Integrated analysis identifies a class of androgen-responsive genes regulated by short combinatorial long-range mechanism facilitated by CTCF.

Nucleic Acids Research
Cenny TaslimShili Lin

Abstract

Recently, much attention has been given to elucidate how long-range gene regulation comes into play and how histone modifications and distal transcription factor binding contribute toward this mechanism. Androgen receptor (AR), a key regulator of prostate cancer, has been shown to regulate its target genes via distal enhancers, leading to the hypothesis of global long-range gene regulation. However, despite numerous flows of newly generated data, the precise mechanism with respect to AR-mediated long-range gene regulation is still largely unknown. In this study, we carried out an integrated analysis combining several types of high-throughput data, including genome-wide distribution data of H3K4 di-methylation (H3K4me2), CCCTC binding factor (CTCF), AR and FoxA1 cistrome data as well as androgen-regulated gene expression data. We found that a subset of androgen-responsive genes was significantly enriched near AR/H3K4me2 overlapping regions and FoxA1 binding sites within the same CTCF block. Importantly, genes in this class were enriched in cancer-related pathways and were downregulated in clinical metastatic versus localized prostate cancer. Our results suggest a relatively short combinatorial long-range regulation mechanism fac...Continue Reading

References

Aug 1, 1997·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·H I ScherM Schwartz
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Apr 13, 2004·Proceedings of the National Academy of Sciences of the United States of America·Andrew I SuJohn B Hogenesch
Nov 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Peter J SaboJohn A Stamatoyannopoulos
Jul 19, 2005·Genome Research·Adam SiepelDavid Haussler
Jul 18, 2006·Nucleic Acids Research·Xuwo JiX Shirley Liu
Aug 10, 2006·Proceedings of the National Academy of Sciences of the United States of America·W Evan JohnsonX Shirley Liu
Dec 19, 2006·Nature Genetics·Scott A TomlinsArul M Chinnaiyan
Apr 20, 2007·Proceedings of the National Academy of Sciences of the United States of America·Xiaohui XieEric S Lander
Aug 8, 2008·Nucleic Acids Research·Raja JothiKeji Zhao
Sep 19, 2008·Genome Biology·Yong ZhangX Shirley Liu
Nov 1, 2008·Cancer Research·Chang S Chan, Jun S Song
Jul 1, 2009·Cell·Jennifer E Phillips, Victor G Corces
Nov 6, 2009·Nature·Melissa J FullwoodYijun Ruan
Feb 9, 2010·Trends in Endocrinology and Metabolism : TEM·Karen E Knudsen, Trevor M Penning
Mar 9, 2010·Nature Genetics·Housheng Hansen HeX Shirley Liu
Jan 15, 2011·Genome Research·Aurélien A SérandourJérôme Eeckhoute
Feb 8, 2011·Cell·Michael Bulger, Mark Groudine
Jun 21, 2011·Nature Genetics·Lusy HandokoChia-Lin Wei
Sep 6, 2011·Trends in Endocrinology and Metabolism : TEM·Dayong WuQianben Wang
Sep 22, 2011·The EMBO Journal·Michael A AugelloKaren E Knudsen

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Citations

Nov 21, 2012·BMC Genomics·Cenny TaslimTim Hui-Ming Huang
Mar 13, 2014·Nature Reviews. Genetics·Chin-Tong Ong, Victor G Corces
Sep 4, 2014·European Journal of Medical Research·Yu ZhangYuhai Zhang
Sep 17, 2016·Molecular and Cellular Endocrinology·Damien A LeachGrant Buchanan
Feb 20, 2019·Endocrine-related Cancer·Peder Rustøen Braadland, Alfonso Urbanucci
Jun 26, 2013·Nature Reviews. Cancer·Eric W-F LamChuay-Yeng Koo
Sep 29, 2015·EMBO Molecular Medicine·Suzan StellooWilbert Zwart
Apr 26, 2020·Molecular Oncology·Simon J BaumgartBernard Haendler
Mar 8, 2019·Endocrine-related Cancer·Peder Rustøen Braadland, Alfonso Urbanucci
Nov 19, 2019·Molecular Oncology·Doris HöflmayerCornelia Schroeder
Apr 24, 2020·Biochimica Et Biophysica Acta. Reviews on Cancer·Bing GaoJianping Guo

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Datasets Mentioned

BETA
GSE6099

Methods Mentioned

BETA
immunoprecipitation
ChIP-seq
PCR
ChIP
ChIP-chip
laser-capture microdissection

Software Mentioned

Significance Analysis of Microarrays ( SAM )

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