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Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes.

Ganapathi M, Srivastava P, Das Sutar SK, Kumar K, Dasgupta D, Pal Singh G, Brahmachari V, Brahmachari SK - BMC Bioinformatics (2005)

Bottom Line: The differences in the chromatin features between the two groups of genes indicate the involvement of chromatin organisation in the control of gene expression.The presence of global regulatory mechanisms mediated through chromatin organisation can decrease the burden of invoking gene specific regulators for maintenance of the active/silenced state of gene expression.This could partially explain the lower number of genes estimated in the human genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India. mythilyg@igib.res.in

ABSTRACT

Background: Global regulatory mechanisms involving chromatin assembly and remodelling in the promoter regions of genes is implicated in eukaryotic transcription control especially for genes subjected to spatial and temporal regulation. The potential to utilise global regulatory mechanisms for controlling gene expression might depend upon the architecture of the chromatin in and around the gene. In-silico analysis can yield important insights into this aspect, facilitating comparison of two or more classes of genes comprising of a large number of genes within each group.

Results: In the present study, we carried out a comparative analysis of chromatin characteristics in terms of the scaffold/matrix attachment regions, nucleosome formation potential and the occurrence of repetitive sequences, in the upstream regulatory regions of housekeeping and tissue specific genes. Our data show that putative scaffold/matrix attachment regions are more abundant and nucleosome formation potential is higher in the 5' regions of tissue specific genes as compared to the housekeeping genes.

Conclusion: The differences in the chromatin features between the two groups of genes indicate the involvement of chromatin organisation in the control of gene expression. The presence of global regulatory mechanisms mediated through chromatin organisation can decrease the burden of invoking gene specific regulators for maintenance of the active/silenced state of gene expression. This could partially explain the lower number of genes estimated in the human genome.

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Nucleosome formation potential score distributions for 5' regions of housekeeping and tissue specific genes. The 5' sequences of human housekeeping and tissue specific genes were analysed by Recon for distribution of nucleosome formation potential scores. Frequency distribution histograms were plotted for scores in various intervals (range -3.2 to +3.2). (A) and (B) show the distribution of nucleosome formation potential scores at 400 and 2000 bp upstream from the gene start site respectively. Nucleosomal density is significantly lower for housekeeping genes as compared to tissue specific ones, in regions close to the gene start site.
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Figure 1: Nucleosome formation potential score distributions for 5' regions of housekeeping and tissue specific genes. The 5' sequences of human housekeeping and tissue specific genes were analysed by Recon for distribution of nucleosome formation potential scores. Frequency distribution histograms were plotted for scores in various intervals (range -3.2 to +3.2). (A) and (B) show the distribution of nucleosome formation potential scores at 400 and 2000 bp upstream from the gene start site respectively. Nucleosomal density is significantly lower for housekeeping genes as compared to tissue specific ones, in regions close to the gene start site.

Mentions: The Tsg and Hkg sequences show a considerable difference in their nucleosome formation potential scores over an extended upstream region of 2000 bp (Figures 1 and 2). The Tsg region is enriched in nucleosome formation potential scores (peak at 1) in all upstream positions analysed (till 2000 bp). For Hkg, the distribution seems to be shifted towards the negative scores at 400 bp region and this shift diminishes gradually as we move further upstream to finally peak at 1 in 2000 bp upstream region (Figure 1). t-test was applied to ascertain the difference in distribution of Recon scores between Hkg and Tsg (Table 3). The resultant P-values in various intervals of relevance (0.8 to 1, 1 to 1.2, -0.8 to -1 and -1 to -1.2) reflect that the scores in the upstream 400 bp from the gene start site show the maximum difference in all the intervals and at 2000 bp, the difference gradually fades away in intervals 0.8 to 1 and 1 to 1.2 (Table 3).


Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes.

Ganapathi M, Srivastava P, Das Sutar SK, Kumar K, Dasgupta D, Pal Singh G, Brahmachari V, Brahmachari SK - BMC Bioinformatics (2005)

Nucleosome formation potential score distributions for 5' regions of housekeeping and tissue specific genes. The 5' sequences of human housekeeping and tissue specific genes were analysed by Recon for distribution of nucleosome formation potential scores. Frequency distribution histograms were plotted for scores in various intervals (range -3.2 to +3.2). (A) and (B) show the distribution of nucleosome formation potential scores at 400 and 2000 bp upstream from the gene start site respectively. Nucleosomal density is significantly lower for housekeeping genes as compared to tissue specific ones, in regions close to the gene start site.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1173084&req=5

Figure 1: Nucleosome formation potential score distributions for 5' regions of housekeeping and tissue specific genes. The 5' sequences of human housekeeping and tissue specific genes were analysed by Recon for distribution of nucleosome formation potential scores. Frequency distribution histograms were plotted for scores in various intervals (range -3.2 to +3.2). (A) and (B) show the distribution of nucleosome formation potential scores at 400 and 2000 bp upstream from the gene start site respectively. Nucleosomal density is significantly lower for housekeeping genes as compared to tissue specific ones, in regions close to the gene start site.
Mentions: The Tsg and Hkg sequences show a considerable difference in their nucleosome formation potential scores over an extended upstream region of 2000 bp (Figures 1 and 2). The Tsg region is enriched in nucleosome formation potential scores (peak at 1) in all upstream positions analysed (till 2000 bp). For Hkg, the distribution seems to be shifted towards the negative scores at 400 bp region and this shift diminishes gradually as we move further upstream to finally peak at 1 in 2000 bp upstream region (Figure 1). t-test was applied to ascertain the difference in distribution of Recon scores between Hkg and Tsg (Table 3). The resultant P-values in various intervals of relevance (0.8 to 1, 1 to 1.2, -0.8 to -1 and -1 to -1.2) reflect that the scores in the upstream 400 bp from the gene start site show the maximum difference in all the intervals and at 2000 bp, the difference gradually fades away in intervals 0.8 to 1 and 1 to 1.2 (Table 3).

Bottom Line: The differences in the chromatin features between the two groups of genes indicate the involvement of chromatin organisation in the control of gene expression.The presence of global regulatory mechanisms mediated through chromatin organisation can decrease the burden of invoking gene specific regulators for maintenance of the active/silenced state of gene expression.This could partially explain the lower number of genes estimated in the human genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India. mythilyg@igib.res.in

ABSTRACT

Background: Global regulatory mechanisms involving chromatin assembly and remodelling in the promoter regions of genes is implicated in eukaryotic transcription control especially for genes subjected to spatial and temporal regulation. The potential to utilise global regulatory mechanisms for controlling gene expression might depend upon the architecture of the chromatin in and around the gene. In-silico analysis can yield important insights into this aspect, facilitating comparison of two or more classes of genes comprising of a large number of genes within each group.

Results: In the present study, we carried out a comparative analysis of chromatin characteristics in terms of the scaffold/matrix attachment regions, nucleosome formation potential and the occurrence of repetitive sequences, in the upstream regulatory regions of housekeeping and tissue specific genes. Our data show that putative scaffold/matrix attachment regions are more abundant and nucleosome formation potential is higher in the 5' regions of tissue specific genes as compared to the housekeeping genes.

Conclusion: The differences in the chromatin features between the two groups of genes indicate the involvement of chromatin organisation in the control of gene expression. The presence of global regulatory mechanisms mediated through chromatin organisation can decrease the burden of invoking gene specific regulators for maintenance of the active/silenced state of gene expression. This could partially explain the lower number of genes estimated in the human genome.

Show MeSH