ISSN 0006-2979, Biochemistry (Moscow), 2023, Vol. 88, No. 11, pp. 1739-1753 © The Author(s) 2023. This article is an open access publication.
Published in Russian in Biokhimiya, 2023, Vol. 88, No. 11, pp. 2109-2126.
1739
REVIEW
Retrotransposons and Telomeres
Alla I. Kalmykova
1,a
* and Olesya A. Sokolova
1
1
Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
a
e-mail: allakalm@idbras.ru
Received June 19, 2023
Revised July 24, 2023
Accepted August 12, 2023
Abstract— Transposable elements (TEs) comprise a significant part of eukaryotic genomes being a major source of ge-
nome instability and mutagenesis. Cellular defense systems suppress the TE expansion at all stages of their life cycle.
Piwi proteins and Piwi-interacting RNAs (piRNAs) are key elements of the anti-transposon defense system, which con-
trol TE activity in metazoan gonads preventing inheritable transpositions and developmental defects. In this review, we
discuss various regulatory mechanisms by which small RNAs combat TE activity. However, active transposons persist,
suggesting these powerful anti-transposon defense mechanisms have a limited capacity. A growing body of evidence sug-
gests that increased TE activity coincides with genome reprogramming and telomere lengthening in different species. In the
Drosophila fruit fly, whose telomeres consist only of retrotransposons, a piRNA-mediated mechanism is required for telo-
mere maintenance and their length control. Therefore, the efficacy of protective mechanisms must be finely balanced in order
not only to suppress the activity of transposons, but also to maintain the proper length and stability of telomeres. Structural
and functional relationship between the telomere homeostasis and LINE1 retrotransposon in human cells indicates a close
link between selfish TEs and the vital structure of the genome, telomere. This relationship, which permits the retention of
active TEs in the genome, is reportedly a legacy of the retrotransposon origin of telomeres. The maintenance of telomeres
and the execution of other crucial roles that TEs acquired during the process of their domestication in the genome serve
as a type of payment for such a “service.”
DOI: 10.1134/S0006297923110068
Keywords: retrotransposons, telomeres, telomerase, polyploidy, Piwi, piRNA, germline, chromatin, LINE1, Drosophila
* To whom correspondence should be addressed.
INTRODUCTION
Currently, a bulk of data has been accumulated to
demonstrate a close relationship between the key cellular
processes and the regulation of the activity of transpos-
able elements (TEs). This relationship enables survival
of TEs in the genomes despite strong defense mecha-
nisms limiting their activity. What mechanism underlies
this global genomic trade-off? TEs serve as a rich source
of evolutionary changes in the genome: they offer en-
hancers, promoters, exons, splicing sites, architectural
elements and participate in the key mechanisms of de-
velopment and immune response [1-4]. TEs contribute
to the maintenance of essential chromosome structures
such as centromeres and ribosomal RNA gene loci [5-8].
In this review, we focus on the origin and maintenance
of telomeres, one of the most compelling cases of the
role of retrotransposons in genome evolution.
Telomeres – the ends of linear chromosomes – have
captivated attention of many scientists for more than
50years. In 1971-1973, Aleksey M. Olovnikov published
his brilliant prediction regarding the “Achilles’ heel of
the double helix,” or chromosome end under-replica-
tion [9, 10]. He also suggested existence of a specialized
DNA polymerase, which compensates for the shortening
of telomeric DNA. Much later this enzyme, now known
as telomerase, was discovered. It turned out that this was
a reverse transcriptase, which acts in a complex with
the RNA template [11]. The ends of the primary linear
chromosomes are thought to be protected by the attach-
ments of retroelements. From this point of view, the
telomerase ribonucleoprotein complex can be consid-
ered as a specialized retroelement that evolved to protect
the chromosome ends [12]. In fact, phylogenetic analy-
sis of the reverse transcriptase of retrotransposons and
telomerase revealed that they originated from a common
ancient retroelement enzyme [13-15]. Telomerase main-
tains telomeres in most organisms, but there are other
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ways to elongate chromosome ends. There are many
modern species of animals whose telomeres are support-
ed by the retrotransposon attachments. These are many
species of insects and, in particular, the Drosophilidae
family. It is believed that Drosophila has lost telomerase,
and the specialized telomeric retrotransposons are used
to maintain telomeres. The telomeres of the silkworm
Bombyx mori are of mixed type, and they are maintained
by the specific telomeric retroelements and low-activity
telomerase. Under certain conditions, retroelements are
also attached to the human telomeres and to telomeres
of other species using telomerase [16, 17]. In these cases,
the double strand break at the chromosome end is used
as a convenient target for TE retrotranspositions. How-
ever, mosquitoes do not have telomerase or telomeric
retroelements, and the telomeres lengthening appeared
to be mediated by the recombination of short satel-
lite-like repeats [18,19].
Telomeres maintained by TE transpositions differ
in the nature of telomeric repeats from telomeres main-
tained by telomerase, but they serve as a reminder of
the retrotransposon origin of telomeres. The study of
the regulation of Drosophila telomeres, which consist of
retrotransposons, reveals a surprising similarity, if not
identity, between the mechanisms that control telomere
maintenance and TE activity. This similarity leads us to
the conclusion that there is a close functional link be-
tween retrotransposons and telomeres in the genome,
which, according to recent evidence, is found not only
in Drosophila but also in mammals.
WHY IS TELOMERASE LOST
IN MANY INSECT AND DROSOPHILA SPECIES?
Telomerase has been lost in many plants and ani-
mals in the process of evolution. Instead, telomeres are
extended by other mechanisms in these cases. In Dip-
tera the telomerase gene was lost about 270 million years
ago[20]. Members of the Diptera group are one of the
most numerous and prosperous species of animals, de-
spite their lack of telomerase. The gene coding for telo-
merase has not been detected in the genome of Drosoph-
ila, and telomere elongation occurs due to transpositions
of specialized TEs. The most thoroughly studied are the
telomeric retroelements of Drosophila melanogaster. They
are represented by three families of LINE retrotrans-
posons (Long Interspersed Nuclear Elements)– HeT-A,
TART, and TAHRE [21, 22]. At the same time, Bombyx
mori has low-activity telomerase, with telomeric niches
actively filled with specialized telomere retrotransposons
SART and TRAS [23]. At present, the evolutionary pres-
sures underlying the apparent reverse evolution and re-
jection of telomerase remain unknown.
Alexey M. Olovnikov was always interested in ex-
ceptions to the rules as he endeavored to explain vari-
ous mysterious phenomena of nature. In this chapter,
we would like to cite his interesting ideas concerning the
loss of telomerase in Drosophila, which he expressed in
personal correspondence: “It is known that the chromo-
somes of the salivary gland cells in D. melanogaster lar-
va are able to undergo many of endoreplication rounds.
In addition, there is a somatic synapse of homologous
chromosomes. Therefore, the lateral conjugation of sis-
ter chromatids, tightly connected together along their
entire length, should necessarily create a mechanical
barrier for the formation of a telomerase telomere. Such
telomere should have a three-dimensional telomere loop.
In the formation of a three-dimensional telomeric com-
plex, hundreds of conjugated chromatid ends, tightly
united in a single polytenic bunch, would create com-
pelling steric obstacles to each other in the formation of
their 3D telomeric complex. Therefore, polytenization
forced Drosophila to abandon telomerase. In contrast,
the G-quadruplex formation, which protects the telo-
meric retrotransposon end on each chromatid, does not
require the telomeric loop and is therefore easily com-
patible with lateral chromatid conjugation. Presumably,
polytenization was the main reason for choosing an
alternative method of protecting Drosophila telomeres.
As it is well known, chromosome polytenization in sali-
vary gland cells in Drosophila larva is necessary for pro-
duction of large amounts of glue before pupation. It is
likely that organisms that need increased gene copy
number and have telomerase telomeres do not use dense
chromatid packaging. For example, in ciliates that have
a polyploid macronucleus and telomerase, chromo-
somes are fragmented. In theory, the following alterna-
tive is also acceptable: if telomeres, unlike the rest of the
polytenized chromatids, are not side-conjugated (and,
therefore, free from the previously mentioned steric hin-
drance), then this expands the possibilities of using the
telomerase method of telomere protection. Therefore,
there may be species in which polytene chromosomes
and telomerase-like proteins are used at some develop-
mental stages, but the ends of the chromosomes are not
paired. Such termini have been cytogenetically observed,
for example, in specialized polytene cells and at the ends
of meiotic pachytene chromosomes of the legume plant
Vigna unguiculata [24, 25]. A tendency to split some
chromosomal ends into oligotene bundles, can be seen
in the polytene chromosomes of certain species [26]”
(from the letter of A. M. Olovnikov to A.I. Kalmykova,
September 2017).
Indeed, recently it was reported that telomeric ret-
rotransposons tend to form G-quadruplexes (secondary
structures formed by guanine-rich DNA sequences) not
only in the Drosophila species, but also in other spe-
cies [27]. Such structures can protect the ends of linear
chromosomes in the absence of a telomeric loop typi-
cal for the telomeres maintained by telomerase. Exis-
tence of alternative ways of telomere maintenance gives
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BIOCHEMISTRY (Moscow) Vol. 88 No. 11 2023
a unique opportunity to explore emergence of the func-
tional analogues in nature. Researching Drosophila telo-
meres allowed us to take a fresh look at the protective
mechanisms of TE control and their roles in telomere
function. The most striking example is the involvement
of small Piwi-interacting RNA (piRNA) and the piRNA
pathway in the control of Drosophila telomere length in
the germline.
piRNA PATHWAY:
SOURCES AND TARGETS OF piRNAs
TEs were found in all studied species and are rep-
resented by several classes and numerous families [28].
TEs make up half of the human genome and 20% of the
D.melanogaster genome [29] and are the primary source
of mutations that can cause both cancer and severe de-
velopmental disorders [30, 31]. Various mechanisms are
used to limit the activity of TEs in somatic cells and
prevent inherited transpositions in the germline. Mech-
anisms which work at the level of transcription of TEs
are key to prevent the initial stage of their reproduction.
