Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Tiwari, Vijay K, McGarvey, Kelly M, Licchesi, Julien D.F, Ohm, Joyce E, Herman, James G, Schübeler, Dirk, Baylin, Stephen B
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2008
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
_version_ 1782161546335485952
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
work_keys_str_mv AT tiwarivijayk pcgproteinsdnamethylationandgenerepressionbychromatinlooping
AT mcgarveykellym pcgproteinsdnamethylationandgenerepressionbychromatinlooping
AT licchesijuliendf pcgproteinsdnamethylationandgenerepressionbychromatinlooping
AT ohmjoycee pcgproteinsdnamethylationandgenerepressionbychromatinlooping
AT hermanjamesg pcgproteinsdnamethylationandgenerepressionbychromatinlooping
AT schubelerdirk pcgproteinsdnamethylationandgenerepressionbychromatinlooping
AT baylinstephenb pcgproteinsdnamethylationandgenerepressionbychromatinlooping