Large Differences between LINE-1 Amplification Rates in the Human and Chimpanzee Lineages

Mathews, Lauren M.; Susan, Y.; Greenberg, Noam; Ovchinnikov, Igor V.; Swergold, Gary D.

doi:10.1086/368275

Cited by 30 publications

(25 citation statements)

References 48 publications

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“…These figures compare favorably with previous estimates, considering the differences in the computational methodologies and requirements for validation of candidate loci used in the different studies (Mathews et al, 2003;CSAC, 2005;Mills et al, 2006). Because L1 elements are often truncated or rearranged (Smit et al, 1995;Szak et al, 2002), we based our analyses of L1 subfamily diversity and relationships on 864 bp-long sequences encompassing the last 665 bp of ORF2 and the entire 3′ UTR, to maximize the number of elements included in the analyses.…”

Section: L1 Elements and Nomenclature Used In This Studysupporting

confidence: 54%

“…The L1 family emerged around 120 million years (myrs) ago (Smit et al, 1995;Khan et al, 2006) and is still actively expanding in humans, as demonstrated by the existence of highly polymorphic L1 elements in human populations (Sheen et al, 2000;Myers et al, 2002;Badge et al, 2003;Boissinot et al, 2004;Seleme et al, 2006;Wang et al, 2006) and de novo L1 insertions responsible for genetic disorders (Chen et al, 2005). The detection of several hundred species-specific L1 insertions in both the human and chimpanzee genomes further supports the recent mobilization of this family of retrotransposons (Mathews et al, 2003;CSAC, 2005;Mills et al, 2006). Contrary to the non-autonomous Alu retrotransposons in which different subfamilies are capable of concomitant expansions (Batzer and Deininger, 2002;Xing et al, 2004;Hedges et al, 2005), a single line of successive L1 subfamilies has amplified within the past 40 myrs in the primate lineage leading to humans (Khan et al, 2006).…”

Section: Introductionmentioning

confidence: 78%

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Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons

Lee

Cordaux

Han

et al. 2007

Gene

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The long interspersed element-1 (LINE-1 or L1) is a highly successful retrotransposon in mammals. L1 elements have continued to actively propagate subsequent to the human-chimpanzee divergence, 6 million years ago, resulting in species-specific inserts. Here, we report a detailed characterization of chimpanzee-specific L1 subfamily diversity and a comparison with their human-specific counterparts. Our results indicate that L1 elements have experienced different evolutionary fates in humans and chimpanzees within the past ~6 million years. Although the species-specific L1 copy numbers are on the same order in both species (1200-2000 copies), the number of retrotranspositioncompetent elements appears to be much higher in the human genome than in the chimpanzee genome. Also, while human L1 subfamilies belong to the same lineage, we identified two lineages of recently integrated L1 subfamilies in the chimpanzee genome. The two lineages seem to have coexisted for several million years, but only one shows evidence of expansion within the past three million years. These differential evolutionary paths may be the result of random variation, or the product of competition between L1 subfamily lineages. Our results suggest that the coexistence of several L1 subfamily lineages within a species may be resolved in a very short evolutionary period of time, perhaps in just a few million years. Therefore, the chimpanzee genome constitutes an excellent model in which to analyze the evolutionary dynamics of L1 retrotransposons.

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Section: L1 Elements and Nomenclature Used In This Studysupporting

confidence: 54%

Section: Introductionmentioning

confidence: 78%

Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons

Lee

Cordaux

Han

et al. 2007

Gene

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“…Unlike the human lineage-specific Alu expansion, the rate of L1 element retrotranspositional activity has been relatively similar in the genomes of human and chimpanzee; they both possess $2,000 lineage-specific L1 elements . This contrasts with earlier assertions of a higher rate of L1 insertion in the chimpanzee lineage [Mathews et al, 2003;Mills et al, 2006]. However, chromosome-specific differences may be assumed, since on the chimpanzee Y chromosome, insertions of L1 elements and endogenous retroviruses have been significantly more frequent than on the human Y chromosome [Hughes et al, 2005].…”

Section: Line Element Insertionscontrasting

confidence: 84%

Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons

Kehrer‐Sawatzki¹,

Cooper²

2007

Hum. Mutat.

