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Transcriptome map of mouse isochores

Please always quote using this URN: urn:nbn:de:bvb:20-opus-142773
  • Background: The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest. Results: We present the transcriptome map of the mouse isochores (DNA segments with a fairlyBackground: The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest. Results: We present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of isochores' base composition on their expression activity. Our analyses also cover the relations between the genes' expression activity and their localization in the isochore families. Conclusions: This study is the first where next-generation sequencing data are used to associate the effects of both genomic and genic compositional properties to their corresponding expression activity. Our findings confirm previous results, and further support the existence of a relationship between isochores and gene expression. This relationship corroborates that isochores are primarily a product of evolutionary adaptation rather than a simple by-product of neutral evolutionary processes.show moreshow less

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Metadaten
Author: Stilianos Arhondakis, Kimon Frousios, Costas S. Iliopoulos, Solon P. Pissis, German Tischler, Sophia Kossida
URN:urn:nbn:de:bvb:20-opus-142773
Document Type:Journal article
Faculties:Fakultät für Mathematik und Informatik / Institut für Informatik
Language:English
Parent Title (English):BMC Genomics
Year of Completion:2011
Volume:12
Issue:511
Pagenumber:1-9
Source:BMC Genomics 2011, 12:511
DOI:https://doi.org/10.1186/1471-2164-12-511
Dewey Decimal Classification:6 Technik, Medizin, angewandte Wissenschaften / 61 Medizin und Gesundheit / 610 Medizin und Gesundheit
Tag:Base composition; Biased gene conversion; Evolution; Expresses genes; GC-Content; Higher rates; Human genome; Mammalian genomes; RNA-SEQ; Rodents
Release Date:2019/02/05
Licence (German):License LogoCC BY: Creative-Commons-Lizenz: Namensnennung