ArticleNature communications2014
CpG island-mediated global gene regulatory modes in mouse embryonic stem cells.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed, 29 citations in OpenAlex.
- PCGF1-mediated bivalent promoter remodeling enables NK cell immune evasion in non-small cell lung cancer.Cell death & disease · 2026Article
- In vivo CRISPR/Cas9-mediated screen reveals a critical function of TFDP1 and E2F4 transcription factors in hematopoiesis.Leukemia · 2024Article
- The arginine methyltransferase Prmt1 coordinates the germline arginine methylome essential for spermatogonial homeostasis and male fertility.Nucleic acids research · 2023Article
- A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs.Communications biology · 2023Article
- Lima1 mediates the pluripotency control of membrane dynamics and cellular metabolism.Nature communications · 2022Article
- Misexpression of genes lacking CpG islands drives degenerative changes during aging.Science advances · 2021Article
- Cooperation between HDAC3 and DAX1 mediates lineage restriction of embryonic stem cells.The EMBO journal · 2021Article
- Conserved dual-mode gene regulation programs in higher eukaryotes.Nucleic acids research · 2021Article
- Pluripotency-State-Dependent Role of Dax1 in Embryonic Stem Cells Self-Renewal.Stem cells international · 2021Article
- Activity of PRC1 and Histone H2AK119 Monoubiquitination: Revising Popular Misconceptions.BioEssays : news and reviews in molecular, cellular and developmental biology · 2020Review
- Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle.eLife · 2019Article
- NOMePlot: analysis of DNA methylation and nucleosome occupancy at the single molecule.Scientific reports · 2019Article
- Chromatin folding and nuclear architecture: PRC1 function in 3D.Current opinion in genetics & development · 2019Review
- Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes.Genome research · 2018Article
- Implications of CpG islands on chromosomal architectures and modes of global gene regulation.Nucleic acids research · 2018Article
- Fosl1 overexpression directly activates trophoblast-specific gene expression programs in embryonic stem cells.Stem cell research · 2018Article
- Fbxl19 recruitment to CpG islands is required for Rnf20-mediated H2B mono-ubiquitination.Nucleic acids research · 2017Article
- The logic of transcriptional regulator recruitment architecture atGenome research · 2017Article
- Intragenic CpG islands play important roles in bivalent chromatin assembly of developmental genes.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Novel functions for the transcription factor E2F4 in development and disease.Cell cycle (Georgetown, Tex.) · 2016Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Both transcriptional and epigenetic regulations are fundamental for the control of eukaryotic gene expression. Here we perform a compendium analysis of >200 large sequencing data sets to elucidate the regulatory logic of global gene expression programs in mouse embryonic stem (ES) cells. We define four major classes of DNA-binding proteins (Core, PRC, MYC and CTCF) based on their target co-occupancy, and discover reciprocal regulation between the MYC and PRC classes for the activity of nearly all genes under the control of the CpG island (CGI)-containing promoters. This CGI-dependent regulatory mode explains the functional segregation between CGI-containing and CGI-less genes during early development. By defining active enhancers based on the co-occupancy of the Core class, we further demonstrate their additive roles in CGI-containing gene expression and cell type-specific roles in CGI-less gene expression. Altogether, our analyses provide novel insights into previously unknown CGI-dependent global gene regulatory modes.
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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.