Genomics

Dataset Information

101

A prostate cancer risk element functions as a repressive loop that regulates HOXA13


ABSTRACT: Prostate cancer (PCa) is the leading cancer among men in the United States, with genetic factors contributing to ~42% of the susceptibility to PCa. To understand the causal genetic factors associated with PCa, we have focused on a PCa risk region located at 7p15.2. We performed Hi-C analysis and demonstrated that this region has long range interactions with the HOXA locus, located ~873 kb away. Using the CRISPR/Cas9 system, we deleted a 4 kb region encompassing several prostate cancer risk-associated SNPs and performed RNA-seq to investigate transcriptomic changes in RWPE1 prostate cells lacking the regulatory element. Our results suggest that the risk element affects the expression of HOXA13 and HOTTIP, but not other genes in the HOXA locus, via a repressive loop. Forced expression of HOXA13 was also performed to gain insight into the mechanisms by which this risk element affects prostate cancer risk. Overall design: Examination of normal prostate epithelial cell RWPE-1 genomic interactions by Hi-C. A prostate cancer risk region at 7p15.2 was deleted and HOXA13 gene was forced expressed in RWPE-1 cells, the transcriptomic changes were investigated by RNA-seq.

REANALYSED by: GSE118514

INSTRUMENT(S): Illumina HiSeq 2000 (Homo sapiens)

SUBMITTER: Zhifei Luo  

PROVIDER: GSE98898 | GEO | 2017-11-01

SECONDARY ACCESSION(S): PRJNA386902

REPOSITORIES: GEO

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Publications

A Prostate Cancer Risk Element Functions as a Repressive Loop that Regulates HOXA13.

Luo Zhifei Z   Rhie Suhn Kyong SK   Lay Fides D FD   Farnham Peggy J PJ  

Cell reports 20171101 6


Prostate cancer (PCa) is the leading cancer among men in the United States, with genetic factors contributing to ∼42% of the susceptibility to PCa. We analyzed a PCa risk region located at 7p15.2 to gain insight into the mechanisms by which this noncoding region may affect gene regulation and contribute to PCa risk. We performed Hi-C analysis and demonstrated that this region has long-range interactions with the HOXA locus, located ∼873 kb away. Using the CRISPR/Cas9 system, we deleted a 4-kb re  ...[more]

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