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Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs
We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibrob...
Autores principales: | , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885280/ https://www.ncbi.nlm.nih.gov/pubmed/17542650 http://dx.doi.org/10.1371/journal.pgen.0030089 |
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author | O'Geen, Henriette Squazzo, Sharon L Iyengar, Sushma Blahnik, Kim Rinn, John L Chang, Howard Y Green, Roland Farnham, Peggy J |
author_facet | O'Geen, Henriette Squazzo, Sharon L Iyengar, Sushma Blahnik, Kim Rinn, John L Chang, Howard Y Green, Roland Farnham, Peggy J |
author_sort | O'Geen, Henriette |
collection | PubMed |
description | We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibroblasts. We found that in each of the cell types the two modifications were differentially enriched at the promoters of the two largest classes of transcription factors. Specifically, zinc finger (ZNF) genes were bound by H3me3K9 and homeobox genes were bound by H3me3K27. We have previously shown that the Polycomb repressive complex 2 is responsible for mediating trimethylation of lysine 27 of histone H3 in human cancer cells. In contrast, there is little overlap between H3me3K9 targets and components of the Polycomb repressive complex 2, suggesting that a different histone methyltransferase is responsible for the H3me3K9 modification. Previous studies have shown that SETDB1 can trimethylate H3 on lysine 9, using in vitro or artificial tethering assays. SETDB1 is thought to be recruited to chromatin by complexes containing the KAP1 corepressor. To determine if a KAP1-containing complex mediates trimethylation of the identified H3me3K9 targets, we performed ChIP-chip assays and identified KAP1 target genes using human 5-kb promoter arrays. We found that a large number of genes of ZNF transcription factors were bound by both KAP1 and H3me3K9 in normal and cancer cells. To expand our studies of KAP1, we next performed a complete genomic analysis of KAP1 binding using a 38-array tiling set, identifying ~7,000 KAP1 binding sites. The identified KAP1 targets were highly enriched for C(2)H(2) ZNFs, especially those containing Krüppel-associated box (KRAB) domains. Interestingly, although most KAP1 binding sites were within core promoter regions, the binding sites near ZNF genes were greatly enriched within transcribed regions of the target genes. Because KAP1 is recruited to the DNA via interaction with KRAB-ZNF proteins, we suggest that expression of KRAB-ZNF genes may be controlled via an auto-regulatory mechanism involving KAP1. |
format | Text |
id | pubmed-1885280 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-18852802007-06-30 Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs O'Geen, Henriette Squazzo, Sharon L Iyengar, Sushma Blahnik, Kim Rinn, John L Chang, Howard Y Green, Roland Farnham, Peggy J PLoS Genet Research Article We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibroblasts. We found that in each of the cell types the two modifications were differentially enriched at the promoters of the two largest classes of transcription factors. Specifically, zinc finger (ZNF) genes were bound by H3me3K9 and homeobox genes were bound by H3me3K27. We have previously shown that the Polycomb repressive complex 2 is responsible for mediating trimethylation of lysine 27 of histone H3 in human cancer cells. In contrast, there is little overlap between H3me3K9 targets and components of the Polycomb repressive complex 2, suggesting that a different histone methyltransferase is responsible for the H3me3K9 modification. Previous studies have shown that SETDB1 can trimethylate H3 on lysine 9, using in vitro or artificial tethering assays. SETDB1 is thought to be recruited to chromatin by complexes containing the KAP1 corepressor. To determine if a KAP1-containing complex mediates trimethylation of the identified H3me3K9 targets, we performed ChIP-chip assays and identified KAP1 target genes using human 5-kb promoter arrays. We found that a large number of genes of ZNF transcription factors were bound by both KAP1 and H3me3K9 in normal and cancer cells. To expand our studies of KAP1, we next performed a complete genomic analysis of KAP1 binding using a 38-array tiling set, identifying ~7,000 KAP1 binding sites. The identified KAP1 targets were highly enriched for C(2)H(2) ZNFs, especially those containing Krüppel-associated box (KRAB) domains. Interestingly, although most KAP1 binding sites were within core promoter regions, the binding sites near ZNF genes were greatly enriched within transcribed regions of the target genes. Because KAP1 is recruited to the DNA via interaction with KRAB-ZNF proteins, we suggest that expression of KRAB-ZNF genes may be controlled via an auto-regulatory mechanism involving KAP1. Public Library of Science 2007-06 2007-06-01 /pmc/articles/PMC1885280/ /pubmed/17542650 http://dx.doi.org/10.1371/journal.pgen.0030089 Text en © 2007 O'Geen 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 O'Geen, Henriette Squazzo, Sharon L Iyengar, Sushma Blahnik, Kim Rinn, John L Chang, Howard Y Green, Roland Farnham, Peggy J Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs |
title | Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs |
title_full | Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs |
title_fullStr | Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs |
title_full_unstemmed | Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs |
title_short | Genome-Wide Analysis of KAP1 Binding Suggests Autoregulation of KRAB-ZNFs |
title_sort | genome-wide analysis of kap1 binding suggests autoregulation of krab-znfs |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1885280/ https://www.ncbi.nlm.nih.gov/pubmed/17542650 http://dx.doi.org/10.1371/journal.pgen.0030089 |
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