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Regional regulation of transcription in the bovine genome.

Kommadath A, Nie H, Groenen MA, te Pas MF, Veerkamp RF, Smits MA - PLoS ONE (2011)

Bottom Line: The objectives here were to provide evidence for the existence of chromosomal regional regulation of transcription in the bovine genome, to analyse the genomic features of genes located within RIDGEs versus anti-RIDGEs and tissue-specific genes versus housekeeping and to examine the genomic distribution of genes subject to positive selection in bovines.Housekeeping genes (defined here as genes expressed in all five tissues) were over-represented within RIDGEs but tissue-specific genes (genes expressed in only one of the five tissues) were not.Housekeeping genes and genes within RIDGEs had, in general, higher expression levels and GC content but shorter gene lengths and intron lengths than tissue-specific genes and genes within anti-RIDGES.

View Article: PubMed Central - PubMed

Affiliation: Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Lelystad, The Netherlands. arun.kommadath@wur.nl

ABSTRACT
Eukaryotic genes are distributed along chromosomes as clusters of highly expressed genes termed RIDGEs (Regions of IncreaseD Gene Expression) and lowly expressed genes termed anti-RIDGEs, interspersed among genes expressed at intermediate levels or not expressed. Previous studies based on this observation suggested a dual mechanism of gene regulation, where, in addition to transcription factors, the chromosomal domain influences the expression level of their embedded genes. The objectives here were to provide evidence for the existence of chromosomal regional regulation of transcription in the bovine genome, to analyse the genomic features of genes located within RIDGEs versus anti-RIDGEs and tissue-specific genes versus housekeeping and to examine the genomic distribution of genes subject to positive selection in bovines. Gene expression analysis of four brain tissues and the anterior pituitary of 28 cows identified 70 RIDGEs and 41 anti-RIDGEs (harbouring 3735 and 1793 bovine genes respectively) across the bovine genome which are significantly higher than expected by chance. Housekeeping genes (defined here as genes expressed in all five tissues) were over-represented within RIDGEs but tissue-specific genes (genes expressed in only one of the five tissues) were not. Housekeeping genes and genes within RIDGEs had, in general, higher expression levels and GC content but shorter gene lengths and intron lengths than tissue-specific genes and genes within anti-RIDGES. Our findings suggest the existence of chromosomal regional regulation of transcription in the bovine genome. The genomic features observed for genes within RIDGEs and housekeeping genes in bovines agree with previous studies in several other species further strengthening the hypothesis of selective pressure to keep the highly and widely expressed genes short and compact for transcriptional efficiency. Further, positively selected genes were found non-randomly distributed on the genome with a preference for RIDGEs and regions of intermediate gene expression compared to anti-RIDGEs.

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Related in: MedlinePlus

Tissue wise transcriptome maps for chromosome 2.Transcriptome maps for AP, HC, AM, DH, VH and one based on the average of the median gene expressions across all 5 tissues. The y-axis shows the median gene expression levels (log transformed normalised gene intensities ranging from 9 to 14) for the 579 Ensembl genes on chromosome 2 represented on the array (AP-Anterior Pituitary, AM-Amygdala, HC-Hippocampus, DH- Dorsal Hypothalamus, VH-Ventral Hypothalamus).
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pone-0020413-g004: Tissue wise transcriptome maps for chromosome 2.Transcriptome maps for AP, HC, AM, DH, VH and one based on the average of the median gene expressions across all 5 tissues. The y-axis shows the median gene expression levels (log transformed normalised gene intensities ranging from 9 to 14) for the 579 Ensembl genes on chromosome 2 represented on the array (AP-Anterior Pituitary, AM-Amygdala, HC-Hippocampus, DH- Dorsal Hypothalamus, VH-Ventral Hypothalamus).

Mentions: Spearman rank correlation test on pair-wise comparisons of transcriptome maps of all tissues showed high correlations (Figure 3), with an average correlation of 0.91 (all p-values below 2.2e-16). The highest correlations are between DH and VH and between AM and HC. All brain areas are more correlated with each other than with the anterior pituitary. The similarity in the transcriptome maps across tissues was clearly visible taking chromosome 2 as an example (Figure 4).


