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

Hameed Khan, Arian Smit, Stephane Boissinot

    Research output: Contribution to journalArticle

    Abstract

    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 (5′UTR) 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 5′UTRs. We propose that L1 families with different 5′UTR 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.

    Original languageEnglish (US)
    Pages (from-to)78-87
    Number of pages10
    JournalGenome Research
    Volume16
    Issue number1
    DOIs
    StatePublished - Jan 1 2006

    Fingerprint

    Retroelements
    Molecular Evolution
    Primates
    Nucleic Acid Regulatory Sequences
    Open Reading Frames
    Haplorhini
    Transcription Factors
    Genome

    ASJC Scopus subject areas

    • Genetics
    • Genetics(clinical)

    Cite this

    Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. / Khan, Hameed; Smit, Arian; Boissinot, Stephane.

    In: Genome Research, Vol. 16, No. 1, 01.01.2006, p. 78-87.

    Research output: Contribution to journalArticle

    Khan, Hameed ; Smit, Arian ; Boissinot, Stephane. / Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. In: Genome Research. 2006 ; Vol. 16, No. 1. pp. 78-87.
    @article{2a4bbe85af584f739822b41c7ae9ad0a,
    title = "Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates",
    abstract = "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 (5′UTR) 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 5′UTRs. We propose that L1 families with different 5′UTR 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.",
    author = "Hameed Khan and Arian Smit and Stephane Boissinot",
    year = "2006",
    month = "1",
    day = "1",
    doi = "10.1101/gr.4001406",
    language = "English (US)",
    volume = "16",
    pages = "78--87",
    journal = "Genome Research",
    issn = "1088-9051",
    publisher = "Cold Spring Harbor Laboratory Press",
    number = "1",

    }

    TY - JOUR

    T1 - Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates

    AU - Khan, Hameed

    AU - Smit, Arian

    AU - Boissinot, Stephane

    PY - 2006/1/1

    Y1 - 2006/1/1

    N2 - 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 (5′UTR) 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 5′UTRs. We propose that L1 families with different 5′UTR 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.

    AB - 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 (5′UTR) 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 5′UTRs. We propose that L1 families with different 5′UTR 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.

    UR - http://www.scopus.com/inward/record.url?scp=30044433182&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=30044433182&partnerID=8YFLogxK

    U2 - 10.1101/gr.4001406

    DO - 10.1101/gr.4001406

    M3 - Article

    VL - 16

    SP - 78

    EP - 87

    JO - Genome Research

    JF - Genome Research

    SN - 1088-9051

    IS - 1

    ER -