TY - JOUR
T1 - Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function
AU - Browne, James A.
AU - Yang, Rui
AU - Song, Lingyun
AU - Crawford, Gregory E.
AU - Leir, Shih Hsing
AU - Harris, Ann
N1 - Funding Information:
This work was supported by National Institutes of Health (R01HD068901 to A.H) and the Cystic Fibrosis Foundation (Harris11G0 to A.H.).
PY - 2014/12/1
Y1 - 2014/12/1
N2 - 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 generatedgenome-wide maps of open chromatin in primaryhumanepididymis epithelial (HEE) 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, including the motif for paired box 2 (PAX2). PAX2is a critical transcriptional regulator of urogenital tract development, which has been well studied in the kidney but is unexplored in the epididymis.Dueto the limited lifespan of primary HEE cells in culture,we investigated the role of PAX2 in an immortalized HEE cell line (REP). First, REP cellswere evaluated by DNase I digestion followed by high-throughput sequencing and the PAX2-binding motif was again identified as an over-represented 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 and compared with that with a non-targeting siRNA. In response to PAX2-represssion, 3135 transcripts were differentially expressed (1333 up-regulated and 1802 down-regulated). Novel PAX2 targets included multiple genes encoding proteins with predicted functions in the epididymis epithelium.
AB - 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 generatedgenome-wide maps of open chromatin in primaryhumanepididymis epithelial (HEE) 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, including the motif for paired box 2 (PAX2). PAX2is a critical transcriptional regulator of urogenital tract development, which has been well studied in the kidney but is unexplored in the epididymis.Dueto the limited lifespan of primary HEE cells in culture,we investigated the role of PAX2 in an immortalized HEE cell line (REP). First, REP cellswere evaluated by DNase I digestion followed by high-throughput sequencing and the PAX2-binding motif was again identified as an over-represented 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 and compared with that with a non-targeting siRNA. In response to PAX2-represssion, 3135 transcripts were differentially expressed (1333 up-regulated and 1802 down-regulated). Novel PAX2 targets included multiple genes encoding proteins with predicted functions in the epididymis epithelium.
KW - Epididymis epithelium
KW - Open chromatin
KW - PAX2
KW - Transcriptional network
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U2 - 10.1093/molehr/gau075
DO - 10.1093/molehr/gau075
M3 - Article
C2 - 25180270
AN - SCOPUS:84961377607
VL - 20
SP - 1198
EP - 1207
JO - Molecular Human Reproduction
JF - Molecular Human Reproduction
SN - 1360-9947
IS - 12
ER -