ArticleProceedings of the National Academy of Sciences of the United States of America2014
Identifying and mapping cell-type-specific chromatin programming of gene expression.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 47 citations in OpenAlex.
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- Directing stem cell differentiation by chromatin state approximation.Nucleic acids research · 2026Article
- Iterative assay for transposase-accessible chromatin by sequencing to isolate functionally relevant neuronal subtypes.Science advances · 2024Article
- The complex biology of aryl hydrocarbon receptor activation in cancer and beyond.Biochemical pharmacology · 2023Review
- Identifying polymorphic cis-regulatory variants as risk markers for lung carcinogenesis and chemotherapy responses in tobacco smokers from eastern India.Scientific reports · 2023Article
- Identifying potential risk genes and pathways for neuropsychiatric and substance use disorders using intermediate molecular mediator information.Frontiers in genetics · 2023Article
- Transcriptomic profiling implicates PAF1 in both active and repressive immune regulatory networks.BMC genomics · 2022Article
- Normal and Pathological NRF2 Signalling in the Central Nervous System.Antioxidants (Basel, Switzerland) · 2022Review
- Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei.BMC genomics · 2022Article
- Promoter/enhancer-based controllability of regulatory networks.Scientific reports · 2022Article
- HNF4A defines tissue-specific circadian rhythms by beaconing BMAL1::CLOCK chromatin binding and shaping the rhythmic chromatin landscape.Nature communications · 2021Article
- Genetic and epigenetic features of promoters with ubiquitous chromatin accessibility support ubiquitous transcription of cell-essential genes.Nucleic acids research · 2021Article
- Heat-Triggered Remote Control of CRISPR-dCas9 for Tunable Transcriptional Modulation.ACS chemical biology · 2020Article
- A possible role for epigenetic feedback regulation in the dynamics of the epithelial-mesenchymal transition (EMT).Physical biology · 2019Article
- Predicting gene expression in massively parallel reporter assays: A comparative study.Human mutation · 2017Article
- Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data.PeerJ · 2017Article
- Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data.National science review · 2016Article
- Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases.Nature methods · 2016Article
- Techniques and Approaches to Genetic Analyses in Nephrological Disorders.Journal of pediatric genetics · 2016Review
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
A problem of substantial interest is to systematically map variation in chromatin structure to gene-expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for determining the existence, strength, and type of relationship between high-resolution chromatin structure in terms of DNaseI hypersensitivity and genome-wide gene-expression levels in 20 diverse human cell types. We show that ∼25% of genes show cell-type-specific expression explained by alterations in chromatin structure. We find that distal regions of chromatin structure (e.g., ±200 kb) capture more genes with this relationship than local regions (e.g., ±2.5 kb), yet the local regions show a more pronounced effect. By exploiting variation across cell types, we were capable of pinpointing the most likely hypersensitive sites related to cell-type-specific expression, which we show have a range of contextual uses. This quantitative framework is likely applicable to other settings aimed at relating continuous genomic measurements to gene-expression variation.
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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.