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L1 repeat is a basic unit of heterochromatin satellites in cetaceans

Mol. Biol. Evol. 15(5):611–612. 1998
1998 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
Letter to the Editor
L1 Repeat Is a Basic Unit of Heterochromatin Satellites in Cetaceans
Vladimir V. Kapitonov,* Gerald P. Holmquist, and Jerzy Jurka*
*Genetic Information Research Institute, Palo Alto, California; and †Department of Biology, Beckman Institute of the City of
Hope, Duarte, California
. 1.—Alignment of dolphin satellite monomer and L1 consen-
sus sequence. The top sequence is the satellite monomer (GenBank
sequence M36451; opposite orientation) and the bottom sequence is
the L1MA9 consensus sequence (Smit et al. 1995) (positions 81–685;
RepBase Update: Numbering refers to satellite
sequence positions. Identical nucleotides are indicated by asterisks,
transversions by dots, transitions by colons, and alignment gaps by
Mammalian heterochromatin, pericentric, telomer-
ic, or intercalary, is usually composed of long arrays of
tandemly repeated DNA sequences called satellites,
which contribute up to 15%–30% of the entire genome.
Rapid divergence of heterochromatin satellites, some-
times between closely related species, raises the funda-
mental question of whether satellite monomers rapidly
evolve from the preexisting pool of satellites or some
of them are recruited from nonsatellite DNA. Previous
analyses of sequence periodicities indicate that alphoid
satellites might have evolved from smaller heptanucleo-
tide units (Zaitsev and Rogaev 1986), which suggests
continuous evolution of satellites from the preexisting
satellites. The alternative model is that individual sat-
ellite units can be recruited from a wide spectrum of
nonsatellite DNA and propagated into satellites by un-
equal crossing over (Smith 1976). This model is rooted
in the fact that no stringent functional requirements
seem to be imposed on individual satellite units, and
many DNA fragments, particularly abundant inter-
spersed repeats, should occasionally be expanded into
satellites. However, to date, no evidence of such events
has been recorded. In this correspondence, we report
that the so-called ‘common satellite’ in cetaceans orig-
inated by amplification of a DNA fragment which in-
cludes the L1 interspersed repetitive element (Boeke
The common cetacean satellites, constituting about
15% of all cetacean genomes, of both odontocetes
(toothed whales) and mysticetes (whalebone whales)
were first used to prove a monophyletic origin of the
Cetacea at the DNA level (Arnason, Hoglund, and Wid-
egren 1984). These satellites are predominantly located
in most interstitial and terminal heterochromatin C-
bands. The monomeric repeat is
1,760 bp long in all
cetaceans except dolphins, where its length is
bp (Arnason, Gretarsdottir, and Widegren 1992; Gre-
tarsdottir and Arnason 1992). There is no reported sat-
ellite DNA similar to the common cetacean satellite in
other mammalian species.
We have found that a 540-bp DNA fragment of the
common cetacean satellite monomer is 63% similar to
the 3
-terminal portion of the mammalian L1 (LINE-1)
retrotransposon (figs. 1 and 2). This is also the first se-
quence record of the L1 retroelement in the genome of
marine mammals. In addition to the nucleotide similar-
ity, we have found protein sequence similarity to the
Key words: LINE1 elements, retrotransposons and satellite DNA,
heterochromatin evolution, unequal crossing over, marine mammals.
Address for correspondence and reprints: Jerzy Jurka, Genetic In-
formation Research Institute, 440 Page Mill Road, Palo Alto, Califor-
nia 94306. E-mail:
beginning and end of the L1 ORF2-encoded protein se-
quence in mammals (fig. 2). The distance between the
homologous patterns corresponds to the size of the basic
satellite unit (
1,580 bp). The most likely interpretation
of these facts is that the entire unit was derived from an
L1-ORF2 fragment which underwent extensive internal
deletions and other mutational events. Given the 80%
similarity between dolphin and whale satellites, it is rea-
sonable to assume a common origin of satellites in both
species from a rearranged L1 fragment.
