ArticleGenome research2013
Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting.
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 68 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
68 citing papers in PubMed, 122 citations in OpenAlex.
- Epigenetic control of cell identities from epiblast to gastrulation.The FEBS journal · 2025Review
- An evolving landscape of PRC2-RNA interactions in chromatin regulation.Nature reviews. Molecular cell biology · 2025Review
- Regulatory mechanisms of steroid hormone receptors on gene transcription through chromatin interaction and enhancer reprogramming.Cellular oncology (Dordrecht, Netherlands) · 2024Review
- Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis.Nature genetics · 2023Article
- scANANSE gene regulatory network and motif analysis of single-cell clusters.F1000Research · 2023Article
- Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation.Molecular omics · 2022Article
- Annotating functional effects of non-coding variants in neuropsychiatric cell types by deep transfer learning.PLoS computational biology · 2022Article
- Distal regulation, silencers, and a shared combinatorial syntax are hallmarks of animal embryogenesis.Genome research · 2022Article
- Article
- Scrt1, a transcriptional regulator of β-cell proliferation identified by differential chromatin accessibility during islet maturation.Scientific reports · 2021Article
- Mammalian SWI/SNF continuously restores local accessibility to chromatin.Nature genetics · 2021Article
- Article
- Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo.Molecular cell · 2021Article
- Article
- A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity.Nature communications · 2020Article
- Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities.An international journal on information fusion · 2019Article
- Polycomb/Trithorax Antagonism: Cellular Memory in Stem Cell Fate and Function.Cell stem cell · 2019Review
- CG dinucleotides enhance promoter activity independent of DNA methylation.Genome research · 2019Article
- Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation.Cancer cell · 2019Article
- PTE, a novel module to target Polycomb Repressive Complex 1 to the human cyclin D2 (The Journal of biological chemistry · 2018Article
8 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 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. To systematically identify transcription factors (TFs) that can direct chromatin changes during cell fate decisions, we model the relationship between genome-wide dynamics of chromatin marks and the local occurrence of computationally predicted TF binding sites. By applying this computational approach to a time course of Polycomb-mediated H3K27me3 marks during neuronal differentiation of murine stem cells, we identify several motifs that likely regulate the dynamics of this chromatin mark. Among these, the sites bound by REST and by the SNAIL family of TFs are predicted to transiently recruit H3K27me3 in neuronal progenitors. We validate these predictions experimentally and show that absence of REST indeed causes loss of H3K27me3 at target promoters in trans, specifically at the neuronal progenitor state. Moreover, using targeted transgenic insertion, we show that promoter fragments containing REST or SNAIL binding sites are sufficient to recruit H3K27me3 in cis, while deletion of these sites results in loss of H3K27me3. These findings illustrate that the occurrence of TF binding sites can determine chromatin dynamics. Local determination of Polycomb activity by REST and SNAIL motifs exemplifies such TF based regulation of chromatin. Furthermore, our results show that key TFs can be identified ab initio through computational modeling of epigenome data sets using a modeling approach that we make readily accessible.
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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.