Transcriptional silencing is achieved by two main mech-
anisms leading to the formation of an inactive chromatin
structure. The first and most conservative mechanism
of chromatin compaction is associated with changes in
histone modifications, in particular with methylation
of lysine 9 of histone 3 (H3K9me), which next leads to
the binding and spread of the heterochromatin pro-
tein 1 (HP1) [32]. Another powerful mechanism of re-
pression of transcription is DNA methylation by cyto-
sine-5′-methyltransferases [33]. In the genome, both
DNA methylation and histone modifications target TEs
to prevent their transcription. The main question is how
are these general mechanisms recruited to the TEs?
The KRAB-ZFP (KRAB-containing zinc finger pro-
teins) family proteins play an important role in the recog-
nition and methylation of DNA and histones at endoge-
nous retroviruses in somatic cells of vertebrates [34, 35].
For most plants and animals, RNA interference
is the most conservative and nearly universal mecha-
nism for distinguishing between “self” and “non-self”.
The pathways involving Argonaute family proteins and
associated short RNAs are termed nucleic acid immuni-
ty because these mechanisms may recognize and elimi-
nate foreign nucleic acids belonging to viruses, TEs, or
transgenes based on nucleic acid sequence. siRNA (small
interfering RNA) of 21 nucleotides in length and RNA
interference protect somatic cells from viruses. The pro-
teins of the Piwi subfamily of the Argonaute family and
the associated piRNAs with a length of 24-30 nucleotides
provide protection against TEs and viruses in the animal
gonads [36, 37]. The distinctive feature of this system
is that the Piwi–piRNA complex is able to induce TE
chromatin modifications in a sequence-specific manner,
i.e., to cause transcriptional silencing. Piwi nuclear pro-
teins in complex with piRNAs induce the formation of
heterochromatin, using the complementarity of piRNA
and nascent mRNA of TEs. This is a multi-stage process
that requires the interaction of several linker and acces-
sory proteins, post-translational modifications that result
in assembly, conformational changes, and eventually sta-
bilization of the Piwi-piRNA-driven chromatin protein
complex, and, finally, recruitment of universal heteroch-
romatin factors to TEs [36,38]. Such tight regulation is
essential to turn off the TEs and prevent erroneous re-
pression of cellular genes.
piRNA-mediated silencing is a multi-stage pro-
cess. The main steps of this process are the formation of
long single-strand RNA precursors in the nucleus, their
processing into mature piRNAs in the cytoplasm, and
piRNA-mediated silencing, which can occur both in the
nucleus (transcriptional silencing) and in the cytoplasm
(post-transcriptional silencing).
To perform their functions, mature piRNAs should
complementarily interact with the transcripts of TE, i.e.,
they should be antisense to the mRNA of TEs. Indeed,
a significant portion of piRNAs in the gonads corre-
sponds to TEs, but are not generated from the mRNA
of TEs. The origin of such antisense TE RNAs in the
genome is not quite clear but may involve the follow-
ing mechanisms. piRNAs are thought to be formed
from long single-strand endogenous RNAs known as
piRNAs precursors (pre-piRNAs) [39, 40]. Our knowl-
edge on this issue is mainly obtained from the D. mela-
nogaster oogenesis model. Studies of the genomic ori-
gin of piRNAs in Drosophila have led to the conclusion
that the sources of piRNAs and their targets are locat-
ed at different genomic loci (Fig. 1a). This assumption
was based on the small RNA sequencing data that re-
vealed the regions in pericentromeric heterochromatin
with high density of the single-mapped (in other words,
unique) piRNAs. Such loci were termed piRNA clus-
ters [39]. These extended regions of the genome, up to
200kb in size, enriched in damaged TE copies, encode
unusually long read-through transcripts that are pro-
cessed into mature piRNAs that target euchromatic ac-
tive TEs. This is a remarkable illustration of how the ge-
nome regions that were previously thought of as “junk”
DNA are really being used functionally. It should be
mentioned that this scenario has not been proved to be
universal.
In Drosophila, there are two types of piRNA clusters,
uni-strand and dual-strand, which are transcribed in
one or two directions, respectively. Both types of piRNA
clusters produce predominantly antisense piRNA rela-
tive to TEs. The reason why they are antisense is easier
to understand considering the uni-strand piRNA clus-
ters, in which all TE remnants are in an inverted position
relative to the pre-piRNA transcription direction. The
best-known uni-strand piRNA cluster is the Drosophila
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BIOCHEMISTRY (Moscow) Vol. 88 No. 11 2023
Fig. 1. Where do piRNA precursors come from? a)Heterochromatic pericentromeric piRNA clusters are the sources of anti-transposon piRNAs
that target the TE active copies. The mapping of small RNAs to the chromosome is schematically shown with the activity of uni- and dual-strand
piRNA clusters depicted below. The Piwi–piRNA complex recognizes and silences TE active copies (black triangle). b)TE active copies form
denovo piRNA clusters. piRNA signature of the TE-associated piRNA clusters is schematically shown. sRNAseq – small RNA sequencing.
c)Transgenic model demonstrates how active TEs in euchromatin could become piRNA clusters. Piwi protein in complex with endogenous piRNA
to I-element recognizes RNA in the complementary transgenic locus, promoting generation of transcripts from both genomic strands, which
are then processed into mature piRNAs.
flamenco locus, which operates in ovarian follicular cells.
It contains many inactive TE copies on the minus genomic
strand relative to the direction of transcription, therefore
the piRNAs processed from long precursor transcripts
are complementary to the transposon mRNAs and guide
their transcriptional silencing [39, 41]. flamenco-like loci
generate piRNAs against endogenous retroviruses related
to the gypsy family. This intricate scenario nevertheless is
recurring in evolution. flamenco-like uni-strand piRNA
clusters have been found in mosquitoes and other Dro-
sophila species [42-44]. Moreover, during mouse sper-
matogenesis, two flamenco-like uni-strand piRNA clus-
ters produce anti-transposon piRNAs [45]. The second
type of heterochromatic piRNA clusters – dual-strand
clusters– are considered as principal players in the an-
ti-transposon defense in the Drosophila germline. These
loci contain chaotically oriented TE copies disrupted by
other TE insertions. Dual-strand piRNA clusters are bi-
directionally transcribed resulting in the generation of
long non-coding piRNA precursors from both genomic
strands [46]. Long piRNA precursors are exported to the
cytoplasm where they are processed into mature piRNAs.
piRNA processing is a conserved well-established mech-
anism in different species. The outer mitochondrial mem-
brane and perinuclear compartment serve as platform for
compartmentalization of piRNA generation and matura-
tion. piRNAs are cleaved as a result of activity of various
specialized ribonucleases. Cytoplasmic Piwi subfamily
proteins perform piRNA amplification using sense and
antisense TE transcripts and piRNA precursors from
clusters, which leads to the formation of both sense and
antisense piRNAs. This mechanism, known as “ping-
pong,” is found in the gonads of all the species stud-
ied, and leads not only to cleavage of TE mRNA (post-
transcriptional silencing), but also to production of new
piRNAs. Recent comprehensive reviews describe in details
the processes of piRNA formation and amplification, as
well as the piRNA processing machinery [36, 37, 47].
Dual-strand piRNA clusters are thought to repre-
sent a repository of information in the genome about
prior TE invasions, as well as a kind of trap for TEs, be-
cause their insertions in the piRNA cluster would lead
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to the production of piRNAs and the suppression of
the activity of cognate copies in the genome [48]. While
dual-strand piRNA clusters were shown to be species-
specific for Drosophila and a few arthropod species,
these types of transposon-specific piRNA sources have
not been identified in other investigated species, includ-
ing mammals. The existence of a conservative mecha-
nism for the synthesis of piRNA precursors that are an-
tisense to TEs is still a matter of debate. For example,
sense and antisense piRNAs are produced from indi-
vidual copies of evolutionarily young active retrotrans-
posons in mammals, despite the presence of a signifi-
cant number of damaged TE copies in the genome [45].
In the piRNA pathway mechanism for transposon
silencing, active transposons are expected to be the pri-
mary targets of piRNAs. A more thorough examination
of small RNA libraries derived from D. melanogaster
ovaries revealed that not only heterochromatic piRNA
clusters, but also full-length euchromatic TEs generate
short RNAs, both piRNAs and siRNAs. This shows that
at the sites of recent TE insertions, local dual-strand
piRNA clusters occur [49], which is similar to the sce-
nario of piRNA generation from the active copies of
LINE1 in mammals [45]. A distinctive feature of the
TE-associated piRNA clusters is a “piRNA signature”.
It is an asymmetric profile of small RNA distribution
upstream and downstream of TEs resulting from the
read-through transcription of piRNA precursors into the
TE flanking genomic regions (Fig. 1b). This signature
was successfully used for the prediction of non-annotat-
ed TE insertions. Moreover, the expansion of small RNA
production outside TEs can suppress the expression of
the neighboring genes [49]. Thus, active TEs serve not
only as targets for the piRNA system, which promotes
chromatin compaction, but also as a source of small
RNAs, as they can produce de novo si- and piRNAs.
The Drosophila telomeric retrotransposons, which are
arrayed as tandem repeats in the telomere, are also the
target and source of piRNAs, which allow feedback reg-
ulation of the telomeric retrotransposons expression, as
addressed in more depth in the following section.
The mechanism underlying the formation of new
TE-associated piRNA clusters, particularly the mech-
anism of activation of bidirectional transcription, is not
totally understood. Antisense promoters are known only
for a few TEs and are rather an exception. For example,
the LINE1 human retrotransposon antisense promoter
and the transcripts derived from it are involved in siRNA-
mediated LINE1 transposition suppression [50, 51].
