title: Transcriptome map of mouse isochores in embryonic and neonatal cortex.
abstract: Several studies on adult tissues agree on the presence of a positive effect of the genomic and genic base composition on mammalian gene expression. Recent literature supports the idea that during developmental processes GC-poor genomic regions are preferentially implicated. We investigate the relationship between the compositional properties of the isochores and of the genes with their respective expression activity during developmental processes. Using RNA-seq data from two distinct developmental stages of the mouse cortex, embryonic day 18 (E18) and postnatal day 7 (P7), we established for the first time a developmental-related transcriptome map of the mouse isochores. Additionally, for each stage we estimated the correlation between isochores' GC level and their expression activity, and the genes' expression patterns for each isochore family. Our analyses add evidence supporting the idea that during development GC-poor isochores are preferentially implicated, and confirm the positive effect of genes' GC level on their expression activity.
authors.affiliation: Department of Informatics, King's College London, The Strand, London WC2R 2LS, UK.
authors.forename: Kimon
authors.initials: K
authors.lastname: Frousios
authors.affiliation: Department of Informatics, King's College London, The Strand, London WC2R 2LS, UK; School of Mathematics and Statistics, University of Western Australia, 35 Stirling Highway, Crawley, Perth WA 6009, Australia.
authors.forename: Costas S
authors.initials: CS
authors.lastname: Iliopoulos
authors.affiliation: Lehrstuhl für Informatik 2, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
authors.forename: German
authors.initials: G
authors.lastname: Tischler
authors.affiliation: Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, Athens 115 27, Greece.
authors.forename: Sophia
authors.initials: S
authors.lastname: Kossida
authors.affiliation: Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA; Heidelberg Institute for Theoretical Studies, 35 Schloss-Wolfsbrunnenweg, Heidelberg D-69118, Germany.
authors.forename: Solon P
authors.initials: SP
authors.lastname: Pissis
authors.affiliation: Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, Athens 115 27, Greece. Electronic address: sarhondakis@bioacademy.gr.
authors.forename: Stilianos
authors.initials: S
authors.lastname: Arhondakis
mesh_terms: D000818:Animals; D001482:Base Composition; D001921:Brain / Q000196:embryology / Q000378:metabolism*; D002874:Chromosome Mapping; D004622:Embryo, Mammalian; D018507:Gene Expression Regulation, Developmental; D015723:Gene Library; D032085:Isochores / Q000235:genetics*; D051379:Mice; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D032085:Isochores