Generally, infrequent insertions of retroelements
constitute only a tiny fraction of C-band-positive regions
of mammalian heterochromatin (Bickmore and Craif
1997, p. 164). Recently, the presence of separate clusters
612 Kapitonov et al.
. 2—Schematic structure of the dolphin satellite DNA from heterochromatin C-bands. The satellite monomer is represented by an arrow
(GenBank accession number M36451; opposite orientation). The 3
region of the monomer (540 bp; gray in the figure) is 63% similar at the
nucleotide level to the mammalian L1 non-LTR retrotransposon, L1MA9 subfamily. The hatched areas indicate significant protein similarity to
the L1 ORF2 protein (PIR accession number S65824; BLASTX P value is 10
of retrotransposons in invertebrate and plant alpha-het-
erochromatin has been reported (Carmena and Gonzalez
1995; Pimpinelli et al. 1995; Pearce et al. 1996; Terri-
noni et al. 1997). It has been proposed that they could
be stable structural components of heterochromatin
(Pimpinelli et al. 1995) or telomeric elements partici-
pating in the compensation of the systematic chromo-
some shortening (Pardue et al. 1996). However, as in-
dicated before (Lohe and Hilliker 1995), there are no
reported data demonstrating that retroelements may
serve as the basic core of satellite monomers, and there
are no reported relationships between retrotransposons
and heterochromatin satellite formation.
The major aspect of our finding is that it revives
the Smith (1976) mechanism of unequal crossing over,
which predicts that if an individual sequence of the sat-
ellite monomer is to some extent arbitrary, then common
interspersed repeats should occasionally be found fixed
in alpha-heterochromatin. Since none were found before
our finding, this prediction lacked evidence, and the role
of the Smith mechanism in satellite evolution remained
We thank anonymous reviewers for their useful
suggestions. This work was supported by grant P41
LM06252 from the National Institutes of Health.
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, reviewing editor
Accepted January 16, 1998
... This approach through chromosomal mapping of LINE-1 has shown different distribution patterns in mammals; 24-32 some LINE-1 are insertions in Adenine and Thymine (AT) rich regions, in euchromatic G-positive bands, on some autosomes and on the X chromosome; 25,26 many other LINE-1 insertions occur in heterochromatic regions, especially in the centromeric regions presumably having a role at the centromeric position. [27][28][29][30][31] Furthermore, it has been hypothesized through the FISH approach that LINE-1 play a role during evolution and are linked with chromosomal rearrangements. 8,9,32 Platyrrhini are small anthropoids grouped into three families: Cebidae, Atelidae and Pitheciidae. ...
... In both A. geoffroyi and A. fusciceps (Figure 1a, 2a), we found almost all non-centromeric LINE-1 signals along chromosomal arms on the X chromosome and in autosomes with a few exception; these signals were, in euchromatic regions either in DAPI positive bands or in CMA3-positive regions and also with a partial correspondence with C positive bands ( Figure 2a, b, c; Figure3b), in agreement with what was observed in many mammals groups, [25][26][27]33 including NMWs. [37][38] These interstitial LINE-1 signals found along chromosomes at non-centromeric regions, through a comparison with the human chromosomal homology extrapolated from previously obtained painting data for A. geoffroyi and A. fusciceps, 42,43 led us to show they overlap with breakpoint regions at the junction of human syntenic blocks (Figure 1a). ...
Full-text available
To investigate the distribution of LINE-1 repeat sequences, a LINE-1 probe was Fluorescence In Situ Hybridized (FISH) on the chromosomes of Ateles geoffroyi and Ateles fusciceps (Atelidae); a LINE-1 probe was also mapped on Cebuella pygmaea (Cebidae) and used as an outgroup for phylogenetic comparison. Ateles spider monkeys have a highly rearranged genome and are an ideal model for testing whether LINE-1 is involved in genome evolution. The LINE-1 probe has been mapped in the two Atelidae species for the first time, revealing a high accumulation of LINE-1 sequences along chromosomal arms, including telomeres, and a scarcity of LINE-1 signals at centromere positions. LINE-1 mapping in C. pygmaea (Cebidae) revealed signals at centromere positions and along chromosome arms, which was consistent with previous published data from other Cebidae species. In a broader sense, the results were analyzed in light of published data on whole-chromosomal human probes mapped in these genomes. This analysis allows us to speculate about the presence of LINE-1 sequences at the junction of human chromosomal syntenies, as well as a possible link between these sequences and chromosomal rearrangements.
