ArticleGenome research2013
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 156 papers, 3 of them syntheses that pooled it.
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Who cites it
156 citing papers in PubMed, 3 syntheses or guidelines pooled it, 235 citations in OpenAlex.
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- New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk.Nature communications · 2016Pooled it
- Sequence variants in the PTCH1 gene associate with spine bone mineral density and osteoporotic fractures.Nature communications · 2016Pooled it
- Prioritizing context-specific genetic risk mechanisms in 11 solid cancers.Journal of the National Cancer Institute · 2026Article
- Article
- Mapping enhancer-gene regulatory interactions from single-cell data.Nature genetics · 2026Article
- Deciphering the regulatory landscape of enhancer RNAs in health and disease.Signal transduction and targeted therapy · 2026Review
- Prioritizing context-specific genetic risk mechanisms in 11 solid cancers.medRxiv : the preprint server for health sciences · 2025Article
- Comparative genomics sheds light on mammalian and avian gene regulation and phenotypic evolution.Nature communications · 2025Article
- Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties.BMC biology · 2025Article
- p53motifDB: integration of genomic information and tumour suppressor p53 binding motifs.Database : the journal of biological databases and curation · 2025Article
- EPI-DynFusion: enhancer-promoter interaction prediction model based on sequence features and dynamic fusion mechanisms.Frontiers in genetics · 2025Article
- Altered chromatin landscape and 3D interactions associated with primary constitutional MLH1 epimutations.Clinical epigenetics · 2024Article
- Crosstalk between paralogs and isoforms influences p63-dependent regulatory element activity.Nucleic acids research · 2024Article
- Increased DNA damage in full-grown oocytes is correlated with diminished autophagy activation.Nature communications · 2024Article
- Methods for evaluating unsupervised vector representations of genomic regions.NAR genomics and bioinformatics · 2024Article
- Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits.Nature communications · 2024Article
- OncogeneScience advances · 2024Article
- Probabilistic association of differentially expressed genes withGenome research · 2024Article
- Context dependent activity of p63-bound gene regulatory elements.bioRxiv : the preprint server for biology · 2024Article
96 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 4 institutions in 3 countries.
Funding
Abstract
Regulatory elements recruit transcription factors that modulate gene expression distinctly across cell types, but the relationships among these remains elusive. To address this, we analyzed matched DNase-seq and gene expression data for 112 human samples representing 72 cell types. We first defined more than 1800 clusters of DNase I hypersensitive sites (DHSs) with similar tissue specificity of DNase-seq signal patterns. We then used these to uncover distinct associations between DHSs and promoters, CpG islands, conserved elements, and transcription factor motif enrichment. Motif analysis within clusters identified known and novel motifs in cell-type-specific and ubiquitous regulatory elements and supports a role for AP-1 regulating open chromatin. We developed a classifier that accurately predicts cell-type lineage based on only 43 DHSs and evaluated the tissue of origin for cancer cell types. A similar classifier identified three sex-specific loci on the X chromosome, including the XIST lincRNA locus. By correlating DNase I signal and gene expression, we predicted regulated genes for more than 500K DHSs. Finally, we introduce a web resource to enable researchers to use these results to explore these regulatory patterns and better understand how expression is modulated within and across human cell types.
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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.