Open Access Research article

Transcriptome map of mouse isochores

Stilianos Arhondakis1*, Kimon Frousios2, Costas S Iliopoulos23, Solon P Pissis2, German Tischler4 and Sophia Kossida1*

Author Affiliations

1 Bioinformatics and Medical Informatics Team, Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, 115 27, Athens, Greece

2 Department of Informatics, King's College London, Strand, WC2R 2LS, London, UK

3 Digital Ecosystems & Business Intelligence Institute, Centre for Stringology & Applications, Curtin University, GPO Box U1987 Perth WA 6845, Australia

4 Department of Informatics, University of Würzburg, 97074 Würzburg, Germany

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BMC Genomics 2011, 12:511  doi:10.1186/1471-2164-12-511

Published: 17 October 2011



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.


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.


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.