title: Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.
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 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.
authors.affiliation: Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
authors.forename: James A
authors.initials: JA
authors.lastname: Browne
authors.affiliation: Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
authors.forename: Rui
authors.initials: R
authors.lastname: Yang
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Duke University Medical School, Durham, NC, USA Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC, USA.
authors.forename: Lingyun
authors.initials: L
authors.lastname: Song
authors.affiliation: Department of Pediatrics, Division of Medical Genetics, Duke University Medical School, Durham, NC, USA Center for Genomic and Computational Biology, Duke University Medical School, Durham, NC, USA.
authors.forename: Gregory E
authors.initials: GE
authors.lastname: Crawford
authors.affiliation: Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
authors.forename: Shih-Hsing
authors.initials: SH
authors.lastname: Leir
authors.affiliation: Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA ann-harris@northwestern.edu.
authors.forename: Ann
authors.initials: A
authors.lastname: Harris
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites; D002460:Cell Line; D042002:Chromatin Assembly and Disassembly; D004822:Epididymis / Q000166:cytology / Q000378:metabolism*; D004847:Epithelial Cells / Q000378:metabolism*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D051762:PAX2 Transcription Factor / Q000235:genetics / Q000378:metabolism*; D034622:RNA Interference; D014158:Transcription, Genetic; D014162:Transfection
chemical_list: D051762:PAX2 Transcription Factor; C497318:PAX2 protein, human
keywords: PAX2; epididymis epithelium; open chromatin; transcriptional network