... Mobile elements, also known as transposable elements (TEs), are recognised among the variety of repetitive elements in genomes. These sequences are quite abundant in the complex genomes of animals such as primates, and the first account has estimated they make up about 26% of the human genome [1], though more recent estimates claim they account for [45][46][47][48][49][50][51][52].1% [2,3]. With improvements in genome assemblies, it has been shown that this region is responsible for the different genome sizes, especially due to TE activity [4]. ...
... LINE-1 and C patterns obtained for the two NWMs are reported on ideograms in Figure 3; in the two Cebidae species analysed in the present work, we found an accumulation of LINE-1 elements displaying a nonrandom distribution by accumulating primarily in CMA-3 and C-positive bands at centromeres or pericentromeric regions (chromosome pairs 13-26 in both species, with some exceptions) (Figures 1a-h, 2 and 3). This result is in agreement with what was previously shown in many other mammals, such as bats, rodents [27,28], and primates [15,22,40,41,[46][47][48]. The comparison of the LINE-1 mapping with previously published data, in particular in species from the Cebidae family, such as Saguinus midas, S. bicolour [41], S. mystax, Leontocebus fuscicollis, Leontopithecus rosalia [15], Aotus nancymaae, and an Atelidae, Alouatta belzebul [22], showed predominantly centromeric distribution in all species. ...
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This work focuses on the distribution of LINE-1 (a Long Interspersed Nuclear Element) in primates and its role during evolution and as a constituent of the architecture of primate genomes. To pinpoint the LINE-1 repeat distribution and its role among primates, LINE-1 probes were mapped onto chromosomes of Homo sapiens (Hominidae, Catarrhini), Sapajus apella, and Cebus capucinus (Cebidae, Platyrrhini) using fluorescence in situ hybridisation (FISH). The choice of platyrrhine species are due to the fact they are taxa characterised by a high level of rearrangements; for this reason, they could be a useful model for the study of LINE-1 and chromosome evolution. LINE-1 accumulation was found in the two Cebidae at the centromere of almost all acrocentric chromosomes 16-22 and on some bi-armed chromosomes. LINE-1 pattern was similar in the two species but only for chromosomes 6, 8, 10, and 18, due to intrachromosomal rearrangements in agreement with what was previously hypothesised as through g banding. LINE-1 interstitial accumulation was found in humans on the 1, 8, 9, 13-15, and X chromosomes; on chromosomes 8, 9, and 13-15, the signal was also at the centromeric position. This is in agreement with recent and complete molecular sequence analysis of human chromosomes 8 and some acrocentric ones. Thus, the hypothesis regarding a link between LINE-1 and centromeres as well as a link with rearrangements are discussed. Indeed, data analysis leads us to support a link between LINE-1 and inter-and intrachromosomal rearrangements, as well as a link between LINE-1 and structural functions at centromeres in primates.
... Sequence similarities between tandem repeats and TEs [76][77][78] indicate a strong evolutionary relationship between these repetitive sequences. In addition, it is also believed that TEs are involved in the origin of some sequence motifs that characterized some satDNAs, as the CENP-B box, presenting this sequence motif strong similarity with the terminal inverted repeats of pogo transposons [79]. ...
... In fact, computer simulations have suggested that satDNA monomers could be generated from a wide variety of non-satellite sequences and propagated into an array by unequal crossing-over [80]. These non-satellite sequences are often TEs [26,31,76,[81][82][83][84][85][86][87][88]. In Table 1, different examples known in the literature are listed where TEs or parts of TEs were converted into other repetitive sequence or altered genes. ...
... The evidence available for the pea, Pisum sativum, indicates that the satDNA PisTR-A originated through the amplification and homogenization of tandem repeats present in the hypervariable 3 UTR of the Ty3/gypsy-like Ogre elements [59]. The 3 terminal may also play a key role in this process, as observed in Drosophila melanogaster, in which the emergence of new satDNA corresponded to the 3 non-coding region of the transposable element HeT-A [87], and in the cetaceans, the DNA of the common satellite monomer is similar to the 3'-terminal portion of the mammalian L1 (LINE-1) retrotransposon [82] (Figure 2). ...