When the Piwi–piRNA complex recognizes complemen-
tary transcripts, an uncommon type of transcription,
convergent transcription, is thought to be triggered at
genomic loci harboring active copies of TEs. This pro-
cess depends on the genomic environment of the TE in-
sertion: endogenous convergent transcription at the TE
insertion locus promotes the formation of a new piRNA
cluster [52]. Transcripts generated from both genomic
strands are then processed into mature pi/siRNAs. Such
a scenario has an obvious biological significance, as it
would result in amplification of protective small RNAs
against most dangerous, transcriptionally active TEs.
Atransgenic model containing a DNA fragment target-
ed by endogenous piRNAs elucidated some details of the
denovo piRNA cluster formation [53-55]. It was shown
that transgenic constructs containing a fragment of I-ele-
ment can become new piRNA clusters. The formation of
piRNA clusters de novo is accompanied by the appear-
ance of weak transcription from the minus strand and the
generation of sense and antisense pi/siRNAs from the
entire transgene and from genomic sequences at a dis-
tance of 1 to 10kb from the transgene [56,57] (Fig.1c).
A scenario in which an active TE is a source of
piRNAs should be evolutionarily beneficial and have
selective advantages. It is unclear why extended hete-
rochromatic piRNA clusters, which are maintained by
aunique transcription mechanism, have survived through-
out evolution in Drosophila and other arthropods. There-
moval of the most extended pericentromeric piRNA
clusters in D. melanogaster were found to not lead to TE
derepression [58]. This suggests that TE silencing in the
stable laboratory line is not primarily mediated by heter-
ochromatic piRNA clusters. This function is most likely
carried out by TE-associated piRNA clusters, which are
generated via the assistance of piRNAs acquired from the
mother with the oocyte cytoplasm [59].
Differences in TE silencing strategies between spe-
cies may be related to different habitats. Horizontal TE
transfer has an impact on natural arthropod populations,
including the re-invasion of previously lost TEs in the
genome [60, 61]. The memory of earlier TE invasions,
which is kept in the form of TE fragments in piRNA
clusters, can protect the population from TE re-infec-
tion due to the existence of complementary piRNAs and
the activation of piRNA-silencing [39, 52, 57, 59, 62].
The idea that active TE copies serve as the prima-
ry targets of the piRNA pathway is emphasized by the
recently discovered mechanism of a co-transcriptional
degradation of TE transcripts [63]. Despite the estab-
lishment of heterochromatin in loci with active copies of
TEs, they can still be transcribed in the germline. Theex-
cess of the TE transcripts in the Drosophila germline is
removed through the activity of the nuclear Ccr4–Not
complex, which has deadenylase activity [64]. Ccr4–Not
is recruited to the transposon transcripts co-transcrip-
tionally by the Piwi-piRNA nuclear complex. Most
likely, the polyA tail at the 3′-end of the TE mRNA is
eliminated due to deadenylase activity of the Ccr4–Not
complex. The nuclear RNA quality control system can
identify these transcripts as aberrant and subject them
to exonuclease cleavage. Noteworthy, the targets of nu-
clear Ccr4–Not are mainly active full-length TEs and
telomeric retrotransposons [63].
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Fig. 2. The piRNA silencing system is a multi-level mechanism. In Drosophila, piRNAs can induce the following processes: a)transcriptional
silencing and chromatin compaction; b)co-transcriptional degradation of nascent RNA in the nucleus via assistance of the deadenylase nuclear
complex Ccr4–Not; c)post-transcriptional RNA degradation and amplification of piRNAs in the cytoplasm; d)de novo piRNA production
at active TEs due to activation of antisense transcription; e)epigenetic transgenerational memory (transfer of maternal piRNAs in complex with
Piwi proteins to offspring through the germ plasm of the oocyte).
To summarize, piRNAs can trigger a number of
important processes aimed at suppressing TE activity
(Fig. 2). In the nucleus, piRNAs induce transcription-
al silencing leading to heterochromatin assembly at the
TE loci [65-67]. The piRNA system also functions at
the co-transcriptional level, causing nucleases to de-
grade TE transcripts at transcription sites [63]. In the
cytoplasm, the piRNA system cleaves TE transcripts
(post-transcriptional silencing), resulting in piRNA am-
plification and their subsequent inheritance through the
oocyte cytoplasm [39, 59, 68-71]. Importantly, piRNAs
can initiate denovo piRNA cluster establishment at full-
length euchromatic TE insertions leading to the expres-
sion of antisense TE transcripts and a burst of piRNA
production against most active TEs [49]. Furthermore,
the fast evolution of proteins participating in the piRNA
pathway allows this system to be highly adaptable to new
targets [72-74]. Despite the high capacity of piRNAs and
other anti-transposon defense systems, selfish TEs suc-
cessfully bypass them, continuing their propagation, re-
sulting in deleterious mutations, diseases, and develop-
mental disorders. A paradoxical situation has emerged in
which the suppression of TE activity requires its activity,
and as a result, the piRNA system operates. Apparently,
the far from perfect efficacy of these and other defense
systems allows TEs to multiply within the tolerable lim-
its, producing material for genome evolution and posi-
tive selection, while also allowing some critical systems,
such as telomeres, to function. The latter phenomenon
will be discussed below.
ROLE OF piRNAs IN REGULATION
OF Drosophila TELOMERES
In Drosophila, disruption of the piRNA system
causes not only TE activation but also excessive telo-
mere extension due to the increased frequency of retro-
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transposon attachments to chromosome ends [75].
This occurs because the germline pool of piRNAs com-
plementary to telomeric retrotransposons is reduced.
The piRNA pathway processes all TE transcripts in the
germline, producing piRNA without differentiating be-
tween telomeric and parasitic retrotransposons. Disrup-
tion of the piRNA pathway leads to a decrease in piRNA
abundance, which is accompanied by the accumulation
of telomeric TE transcripts. These transcripts serve as
intermediates for the extension of telomeres. Drosophila
telomeres are maintained by the retrotranspositions of
specialized telomeric TEs that are not found in other ge-
nomic loci. Telomeric retroelements are both the sources
and the targets of piRNAs, making them a unique ex-
ample of a self-regulated TE-associated piRNA cluster.
Bidirectional promoters of Drosophila telomeric retro-
transposons organized in head-to-tail arrays ensure
the generation of both sense and antisense transcripts,
which are then used to produce telomeric piRNAs [76-
79]. Drosophila is not the only example of such regula-
tion. Piwi proteins are also involved in the regulation of
SART and TRAS telomeric retrotransposon transposi-
tions in the silkworms [80].
The heterochromatin state is a characteristic of
telomeres. Heterochromatin factors are recruited to telo-
meric retrotransposons via the assistance of the piRNA
system in the Drosophila germline [81]. When the piRNA
system is disrupted, the levels of the key heterochroma-
tin protein HP1 and the histone modification H3K9me3
decrease at telomeres. The shift of telomeric clusters
from the nuclear periphery, along with a global change
in telomeric chromatin structure, is found in the germ-
line of Drosophila piRNA mutants [81]. Furthermore, the
most abundant D. melanogaster telomeric repeat, HeT-A,
is co-transcriptionally regulated in the nucleus by recruit-
ing the Ccr4–Not deadenylase complex [63]. Confocal
microscopy revealed the presence of structures nearby
telomeres that contained the Ccr4–Not protein complex,
the Piwi protein, and RNA nuclear export factors [63].
Interestingly, non-canonical deadenylases Ccr4 and Caf1,
which are localized in Cajal nuclear bodies, are involved
in the biogenesis of human telomerase RNA compo-
nent[82]. Thus, the piRNA system and Ccr4–Not dead-
enylase are implicated in both the reduction of activity
of selfish TEs and in the Drosophila telomere regulation.
Telomere length in Drosophila is negatively regulated
by the piRNA system; the more actively it functions, the
less frequently telomere lengthening takes place. Inor-
der to maintain the frequency of attachment of telomeric
retroelements to the ends of chromosomes required for
normal development, a complicated feedback mecha-
nism controls the level of telomeric transcripts, telomeric
piRNAs, and the state of telomeric chromatin. The fact
that the piRNA-mediated mechanism should effectively
suppress TE activity complicates telomere length control
even more. Indeed, piRNA system disruption causes not
only an increase in the frequency of telomeric attach-
ments, but also TE activation and sterility [75]. The op-
posite situation, i.e., activation of the piRNA system and
excessive telomere shortening, was observed in one of
the natural Drosophila strains. Differences in the extent
of anti-transposon protection among natural Drosophila
Fig. 3. The mechanisms regulating telomere maintenance and transposon control are tightly linked. The piRNA system controls both activity
of selfish TEs and telomeric retrotransposon attachments to the chromosome ends in the Drosophila germline.
KALMYKOVA, SOKOLOVA1746
BIOCHEMISTRY (Moscow) Vol. 88 No. 11 2023
populations can be explained by the high variability of
proteins involved in the piRNA pathway and variable ef-
ficacy of primary piRNA processing [83]. Flies, which
had the most efficient piRNA processing, lacked full-
length copies of the HeT-A retrotransposon, the main
structural element of telomeres. This strain had re-
duced fertility and viability. Therefore, enhancement of
piRNA-mediated protection leading to strong repres-
sion of transposons, can also cause telomere shortening.
This result implies that limits exist for improvements
in the efficiency of the piRNA defense system because
it needs to achieve a balance between protecting the ge-
nome against transposon propagation and allowing ade-
quate telomere maintenance (Fig.3).
WHEN AND WHY
ARE TRANSPOSABLE ELEMENTS
ACTIVATED DURING DEVELOPMENT?
The stages of development during which TEs are
activated could point to the mechanisms of TE control
(Fig.4,a-c). Surprisingly, short-term transposon activa-
tion is observed during early stages of gametogenesis in
a variety of species [84]. There is a brief developmental
window at the early stages of D. melanogaster oogene-
sis when Piwi levels decrease and TEs mobilize [85].
