IsoXpressor: A Tool to Assess Transcriptional Activity within Isochores

Genomes are characterized by large regions of homogeneous base compositions known as isochores. The latter are divided into GC-poor and GC-rich classes linked to distinct functional and structural properties. Several studies have addressed how isochores shape function and structure. To aid in this important subject, we present IsoXpressor, a tool designed for the analysis of the functional property of transcription within isochores. IsoXpressor allows users to process RNA-Seq data in relation to the isochores, and it can be employed to investigate any biological question of interest for any species. The results presented herein as proof of concept are focused on the preimplantation process in Homo sapiens (human) and Macaca mulatta (rhesus monkey)

Transcriptome map of mouse isochores

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p

Transcriptome map of mouse isochores in embryonic and neonatal cortex

AbstractSeveral 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