Regional regulation of transcription in the bovine genome.

Kommadath A, Nie H, Groenen MA, te Pas MF, Veerkamp RF, Smits MA - PLoS ONE (2011)

Tissue wise transcriptome maps for chromosome 2.Transcriptome maps for AP, HC, AM, DH, VH and one based on the average of the median gene expressions across all 5 tissues. The y-axis shows the median gene expression levels (log transformed normalised gene intensities ranging from 9 to 14) for the 579 Ensembl genes on chromosome 2 represented on the array (AP-Anterior Pituitary, AM-Amygdala, HC-Hippocampus, DH- Dorsal Hypothalamus, VH-Ventral Hypothalamus).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3108615&req=5

pone-0020413-g004: Tissue wise transcriptome maps for chromosome 2.Transcriptome maps for AP, HC, AM, DH, VH and one based on the average of the median gene expressions across all 5 tissues. The y-axis shows the median gene expression levels (log transformed normalised gene intensities ranging from 9 to 14) for the 579 Ensembl genes on chromosome 2 represented on the array (AP-Anterior Pituitary, AM-Amygdala, HC-Hippocampus, DH- Dorsal Hypothalamus, VH-Ventral Hypothalamus).
Mentions: Spearman rank correlation test on pair-wise comparisons of transcriptome maps of all tissues showed high correlations (Figure 3), with an average correlation of 0.91 (all p-values below 2.2e-16). The highest correlations are between DH and VH and between AM and HC. All brain areas are more correlated with each other than with the anterior pituitary. The similarity in the transcriptome maps across tissues was clearly visible taking chromosome 2 as an example (Figure 4).

Bottom Line: The objectives here were to provide evidence for the existence of chromosomal regional regulation of transcription in the bovine genome, to analyse the genomic features of genes located within RIDGEs versus anti-RIDGEs and tissue-specific genes versus housekeeping and to examine the genomic distribution of genes subject to positive selection in bovines.Housekeeping genes (defined here as genes expressed in all five tissues) were over-represented within RIDGEs but tissue-specific genes (genes expressed in only one of the five tissues) were not.Housekeeping genes and genes within RIDGEs had, in general, higher expression levels and GC content but shorter gene lengths and intron lengths than tissue-specific genes and genes within anti-RIDGES.

View Article: PubMed Central - PubMed

Affiliation: Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, Lelystad, The Netherlands. arun.kommadath@wur.nl

ABSTRACT
Eukaryotic genes are distributed along chromosomes as clusters of highly expressed genes termed RIDGEs (Regions of IncreaseD Gene Expression) and lowly expressed genes termed anti-RIDGEs, interspersed among genes expressed at intermediate levels or not expressed. Previous studies based on this observation suggested a dual mechanism of gene regulation, where, in addition to transcription factors, the chromosomal domain influences the expression level of their embedded genes. The objectives here were to provide evidence for the existence of chromosomal regional regulation of transcription in the bovine genome, to analyse the genomic features of genes located within RIDGEs versus anti-RIDGEs and tissue-specific genes versus housekeeping and to examine the genomic distribution of genes subject to positive selection in bovines. Gene expression analysis of four brain tissues and the anterior pituitary of 28 cows identified 70 RIDGEs and 41 anti-RIDGEs (harbouring 3735 and 1793 bovine genes respectively) across the bovine genome which are significantly higher than expected by chance. Housekeeping genes (defined here as genes expressed in all five tissues) were over-represented within RIDGEs but tissue-specific genes (genes expressed in only one of the five tissues) were not. Housekeeping genes and genes within RIDGEs had, in general, higher expression levels and GC content but shorter gene lengths and intron lengths than tissue-specific genes and genes within anti-RIDGES. Our findings suggest the existence of chromosomal regional regulation of transcription in the bovine genome. The genomic features observed for genes within RIDGEs and housekeeping genes in bovines agree with previous studies in several other species further strengthening the hypothesis of selective pressure to keep the highly and widely expressed genes short and compact for transcriptional efficiency. Further, positively selected genes were found non-randomly distributed on the genome with a preference for RIDGEs and regions of intermediate gene expression compared to anti-RIDGEs.

Show MeSH
Related in: MedlinePlus