Genomics

Dataset Information

350

Next Generation Sequencing Facilitates Quantitative Analysis of effect of knockdown of GATA2 on AR binding sites


ABSTRACT: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare AR binding activity in LNCaP cells with and without knockdown of GATA2. Methods: LNCaP cells between passage number 32-34 were used for assay. Cells are transfected with GATA2 specific or nonspecific siRNA and ChIP was performed, the ChIP producted was further used to generate library with illumina ChIP-seq kit. Hi-seq 2500 was used for sequencing and the data was analyzed by MACs for peaks. Results: GATA2 knockdown lead to changes of AR binding activity , in most AR binding sites, AR shows decreased bindig activity. Only small percent sites show increased binding. Conclusions: Our study represents the first detailed analysis of the relationship between GATA2 and AR binding in whole genomic DNA.These results demostrate GATA2 play a critical role in AR activity in prostate cancer. LNCaP cells was used as cell model were treated with specific GATA2 siRNA.Library was sequenced using Illumina HI-seq 2500.

ORGANISM(S): Homo sapiens  

SUBMITTER: Xiangtal Liu   Dayong Wu  Qianben Wang 

PROVIDER: E-GEOD-52725 | ArrayExpress | 2014-01-21

SECONDARY ACCESSION(S): SRP033312GSE52725PRJNA229904

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Three-tiered role of the pioneer factor GATA2 in promoting androgen-dependent gene expression in prostate cancer.

Wu Dayong D   Sunkel Benjamin B   Chen Zhong Z   Liu Xiangtao X   Ye Zhenqing Z   Li Qianjin Q   Grenade Cassandra C   Ke Jingdong J   Zhang Chunpeng C   Chen Hongyan H   Nephew Kenneth P KP   Huang Tim H-M TH   Liu Zhihua Z   Jin Victor X VX   Wang Qianben Q  

Nucleic acids research 20140113 6


In prostate cancer, androgen receptor (AR) binding and androgen-responsive gene expression are defined by hormone-independent binding patterns of the pioneer factors FoxA1 and GATA2. Insufficient evidence of the mechanisms by which GATA2 contributes to this process precludes complete understanding of a key determinant of tissue-specific AR activity. Our observations suggest that GATA2 facilitates androgen-responsive gene expression by three distinct modes of action. By occupying novel binding si  ...[more]

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