Transcriptome map of mouse isochores.

Abstract:

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 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.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Arhondakis S,Frousios K,Iliopoulos CS,Pissis SP,Tischler G,Kossida S

doi

10.1186/1471-2164-12-511

subject

Has Abstract

pub_date

2011-10-17 00:00:00

pages

511

issn

1471-2164

pii

1471-2164-12-511

journal_volume

12

pub_type

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