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

Publication ,  Journal Article
Browne, JA; Yang, R; Song, L; Crawford, GE; Leir, S-H; Harris, A
Published in: Mol Hum Reprod
December 2014

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 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). PAX2 is a critical transcriptional regulator of urogenital tract development, which has been 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 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-repression, 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.

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Published In

Mol Hum Reprod

DOI

EISSN

1460-2407

Publication Date

December 2014

Volume

20

Issue

12

Start / End Page

1198 / 1207

Location

England

Related Subject Headings

  • Transfection
  • Transcription, Genetic
  • RNA Interference
  • PAX2 Transcription Factor
  • Obstetrics & Reproductive Medicine
  • Male
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genome-Wide Association Study
  • Gene Regulatory Networks
 

Citation

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Browne, J. A., Yang, R., Song, L., Crawford, G. E., Leir, S.-H., & Harris, A. (2014). Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function. Mol Hum Reprod, 20(12), 1198–1207. https://doi.org/10.1093/molehr/gau075
Browne, James A., Rui Yang, Lingyun Song, Gregory E. Crawford, Shih-Hsing Leir, and Ann Harris. “Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.Mol Hum Reprod 20, no. 12 (December 2014): 1198–1207. https://doi.org/10.1093/molehr/gau075.
Browne JA, Yang R, Song L, Crawford GE, Leir S-H, Harris A. Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function. Mol Hum Reprod. 2014 Dec;20(12):1198–207.
Browne, James A., et al. “Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.Mol Hum Reprod, vol. 20, no. 12, Dec. 2014, pp. 1198–207. Pubmed, doi:10.1093/molehr/gau075.
Browne JA, Yang R, Song L, Crawford GE, Leir S-H, Harris A. Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function. Mol Hum Reprod. 2014 Dec;20(12):1198–1207.
Journal cover image

Published In

Mol Hum Reprod

DOI

EISSN

1460-2407

Publication Date

December 2014

Volume

20

Issue

12

Start / End Page

1198 / 1207

Location

England

Related Subject Headings

  • Transfection
  • Transcription, Genetic
  • RNA Interference
  • PAX2 Transcription Factor
  • Obstetrics & Reproductive Medicine
  • Male
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Genome-Wide Association Study
  • Gene Regulatory Networks