ArticleProceedings of the National Academy of Sciences of the United States of America2014
Analysis of chromatin-state plasticity identifies cell-type-specific regulators of H3K27me3 patterns.
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 51 papers.
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51 citing papers in PubMed, 76 citations in OpenAlex.
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- A MTA2-SATB2 chromatin complex restrains colonic plasticity toward small intestine by retaining HNF4A at colonic chromatin.Nature communications · 2024Article
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- Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning.PLoS computational biology · 2022Article
- Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators.Bioinformatics (Oxford, England) · 2021Article
- Comparison of Global DNA Methylation Patterns in Human Melanoma Tissues and Their Derivative Cell Lines.Cancers · 2021Article
- Integrative analysis reveals novel driver genes and molecular subclasses of hepatocellular carcinoma.Aging · 2020Article
- A Platelet Function Modulator of Thrombin Activation Is Causally Linked to Cardiovascular Disease and Affects PAR4 Receptor Signaling.American journal of human genetics · 2020Article
- Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis.Molecular cell · 2020Article
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- Krüppel-like Factor 5 Regulates Stemness, Lineage Specification, and Regeneration of Intestinal Epithelial Stem Cells.Cellular and molecular gastroenterology and hepatology · 2020Article
- Epigenetic Changes Induced byInfection and immunity · 2019Article
- Extensive Recovery of Embryonic Enhancer and Gene Memory Stored in Hypomethylated Enhancer DNA.Molecular cell · 2019Article
- Genome-wide analysis of epigenetic dynamics across human developmental stages and tissues.BMC genomics · 2019Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Chromatin states are highly cell-type-specific, but the underlying mechanisms for the establishment and maintenance of their genome-wide patterns remain poorly understood. Here we present a computational approach for investigation of chromatin-state plasticity. We applied this approach to investigate an ENCODE ChIP-seq dataset profiling the genome-wide distributions of the H3K27me3 mark in 19 human cell lines. We found that the high plasticity regions (HPRs) can be divided into two functionally and mechanistically distinct subsets, which correspond to CpG island (CGI) proximal or distal regions, respectively. Although the CGI proximal HPRs are typically associated with continuous variation across different cell-types, the distal HPRs are associated with binary-like variations. We developed a computational approach to predict putative cell-type-specific modulators of H3K27me3 patterns and validated the predictions by comparing with public ChIP-seq data. Furthermore, we applied this approach to investigate mechanisms for poised enhancer establishment in primary human erythroid precursors. Importantly, we predicted and experimentally validated that the principal hematopoietic regulator T-cell acute lymphocytic leukemia-1 (TAL1) is involved in regulating H3K27me3 variations in collaboration with the transcription factor growth factor independent 1B (GFI1B), providing fresh insights into the context-specific role of TAL1 in erythropoiesis. Our approach is generally applicable to investigate the regulatory mechanisms of epigenetic pathways in establishing cellular identity.
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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.