Genomics

Dataset Information

162

VHL restoration alters cis-regulatory landscape


ABSTRACT: VHL loss is the most common genetic alteration event in ccRCC. By profiling histone modifications from VHL-deficient ccRCC primary tumors and cell lines, we identifed tumor-associated promoters and enhancers. We next investigate whether VHL restoration alters tumor associated promoters and enhancers. We compared H3K27ac ChIP-seq with and without VHL restoration in 786-O cells. Restoration of wild-type VHL significantly altered a subset of tumor enhancers but affected promoters to a less extent. Overall design: H3K27ac ChIP-Seq in ccRCC cell line, 786-O, with wild-type VHL restoration

INSTRUMENT(S): Illumina HiSeq 2500 (Homo sapiens)

SUBMITTER: Xiaosai Yao  

PROVIDER: GSE102095 | GEO | 2017-08-22

SECONDARY ACCESSION(S): PRJNA396574

REPOSITORIES: GEO

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Publications

VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma.

Yao Xiaosai X   Tan Jing J   Lim Kevin Junliang KJ   Koh Joanna J   Ooi Wen Fong WF   Li Zhimei Z   Huang Dachuan D   Xing Manjie M   Chan Yang Sun YS   Qu James Zhengzhong JZ   Tay Su Ting ST   Wijaya Giovani G   Lam Yue Ning YN   Hong Jing Han JH   Lee-Lim Ai Ping AP   Guan Peiyong P   Ng Michelle Shu Wen MSW   He Cassandra Zhengxuan CZ   Lin Joyce Suling JS   Nandi Tannistha T   Qamra Aditi A   Xu Chang C   Myint Swe Swe SS   Davies James O J JOJ   Goh Jian Yuan JY   Loh Gary G   Tan Bryan C BC   Rozen Steven G SG   Yu Qiang Q   Tan Iain Bee Huat IBH   Cheng Christopher Wai Sam CWS   Li Shang S   Chang Kenneth Tou En KTE   Tan Puay Hoon PH   Silver David Lawrence DL   Lezhava Alexander A   Steger Gertrud G   Hughes Jim R JR   Teh Bin Tean BT   Tan Patrick P  

Cancer discovery 20170911 11


Protein-coding mutations in clear cell renal cell carcinoma (ccRCC) have been extensively characterized, frequently involving inactivation of the von Hippel-Lindau (VHL) tumor suppressor. Roles for noncoding cis-regulatory aberrations in ccRCC tumorigenesis, however, remain unclear. Analyzing 10 primary tumor/normal pairs and 9 cell lines across 79 chromatin profiles, we observed pervasive enhancer malfunction in ccRCC, with cognate enhancer-target genes associated with tissue-specific aspects o  ...[more]

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