{"doi":"10.1073/pnas.2006038117","title":"Co-option of the lineage-specific\n                    <i>LAVA</i>\n                    retrotransposon in the gibbon genome","abstract":"<jats:title>Significance</jats:title>\n                  <jats:p>\n                    Transposable elements (TEs) are genetic units that can selfishly propagate in a host genome. Despite often being considered “junk,” TEs can occasionally acquire useful functions such as regulating expression of nearby host genes. Here, we study gibbons, small apes whose genome contains a unique TE called\n                    <jats:italic>LAVA</jats:italic>\n                    (LINE-\n                    <jats:italic>Alu</jats:italic>\n                    Sz-VNTR-\n                    <jats:italic>Alu</jats:italic>\n                    <jats:sub>LIKE</jats:sub>\n                    ). We present evidence indicating that several LAVA insertions function as gene regulatory elements in the gibbon genome. Two of these insertions were also favored/preserved by natural selection, further indicating their functional importance for gibbons. Both of these LAVA elements were found inside genes that facilitate correct repair of DNA breaks, suggesting that LAVA’s incorporation in these genes may have influenced the regulation of biological processes that are crucial for maintaining genome integrity.\n                  </jats:p>","journal":"Proceedings of the National Academy of Sciences","year":2020,"id":32756,"datarank":0.723555967211706,"base_score":3.1780538303479458,"endowment":3.1780538303479458,"self_citation_contribution":0.47670807455219194,"citation_network_contribution":0.246847892659514,"self_endowment_contribution":0.47670807455219194,"citer_contribution":0.246847892659514,"corpus_percentile":null,"corpus_rank":null,"citation_count":23,"citer_count":14,"citers_with_citation_signal":12,"citers_with_endowment":12,"datacite_reuse_total":1,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":172774,"name":"Kimberly A. Nevonen","orcid":null,"position":1,"is_corresponding":false},{"id":172775,"name":"Brett A. Davis","orcid":null,"position":2,"is_corresponding":false},{"id":172776,"name":"Pryce Michener","orcid":null,"position":3,"is_corresponding":false},{"id":172777,"name":"Samantha Ward","orcid":null,"position":4,"is_corresponding":false},{"id":172778,"name":"Mark Milhaven","orcid":null,"position":5,"is_corresponding":false},{"id":172779,"name":"Lana Harshman","orcid":null,"position":6,"is_corresponding":false},{"id":172780,"name":"Ajuni Sohota","orcid":null,"position":7,"is_corresponding":false},{"id":109835,"name":"Jason D. Fernandes","orcid":"0000-0002-8625-1796","position":8,"is_corresponding":false},{"id":89178,"name":"Sofie R. Salama","orcid":"0000-0001-6999-7193","position":9,"is_corresponding":false},{"id":49048,"name":"Rachel J. O’Neill","orcid":"0000-0002-1525-6821","position":10,"is_corresponding":false},{"id":6730,"name":"Nadav Ahituv","orcid":"0000-0002-7434-8144","position":11,"is_corresponding":false},{"id":91087,"name":"Krishna R. Veeramah","orcid":"0000-0002-6768-4000","position":12,"is_corresponding":false},{"id":51330,"name":"Lucia Carbone","orcid":"0000-0002-2118-107X","position":13,"is_corresponding":false},{"id":172773,"name":"Mariam Okhovat","orcid":"0000-0002-3145-9397","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":3.1780538303479458,"endowment":3.1780538303479458,"datacite_reuse_total":1,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"32690705","pmcid":"PMC7431028","openalex_id":"https://openalex.org/W3042284795","authors":[],"funders":[{"funder_name":"Leakey Foundation","grant_id":"N/A","title":null},{"funder_name":"National Science Foundation","grant_id":"1613856","title":null},{"funder_name":"HHS | NIH | National Human Genome Research Institute","grant_id":"R01HG010333","title":null},{"funder_name":"HHS | NIH | NIH Office of the Director","grant_id":"P51 OD011092","title":null},{"funder_name":"HHS | National Institutes of Health","grant_id":"F32GM125388","title":null},{"funder_name":"HHS | NIH | National Human Genome Research Institute","grant_id":"1R01HG010329","title":null},{"funder_name":"NHGRI NIH HHS","grant_id":"R01 HG010329","title":null},{"funder_name":"National Institutes of Health","grant_id":"5R01HG010333-02","title":"Comparative and functional analysis of conservation and rearrangement of topologically associating domains across mammals."