Full-text available
The impact of transposable elements (TEs) on the evolution of the eukaryote genome has been observed in a number of biological processes, such as the recruitment of the host’s gene expression network or the rearrangement of genome structure. However, TEs may also provide a substrate for the emergence of novel repetitive elements, which contribute to the generation of new genomic components during the course of the evolutionary process. In this review, we examine published descriptions of TEs that give rise to tandem sequences in an attempt to comprehend the relationship between TEs and the emergence of de novo satellite DNA families in eukaryotic organisms. We evaluated the intragenomic behavior of the TEs, the role of their molecular structure, and the chromosomal distribution of the paralogous copies that generate arrays of repeats as a substrate for the emergence of new repetitive elements in the genome. We highlight the involvement and importance of TEs in the eukaryote genome and its remodeling processes.
... In our work, we found LINE-1 elements by FISH in the two species analyzed of both the Cebidae and Atelidae families, at centromeric position in agreement with previous cytogenetic molecular data (Serfaty et al. 2017, Ceraulo et al., 2021b and supporting also previous molecular data (Sookdeo et al. 2018). LINE-1 probes displayed a non-random distribution by accumulating primarily in CMA3 positive bands at centromeres or pericentromeric regions, co-localizing with C-positive heterochromatin bands (Fig 1, 2); the co-localization of LINE-1 with C-positive bands was previously identified not only in primates but also in other taxa (Kapitonov et al. 1998;Serfaty et al. 2017). The finding of the centromeric enrichment of LINEs in all analyzed platyrrhine species permitted us to hypothesize that this accumulation might have occurred in the common ancestor of all Platyrrhini, contributing to their current karyotype features. ...
Full-text available
LINE-1 sequences have been linked to genome evolution, plasticity and speciation; however, despite their importance, their chromosomal distribution is poorly known in primates. In this perspective, we used fluorescence in situ hybridiza-tion (FISH) to map LINE-1 probes onto two representative platyrrhine species, Aotus nancymaae (Cebidae) and Alouatta belzebul (Atelidae), both characterized with high-ly rearranged karyotypes, in order to investigate their chromosomal distribution and role and to better characterize the two genomes. We found centromeric enrichment of LINE-1 sequences on all biarmed and acrocentric chromosomes co-localized with heterochromatin C-positive bands. This distribution led us to hypothesize that LINE 1 sequences may have a role in the centromere architecture and karyotype organization of platyrrhine genomes.Keyword:transposable elements, C-banding, molecular cytogenetics probes, genome evolution.INTRODUCTIONThrough classic and molecular cytogenetics, many primates have been shown to have variable karyotypes; many kinds of probes have been mapped, including single locus probes (Dumas and Sineo 2010, 2012), and Bacterial Artificial Chromosomes (BAC) (Dumas and Sineo 2014; Dumas et al. 2015) and whole chromosome paints have been used (Dumas et al. 2007; Dumas et al. 2012), showing a high rate of intrachromosomal and intrachromosomal rearrangements. In particular, among Platyrrhini (New World primates) liv-ing in tropical and neotropical regions, the genera Alouatta (howler mon-keys) (Cebidae) and Aotus (owl monkey) (Cebidae) have very derived kary-otypes. Originally, one or only a few species were recognized in these two genera: in Aotus there was just one, while later up to eleven species were described, with many of them showing different karyomorphs and having diploid numbers ranging between 2n=46 to 56; Alouatta went from five rec-
... In the plant Aegilops speltoides, the 250 bp centromeric satellite shares high similarity to portions of a Ty3/gypsy-like retrotransposons [49]. TEs homologous to centromeric repeats have also been identified in other plant species, such as the Atenspm element in A. thaliana [50] and ATCOPIA93 in A. lyrata [51], as well as in animals such as the pDv element in D. virilis [52], and in cetaceans [53]. ...
