title: Identification of ELF3 as an early transcriptional regulator of human urothelium.
abstract: Despite major advances in high-throughput and computational modelling techniques, understanding of the mechanisms regulating tissue specification and differentiation in higher eukaryotes, particularly man, remains limited. Microarray technology has been explored exhaustively in recent years and several standard approaches have been established to analyse the resultant datasets on a genome-wide scale. Gene expression time series offer a valuable opportunity to define temporal hierarchies and gain insight into the regulatory relationships of biological processes. However, unless datasets are exactly synchronous, time points cannot be compared directly. Here we present a data-driven analysis of regulatory elements from a microarray time series that tracked the differentiation of non-immortalised normal human urothelial (NHU) cells grown in culture. The datasets were obtained by harvesting differentiating and control cultures from finite bladder- and ureter-derived NHU cell lines at different time points using two previously validated, independent differentiation-inducing protocols. Due to the asynchronous nature of the data, a novel ranking analysis approach was adopted whereby we compared changes in the amplitude of experiment and control time series to identify common regulatory elements. Our approach offers a simple, fast and effective ranking method for genes that can be applied to other time series. The analysis identified ELF3 as a candidate transcriptional regulator involved in human urothelial cytodifferentiation. Differentiation-associated expression of ELF3 was confirmed in cell culture experiments and by immunohistochemical demonstration in situ. The importance of ELF3 in urothelial differentiation was verified by knockdown in NHU cells, which led to reduced expression of FOXA1 and GRHL3 transcription factors in response to PPARγ activation. The consequences of this were seen in the repressed expression of late/terminal differentiation-associated uroplakin 3a gene expression and in the compromised development and regeneration of urothelial barrier function.
authors.affiliation: Institute of Computer Science I12, Technische Universität München, Boltzmannstr. 3, 85748 Garching, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Böck
authors.affiliation: Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, UK.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Hinley
authors.affiliation: Institute of Computer Science I12, Technische Universität München, Boltzmannstr. 3, 85748 Garching, Germany.
authors.forename: Constanze
authors.initials: C
authors.lastname: Schmitt
authors.affiliation: Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, UK.
authors.forename: Tom
authors.initials: T
authors.lastname: Wahlicht
authors.affiliation: Institute of Computer Science, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128 Mainz, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Kramer
authors.affiliation: Jack Birch Unit for Molecular Carcinogenesis, Department of Biology, University of York, York YO10 5DD, UK. Electronic address: jennifer.southgate@york.ac.uk.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Southgate
mesh_terms: D002454:Cell Differentiation / Q000502:physiology*; D017931:DNA Primers / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D017097:Electric Impedance; D018507:Gene Expression Regulation, Developmental / Q000235:genetics / Q000502:physiology*; D055785:Gene Knockdown Techniques; D051541:Hepatocyte Nuclear Factor 3-alpha / Q000378:metabolism; D006801:Humans; D007150:Immunohistochemistry; D046228:Microarray Analysis; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism*; D050783:Proto-Oncogene Proteins c-ets; D034741:RNA, Small Interfering / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D019459:Urothelium / Q000166:cytology / Q000196:embryology*
chemical_list: D017931:DNA Primers; D004268:DNA-Binding Proteins; C105529:ELF3 protein, human; C496499:FOXA1 protein, human; C473143:GRHL3 protein, human; D051541:Hepatocyte Nuclear Factor 3-alpha; D011518:Proto-Oncogene Proteins; D050783:Proto-Oncogene Proteins c-ets; D034741:RNA, Small Interfering; D014157:Transcription Factors
keywords: Differentiation; ELF3; Gene expression; Microarray analysis; Normal Human Urothelium; PPARγ; Time series