ArticleNucleic acids research2013
Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 37 citations in OpenAlex.
- Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.Annual review of biophysics · 2025Review
- Integrative approaches based on genomic techniques in the functional studies on enhancers.Briefings in bioinformatics · 2023Review
- Review
- An intriguing characteristic of enhancer-promoter interactions.BMC genomics · 2021Article
- Enhancer occlusion transcripts regulate the activity of human enhancer domains via transcriptional interference: a computational perspective.Nucleic acids research · 2020Article
- Eukaryotic transcription factors can track and control their target genes using DNA antennas.Nature communications · 2020Article
- SIRT1/2 orchestrate acquisition of DNA methylation and loss of histone H3 activating marks to prevent premature activation of inflammatory genes in macrophages.Nucleic acids research · 2020Article
- Fine mapping chromatin contacts in capture Hi-C data.BMC genomics · 2019Article
- Canonical and single-cell Hi-C reveal distinct chromatin interaction sub-networks of mammalian transcription factors.Genome biology · 2018Article
- Intergenic disease-associated regions are abundant in novel transcripts.Genome biology · 2017Article
- A pathway-centric view of spatial proximity in the 3D nucleome across cell lines.Scientific reports · 2016Article
- Transcriptome of the inner circular smooth muscle of the developing mouse intestine: Evidence for regulation of visceral smooth muscle genes by the hedgehog target gene, cJun.Developmental dynamics : an official publication of the American Association of Anatomists · 2016Article
- Early enhancer establishment and regulatory locus complexity shape transcriptional programs in hematopoietic differentiation.Nature genetics · 2015Article
- Histone H2A.Z deregulation in prostate cancer. Cause or effect?Cancer metastasis reviews · 2014Review
- Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells.BMC genomics · 2014Article
- Next-generation sequencing and epigenomics research: a hammer in search of nails.Genomics & informatics · 2014Review
- The missing story behind Genome Wide Association Studies: single nucleotide polymorphisms in gene deserts have a story to tell.Frontiers in genetics · 2014Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Mammalian gene expression is often regulated by distal enhancers. However, little is known about higher order functional organization of enhancers. Using ∼100 K P300-bound regions as candidate enhancers, we investigated their correlated activity across 72 cell types based on DNAse hypersensitivity. We found widespread correlated activity between enhancers, which decreases with increasing inter-enhancer genomic distance. We found that correlated enhancers tend to share common transcription factor (TF) binding motifs, and several chromatin modification enzymes preferentially interact with these TFs. Presence of shared motifs in enhancer pairs can predict correlated activity with 73% accuracy. Also, genes near correlated enhancers exhibit correlated expression and share common function. Correlated enhancers tend to be spatially proximal. Interestingly, weak enhancers tend to correlate with significantly greater numbers of other enhancers relative to strong enhancers. Furthermore, strong/weak enhancers preferentially correlate with strong/weak enhancers, respectively. We constructed enhancer networks based on shared motif and correlated activity and show significant functional enrichment in their putative target gene clusters. Overall, our analyses show extensive correlated activity among enhancers and reveal clusters of enhancers whose activities are coordinately regulated by multiple potential mechanisms involving shared TF binding, chromatin modifying enzymes and 3D chromatin structure, which ultimately co-regulate functionally linked genes.
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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.