{"doi":"10.1101/2025.05.19.654775","title":"Transposable elements drive species-specific and tissue-specific transcriptomes in human development","abstract":"Background: Transposable elements (TEs) are an abundant and crucial regulatory resource in the human genome. Serving as alternative promoters, TEs can be reactivated and produce TE-initiated transcripts, which play importance roles in early development and differentiated tissues. However, the prevalence and function of TE-initiated transcription in human development are poorly characterized. Results: We identified 12,918 TE-initiated transcripts across 40 human body sites and embryonic stem cells. Among TE-initiated transcripts, 80% were activated in a tissue-specific manner. TEs with tissue-specific transcription factor binding motifs were enriched in particular tissues. Additionally, approximately half of TE-derived TSSs were primates-specific. Notably, 375 primates-specific TE-derived TSSs were found to create novel tissue-specific gene expression patterns during evolution. Conclusions: Our results characterize the global profile of TE-initiated transcription and enhance our understanding of TE contribution to the primate-specific gene regulatory networks in human development.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":566658,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.943,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":867623,"name":"Jianqi She","orcid":"0000-0001-7210-6638","position":1,"is_corresponding":false},{"id":1418868,"name":"Xueyan Hu","orcid":"0000-0002-4253-3564","position":2,"is_corresponding":false},{"id":867625,"name":"Yueqi Jin","orcid":"0000-0003-0225-6512","position":3,"is_corresponding":false},{"id":1418869,"name":"Jiaming Zhao","orcid":"0000-0002-5295-2535","position":4,"is_corresponding":false},{"id":1419391,"name":"Songyan Hou","orcid":null,"position":5,"is_corresponding":false},{"id":867628,"name":"Changyu Tao","orcid":"0000-0001-7333-6822","position":6,"is_corresponding":false},{"id":867624,"name":"Minghao Du","orcid":"0000-0002-7478-5539","position":7,"is_corresponding":false},{"id":867631,"name":"Ence Yang","orcid":"0000-0002-9526-2737","position":8,"is_corresponding":false},{"id":1470687,"name":"Yun Zhang","orcid":"0009-0001-5981-2279","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T02:56:40.491968Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}