Transcriptomics,Multiomics

Dataset Information

57

Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function [Agilent expression]


ABSTRACT: The epithelium lining the epididymis in the male reproductive tract maintains a luminal environment that promotes sperm cell maturation. This process is dependent on the coordinated expression of many genes that encode proteins with a role in epithelial transport. We previously generated genome-wide maps of open chromatin in primary human fetal epididymis epithelial cells to identify potential regulatory elements controlling coordinated gene expression in the epididymis epithelium. Subsequent in silico analysis identified transcription factor binding sites (TFBS) that were over-represented in the HEE open chromatin, include the motif for paired box 2 (PAX2). PAX2 is a critical transcriptional regulator of urogenital tract development, which is well studied in the kidney but is unexplored in the epididymis. Due to the limited lifespan of primary HEE cells in culture we investigated the role of PAX2 in an immortalized HEE cell line (REP). First, REP cells were evaluated by DNase-seq and their open chromatin map overlapped that of primary HEE cells at ~ 65% of sites. Moreover, the PAX2-binding motif was again identified as an overrepresented TFBS within intergenic open chromatin, though on fewer chromosomes than in the primary HEE cells. To identify PAX2-target genes in REP cells, RNA-seq analysis was performed after siRNA-mediated depletion of PAX2 in comparison to a non-targeting siRNA. In response to PAX2-represssion, 3142 transcripts were differentially expressed (1334 up-regulated and 1808 down-regulated). Novel PAX2 targets included multiple genes encoding proteins with a predicted function in the epididymis epithelium. Gene expression in REP cells was measured at 16 hours after exposure to 1nM R1881 or vehicle control.

OTHER RELATED OMICS DATASETS IN: E-GEOD-59781

ORGANISM(S): Homo sapiens  

SUBMITTER: James Browne  Rui Yang   Ann Harris    

PROVIDER: E-GEOD-60381 | ArrayExpress| 2015-01-10

SECONDARY ACCESSION(S): GSE60381PRJNA258154

REPOSITORIES: GEO, ArrayExpress

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Publications

Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.

Browne James A JA   Yang Rui R   Song Lingyun L   Crawford Gregory E GE   Leir Shih-Hsing SH   Harris Ann A  

Molecular human reproduction 20140901 12


The epithelium lining the epididymis in the male reproductive tract maintains a luminal environment that promotes sperm cell maturation. This process is dependent on the coordinated expression of many genes that encode proteins with a role in epithelial transport. We previously generated genome-wide maps of open chromatin in primary human epididymis epithelial (HEE) cells to identify potential regulatory elements controlling coordinated gene expression in the epididymis epithelium. Subsequent in  ...[more]

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