TheTE transcripts produced at this stage are processed
into piRNAs by the cytoplasmic piRNA amplification
machinery. When Piwi expression is restored these
piRNAs mediate transcriptional silencing of TEs at later
stages of oogenesis [86]. When the Piwi protein is ab-
sent during the early stages of oogenesis, transcriptional
activation of telomeric retroelements (HeT-A and TART)
is detected, which leads to the formation of telomere
elongation intermediates [66, 87, 88]. In D. melanogas-
ter, such intermediates are spherical ribonucleopro-
tein (RNP) particles composed of the retrotransposon
HeT-A-encoded Gag protein, packed with HeT-A RNA,
and capable of being targeted to telomeres [89,90]. For
the first time, such HeT-A spheres were found in active-
ly proliferating larval brain cells, and their appearance
on telomeres coincided with telomere replication [89].
The main structural component of Drosophila telomeres
is the non-autonomous retroelement HeT-A, lacking re-
verse transcriptase. Reverse transcriptase is provided by
other telomeric retroelements– TART and/or TAHRE.
TART reverse transcriptase was also discovered in the
HeT-A spheres in neuroblasts [91]. Most likely, HeT-A
spheres are necessary for the retrotransposition of telo-
meric elements to the chromosome ends to elongate
Drosophila telomeres. Transcription of Drosophila telo-
meric retrotransposons HeT-A and TART is normally
detected in the ovarian germ cysts, and when the piRNA
system is disrupted, spherical particles containing RNA
and the Gag protein encoded by HeT-A arise [87].
Telomere elongation occurs at the same stages at which
TEs are activated. This is most likely due to a decrease
in piRNA protection and the accumulation of telomer-
ic element transcripts, as well as global heterochromatin
decompaction and greater accessibility of chromosom-
al ends in mitotically active gamete progenitor cells.
Indeed, disruption of various heterochromatin factors
such as HP1, histone demethylase Lsd1 and its cofac-
tor Ova, methyltransferases dSetdB1 and Su(var)3-9
lead to both TE activation and telomeric transcript ac-
cumulation [92-98]. Mutation of Su(var)2-5 gene en-
coding HP1, causes telomere elongation [98]. A similar
scenario has been observed in other animals. In mam-
mals, a wave of de novo DNA methylation is typical
for prenatal male germline development. As a result,
expression of young active subfamilies of retroelement
LINE1 occurs in primordial germ cells [99]. At later
stages of spermatogenesis, emergence of Piwi subfamily
protein, MILI2 in mouse, triggers piRNA production,
recruitment of DNA methylase and establishment of
piRNA-mediated denovo DNA methylation at LINE1
sequences [100].
In the mammalian development, two waves of de-
methylation and remethylation of DNA occur– in pri-
mordial germ cells and in the early embryogenesis [101].
Global demethylation of the genome in the primordial
germ cells during prenatal development is believed to be
required for epigenome reprogramming and the estab-
lishment denovo DNA methylation patterns [102, 103].
DNA demethylation is also required for telomere exten-
sion in embryonic stem cells which is associated with in-
creased levels of transcription of many retrotransposons
[104-106]. The transcription factor Zscan4 (Zinc finger
and SCAN domain containing 4) plays a critical role
in maintaining the DNA demethylation state and het-
erochromatin derepression in embryonic stem cells and
2-cell embryos [107]. Zscan4 increases the expression
of genes involved in homologous recombination, which
stimulates the recombination mechanism of telomere
lengthening in embryonic stem cells, 2-cell embryos,
and ALT (alternative lengthening of telomeres) tumor
cells that use recombination for telomere lengthening
[105, 106, 108]. In preimplantation embryos, the activa-
tion of LINE1 retrotransposons and endogenous retro-
viruses is also observed [109-112]. Interestingly, LINE1
inhibition leads to impaired expression of pluripotency
factors, including Zscan4, and blocks telomere elon-
gation in embryonic stem cells [113]. In turn, LINE1
RNA acts as a transcriptional repressor of the Dux gene,
which is required for embryonic cells to exit the 2C state
and continue development [114]. It was also shown that
early differentiation gene promoters contain regulato-
ry regions of endogenous retroviruses and are regulated
by retroviral proteins [115]. Thus, transposon activation
occurs during brief periods of development associated
with genome reprogramming and telomere elongation.
RETROTRANSPOSONS AND TELOMERES 1747
BIOCHEMISTRY (Moscow) Vol. 88 No. 11 2023
Fig. 4. Developmental stages of transposon activation. a)When Piwi protein levels fall during Drosophila oogenesis, TEs and telomeric retrotrans-
posons are activated in the germ cysts. At this step, piRNAs are produced, which cause transcriptional silencing at the later stages of oogenesis.
Telomere elongation is anticipated to occur at the same stage due to retrotranspositions of telomeric retroelements to the chromosome ends.
b)TE activation is associated with global demethylation in mouse primordial germ cells during spermatogenesis. Then, piRNA-mediated denovo
DNA methylation of LINE1 active copies is established. c)Transposon mobilization and telomere elongation are observed during first zygotic
divisions in mammalian embryogenesis. d) The inhibition of LINE1 by piRNAs may have an indirect effect on LINE1 telomeric functions
in mammalian germ cells (hypothesis).
Furthermore, these processes are linked by a sophisti-
cated regulatory network, the proper balance of which is
required for normal development.
Natural aging and premature aging syndromes both
exhibit chromatin decompaction and activation of ex-
pression of TEs and telomeric repeats, resulting in DNA
damage and cell death [116,117], which emphasizes the
commonality of epigenetic regulation of telomeres and
TEs at different developmental stages.
INVOLVEMENT OF LINE1
IN THE MAINTENANCE
OF MAMMALIAN TELOMERES
Similarities between TE control and telomere reg-
ulation mechanisms are evident in Drosophila where
telomeres are elongated by the retrotranspositions of
retroelements. However, in the vast majority of species,
telomeres are maintained by the activity of a specialized
reverse transcriptase – telomerase – the components
of which are encoded by cellular genes. New evidence
demonstrates that the retrotransposons are involved in
the functioning of telomeres in mammalian cells. Inthe
absence of the components of the protective telomere
complex shelterin, the LINE1 retrotransposon can at-
tach to the telomere in human cells via reverse tran-
scription and become a structural part of telomeric
DNA [17]. In addition, LINE1 is also able to play a role
in telomere function. LINE1 knockdown in cancer cells
resulted in a reduced expression of shelterin proteins,
decreased telomerase activity and telomere shortening
[118]. In line with this observation, inhibition of LINE1
activity in the mouse 2-cell embryos blocked telomere
elongation and genome reprogramming [113]. Further-
more, LINE1 RNPs were found directly at telomeric
KALMYKOVA, SOKOLOVA1748
BIOCHEMISTRY (Moscow) Vol. 88 No. 11 2023
ends in human cancer cells and mouse 2-cell embryos,
where they interacted with telomeric repeat-contain-
ing RNA (TERRA) [113, 119]. LINE1 appears to be
involved in telomere biogenesis, however it is unknown
how LINE1 is targeted there or which telomere compo-
nents it recognizes. Given the role of LINE1 in telomere
function, it is tempting to speculate about a potential
relationship between the piRNA system that regulates
LINE1 expression and telomeres in telomerase-using
mammals (Fig.4d).
All together, these findings indicate that the systems
regulating telomere maintenance and transposon control
in the mammalian genome are connected with respect
to temporal regulation and function. Research on this
relationship will contribute to a better understanding of
the mechanisms of telomere regulation in development,
aging, and cancer cells.
CONCLUSION
The interaction between the host genome and TEs
is commonly referred to as a genomic conflict, and the
processes behind this conflict are complicated and de-
batable [120]. When the molecular mechanisms of TE
control were not yet known, analysis of TE population
dynamics revealed a balance between TE spread rate
and the mechanisms that limit this process. As a result,
the genome has a rather stable amount of TE copies
[121]. Excessive reduction of TE activity and their copy
number does not appear to provide a selective benefit to
the host, as recent methods of genomic data analysis of
natural Drosophila populations indicate. For example,
the amount of piRNA does not correlate with TE trans-
position activity, therefore, the piRNA system is not op-
timally adapted to protect the genome from TEs [122].
The continuous improvement of the adaptable piRNA
system is probably limited by its participation in key reg-
ulatory functions, which creates a conflict between TEs
and the genome. Incomplete suppression of TEs allows
important cellular functions to be performed by the do-
mesticated TEs and consequently ensures the survival of
selfish TEs in the genome. What is the mechanism of
this global genomic compromise? Part of the solution,
we believe, can be found in the retrotransposon origin of
telomeres and telomerase. Transposon activity is asso-
ciated with genome reprogramming, erasing of epigen-
etic marks and telomere elongation. A dual role of the
piRNA system in telomere protection and transposon
silencing in Drosophila resulted from the nature of Dro-
sophila telomeres which are made up of retrotransposons
perse. However, telomerase can also be considered as a
specialized retroelement that retained its functional rela-
tionship with genomic retrotransposons. Thus, we con-
clude that protective systems can only partially suppress
the activity of selfish TEs since they must be balanced
to carry out essential tasks, like those related to telomere
maintenance. However, this is a blessing in disguise:
anincreasing body of evidence indicates that domesti-
cated TEs make a significant contribution to the diversi-
ty of regulatory mechanisms that ultimately confer evo-
lutionary benefits to the host genome.
Contributions. A.I.K. conception and writing the
manuscript; O.A.S. writing and editing the manuscript.
Funding. This work was financially supported by the
Russian Science Foundation (project no.23-24-00025).
Ethics declarations. The authors declare no conflict
of interest in financial or any other sphere. This article
does not contain any studies with human participants
oranimals performed by any of the authors.
