ArticleCell genomics2024
Human gene regulatory evolution is driven by the divergence of regulatory element function in both cis and trans.
Article in Cell genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
15 citing papers in PubMed, 17 citations in OpenAlex.
- Massively parallel assessment of gene regulatory activity at human cortical-structure-associated variants.Nature neuroscience · 2026Article
- Trans-regulation of heterochromatin underlies genetic variation in 3D genome contacts in mouse embryonic stem cells.Genome biology · 2026Article
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- Decoding the germline genetic architecture of prostate cancer at a single cell resolution.PLoS genetics · 2025Article
- Addressing missing context in regulatory variation across primate evolution.Current opinion in genetics & development · 2025Review
- Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes.Genome research · 2025Article
- Lineage-specific regulatory evolution: insights from massively parallel reporter assays.Current opinion in genetics & development · 2025Review
- Article
- Comprehensive mapping of genetic variation at Epromoters reveals pleiotropic association with multiple disease traits.Nucleic acids research · 2025Article
- Novelty versus innovation of gene regulatory elements in human evolution and disease.Current opinion in genetics & development · 2025Review
- Structural heterogeneity and functional convergence of transposable elements.Frontiers in genetics · 2025Article
- Review
- Comparative genomics illuminates karyotype and sex chromosome evolution of sharks.Cell genomics · 2024Article
- Transforming our understanding of species-specific gene regulation.Cell genomics · 2024Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Gene regulatory divergence between species can result from cis-acting local changes to regulatory element DNA sequences or global trans-acting changes to the regulatory environment. Understanding how these mechanisms drive regulatory evolution has been limited by challenges in identifying trans-acting changes. We present a comprehensive approach to directly identify cis- and trans-divergent regulatory elements between human and rhesus macaque lymphoblastoid cells using assay for transposase-accessible chromatin coupled to self-transcribing active regulatory region (ATAC-STARR) sequencing. In addition to thousands of cis changes, we discover an unexpected number (∼10,000) of trans changes and show that cis and trans elements exhibit distinct patterns of sequence divergence and function. We further identify differentially expressed transcription factors that underlie ∼37% of trans differences and trace how cis changes can produce cascades of trans changes. Overall, we find that most divergent elements (67%) experienced changes in both cis and trans, revealing a substantial role for trans divergence-alone and together with cis changes-in regulatory differences between species.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.