Evolutionary insights from profiling LINE-1 activity at allelic resolution in a single human genome

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Abstract

Transposable elements have created the majority of the sequence in many genomes. In mammals, LINE-1 retrotransposons have been expanding for more than 100 million years as distinct, consecutive lineages; however, the drivers of this recurrent lineage emergence and disappearance are unknown. Most human genome assemblies provide a record of this ancient evolution, but fail to resolve ongoing LINE-1 retrotranspositions. Utilizing the human CHM1 long-read-based haploid assembly, we identified and cloned all full-length, intact LINE-1s, and found 29 LINE-1s with measurable in vitro retrotransposition activity. Among individuals, these LINE-1s varied in their presence, their allelic sequences, and their activity. We found that recently retrotransposed LINE-1s tend to be active in vitro and polymorphic in the population relative to more ancient LINE-1s. However, some rare allelic forms of old LINE-1s retain activity, suggesting older lineages can persist longer than expected. Finally, in LINE-1s with in vitro activity and in vivo fitness, we identified mutations that may have increased replication in ancient genomes and may prove promising candidates for mechanistic investigations of the drivers of LINE-1 evolution and which LINE-1 sequences contribute to human disease.

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    Reply to the reviewers

    We would like to thank the Review Commons editor and three reviewers for their enthusiastic response, including their constructive suggestions and appreciation of the high impact and originality of our study. We have completed the revisions and new analyses suggested by the reviewers, and we thank the reviewers for their suggestions to increase the impact and interest in this work and for guiding us towards this much improved manuscript.

    In this response letter, we present the response to each reviewer comment and associated revisions made to the text and figures as bullet points below the reviewers' text (black text).

    Reviewer #1 (Evidence, reproducibility …

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    Referee #3

    Evidence, reproducibility and clarity

    Yang et al. perform an in-depth analysis of potentially mobile source L1 alleles in a single human genome (CHM1) previously subjected to Pacbio whole genome sequencing. The retrotransposition efficiencies of source L1 alleles with intact ORFs were tested in vitro, and these efficiencies compared to a model of in vivo activity based on Hamming distance to other ORF-intact L1 alleles. Comparisons of CHM1 L1 alleles are made to CHM13 (used for the recent T2T reference assembly), and also to population-scale sequencing efforts to establish how widespread each source L1 allele is. These data showcase the advantages of being able to …

  3. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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    Referee #2

    Evidence, reproducibility and clarity

    This manuscript is an interesting and well-crafted study of LINE-1 activity at the single genome human genome level using long read-based haploid assemblies. The manuscript has some real gems and address critical aspects of LINE- biology that are typically not rigorously examined. The authors are to be commended for undertaking this exercise and for providing interesting perspectives that challenge the dogma that dominates the field in several areas. Despite the noted strengths of the contributions, the manuscript ignores the clear limitations inherent to the approaches taken and at times appears as dogmatic as the dogma that they …

  4. Note: This preprint has been reviewed by subject experts for Review Commons. Content has not been altered except for formatting.

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    Referee #1

    Evidence, reproducibility and clarity

    Summary:

    Yang et al. took advantage of recently published long-read-based genomic sequences of nearly homozygous genomes from complete hydatidiform moles to retrieve allelic sequences of LINE-1, the currently only active and autonomous retrotransposon of the human genome, and produced the repertoire of intact LINE-1 in a genome. The authors performed cell-culture-based retrotransposition assays measurements and in vivo fitness estimations of all identified intact LINE-1 to infer evolutionary dynamics. In this article, the authors further validate the major contribution of polymorphic LINE-1 to the de novo retrotransposition events …