Open access. This article is licensed under a Cre-
ative Commons Attribution 4.0 International License,
which permits use, sharing, adaptation, distribution, and
reproduction in any medium or format, as long as you
give appropriate credit to the original author(s) and the
source, provide a link to the Creative Commons license,
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REFERENCES
1. Fueyo, R., Judd, J., Feschotte, C., and Wysocka, J.
(2022) Roles of transposable elements in the regulation
of mammalian transcription, Nat. Rev. Mol. Cell Biol., 23,
481-497, doi: 10.1038/s41580-022-00457-y.
2. Modzelewski, A. J., Gan Chong, J., Wang, T., and He,L.
(2022) Mammalian genome innovation through trans-
poson domestication, Nat. Cell Biol., 24, 1332-1340,
doi: 10.1038/s41556-022-00970-4.
3. Almojil, D., Bourgeois, Y., Falis, M., Hariyani, I., Wil-
cox, J., and Boissinot, S. (2021) The structural, func-
tional and evolutionary impact of transposable elements
in eukaryotes, Genes (Basel), 12, 918, doi: 10.3390/
genes12060918.
4. Nishihara, H. (2020) Transposable elements as genet-
ic accelerators of evolution: contribution to genome size,
gene regulatory network rewiring and morphological in-
novation, Genes Genet. Syst., 94, 269-281, doi: 10.1266/
ggs.19-00029.
5. Hartley, G., and O’Neill, R. J. (2019) Centromere re-
peats: hidden gems of the genome, Genes (Basel), 10, 223,
doi: 10.3390/genes10030223.
RETROTRANSPOSONS AND TELOMERES 1749
BIOCHEMISTRY (Moscow) Vol. 88 No. 11 2023
6. Chang, C. H., Chavan, A., Palladino, J., Wei, X., Martins,
N. M. C., Santinello, B., Chen, C. C., Erceg, J., Beliveau,
B. J., Wu, C. T., Larracuente, A. M., and Mellone, B.G.
(2019) Islands of retroelements are major components
of Drosophila centromeres, PLoS Biol., 17, e3000241,
doi: 10.1371/journal.pbio.3000241.
7. Chueh, A. C., Northrop, E. L., Brettingham-Moore,
K.H., Choo, K. H., and Wong, L. H. (2009) LINE ret-
rotransposon RNA is an essential structural and function-
al epigenetic component of a core neocentromeric chro-
matin, PLoS Genet., 5, e1000354, doi: 10.1371/journal.
pgen.1000354.
8. Nelson, J. O., Slicko, A., and Yamashita, Y. M. (2023) The
retrotransposon R2 maintains Drosophila ribosomal DNA
repeats, Proc. Natl. Acad. Sci. USA, 120, e2221613120,
doi: 10.1073/pnas.2221613120.
9. Olovnikov, A. M. (1971) Principle of marginotomy in
template synthesis of polynucleotides [in Russian], Dokl.
Akad. Nauk SSSR, 201, 1496-1499.
10. Olovnikov, A. M. (1973) A theory of marginotomy. The
incomplete copying of template margin in enzymic syn-
thesis of polynucleotides and biological significance of the
phenomenon, J. Theor. Biol., 41, 181-190, doi: 10.1016/
0022-5193(73)90198-7.
11. Blackburn, E. H. (1992) Telomerases, Annu. Rev. Biochem.,
61, 113-129, doi: 10.1146/annurev.bi.61.070192.000553.
12. Garavis, M., Gonzalez, C., and Villasante, A. (2013) On
the origin of the eukaryotic chromosome: the role of non-
canonical DNA structures in telomere evolution, Genome
Biol. Evol., 5, 1142-1150, doi: 10.1093/gbe/evt079.
13. Gladyshev, E. A., and Arkhipova, I. R. (2007) Telomere-
associated endonuclease-deficient Penelope-like retroele-
ments in diverse eukaryotes, Proc. Natl. Acad. Sci. USA,
104, 9352-9357, doi: 10.1073/pnas.0702741104.
14. Nakamura, T. M., and Cech, T. R. (1998) Reversing time:
origin of telomerase, Cell, 92, 587-590, doi: 10.1016/
s0092-8674(00)81123-x.
15. Eickbush, T. H. (1997) Telomerase and retrotransposons:
which came first? Science, 277, 911-912, doi: 10.1126/
science.277.5328.911.
16. Kordyukova, M., Olovnikov, I., and Kalmykova, A.
(2018) Transposon control mechanisms in telomere bi-
ology, Curr. Opin. Genet. Dev., 49, 56-62, doi: 10.1016/
j.gde.2018.03.002.
17. Morrish, T. A., Garcia-Perez, J. L., Stamato, T. D., Tacci-
oli, G. E., Sekiguchi, J., and Moran, J.V. (2007) Endonu-
clease-independent LINE-1 retrotransposition at mam-
malian telomeres, Nature, 446, 208-212, doi: 10.1038/
nature05560.
18. Roth, C. W., Kobeski, F., Walter, M. F., and Biess-
mann,H. (1997) Chromosome end elongation by recom-
bination in the mosquito Anopheles gambiae, Mol. Cell.
Biol., 17, 5176-5183, doi: 10.1128/MCB.17.9.5176.
19. Compton, A., Liang, J., Chen, C., Lukyanchiko-
va,V., Qi,Y., Potters, M., Settlage, R., Miller, D., De-
schamps, S., Mao, C., Llaca, V., Sharakhov, I. V., and
Tu, Z. (2020) The beginning of the end: a chromosomal
assembly of the new world malaria mosquito ends with
a novel telomere, G3 (Bethesda), 10, 3811-3819, doi:
10.1534/g3.120.401654.
20. Mason, J. M., Randall, T. A., and Capkova Frydrycho-
va,R. (2016) Telomerase lost? Chromosoma, 125, 65-73,
doi: 10.1007/s00412-015-0528-7.
21. Pardue, M. L., and DeBaryshe, P. G. (2008) Drosophi-
la telomeres: a variation on the telomerase theme, Fly,
2, 101-110, doi: 10.4161/fly.6393.
22. Casacuberta, E. (2017) Drosophila: retrotransposons mak-
ing up telomeres, Viruses, 9, 192, doi: 10.3390/v9070192.
23. Fujiwara, H., Osanai, M., Matsumoto, T., and Kojima,
K. K. (2005) Telomere-specific non-LTR retrotrans-
posons and telomere maintenance in the silkworm, Bom-
byx mori, Chromosome Res., 13, 455-467, doi: 10.1007/
s10577-005-0990-9.
24. Guerra, M., Kenton, A., and Bennett, M. D. (1996)
rDNA sites in mitotic and polytene chromosomes of Vigna
unguiculata (L.) Walp. and Phaseolus coccineus L. revealed
by in situ hybridization, Ann. Botany, 78, 157-161, doi:
10.1006/anbo.1996.0108.
25. Iwata-Otsubo, A., Lin, J. Y., Gill, N., and Jackson, S. A.
(2016) Highly distinct chromosomal structures in cowpea
(Vigna unguiculata), as revealed by molecular cytogenet-
ic analysis, Chromosome Res., 24, 197-216, doi: 10.1007/
s10577-015-9515-3.
26. Zhimulev, I. F. (1996) Morphology and structure of poly-
tene chromosomes, Adv. Genet., 34, 1-497, doi: 10.1016/
s0065-2660(08)60533-7.
27. Jedlicka, P., Tokan, V., Kejnovska, I., Hobza, R., and Ke-
jnovsky, E. (2023) Telomeric retrotransposons show pro-
pensity to form G-quadruplexes in various eukaryotic spe-
cies, Mob. DNA, 14, 3, doi: 10.1186/s13100-023-00291-9.
28. Wells, J. N., and Feschotte, C. (2020) A field guide to
eukaryotic transposable elements, Annu. Rev. Genet., 54,
539-561, doi: 10.1146/annurev-genet-040620-022145.
29. Merel, V., Boulesteix, M., Fablet, M., and Vieira, C.
(2020) Transposable elements in Drosophila, Mob. DNA,
11, 23, doi: 10.1186/s13100-020-00213-z.
30. Anwar, S. L., Wulaningsih, W., and Lehmann, U. (2017)
Transposable elements in human cancer: causes and con-
sequences of deregulation, Int.J. Mol. Sci., 18, 974, doi:
10.3390/ijms18050974.
31. Huang, C. R., Burns, K. H., and Boeke, J. D. (2012)
Active transposition in genomes, Annu. Rev. Genet., 46,
651-675, doi: 10.1146/annurev-genet-110711-155616.
32. Lomberk, G., Wallrath, L., and Urrutia, R. (2006) The
heterochromatin protein 1 family, Genome Biol., 7, 228,
doi: 10.1186/gb-2006-7-7-228.
33. Lyko, F. (2018) The DNA methyltransferase family: a ver-
satile toolkit for epigenetic regulation, Nat. Rev. Genet.,
19, 81-92, doi: 10.1038/nrg.2017.80.
34. Ecco, G., Cassano, M., Kauzlaric, A., Duc, J., Coluc-
cio, A., Offner, S., Imbeault, M., Rowe, H. M., Turel-
li, P., and Trono, D. (2016) Transposable elements and
KALMYKOVA, SOKOLOVA1750
BIOCHEMISTRY (Moscow) Vol. 88 No. 11 2023
their KRAB-ZFP controllers regulate gene expression
in adult tissues, Dev. Cell, 36, 611-623, doi: 10.1016/
j.devcel.2016.02.024.
35. Yang, P., Wang, Y., and Macfarlan, T. S. (2017) The
role of KRAB-ZFPs in transposable element repression
and mammalian evolution, Trends Genet., 33, 871-881,
doi: 10.1016/j.tig.2017.08.006.
36. Czech, B., Munafo, M., Ciabrelli, F., Eastwood, E. L.,
Fabry, M. H., Kneuss, E., and Hannon, G. J. (2018)
piRNA-guided genome defense: from biogenesis to silenc-
ing, Annu. Rev. Genet., 52, 131-157, doi: 10.1146/annurev-
genet-120417-031441.
