title: HNF1 regulates critical processes in the human epididymis epithelium.
abstract: The luminal environment of the epididymis participates in sperm maturation and impacts male fertility. It is dependent on the coordinated expression of many genes encoding proteins with a role in epithelial transport. We identified cis-regulatory elements for critical genes in epididymis function, by mapping open chromatin genome-wide in human epididymis epithelial (HEE) cells. Bioinformatic predictions of transcription factors binding to the regulatory elements suggested an important role for hepatocyte nuclear factor 1 (HNF1) in the transcriptional program of these cells. Chromatin immunoprecipitation and deep sequencing (ChIP-seq) revealed HNF1 target genes in HEE cells. In parallel, the contribution of HNF1 to the transcriptome of HEE cells was determined by RNA-seq, following siRNA-mediated depletion of both HNF1α and HNF1β transcription factors. Repression of these factors caused differential expression of 1892 transcripts (902 were downregulated and 990 upregulated) in comparison to non-targeting siRNAs. Differentially expressed genes with HNF1 ChIP-seq peaks within 20 kb were subject to gene ontology process enrichment analysis. Among the most significant processes associated with down-regulated genes were epithelial transport of water, phosphate and bicarbonate, all critical processes in epididymis epithelial function. Measurements of intracellular pH (pHi) confirmed a role for HNF1 in regulating the epididymis luminal environment.
authors.affiliation: Human Molecular Genetics Program, Lurie Children's Research Center, 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.
authors.forename: Rui
authors.initials: R
authors.lastname: Yang
authors.affiliation: Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
authors.forename: Scott E
authors.initials: SE
authors.lastname: Eggener
authors.affiliation: Human Molecular Genetics Program, Lurie Children's Research Center, 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. Electronic address: ann-harris@northwestern.edu.
authors.forename: Ann
authors.initials: A
authors.lastname: Harris
mesh_terms: D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods; D004822:Epididymis / Q000166:cytology / Q000378:metabolism*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D051537:Hepatocyte Nuclear Factor 1 / Q000235:genetics* / Q000378:metabolism*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D050436:Regulatory Elements, Transcriptional; D014158:Transcription, Genetic
chemical_list: D051537:Hepatocyte Nuclear Factor 1
keywords: Cis-regulatory elements; Epididymis epithelium; HNF1; Transcriptional network