Full-text available
Transposable elements (TEs) are abundant components of constitutive heterochromatin of the most diverse evolutionarily distant organisms. TEs enrichment in constitutive heterochromatin was originally described in the model organism Drosophila melanogaster, but it is now considered as a general feature of this peculiar portion of the genomes. The phenomenon of TE enrichment in constitutive heterochromatin has been proposed to be the consequence of a progressive accumulation of transposable elements caused by both reduced recombination and lack of functional genes in constitutive heterochromatin. However, this view does not take into account classical genetics studies and most recent evidence derived by genomic analyses of heterochromatin in Drosophila and other species. In particular, the lack of functional genes does not seem to be any more a general feature of heterochromatin. Sequencing and annotation of Drosophila melanogaster constitutive heterochromatin have shown that this peculiar genomic compartment contains hundreds of transcriptionally active genes, generally larger in size than that of euchromatic ones. Together, these genes occupy a significant fraction of the genomic territory of heterochromatin. Moreover, transposable elements have been suggested to drive the formation of heterochromatin by recruiting HP1 and repressive chromatin marks. In addition, there are several pieces of evidence that transposable elements accumulation in the heterochromatin might be important for centromere and telomere structure. Thus, there may be more complexity to the relationship between transposable elements and constitutive heterochromatin, in that different forces could drive the dynamic of this phenomenon. Among those forces, preferential transposition may be an important factor. In this article, we present an overview of experimental findings showing cases of transposon enrichment into the heterochromatin and their positive evolutionary interactions with an impact to host genomes.
... Retroelements, mobile elements that propagate via an RNA intermediate, have been proposed as major players in centromere evolution because they can provide the material for generation of new satellite families. Such phenomena have been observed in plants (Kapitonov and Jurka 1999;Cheng and Murata 2003), Drosophila (Heikkinen, et al. 1995), and cetaceans (Kapitonov, et al. 1998). Furthermore, centromeric retroelements have been implicated in facilitating chromosome evolution through the introduction of large-scale genomic rearrangements as specific classes of centromeric retroelement have been found to be enriched at evolutionary breakpoints (Longo, et al. 2009). ...
Full-text available
Centromeres are functionally conserved chromosomal loci essential for proper chromosome segregation during cell division, yet they show high sequence diversity across species. Despite their variation, a near universal feature of centromeres is the presence of repetitive sequences, such as DNA satellites and transposable elements (TEs). Because of their rapidly evolving karyotypes, gibbons represent a compelling model to investigate divergence of functional centromere sequences across short evolutionary timescales. In this study, we use ChIP-seq, RNA-seq and fluorescence in situ hybridization to comprehensively investigate the centromeric repeat content of the four extant gibbon genera (Hoolock, Hylobates, Nomascus and Siamang). In all gibbon genera, we find that CENP-A nucleosomes and the DNA-proteins that interface with the inner kinetochore preferentially bind retroelements of broad classes rather than satellite DNA. A previously identified, gibbon-specific composite retrotransposon, LAVA, known to be expanded within the centromere regions of one gibbon genus (Hoolock), displays centromere- and species-specific sequence differences, potentially as a result of its co-option to a centromeric function. When dissecting centromere satellite composition, we discovered the presence of the retroelement-derived macrosatellite SST1 in multiple centromeres of Hoolock, whereas alpha-satellites represent the predominate satellite in the other genera, further suggesting an independent evolutionary trajectory for Hoolock centromeres. Finally, using de novo assembly of centromere sequences, we determined that transcripts originating from gibbon centromeres recapitulate the species-specific TE composition. Combined, our data reveal dynamic shifts in the repeat content which define gibbon centromeres and coincide with the extensive karyotypic diversity within this lineage.
... Although this was not described before, we can observe that several of Repbase Merlin families also have internal tandem repeats (S1 Table). The close relationship of tandem repeats and TEs has been recently well documented, with several micro, mini and satellite DNAs found embedded within TEs [65][66][67][68][69][70]. The existence of tandem repeats in multiple families and copies of Merlin indicates this TE could help to spread tandem repeats by transposition as proto-satellites that could be next amplified and homogenized such as the model suggested by Paço and colleagues [67]. ...
