title: Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers.
abstract: One of the key issues in studying transcriptional regulation during development is how to employ genome-wide assays that reveals sites of open chromatin and transcription factor binding to efficiently identify biologically relevant genes and enhancers. Analysis of Drosophila CNS midline cell development provides a useful system for studying transcriptional regulation at the genomic level due to a large, well-characterized set of midline-expressed genes and in vivo validated enhancers. In this study, FAIRE-seq on FACS-purified midline cells was performed and the midline FAIRE data were compared with whole-embryo FAIRE data. We find that regions of the genome with a strong midline FAIRE peak and weak whole-embryo FAIRE peak overlap with known midline enhancers and provide a useful predictive tool for enhancer identification. In a complementary analysis, we compared a large dataset of fragments that drive midline expression in vivo with the FAIRE data. Midline enhancer fragments with a midline FAIRE peak tend to be near midline-expressed genes, whereas midline enhancers without a midline FAIRE peak were often distant from midline-expressed genes and unlikely to drive midline transcription in vivo.
authors: Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.|Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors: Joseph C
authors: JC
authors: Pearson
authors: Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA dmckay1@email.unc.edu steve_crews@unc.edu.|Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.|Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors: Daniel J
authors: DJ
authors: McKay
authors: Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors: Jason D
authors: JD
authors: Lieb
authors: Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA dmckay1@email.unc.edu steve_crews@unc.edu.|Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors: Stephen T
authors: 0000-0002-1432-401X
authors: ST
authors: Crews
mesh_terms: D000818:Animals; D030801:Animals, Genetically Modified; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D004330:Drosophila; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism*; D004742:Enhancer Elements, Genetic / Q000235:genetics; D005434:Flow Cytometry; D018507:Gene Expression Regulation, Developmental / Q000235:genetics
chemical_list: D002843:Chromatin; D029721:Drosophila Proteins
keywords: CNS; Chromatin; Drosophila; Enhancer; FAIRE-seq; Midline