37. Ozata, D. M., Gainetdinov, I., Zoch, A., O’Carroll, D.,
and Zamore, P. D. (2019) PIWI-interacting RNAs: small
RNAs with big functions, Nat. Rev. Genet., 20, 89-108,
doi: 10.1038/s41576-018-0073-3.
38. Andreev, V. I., Yu, C., Wang, J., Schnabl, J., Tirian,L.,
Gehre, M., Handler, D., Duchek, P., Novatchko-
va, M., Baumgartner, L., Meixner, K., Sienski, G.,
Patel, D. J., and Brennecke, J. (2022) Panoramix
SUMOylation on chromatin connects the piRNA path-
way to the cellular heterochromatin machinery, Nat.
Struct. Mol. Biol., 29, 130-142, doi: 10.1038/s41594-022-
00721-x.
39. Brennecke, J., Aravin, A. A., Stark, A., Dus, M., Kel-
lis, M., Sachidanandam, R., and Hannon, G. J. (2007)
Discrete small RNA-generating loci as master regulators
of transposon activity in Drosophila, Cell, 128, 1089-1103,
doi: 10.1016/j.cell.2007.01.043.
40. Aravin, A., Gaidatzis, D., Pfeffer, S., Lagos-Quintana,M.,
Landgraf, P., Iovino, N., Morris, P., Brownstein, M. J.,
Kuramochi-Miyagawa, S., Nakano, T., Chien, M., Russo,
J.J., Ju, J., Sheridan, R., Sander, C., Zavolan, M., and
Tuschl, T. (2006) A novel class of small RNAs bind to
MILI protein in mouse testes, Nature, 442, 203-207,
doi: 10.1038/nature04916.
41. Sarot, E., Payen-Groschene, G., Bucheton, A., and Pelis-
son, A. (2004) Evidence for a piwi-dependent RNA silenc-
ing of the gypsy endogenous retrovirus by the Drosophila
melanogaster flamenco gene, Genetics, 166, 1313-1321,
doi: 10.1534/genetics.166.3.1313.
42. Aguiar, E., de Almeida, J. P. P., Queiroz, L. R., Oliveira,
L. S., Olmo, R. P., de Faria, I., Imler, J. L., Gruber, A.,
Matthews, B. J., and Marques, J. T. (2020) A single uni-
directional piRNA cluster similar to the flamenco locus is
the major source of EVE-derived transcription and small
RNAs in Aedes aegypti mosquitoes, RNA, 26, 581-594,
doi: 10.1261/rna.073965.119.
43. Rozhkov, N. V., Zelentsova, E. S., Shostak, N. G., and
Evgen’ev, M. B. (2011) Expression of Drosophila virilis
retroelements and role of small RNAs in their intrastrain
transposition, PLoS One, 6, e21883, doi: 10.1371/journal.
pone.0021883.
44. Van Lopik, J., Alizada, A., Trapotsi, M. A., Hannon,
G. J., Bornelöv, S., and Czech Nicholson, B. (2023)
Unistrand piRNA clusters are an evolutionarily conserved
mechanism to suppress endogenous retroviruses across the
Drosophila genus, Nat. Commun., 14, 7337, doi: 10.1038/
s41467-023-42787-1.
45. Aravin, A. A., Sachidanandam, R., Bourc’his, D., Schae-
fer, C., Pezic, D., Toth, K. F., Bestor, T., and Hannon,
G. J. (2008) A piRNA pathway primed by individual trans-
posons is linked to de novo DNA methylation in mice,
Mol. Cell, 31, 785-799, doi: 10.1016/j.molcel.2008.09.003.
46. Andersen, P. R., Tirian, L., Vunjak, M., and Brennecke,J.
(2017) A heterochromatin-dependent transcription ma-
chinery drives piRNA expression, Nature,
549, 54-59,
doi: 10.1038/nature23482.
47. Sato, K., and Siomi, M. C. (2020) The piRNA pathway
in Drosophila ovarian germ and somatic cells, Proc. Jpn.
Acad. Ser. B Phys. Biol. Sci., 96, 32-42, doi: 10.2183/
pjab.96.003.
48. Khurana, J. S., Wang, J., Xu, J., Koppetsch, B. S., Thom-
son, T. C., Nowosielska, A., Li, C., Zamore, P. D.,
Weng,Z., and Theurkauf, W.E. (2011) Adaptation to P
element transposon invasion in Drosophila melanogaster,
Cell, 147, 1551-1563, doi: 10.1016/j.cell.2011.11.042.
49. Shpiz, S., Ryazansky, S., Olovnikov, I., Abramov, Y., and
Kalmykova, A. (2014) Euchromatic transposon insertions
trigger production of novel Pi- and endo-siRNAs at the
target sites in the drosophila germline, PLoS Genet., 10,
e1004138, doi: 10.1371/journal.pgen.1004138.
50. Speek, M. (2001) Antisense promoter of human L1 ret-
rotransposon drives transcription of adjacent cellu-
lar genes, Mol. Cell. Biol., 21, 1973-1985, doi: 10.1128/
MCB.21.6.1973-1985.2001.
51. Yang, N., and Kazazian, H. H., Jr. (2006) L1 retrotrans-
position is suppressed by endogenously encoded small in-
terfering RNAs in human cultured cells, Nat. Struct. Mol.
Biol., 13, 763-771, doi: 10.1038/nsmb1141.
52. Komarov, P. A., Sokolova, O., Akulenko, N., Bras-
set, E., Jensen, S., and Kalmykova, A. (2020) Epigen-
etic requirements for triggering heterochromatinization
and Piwi-interacting RNA production from transgenes
in the Drosophila germline, Cells, 9, 922, doi: 10.3390/
cells9040922.
53. De Vanssay, A., Bouge, A. L., Boivin, A., Hermant, C.,
Teysset, L., Delmarre, V., Antoniewski, C., and Ronsser-
ay, S. (2012) Paramutation in Drosophila linked to emer-
gence of a piRNA-producing locus, Nature, 490, 112-115,
doi: 10.1038/nature11416.
54. Josse, T., Teysset, L., Todeschini, A. L., Sidor, C. M.,
Anxolabehere, D., and Ronsseray, S. (2007) Telomeric
trans-silencing: an epigenetic repression combining RNA
silencing and heterochromatin formation, PLoS Genet.,
3, 1633-1643, doi: 10.1371/journal.pgen.0030158.
55. Muerdter, F., Olovnikov, I., Molaro, A., Rozhkov, N. V.,
Czech, B., Gordon, A., Hannon, G. J., and Aravin, A.A.
(2012) Production of artificial piRNAs in flies and mice,
RNA, 18, 42-52, doi: 10.1261/rna.029769.111.
56. Akulenko, N., Ryazansky, S., Morgunova, V., Komarov,
P.A., Olovnikov, I., Vaury, C., Jensen, S., and Kalmykova, A.
RETROTRANSPOSONS AND TELOMERES 1751
BIOCHEMISTRY (Moscow) Vol. 88 No. 11 2023
(2018) Transcriptional and chromatin changes accompa-
nying de novo formation of transgenic piRNA clusters,
RNA, 24, 574-584, doi: 10.1261/rna.062851.117.
57. Olovnikov, I., Ryazansky, S., Shpiz, S., Lavrov, S.,
Abramov, Y., Vaury, C., Jensen, S., and Kalmykova, A.
(2013) Denovo piRNA cluster formation in the Drosophila
germ line triggered by transgenes containing a transcribed
transposon fragment, Nucleic Acids Res., 41, 5757-5768,
doi: 10.1093/nar/gkt310.
58. Gebert, D., Neubert, L. K., Lloyd, C., Gui, J., Leh-
mann, R., and Teixeira, F. K. (2021) Large Drosophila
germline piRNA clusters are evolutionarily labile and dis-
pensable for transposon regulation, Mol. Cell, 81, 3965-
3978, doi: 10.1016/j.molcel.2021.07.011.
59. Brennecke, J., Malone, C. D., Aravin, A. A., Sachidanan-
dam, R., Stark, A., and Hannon, G.J. (2008) Anepigen-
etic role for maternally inherited piRNAs in transposon
silencing, Science, 322, 1387-1392, doi: 10.1126/science.
1165171.
60. Blumenstiel, J. P. (2019) Birth, school, work, death, and
resurrection: the life stages and dynamics of transpos-
able element proliferation, Genes (Basel), 10, 336, doi:
10.3390/genes10050336.
61. Wallau, G. L., Vieira, C., and Loreto, E. L. S. (2018) Ge-
netic exchange in eukaryotes through horizontal transfer:
connected by the mobilome, Mob. DNA, 9, 6, doi: 10.1186/
s13100-018-0112-9.
62. Jensen, S., Gassama, M. P., and Heidmann, T. (1999)
Taming of transposable elements by homology-dependent
gene silencing, Nat. Genet., 21, 209-212, doi: 10.1038/5997.
63. Kordyukova, M., Sokolova, O., Morgunova, V., Ryazan-
sky, S., Akulenko, N., Glukhov, S., and Kalmykova, A.
(2020) Nuclear Ccr4-Not mediates the degradation of
telomeric and transposon transcripts at chromatin in the
Drosophila germline, Nucleic Acids Res., 48, 141-156,
doi: 10.1093/nar/gkz1072.
64. Collart, M. A., and Panasenko, O. O. (2012) The
Ccr4 – not complex, Gene, 492, 42-53, doi: 10.1016/
j.gene.2011.09.033.
65. Rozhkov, N. V., Hammell, M., and Hannon, G. J.
(2013) Multiple roles for Piwi in silencing Drosophila
transposons, Genes Dev., 27, 400-412, doi: 10.1101/gad.
209767.112.
66. Shpiz, S., Olovnikov, I., Sergeeva, A., Lavrov, S., Abram-
ov, Y., Savitsky, M., and Kalmykova, A. (2011) Mecha-
nism of the piRNA-mediated silencing of Drosophila telo-
meric retrotransposons, Nucleic Acids Res., 39, 8703-8711,
doi: 10.1093/nar/gkr552.