Full-text available
DNA transposons are defined as repeated DNA sequences that can move within the host genome through the action of transposases. The transposon superfamily Merlin was originally found mainly in animal genomes. Here, we describe a global distribution of the Merlin in animals, fungi, plants and protists, reporting for the first time their presence in Rhodophy-ceae, Metamonada, Discoba and Alveolata. We identified a great variety of potentially active Merlin families, some containing highly imperfect terminal inverted repeats and internal tandem repeats. Merlin-related sequences with no evidence of mobilization capacity were also observed and may be products of domestication. The evolutionary trees support that Merlin is likely an ancient superfamily, with early events of diversification and secondary losses, although repeated re-invasions probably occurred in some groups, which would explain its diversity and discontinuous distribution. We cannot rule out the possibility that the Merlin superfamily is the product of multiple horizontal transfers of related prokaryotic insertion sequences. Moreover, this is the first account of a DNA transposon in kinetoplastid flagellates, with conserved Merlin transposase identified in Bodo saltans and Perkinsela sp., whereas it is absent in trypanosomatids. Based on the level of conservation of the transposase and overlaps of putative open reading frames with Merlin, we propose that in protists it may serve as a raw material for gene emergence.
... In addition, the evolution of the variable heterochromatic part of the genome in different groups of marine mammals has been researched actively in whales and less so in pinnipeds. Heterochromatin in whales reaches 25-30% of the genome and is composed of different families of repeated sequences [76][77][78][79][80][81][82]. Heterochromatin is scarcer in pinnipeds than in whales. ...
Full-text available
Pinnipedia karyotype evolution was studied here using human, domestic dog, and stone marten whole-chromosome painting probes to obtain comparative chromosome maps among species of Odobenidae (Odobenus rosmarus), Phocidae (Phoca vitulina, Phoca largha, Phoca hispida, Pusa sibirica, Erignathus barbatus), and Otariidae (Eumetopias jubatus, Callorhinus ursinus, Phocarctos hookeri, and Arctocephalus forsteri). Structural and functional chromosomal features were assessed with telomere repeat and ribosomal-DNA probes and by CBG (C-bands revealed by barium hydroxide treatment followed by Giemsa staining) and CDAG (Chromomycin A3-DAPI after G-banding) methods. We demonstrated diversity of heterochromatin among pinniped karyotypes in terms of localization, size, and nucleotide composition. For the first time, an intrachromosomal rearrangement common for Otariidae and Odobenidae was revealed. We postulate that the order of evolutionarily conserved segments in the analyzed pinnipeds is the same as the order proposed for the ancestral Carnivora karyotype (2n = 38). The evolution of conserved genomes of pinnipeds has been accompanied by few fusion events (less than one rearrangement per 10 million years) and by novel intrachromosomal changes including the emergence of new centromeres and pericentric inversion/centromere repositioning. The observed interspecific diversity of pinniped karyotypes driven by constitutive heterochromatin variation likely has played an important role in karyotype evolution of pinnipeds, thereby contributing to the differences of pinnipeds’ chromosome sets.
To study heterochromatin distribution differences among tamarins, we applied LINE-1 probes using fluorescence in situ hybridization onto chromosomes of Saguinus mystax, Leontocebus fuscicollis, and Leontopithecus rosalia with the aim to investigate possible evolutionary implications. LINE-1 repeats were shown to be involved in genome architecture and in the occurrence of chromosomal rearrangements in many vertebrates. We found bright LINE-1 probe signals at centromeric or pericentromeric areas, GC rich, on almost all chromosomes in three tamarin species. We also found non-centromeric signals along chromosome arms. In a phylogenetic perspective, we analyzed the pattern of LINE-1 distribution considering human chromosomal homologies and C banding patterns. Our data indicate that LINE-1 centromeric expansions and accumulation presumably arose in a common tamarin ancestor and that the presence of LINE-1 at the junction of human chromosome associations is presumably linked to interchromosomal rearrangements. For example, we found bright centromeric signals as well as non-centromeric signals on chromosomes 1 and 2, in all species analyzed, in correspondence to human chromosome associations 13/9/22 and 20/17/13, which are synapomorphic for all tamarins. Furthermore, we found other faint signals that could be apomorphisms linked both to intrachromosomal rearrangements as well as to retro-transposition events. Our results confirm that the three species have similar karyotypes but small differences in LINE-1 and heterochromatin amplification and distribution; in particular on chromosome pairs 19–22, where we show the occurrence of small inversions, in agreement with previous classic cytogenetic hypotheses.
