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.2011 Oct 17:12:511.
doi: 10.1186/1471-2164-12-511.

Transcriptome map of mouse isochores

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Transcriptome map of mouse isochores

Stilianos Arhondakis et al. BMC Genomics..

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.

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Figures

Figure 1
Figure 1
Expression profiles of the isochore for the three tissues on chromosome 10. The Y axis measures the isochores' GC levels (positive values -- light blue line) and their respective expression levels (EL-- Equation (1)) for the brain, liver, and muscle tissues (negative values -- red, dark blue, and green lines, respectively). High expression corresponds to peaks in the lines. The red and black boxes highlight areas where the high GC level is clearly accompanied by high expression. The black vertical line in the red box marks the location of the 10 Mm62 H3 isochore.
Figure 2
Figure 2
Correlation between the solely GC effects on the expression activity of each isochore. Correlation between the expression level (normalized by the gene densityED-- Equation (2)) of each isochore and the respective GC level (red plot for brain, blue plot for liver, and green plot for muscle).
Figure 3
Figure 3
Average genic activity within each isochore for the three tissues. Average genic expression levels after the genes have been binned in the five isochore families. Larger negative values (tall coloured bars) indicate low expression, and small negative values (short coloured bars) indicate high expression.
Figure 4
Figure 4
Isochoric distributions for the non-detected genes and the total number of CDSs. Top: Distribution (%) across the isochore families of the genes not detected to be expressed in any of the three tissues (bars in black), and of the genes not detected to be expressed in a specific tissue only (red bars for brain, blue bars for liver, and green bars for muscle). Bottom: Distribution (%) of the total number of coding sequences across the five isochore families (each coloured bar corresponds to an isochore family).
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References

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