},{"funder_name":"National Institutes of Health","grant_id":"1F32GM125388-01A1","title":"Evolutionary and Mechanistic Investigations of Transposable Element Exaptation by KRAB-Zinc Finger Proteins"},{"funder_name":"National Institutes of Health","grant_id":"1R01HG010329-01","title":"Evolution of new regulatory networks via genetic arms races between KRAB zinc finger proteins and retrotransposons"}],"total_grants":10,"fwci":3.4683,"citation_percentile":0.91983564,"influential_citations":1,"citation_trend":[{"year":2020,"count":1},{"year":2021,"count":3},{"year":2022,"count":7},{"year":2023,"count":4},{"year":2024,"count":3},{"year":2025,"count":4},{"year":2026,"count":1}],"oa_status":"bronze","license":"https://www.pnas.org/site/aboutpnas/licenses.xhtml","oa_locations":[{"url":"https://www.pnas.org/content/pnas/117/32/19328.full.pdf","host_type":"journal"},{"url":"https://www.pnas.org/content/pnas/117/32/19328.full.pdf","host_type":"BRONZE"},{"url":"https://www.pnas.org/content/pnas/117/32/19328.full.pdf","host_type":"publisher"},{"url":"http://www.pnas.org/syndication/doi/10.1073/pnas.2006038117","host_type":"publisher"},{"url":"https://pnas.org/doi/pdf/10.1073/pnas.2006038117","host_type":"publisher"},{"url":"https://doi.org/10.1073/pnas.2006038117","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/32690705","host_type":"repository"},{"url":"http://europepmc.org/pmc/articles/PMC7431028","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7431028","host_type":"repository"},{"url":"https://doi.org/10.1101/765230","host_type":""},{"url":"https://europepmc.org/articles/pmc7431028?pdf=render","host_type":""},{"url":"https://dx.doi.org/10.1101/765230","host_type":""},{"url":"https://dx.doi.org/10.1073/pnas.2006038117","host_type":""},{"url":"https://escholarship.org/uc/item/0611s5jt","host_type":""},{"url":"https://doi.org/https://doi.org/10.1073/pnas.2006038117","host_type":""}],"fields_of_study":["Chromosomal and Genetic Variations","Genomic variations and chromosomal abnormalities","Genomics and Chromatin Dynamics","Medicine","Biology","Environmental Science","0301 basic medicine","03 medical and health sciences","0303 health sciences","Animals","Chromatin","Evolution, Molecular","Gene Expression Regulation","Genome","Hylobates","Mutagenesis, Insertional","Regulatory Sequences, Nucleic Acid","Retroelements","Species Specificity"],"mesh_terms":["Animals","Chromatin","Gene Expression Regulation","Hylobates","Regulatory Sequences, Nucleic Acid","Species Specificity","Mutagenesis, Insertional","Genome","Retroelements","Evolution, Molecular"],"keywords":["Retrotransposon","Lineage (genetic)","Lava","Genome","Evolutionary biology","Biology","Genetics","Paleontology","Transposable element","Gene","DNA repair","cis-regulatory element","Co-option","Transcription Factor Binding","Retroelements","Evolution","1.1 Normal biological development and functioning","Regulatory Sequences, Nucleic Acid","Evolution, Molecular","Species Specificity","Underpinning research","Insertional","Animals","Hylobates","Nucleic Acid","Human Genome","Molecular","Chromatin","Mutagenesis, Insertional","Gene Expression Regulation","Mutagenesis","Regulatory Sequences"],"sdg_mappings":[{"sdg_number":13,"sdg_label":"13. 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