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The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions. Lineage-specific segmental duplications, detected by array comparative genomic hybridization and direct sequence comparison, have made a very significant contribution to this structural divergence, which is at least three-fold greater than that due to nucleotide substitutions. Since structural genomic changes may have given rise to irreversible functional differences between the diverging species, their detailed analysis could help to identify the biological processes that have accompanied speciation. To this end, interspecies comparisons have revealed numerous human-specific gains and losses of genes as well as changes in gene expression. The very considerable structural diversity (polymorphism) evident within both lineages has, however, hampered the analysis of the structural divergence between the human and chimpanzee genomes. The concomitant evaluation of genetic divergence and diversity at the nucleotide level has nevertheless served to identify many genes that have evolved under positive selection and may thus have been involved in the development of human lineage-specific traits. Genes that display signs of weak negative selection have also been identified and could represent candidate loci for complex genomic disorders. Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome.

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“…In murine rodents (Pascale et al 1993;Verneau et al 1998) and in primates (Smit et al 1995;Liu et al 2003;Boissinot et al 2004), bursts of amplification alternate with periods of low activity, and in the human lineage, the rate of L1 amplification seems to have slowly decreased over the last 25 Myr (Lander et al 2001). Correlations between bursts of amplification and evolutionary radiations (Pascale et al 1990) suggest that the history of populations, especially the occurrence of population bottlenecks (Mathews et al 2003), could affect the dynamics of L1 amplification. However, this alone could not explain the large variations in replicative success observed between L1 families, and it was recently suggested that positive or negative interactions of a host factor with L1 replicative machinery could be responsible for the episodic nature of L1 amplification (Pascale et al 1993;Furano 2000;Furano et al 2004;).…”

mentioning

confidence: 99%

Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates

Khan

Smit

Boissinot³

2005

Genome Res.

320

461

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We investigated the evolution of the families of LINE-1 (L1) retrotransposons that have amplified in the human lineage since the origin of primates. We identified two phases in the evolution of L1. From ∼70 million years ago (Mya) until ∼40 Mya, three distinct L1 lineages were simultaneously active in the genome of ancestral primates. In contrast, during the last 40 million years (Myr), i.e., during the evolution of anthropoid primates, a single lineage of families has evolved and amplified. We found that novel (i.e., unrelated) regulatory regions (5ЈUTR) have been frequently recruited during the evolution of L1, whereas the two open-reading frames (ORF1 and ORF2) have remained relatively conserved. We found that L1 families coexisted and formed independently evolving L1 lineages only when they had different 5ЈUTRs. We propose that L1 families with different 5ЈUTR can coexist because they don't rely on the same host-encoded factors for their transcription and therefore do not compete with each other. The most prolific L1 families (families L1PA8 to L1PA3) amplified between 40 and 12 Mya. This period of high activity corresponds to an episode of adaptive evolution in a segment of ORF1. The correlation between the high activity of L1 families and adaptive evolution could result from the coevolution of L1 and a host-encoded repressor of L1 activity.[Supplemental material is available online at www.genome.org.]LINE-1 (L1) retrotransposons (Fig. 1A) constitute the most abundant family of autonomously replicating retroelements in mammals, and their continuous amplification over the last ∼170 million years (Myr) has had a profound impact on the organization and function of mammalian genomes (Smit 1996;Lander et al. 2001;Kazazian 2004). L1 elements replicate via an RNA intermediate that is copied into genomic DNA at the site of insertion (Luan et al. 1993;Luan and Eickbush 1995;Cost et al. 2002). This mechanism of replication is not very efficient and generates mostly defective copies that are truncated at their 5Ј end. These copies can be classified into families of hundreds to thousands of elements based on the shared nucleotide differences they inherit from their common progenitor (or group of closely related progenitors). Because the vast majority of L1 inserts are pseudogenes, they accumulate mutations at the neutral rate (Voliva et al. 1984;Hardies et al. 1986;Pascale et al. 1993;Boissinot et al. 2000). Consequently, older families are more divergent than younger ones. Phylogenetic analyses of L1 families in murine rodents and in primates (see Furano 2000, and references therein) have shown that, over the long-term, a single lineage of L1 families amplifies and evolves, one family replacing its predecessor as the dominant family. This mode of evolution is exemplified in human, where a single lineage of families amplified over the last 25 Myr (Smit et al. 1995;. Families of closely related variants can occasionally coexist for short periods of time (Cabot et al. 1997;Boissinot et al. 2000) until one family prevails...

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Large Differences between LINE-1 Amplification Rates in the Human and Chimpanzee Lineages

Cited by 30 publications

References 48 publications

Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons

Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons

Understanding the recent evolution of the human genome: insights from human-chimpanzee genome comparisons

Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates

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