67. Sienski, G., Donertas, D., and Brennecke, J. (2012) Tran-
scriptional silencing of transposons by piwi and maelstrom
and its impact on chromatin state and gene expression,
Cell, 151, 964-980, doi: 10.1016/j.cell.2012.10.040.
68. Akkouche, A., Mugat, B., Barckmann, B., Varela-
Chavez,C., Li, B., Raffel, R., Pelisson, A., and Chambey-
ron, S. (2017) Piwi is required during Drosophila embryo-
genesis to license dual-strand piRNA clusters for trans-
poson repression in adult ovaries, Mol. Cell, 66, 411-419,
doi: 10.1016/j.molcel.2017.03.017.
69. Gunawardane, L. S., Saito, K., Nishida, K. M., Miy-
oshi,K., Kawamura, Y., Nagami, T., Siomi, H., and Si-
omi, M.C. (2007) A slicer-mediated mechanism for re-
peat-associated siRNA 5′ end formation in Drosophila,
Science, 315, 1587-1590, doi: 10.1126/science.1140494.
70. Han, B. W., Wang, W., Li, C., Weng, Z., and Zamore,
P.D. (2015) Noncoding RNA. piRNA-guided transposon
cleavage initiates Zucchini-dependent, phased piRNA
production, Science, 348, 817-821, doi: 10.1126/science.
aaa1264.
71. Mohn, F., Handler, D., and Brennecke, J. (2015) Non-
coding RNA. piRNA-guided slicing specifies transcripts
for Zucchini-dependent, phased piRNA biogenesis,
Science, 348, 812-817, doi: 10.1126/science.aaa1039.
72. Lewis, S. H., Salmela, H., and Obbard, D. J. (2016) Du-
plication and diversification of dipteran argonaute genes,
and the evolutionary divergence of Piwi and aubergine,
Genome Biol. Evol., 8, 507-518, doi: 10.1093/gbe/evw018.
73. Parhad, S. S., Tu, S., Weng, Z., and Theurkauf, W. E.
(2017) Adaptive evolution leads to cross-species incompat-
ibility in the piRNA transposon silencing machinery, Dev.
Cell, 43, 60-70 e65, doi: 10.1016/j.devcel.2017.08.012.
74. Vermaak, D., Henikoff, S., and Malik, H. S. (2005) Pos-
itive selection drives the evolution of rhino, a member of
the heterochromatin protein1 family in Drosophila, PLoS
Genet., 1, 96-108, doi: 10.1371/journal.pgen.0010009.
75. Savitsky, M., Kwon, D., Georgiev, P., Kalmykova, A., and
Gvozdev, V. (2006) Telomere elongation is under the con-
trol of the RNAi-based mechanism in the Drosophila ger-
mline, Genes Dev., 20, 345-354, doi: 10.1101/gad.370206.
76. Danilevskaya, O. N., Traverse, K. L., Hogan, N. C.,
DeBaryshe, P. G., and Pardue, M. L. (1999) The two
Drosophila telomeric transposable elements have very dif-
ferent patterns of transcription, Mol. Cell. Biol., 19, 873-
881, doi: 10.1128/MCB.19.1.873.
77. Maxwell, P. H., Belote, J. M., and Levis, R. W. (2006)
Identification of multiple transcription initiation, polyad-
enylation, and splice sites in the Drosophila melanogaster
TART family of telomeric retrotransposons, Nucleic Acids
Res., 34, 5498-5507.
78. Radion, E., Ryazansky, S., Akulenko, N., Rozovsky, Y.,
Kwon, D., Morgunova, V., Olovnikov, I., and Kalmyko-
va,A. (2017) Telomeric retrotransposon HeT-A contains
a bidirectional promoter that initiates divergent transcrip-
tion of piRNA precursors in Drosophila germline, J.Mol.
Biol., 429, 3280-3289, doi: 10.1016/j.jmb.2016.12.002.
79. Shpiz, S., Kwon, D., Rozovsky, Y., and Kalmykova, A.
(2009) rasiRNA pathway controls antisense expression of
Drosophila telomeric retrotransposons in the nucleus, Nu-
cleic Acids Res., 37, 268-278, doi: 10.1093/nar/gkn960.
80. Tatsuke, T., Sakashita, K., Masaki, Y., Lee, J. M., Kawa-
guchi, Y., and Kusakabe, T. (2010) The telomere- specific
non-LTR retrotransposons SART1 and TRAS1 are sup-
pressed by Piwi subfamily proteins in the silkworm,
KALMYKOVA, SOKOLOVA1752
BIOCHEMISTRY (Moscow) Vol. 88 No. 11 2023
Bombyx mori, Cell. Mol. Biol. Lett., 15, 118-133, doi:
10.2478/s11658-009-0038-9.
81. Radion, E., Morgunova, V., Ryazansky, S., Akulenko,N.,
Lavrov, S., Abramov, Y., Komarov, P. A., Glukhov,
S. I., Olovnikov, I., and Kalmykova, A. (2018) Key role
of piRNAs in telomeric chromatin maintenance and
telomere nuclear positioning in Drosophila germline,
Epigenetics Chromatin, 11, 40, doi: 10.1186/s13072-
018-0210-4.
82. Wagner, E., Clement, S. L., and Lykke-Andersen, J.
(2007) An unconventional human Ccr4-Caf1 deadenylase
complex in nuclear cajal bodies, Mol. Cell. Biol., 27, 1686-
1695, doi: 10.1128/MCB.01483-06.
83. Ryazansky, S., Radion, E., Mironova, A., Akulenko,N.,
Abramov, Y., Morgunova, V., Kordyukova, M. Y.,
Olovnikov, I., and Kalmykova, A. (2017) Natural variation
of piRNA expression affects immunity to transposable el-
ements, PLoS Genet., 13, e1006731, doi: 10.1371/journal.
pgen.1006731.
84. Maupetit-Mehouas, S., and Vaury, C. (2020) Trans-
poson reactivation in the germline may be useful for
both transposons and their host genomes, Cells, 9, 1172,
doi: 10.3390/cells9051172.
85. Dufourt, J., Dennis, C., Boivin, A., Gueguen, N., Ther-
on, E., Goriaux, C., Pouchin, P., Ronsseray, S., Bras-
set, E., and Vaury, C. (2014) Spatio-temporal require-
ments for transposable element piRNA-mediated silencing
during Drosophila oogenesis, Nucleic Acids Res., 42, 2512-
2524, doi: 10.1093/nar/gkt1184.
86. Theron, E., Maupetit-Mehouas, S., Pouchin, P., Bau-
det, L., Brasset, E., and Vaury, C. (2018) The interplay
between the Argonaute proteins Piwi and Aub within
Drosophila germarium is critical for oogenesis, piRNA
biogenesis and TE silencing, Nucleic acids Res., 46, 10052-
10065, doi: 10.1093/nar/gky695.
87. Kordyukova, M., Morgunova, V., Olovnikov, I., Koma-
rov, P. A., Mironova, A., Olenkina, O. M., and Kalmy-
kova,A. (2018) Subcellular localization and Egl-mediated
transport of telomeric retrotransposon HeT-A ribonuc-
leoprotein particles in the Drosophila germline and early
embryogenesis, PLoS One, 13, e0201787, doi: 10.1371/
journal.pone.0201787.
88. Sokolova, O., Morgunova, V., Sizova, T. V., Komarov,
P.A., Olenkina, O. M., Babaev, D.S., Mikhaleva, E.A.,
Kwon, D.A., Erokhin, M., and Kalmykova, A. (2023) The
insulator BEAF32 controls the spatial-temporal expres-
sion profile of the telomeric retrotransposon TART in the
Drosophila germline, Development, 150, dev201678, doi:
10.1242/dev.201678.
89. Zhang, L., Beaucher, M., Cheng, Y., and Rong, Y. S.
(2014) Coordination of transposon expression with DNA
replication in the targeting of telomeric retrotransposons
in Drosophila, EMBO J., 33, 1148-1158, doi: 10.1002/
embj.201386940.
90. Rashkova, S., Karam, S. E., Kellum, R., and Pardue,
M.L. (2002) Gag proteins of the two Drosophila telomeric
retrotransposons are targeted to chromosome ends, J.Cell
Biol., 159, 397-402, doi: 10.1083/jcb.200205039.
91. Lopez-Panades, E., Gavis, E. R., and Casacuberta, E.
(2015) Specific localization of the Drosophila telomere
transposon proteins and RNAs, give insight in their behav-
ior, control and telomere biology in this organism, PLoS
One, 10, e0128573, doi: 10.1371/journal.pone.0128573.
92. Lepesant, J. M. J., Iampietro, C., Galeota, E., Auge, B.,
Aguirrenbengoa, M., Merce, C., Chaubet, C., Rocher,V.,
Haenlin, M., Waltzer, L., Pelizzola, M., and Di Stefa-
no,L. (2020) A dual role of dLsd1 in oogenesis: regulating
developmental genes and repressing transposons, Nucleic
Acids Res
., 48, 1206-1224, doi: 10.1093/nar/gkz1142.
93. Yang, F., Quan, Z., Huang, H., He, M., Liu, X., Cai, T.,
and Xi, R. (2019) Ovaries absent links dLsd1 to HP1a for
local H3K4 demethylation required for heterochromatic
gene silencing, Elife, 8, e40806, doi: 10.7554/eLife.40806.
94. Sienski, G., Batki, J., Senti, K. A., Donertas, D.,
Tirian,L., Meixner, K., and Brennecke, J. (2015) Silen-
cio/CG9754 connects the Piwi-piRNA complex to the
cellular heterochromatin machinery, Genes Dev., 29,
2258-2271, doi: 10.1101/gad.271908.115.
95. Penke, T. J., McKay, D. J., Strahl, B. D., Matera, A.G.,
and Duronio, R.J. (2016) Direct interrogation of the role
of H3K9 in metazoan heterochromatin function, Genes
Dev., 30, 1866-1880, doi: 10.1101/gad.286278.116.
