title: Characterization of enhancers active in the mouse embryonic cerebral cortex suggests Sox/Pou cis-regulatory logics and heterogeneity of cortical progenitors.
abstract: We aimed to identify cis-regulatory elements that control gene expression in progenitors of the cerebral cortex. A list of 975 putative enhancers were retrieved from a ChIP-Seq experiment performed in NS5 mouse stem cells with antibodies to Sox2, Brn2/Pou3f2, or Brn1/Pou3f3. Through a selection pipeline including gene ontology and expression pattern, we reduced the number of candidate enhancer sequences to 20. Ex vivo electroporation of green fluorescent pProtein (GFP) reporter constructs in the telencephalon of mouse embryos showed that 35% of the 20 selected candidate sequences displayed enhancer activity in the developing cortex at E13.5. In silico transcription factor binding site (TFBS) searches and mutagenesis experiments showed that enhancer activity is related to the presence of Sox/Pou TFBS pairs in the sequence. Comparative genomic analyses showed that enhancer activity is not related to the evolutionary conservation of the sequence. Finally, the combination of in utero electroporation of GFP reporter constructs with immunostaining for Tbr2 (basal progenitor marker) and phospho-histoneH3 (mitotic activity marker) demonstrated that each enhancer is specifically active in precise subpopulations of progenitors in the cortical germinal zone, highlighting the heterogeneity of these progenitors in terms of cis-regulation.
authors.affiliation: Equipe Development and Evolution of the Forebrain.
authors.forename: Amandine
authors.initials: A
authors.lastname: Bery
authors.affiliation: MRC-NIMR, London, UK.
authors.forename: Ben
authors.initials: B
authors.lastname: Martynoga
authors.affiliation: MRC-NIMR, London, UK.
authors.forename: François
authors.initials: F
authors.lastname: Guillemot
authors.affiliation: Equipe Morphogenesis of the Chordate Nervous System, UPR3294 N&D, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France and.
authors.forename: Jean-Stéphane
authors.initials: JS
authors.lastname: Joly
authors.affiliation: Equipe Development and Evolution of the Forebrain.
authors.forename: Sylvie
authors.initials: S
authors.lastname: Rétaux
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D005075:Biological Evolution; D015820:Cadherins / Q000235:genetics / Q000378:metabolism; D002460:Cell Line; D002540:Cerebral Cortex / Q000166:cytology* / Q000196:embryology*; D004622:Embryo, Mammalian; D005260:Female; D018507:Gene Expression Regulation, Developmental / Q000502:physiology*; D006657:Histones / Q000235:genetics / Q000378:metabolism; D066298:In Vitro Techniques; D051379:Mice; D008822:Mice, Transgenic; D016296:Mutagenesis / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D009924:Organ Culture Techniques; D050809:POU Domain Factors / Q000235:genetics / Q000378:metabolism*; D011247:Pregnancy; D055748:SOXB1 Transcription Factors / Q000235:genetics / Q000378:metabolism*; D013234:Stem Cells / Q000502:physiology*; D020825:T-Box Domain Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D015820:Cadherins; C491198:Eomes protein, mouse; D006657:Histones; D009419:Nerve Tissue Proteins; D050809:POU Domain Factors; C083970:R-cadherin; D055748:SOXB1 Transcription Factors; D020825:T-Box Domain Proteins
keywords: ChIP-Seq; Pou; Sox; cis-regulation; electroporation