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We determined the distribution of 11 different transposable elements on Drosophila melanogaster mitotic chromosomes by using high-resolution fluorescent in situ hybridization (FISH) coupled with charge-coupled device camera analysis. Nine of these transposable elements (copia, gypsy, mdg-1, blood, Doc, I, F, G, and Bari-1) are preferentially clustered into one or more discrete heterochromatic regions in chromosomes of the Oregon-R laboratory stock. Moreover, FISH analysis of geographically distant strains revealed that the locations of these heterochromatic transposable element clusters are highly conserved. The P and hobo elements, which are likely to have invaded the D. melanogaster genome at the beginning of this century, are absent from Oregon-R heterochromatin but clearly exhibit heterochromatic clusters in certain natural populations. Together these data indicate that transposable elements are major structural components of Drosophila heterochromatin, and they change the current views on the role of transposable elements in host genome evolution.
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Analysis of the 3'-ends of approximately 900 separate human LINE-1 (L1) elements from primates revealed 47 contiguous but distinct subfamilies with the L1 family. Eight previously described medium reiteration frequency sequences (MERs) were found to be parts of ancient L1 untranslated 3'-regions which show little or no sequence similarity to the presently active L1 3'-end. Some of the major changes in 3'-end sequence can be explained by recombination events between different L1 repeats as well as between L1 and unrelated repetitive sequences. One of these sequences, MER42, is reported in this paper. With the set of consensus sequences for different subfamilies and their diagnostic features, it is possible to estimate the age of individual LINE-1 elements. Contrary to earlier suggestions, the majority of L1 copies in the human genome is very old; more than half of the identifiable elements were inserted into the genome before the mammalian radiation, as evidenced by elements at orthologous sites in human and other mammalian genomes. Multiple distinct L1 source genes seem to have been active simultaneously over long periods of time.
The intragenomic location of the elements of the I, G, jockey, F, and Doc transposon families has been studied by the Southern blot analysis, in 12 laboratory Drosophila melanogaster stocks. Elements located in euchromatin, heterochromatin, and on the Y chromosome are identified, and their stability has been assessed by comparing the autoradiographs detected in different stocks and analysis of individual flies. Evidence is shown suggesting that preferential location in euchromatin or heterochromatin and the distribution within heterochromatin are distinctive of transposon families. Elements located in heterochromatin can be unstable. These results are discussed in the context of the relationship between transposable elements and the host genome.
In Drosophila, chromosome ends (telomeres) are composed of telomere-specific transposable elements (the retroposons HeT-A and TART). These elements are a bona fide part of the cellular machinery yet have many of the hallmarks of retrotransposable elements and retroviruses, raising the possibility that parasitic transposable elements and viruses might have evolved from mechanisms that the cell uses to maintain its chromosomes. It is striking that Drosophila, the model organism for many discoveries in genetics, development and molecular biology (including the classical concept of telomeres), should prove to have chromosome ends different from the generally accepted model. Studies of these telomere-specific retrotransposable elements raise questions about conventional wisdom concerning not only telomeres, but also transposable elements and heterochromatin.
It is often supposed that highly repetitious DNA's arise only as a result of unusual mechanisms or in response to selective pressure. My arguments and simulations suggest, by contrast, that a pattern of tandem repeats is the natural state of DNA whose sequence is not maintained by selection. The simulations show that periodicities can develop readily from nonreptitious DNA as a result of the random accumulation of random mutations and random homology-dependent unequal crossovers. The lengths of these periodicities, and the patterns of subrepeats within them, would fluctuate in evolution, with the probability of a given pattern being dependent on the unknown exact nature of the crossover mechanism. Qualitatively, then, unequal crossover provides a reasonable and uncontrived explanation for the prevalence of highly repeated sequences in DNA and for the patterns of periodicity they evince.
