ArticleNature communications2017
Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
46 citing papers in PubMed, 1 synthesis or guideline pooled it, 73 citations in OpenAlex.
- Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity.Communications biology · 2023Pooled it
- Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation.bioRxiv : the preprint server for biology · 2026Article
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- Evolutionary Analysis of Transcriptional Regulation Mediated by Cdx2 in Rodents.Cell proliferation · 2026Article
- From IL-6 production to IL-6R buffering: a unified IL-6-IL-6R framework for immune homeostasis during viral infection.Frontiers in immunology · 2026Review
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.PLoS computational biology · 2025Article
- ASPEN: Robust detection of allelic dynamics in single cell RNA-seq.bioRxiv : the preprint server for biology · 2025Article
- De novo design of insulated cis-regulatory elements based on deep learning-predicted fitness landscape.Nucleic acids research · 2025Article
- Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis.Genome research · 2025Article
- Article
- Understanding species-specific and conserved RNA-protein interactions in vivo and in vitro.Nature communications · 2024Article
- Alternation of gene expression in brain-derived exosomes after cerebral ischemic preconditioning in mice.Heliyon · 2024Article
- Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids.Nature communications · 2024Article
- The genetic basis of autoimmunity seen through the lens of T cell functional traits.Nature communications · 2024Review
- Understanding species-specific and conserved RNA-protein interactionsbioRxiv : the preprint server for biology · 2024Article
- A compendium of genetic regulatory effects across pig tissues.Nature genetics · 2024Article
- Dominance is common in mammals and is associated with trans-acting gene expression and alternative splicing.Genome biology · 2023Article
- Article
- Decoding enhancer complexity with machine learning and high-throughput discovery.Genome biology · 2023Review
- Article
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
Noncoding regulatory variants play a central role in the genetics of human diseases and in evolution. Here we measure allele-specific transcription factor binding occupancy of three liver-specific transcription factors between crosses of two inbred mouse strains to elucidate the regulatory mechanisms underlying transcription factor binding variations in mammals. Our results highlight the pre-eminence of cis-acting variants on transcription factor occupancy divergence. Transcription factor binding differences linked to cis-acting variants generally exhibit additive inheritance, while those linked to trans-acting variants are most often dominantly inherited. Cis-acting variants lead to local coordination of transcription factor occupancies that decay with distance; distal coordination is also observed and may be modulated by long-range chromatin contacts. Our results reveal the regulatory mechanisms that interplay to drive transcription factor occupancy, chromatin state, and gene expression in complex mammalian cell states.
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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 OpenQuestion graph.