96. Teo, R. Y. W., Anand, A., Sridhar, V., Okamura, K., and
Kai, T. (2018) Heterochromatin protein 1a functions for
piRNA biogenesis predominantly from pericentric and
telomeric regions in Drosophila, Nat. Commun., 9, 1735,
doi: 10.1038/s41467-018-03908-3.
97. Wang, S. H., and Elgin, S. C. (2011) Drosophila Piwi
functions downstream of piRNA production mediating a
chromatin-based transposon silencing mechanism in fe-
male germ line, Proc. Natl. Acad. Sci. USA, 108, 21164-
21169, doi: 10.1073/pnas.1107892109.
98. Savitsky, M., Kravchuk, O., Melnikova, L., and Geor-
giev, P. (2002) Heterochromatin protein 1 is involved
in control of telomere elongation in Drosophila mela-
nogaster, Mol. Cell. Biol., 22, 3204-3218, doi: 10.1128/
MCB.22.9.3204-3218.2002.
99. Molaro, A., Falciatori, I., Hodges, E., Aravin, A. A., Mar-
ran, K., Rafii, S., McCombie, W. R., Smith, A. D., and
Hannon, G. J. (2014) Two waves of de novo methylation
during mouse germ cell development, Genes Dev., 28,
1544-1549, doi: 10.1101/gad.244350.114.
100. Zoch, A., Auchynnikava, T., Berrens, R. V., Kabaya-
ma,Y., Schopp, T., Heep, M., Vasiliauskaite, L., Perez-
Rico, Y. A., Cook, A. G., Shkumatava, A., Rappsilber,J.,
Allshire, R. C., and O’Carroll, D. (2020) SPOCD1 is
an essential executor of piRNA-directed de novo DNA
methylation, Nature, 584, 635-639, doi: 10.1038/s41586-
020-2557-5.
101. Zeng, Y., and Chen, T. (2019) DNA methylation repro-
gramming during mammalian development, Genes (Ba-
sel), 10, 257, doi: 10.3390/genes10040257.
RETROTRANSPOSONS AND TELOMERES 1753
BIOCHEMISTRY (Moscow) Vol. 88 No. 11 2023
102. Shirane, K., Kurimoto, K., Yabuta, Y., Yamaji, M., Sa-
toh,J., Ito, S., Watanabe, A., Hayashi, K., Saitou, M.,
and Sasaki, H. (2016) Global landscape and regulatory
principles of DNA methylation reprogramming for germ
cell specification by mouse pluripotent stem cells, Dev.
Cell, 39, 87-103, doi: 10.1016/j.devcel.2016.08.008.
103. Kohlrausch, F. B., Berteli, T. S., Wang, F., Navarro, P. A.,
and Keefe, D. L. (2022) Control of LINE-1 expression
maintains genome integrity in germline and early embryo
development, Reprod. Sci., 29, 328-340, doi: 10.1007/
s43032-021-00461-1.
104. Akiyama, T., Xin, L., Oda, M., Sharov, A. A., Amano,M.,
Piao, Y., Cadet, J. S., Dudekula, D. B., Qian, Y.,
Wang, W., Ko, S. B., and Ko, M. S. (2015) Transient
bursts of Zscan4 expression are accompanied by the rapid
derepression of heterochromatin in mouse embryonic stem
cells, DNA Res., 22, 307-318, doi: 10.1093/dnares/dsv013.
105. Dan, J., Rousseau, P., Hardikar, S., Veland, N., Wong, J.,
Autexier, C., and Chen, T. (2017) Zscan4 inhibits mainte-
nance DNA methylation to facilitate telomere elongation
in mouse embryonic stem cells, Cell Rep., 20, 1936-1949,
doi: 10.1016/j.celrep.2017.07.070.
106. Zalzman, M., Falco, G., Sharova, L. V., Nishiyama, A.,
Thomas, M., Lee, S. L., Stagg, C. A., Hoang, H. G.,
Yang, H. T., Indig, F. E., Wersto, R. P., and Ko, M. S.
(2010) Zscan4 regulates telomere elongation and genomic
stability in ES cells, Nature, 464, 858-863, doi: 10.1038/
nature08882.
107. Thool, M., Sundaravadivelu, P. K., Sudhagar, S., and
Thummer, R. P. (2022) A comprehensive review on the
role of ZSCAN4 in embryonic development, stem cells,
and cancer, Stem Cell Rev. Rep., 18, 2740-2756, doi:
10.1007/s12015-022-10412-1.
108. Dan, J., Zhou, Z., Wang, F., Wang, H., Guo, R., Keefe,
D. L., and Liu, L. (2022) Zscan4 contributes to telomere
maintenance in telomerase-deficient late generation
mouse escs and human ALT cancer cells, Cells, 11, 456,
doi: 10.3390/cells11030456.
109. Peaston, A. E., Evsikov, A. V., Graber, J. H., de Vries,
W. N., Holbrook, A. E., Solter, D., and Knowles, B. B.
(2004) Retrotransposons regulate host genes in mouse oo-
cytes and preimplantation embryos, Dev Cell., 7, 597-606,
doi: 10.1016/j.devcel.2004.09.004.
110. Kigami, D., Minami, N., Takayama, H., and Imai, H.
(2003) MuERV-L is one of the earliest transcribed genes
in mouse one-cell embryos, Biol. Reprod., 68, 651-654,
doi: 10.1095/biolreprod.102.007906.
111. Fadloun, A., Le Gras, S., Jost, B., Ziegler-Birling, C.,
Takahashi, H., Gorab, E., Carninci, P., and Torres- Padilla,
M. E. (2013) Chromatin signatures and retrotransposon
profiling in mouse embryos reveal regulation of LINE-1
by RNA, Nat. Struct. Mol. Biol., 20, 332-338, doi: 10.1038/
nsmb.2495.
112. Eckersley-Maslin, M. A., Svensson, V., Krueger, C.,
Stubbs, T. M., Giehr, P., Krueger, F., Miragaia, R. J.,
Kyriakopoulos, C., Berrens, R. V., Milagre, I., Walter, J.,
Teichmann, S. A., and Reik, W. (2016) MERVL/Zscan4
network activation results in transient genome-wide DNA
demethylation of mESCs, Cell Rep., 17, 179-192, doi:
10.1016/j.celrep.2016.08.087.
113. Wang, F., Chamani, I. J., Luo, D., Chan, K., Navarro,
P.A., and Keefe, D. L. (2021) Inhibition of LINE-1 ret-
rotransposition represses telomere reprogramming during
mouse 2-cell embryo development, J.Assist Reprod. Gen-
et., 38, 3145-3153, doi: 10.1007/s10815-021-02331-w.
114. Percharde, M., Lin, C. J., Yin, Y., Guan, J., Peixoto, G.A.,
Bulut-Karslioglu, A., Biechele, S., Huang, B., Shen,X.,
and Ramalho-Santos, M. (2018) A LINE1-nucleolin part-
nership regulates early development and ESC identity,
Cell, 174, 391-405, doi: 10.1016/j.cell.2018.05.043.
115. Macfarlan, T. S., Gifford, W. D., Driscoll, S., Lettieri,K.,
Rowe, H. M., Bonanomi, D., Firth, A., Singer, O., Tro-
no,D., and Pfaff, S.L. (2012) Embryonic stem cell poten-
cy fluctuates with endogenous retrovirus activity, Nature,
487, 57-63, doi: 10.1038/nature11244.
116. Ghosh, S., and Zhou, Z. (2014) Genetics of aging, proge-
ria and lamin disorders, Curr. Opin. Genet. Dev., 26, 41-46,
doi: 10.1016/j.gde.2014.05.003.
117. Gorbunova, V., Seluanov, A., Mita, P., McKerrow, W.,
Fenyo, D., Boeke, J. D., Linker, S. B., Gage, F. H., Kreil-
ing, J. A., Petrashen, A. P., Woodham, T. A., Taylor,
J. R., Helfand, S. L., and Sedivy, J. M. (2021) The role
of retrotransposable elements in ageing and age-associ-
ated diseases, Nature, 596, 43-53, doi: 10.1038/s41586-
021-03542-y.
118. Aschacher, T., Wolf, B., Enzmann, F., Kienzl, P., Mess-
ner, B., Sampl, S., Svoboda, M., Mechtcheriakova, D.,
Holzmann, K., and Bergmann, M. (2016) LINE-1 induc-
es hTERT and ensures telomere maintenance in tumour
cell lines, Oncogene, 35, 94-104, doi: 10.1038/onc.2015.65.
119. Aschacher, T., Wolf, B., Aschacher, O., Enzmann, F.,
Laszlo, V., Messner, B., Turkcan, A., Weis, S., Spiegl-
Kreinecker, S., Holzmann, K., Laufer, G., Ehrlich, M.,
and Bergmann, M. (2020) Long interspersed element-1
ribonucleoprotein particles protect telomeric ends in alter-
native lengthening of telomeres dependent cells, Neopla-
sia, 22, 61-75, doi: 10.1016/j.neo.2019.11.002.
120. Cosby, R. L., Chang, N. C., and Feschotte, C. (2019)
Host-transposon interactions: conflict, cooperation,
and cooption, Genes Dev., 33, 1098-1116, doi: 10.1101/
gad.327312.119.
121. Charlesworth, B., and Langley, C. H. (1989) The pop-
ulation genetics of Drosophila transposable elements,
Annu. Rev. Genet., 23, 251-287, doi: 10.1146/annurev.ge.
23.120189.001343.
122. Kelleher, E. S., and Barbash, D. A. (2013) Analysis of
piRNA- mediated silencing of active TEs in Drosophi-
la melanogaster suggests limits on the evolution of host
genome defense, Mol. Biol. Evol., 30, 1816-1829, doi:
10.1093/molbev/mst081.