The genomes of all extant cetaceans are characterized by the presence of the so-called common cetacean DNA satellite. In the mysticetes (whalebone whales) the repeat length of the satellite is 1,760 bp. In the odontocetes (toothed whales), other than the family Delphinidae, the repeat length is usually approximately 1,740 bp. The Delphinidae are characterized by a repeat length of approximately 1,580 bp. It has been shown in odontocetes that the satellite evolves in concert and that differences between species, with respect to the sequence of the satellite, correspond reasonably well to their evolutionary distances. In the present study the sequence of the satellite was determined in three repeats in each of seven mysticete species, and a consensus for each species established. Parsimony and neighbor-joining analyses based upon sequences of all repeats showed that the primary evolutionary distinction among the mysticetes is between the Balaenidae sensu stricto (i.e., the bowhead whale and the right whale) and all remaining species, including the pygmy right whale, a species that usually has been included in the Balaenidae. The comparisons also showed that the humpback whale and the gray whale were approximately equidistant from the blue whale and the fin whale (genus Balaenoptera). Concerted evolution of the satellite was also demonstrated among the mysticetes, but it appeared to evolve more slowly in the mysticetes than in the odontocetes.
The common cetacean highly repetitive DNA component was analyzed with respect to its evolution and value for establishing phylogenetic relationships. The repeat length of the component, which is tandemly organized, is ≈ 1750 by in all cetaceans except the delphinids, in which the repeat length is ≈ 1580 bp. The evolution of the component was studied after sequencing the component in different odontocetes representing the Delphinidae (delphinids), Monodontidae (narwhals), and Ziphiidae (beaked whales). The evolution of this component is very slow, and comparisons showed that sequence divergence among species corresponds closely to their generally accepted phylogenetic relationships and that the component evolves in a concerted manner. The phylogenetic information obtained in this study identified the Irrawaddy dolphin (Orcaella brevirostris) as a delphinid and did not support a close relationship of this species with the Monodontidae.
The nucleotide sequence of two cloned fragments of human alphoid DNA was established. These fragments were earlier characterized in our laboratory as molecular markers of the 3rd (pHS05) and 11th (pHS53) chromosomes. Fragment pHS53 (2546 bp) contains alphoid repeats tandemly arranged and organized into three highly homologous pentamers. The heterogeneity of monomeric sequences within individual pentamers reaches 24-33%. Structural analysis of EcoRI subfragment pHS05 showed that this alphoid tetramer consists of two dimers 340 bp long. These dimers differ up to 16% from each other and from the so-called consensus sequence of the EcoRI-340 bp-restriction fragments family reported earlier by Wu and Manuelidis. The primary structure of four cloned fragments of EcoRI-340 bp-family was established. The data show that human alphoid DNA is highly heterogeneous. This conclusion is opposite to the view suggesting that alphoid DNA is a highly homogeneous class of reiterated sequences of the human genome.
It is controversial whether odontocetes (toothed whales) and mysticetes (whalebone whales) have a common ancestry. Cetacean karyological uniformity, which is unique among mammalian orders, suggests a monophyletic origin; however, several anatomical authorities have maintained that odontocetes and mysticetes are diphyletic. We investigated the issue using Southern blot hybridization. Two labelled restriction fragment probes from the DNA of the sei whale (a mysticete) were hybridized to restricted DNA of cetacean species representing all extant families except the Eschrichtiidae, the gray whales. The probes hybridized to specific restriction fragments in all odontocete and mysticete materials. Hybridization showed preservation of hybridization homologies and a striking conservation of the length of highly repeated DNA sequences. The results are compatible with a common ancestry of odontocetes and mysticetes.
In situ hybridisation to mitotic chromosomes shows that sequences homologous to different Drosophila melanogaster transposable elements are widely distributed not only in beta but also in alpha-heterochromatin. Clusters of these sequences are detected in most proximal positions. They colocalise with known satellite sequences in several regions, but are also located in places where no known sequence has been mapped so far. The pattern of hybridisation is dinstinctive and specific for each element, and presents constant features in six different D. melanogaster strains studied. The entirely heterochromatic Y chromosome contains large amounts of these sequences. Additionally, some of these sequences appear to be present in substantial quantities in the smallest minichromosome of Drosophila, Dp(1;f)1187.