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PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping
Many DNA hypermethylated and epigenetically silenced genes in adult cancers are Polycomb group (PcG) marked in embryonic stem (ES) cells. We show that a large region upstream (∼30 kb) of and extending ∼60 kb around one such gene, GATA-4, is organized—in Tera-2 undifferentiated embryonic carcinoma (E...
Autores principales: | , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2008
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2592355/ https://www.ncbi.nlm.nih.gov/pubmed/19053175 http://dx.doi.org/10.1371/journal.pbio.0060306 |
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author | Tiwari, Vijay K McGarvey, Kelly M Licchesi, Julien D.F Ohm, Joyce E Herman, James G Schübeler, Dirk Baylin, Stephen B |
author_facet | Tiwari, Vijay K McGarvey, Kelly M Licchesi, Julien D.F Ohm, Joyce E Herman, James G Schübeler, Dirk Baylin, Stephen B |
author_sort | Tiwari, Vijay K |
collection | PubMed |
description | Many DNA hypermethylated and epigenetically silenced genes in adult cancers are Polycomb group (PcG) marked in embryonic stem (ES) cells. We show that a large region upstream (∼30 kb) of and extending ∼60 kb around one such gene, GATA-4, is organized—in Tera-2 undifferentiated embryonic carcinoma (EC) cells—in a topologically complex multi-loop conformation that is formed by multiple internal long-range contact regions near areas enriched for EZH2, other PcG proteins, and the signature PcG histone mark, H3K27me3. Small interfering RNA (siRNA)–mediated depletion of EZH2 in undifferentiated Tera-2 cells leads to a significant reduction in the frequency of long-range associations at the GATA-4 locus, seemingly dependent on affecting the H3K27me3 enrichments around those chromatin regions, accompanied by a modest increase in GATA-4 transcription. The chromatin loops completely dissolve, accompanied by loss of PcG proteins and H3K27me3 marks, when Tera-2 cells receive differentiation signals which induce a ∼60-fold increase in GATA-4 expression. In colon cancer cells, however, the frequency of the long-range interactions are increased in a setting where GATA-4 has no basal transcription and the loops encompass multiple, abnormally DNA hypermethylated CpG islands, and the methyl-cytosine binding protein MBD2 is localized to these CpG islands, including ones near the gene promoter. Removing DNA methylation through genetic disruption of DNA methyltransferases (DKO cells) leads to loss of MBD2 occupancy and to a decrease in the frequency of long-range contacts, such that these now more resemble those in undifferentiated Tera-2 cells. Our findings reveal unexpected similarities in higher order chromatin conformation between stem/precursor cells and adult cancers. We also provide novel insight that PcG-occupied and H3K27me3-enriched regions can form chromatin loops and physically interact in cis around a single gene in mammalian cells. The loops associate with a poised, low transcription state in EC cells and, with the addition of DNA methylation, completely repressed transcription in adult cancer cells. |
format | Text |
id | pubmed-2592355 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-25923552008-12-02 PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping Tiwari, Vijay K McGarvey, Kelly M Licchesi, Julien D.F Ohm, Joyce E Herman, James G Schübeler, Dirk Baylin, Stephen B PLoS Biol Research Article Many DNA hypermethylated and epigenetically silenced genes in adult cancers are Polycomb group (PcG) marked in embryonic stem (ES) cells. We show that a large region upstream (∼30 kb) of and extending ∼60 kb around one such gene, GATA-4, is organized—in Tera-2 undifferentiated embryonic carcinoma (EC) cells—in a topologically complex multi-loop conformation that is formed by multiple internal long-range contact regions near areas enriched for EZH2, other PcG proteins, and the signature PcG histone mark, H3K27me3. Small interfering RNA (siRNA)–mediated depletion of EZH2 in undifferentiated Tera-2 cells leads to a significant reduction in the frequency of long-range associations at the GATA-4 locus, seemingly dependent on affecting the H3K27me3 enrichments around those chromatin regions, accompanied by a modest increase in GATA-4 transcription. The chromatin loops completely dissolve, accompanied by loss of PcG proteins and H3K27me3 marks, when Tera-2 cells receive differentiation signals which induce a ∼60-fold increase in GATA-4 expression. In colon cancer cells, however, the frequency of the long-range interactions are increased in a setting where GATA-4 has no basal transcription and the loops encompass multiple, abnormally DNA hypermethylated CpG islands, and the methyl-cytosine binding protein MBD2 is localized to these CpG islands, including ones near the gene promoter. Removing DNA methylation through genetic disruption of DNA methyltransferases (DKO cells) leads to loss of MBD2 occupancy and to a decrease in the frequency of long-range contacts, such that these now more resemble those in undifferentiated Tera-2 cells. Our findings reveal unexpected similarities in higher order chromatin conformation between stem/precursor cells and adult cancers. We also provide novel insight that PcG-occupied and H3K27me3-enriched regions can form chromatin loops and physically interact in cis around a single gene in mammalian cells. The loops associate with a poised, low transcription state in EC cells and, with the addition of DNA methylation, completely repressed transcription in adult cancer cells. Public Library of Science 2008-12 2008-12-02 /pmc/articles/PMC2592355/ /pubmed/19053175 http://dx.doi.org/10.1371/journal.pbio.0060306 Text en © 2008 Tiwari et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Tiwari, Vijay K McGarvey, Kelly M Licchesi, Julien D.F Ohm, Joyce E Herman, James G Schübeler, Dirk Baylin, Stephen B PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping |
title | PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping |
title_full | PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping |
title_fullStr | PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping |
title_full_unstemmed | PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping |
title_short | PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping |
title_sort | pcg proteins, dna methylation, and gene repression by chromatin looping |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2592355/ https://www.ncbi.nlm.nih.gov/pubmed/19053175 http://dx.doi.org/10.1371/journal.pbio.0060306 |
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