A comprehensive analysis of chimpanzee (Pan troglodytes)-specific LINE-1 retrotransposons

Lee, Sun Young; Tang, Wanxiangfu; Liang, Ping; Han, Kyudong

doi:10.1016/j.gene.2019.01.022

Cited by 5 publications

(5 citation statements)

References 37 publications

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“…In particular, raw numbers of LINE-1 elements have been estimated for chimpanzees (5913), orangutans (21,711), crab-eating macaques (782), rhesus macaques (3016), green monkeys (11,981), and humans, based on the most updated reference sequences [ 1 , 61 ]. Other detailed analyses have been recently performed on single species, for example, Pan troglodytes [ 62 ] and Gorilla gorilla [ 63 ], while human-specific elements were previously found [ 7 ] and are still being researched [ 1 ]. In humans, it has been demonstrated that LINE-1 are also responsible for the interindividual variability linked to structural variants, providing a large number of insertions that are informative for fine-scale analysis of human genetic population history [ 12 ], even in extinct hominid species [ 64 ].…”

Section: Discussionmentioning

confidence: 99%

Mapping Retrotransposon LINE-1 Sequences into Two Cebidae Species and Homo sapiens Genomes and a Short Review on Primates

Milioto

Perelman

Paglia³

et al. 2022

Genes

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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.

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Section: Discussionmentioning

confidence: 99%

Mapping Retrotransposon LINE-1 Sequences into Two Cebidae Species and Homo sapiens Genomes and a Short Review on Primates

Milioto

Perelman

Paglia³

et al. 2022

Genes

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“…In contrast, in humans, the active family is the L1HS, consisting of several subfamilies, namely pre-Ta, Ta-0, Ta-1, Ta1-d, and Ta1-nd [9,95], of which about 146 copies are active [5]. Moreover, comparative analysis showed that the activity of human L1 copies is significantly higher than that of chimpanzees [90,94].…”

Section: Line Evolution In Primatesmentioning

confidence: 95%

“…Only in New World South American spider monkeys the absence of L1 activity was found [87,88]. The evolutionary history of the Old World primates began approximately 21-25 myrs and is associated with the distribution of L1PA6-L1PA5 elements [83,[89][90][91]. L1PA5-6 elements, which are evolutionarily closest to their modern active L1 subfamilies, are most widely distributed in the genomes of monkeys (Cercopithecoidea) [89,90].…”

Section: Line Evolution In Primatesmentioning

confidence: 99%

“…The evolutionary history of the Old World primates began approximately 21-25 myrs and is associated with the distribution of L1PA6-L1PA5 elements [83,[89][90][91]. L1PA5-6 elements, which are evolutionarily closest to their modern active L1 subfamilies, are most widely distributed in the genomes of monkeys (Cercopithecoidea) [89,90]. Interestingly, the greatest differences in the number of primate L1 were found among the Cercopithecoidea.…”

Section: Line Evolution In Primatesmentioning

confidence: 99%

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Factors Regulating the Activity of LINE1 Retrotransposons

Protasova

Andreeva

Rogaev

2021

Genes

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LINE-1 (L1) is a class of autonomous mobile genetic elements that form somatic mosaicisms in various tissues of the organism. The activity of L1 retrotransposons is strictly controlled by many factors in somatic and germ cells at all stages of ontogenesis. Alteration of L1 activity was noted in a number of diseases: in neuropsychiatric and autoimmune diseases, as well as in various forms of cancer. Altered activity of L1 retrotransposons for some pathologies is associated with epigenetic changes and defects in the genes involved in their repression. This review discusses the molecular genetic mechanisms of the retrotransposition and regulation of the activity of L1 elements. The contribution of various factors controlling the expression and distribution of L1 elements in the genome occurs at all stages of the retrotransposition. The regulation of L1 elements at the transcriptional, post-transcriptional and integration into the genome stages is described in detail. Finally, this review also focuses on the evolutionary aspects of L1 accumulation and their interplay with the host regulation system.

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“…[19][20][21] Numerous additional species-specific LINE-1 retrotransposons have been discovered in chimpanzees, gorillas (Hominidae), and representative species of the Cercopithecidae family in recent studies using advanced sequencing methods that allow for better detection of repetitive sequences that traditionally have not been easily detected. [22][23] Through molecular sequence data analysis, LINE-1 activity has also been shown in New World Monkeys (NWMs) of the genera Saimiri and Saguinus, but with contrasting results in the Ateles lineage. 19,20 Another approach used to study LINE sequence distribution is the molecular cytogenetic approach by Fluorescence In Situ Hybridization (FISH).…”

Section: Introductionmentioning

confidence: 99%

Retrotransposon mapping in spider monkey genomes of the family Atelidae (Platyrrhini, Primates) shows a high level of LINE-1 amplification

et al. 2022

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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.

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A comprehensive analysis of chimpanzee (Pan troglodytes)-specific LINE-1 retrotransposons

Cited by 5 publications

References 37 publications

Mapping Retrotransposon LINE-1 Sequences into Two Cebidae Species and Homo sapiens Genomes and a Short Review on Primates

Mapping Retrotransposon LINE-1 Sequences into Two Cebidae Species and Homo sapiens Genomes and a Short Review on Primates

Factors Regulating the Activity of LINE1 Retrotransposons

Retrotransposon mapping in spider monkey genomes of the family Atelidae (Platyrrhini, Primates) shows a high level of LINE-1 amplification

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