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Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites.

Shi B, Guo X, Wu T, Sheng S, Wang J, Skogerbø G, Zhu X, Chen R - BMC Genomics (2009)

Bottom Line: Many DHSs appeared to be associated with annotated non-coding RNAs and recently detected transcripts of unknown function.It has been reported that nematode highly conserved non-coding elements were associated with cis-regulatory elements, and we also found that DHSs, particularly distal intergenic DHSs, were significantly enriched in regions that were conserved between the C. elegans and C. briggsae genomes.We describe the first genome-wide analysis of C. elegans DHSs, and show that the distribution of DHSs is strongly associated with functional elements in the genome.

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Affiliation: Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China. shibaochen@moon.ibp.ac.cn

ABSTRACT

Background: A major goal of post-genomics research is the integrated analysis of genes, regulatory elements and the chromatin architecture on a genome-wide scale. Mapping DNase I hypersensitive sites within the nuclear chromatin is a powerful and well-established method of identifying regulatory element candidates.

Results: Here, we report the first genome-wide analysis of DNase I hypersensitive sites (DHSs) in Caenorhabditis elegans. The data was obtained by hybridizing DNase I-treated and end-captured material from young adult worms to a high-resolution tiling microarray. The data show that C. elegans DHSs were significantly enriched within intergenic regions located 2 kb upstream and downstream of coding genes, and also that a considerable fraction of all DHSs mapped to intergenic positions distant to annotated coding genes. Annotated transcribed loci were generally depleted in DHSs relative to intergenic regions, but DHSs were nonetheless enriched in coding exons and UTRs, whereas introns were significantly depleted in DHSs. Many DHSs appeared to be associated with annotated non-coding RNAs and recently detected transcripts of unknown function. It has been reported that nematode highly conserved non-coding elements were associated with cis-regulatory elements, and we also found that DHSs, particularly distal intergenic DHSs, were significantly enriched in regions that were conserved between the C. elegans and C. briggsae genomes.

Conclusion: We describe the first genome-wide analysis of C. elegans DHSs, and show that the distribution of DHSs is strongly associated with functional elements in the genome.

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Chromosomal DHS densities.
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Figure 3: Chromosomal DHS densities.

Mentions: The average DHSs length was 121 bp, with maximum and minimum lengths ranging from 46 bp to 754 bp (see Supplementary Figure S2 in Additional file 1 for the DHS length distributions). The locations of all 7095 DHSs were mapped to the C. elegans genome (WormBase WS140) [8]. The density of DHSs was slightly larger on the chromosome X than on the other chromosomes. This difference was similar to the distribution of highly conserved non-coding elements (CNEs) in the C. elegans genome [16], and could not be entirely explained by the density of annotated coding genes on chromosomes X, as the number of DHSs per 100 annotated coding genes were also higher for chromosomes X than for autosomal chromosomes (Figure 3).


Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites.

Shi B, Guo X, Wu T, Sheng S, Wang J, Skogerbø G, Zhu X, Chen R - BMC Genomics (2009)

Chromosomal DHS densities.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651899&req=5

Figure 3: Chromosomal DHS densities.
Mentions: The average DHSs length was 121 bp, with maximum and minimum lengths ranging from 46 bp to 754 bp (see Supplementary Figure S2 in Additional file 1 for the DHS length distributions). The locations of all 7095 DHSs were mapped to the C. elegans genome (WormBase WS140) [8]. The density of DHSs was slightly larger on the chromosome X than on the other chromosomes. This difference was similar to the distribution of highly conserved non-coding elements (CNEs) in the C. elegans genome [16], and could not be entirely explained by the density of annotated coding genes on chromosomes X, as the number of DHSs per 100 annotated coding genes were also higher for chromosomes X than for autosomal chromosomes (Figure 3).

Bottom Line: Many DHSs appeared to be associated with annotated non-coding RNAs and recently detected transcripts of unknown function.It has been reported that nematode highly conserved non-coding elements were associated with cis-regulatory elements, and we also found that DHSs, particularly distal intergenic DHSs, were significantly enriched in regions that were conserved between the C. elegans and C. briggsae genomes.We describe the first genome-wide analysis of C. elegans DHSs, and show that the distribution of DHSs is strongly associated with functional elements in the genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China. shibaochen@moon.ibp.ac.cn

ABSTRACT

Background: A major goal of post-genomics research is the integrated analysis of genes, regulatory elements and the chromatin architecture on a genome-wide scale. Mapping DNase I hypersensitive sites within the nuclear chromatin is a powerful and well-established method of identifying regulatory element candidates.

Results: Here, we report the first genome-wide analysis of DNase I hypersensitive sites (DHSs) in Caenorhabditis elegans. The data was obtained by hybridizing DNase I-treated and end-captured material from young adult worms to a high-resolution tiling microarray. The data show that C. elegans DHSs were significantly enriched within intergenic regions located 2 kb upstream and downstream of coding genes, and also that a considerable fraction of all DHSs mapped to intergenic positions distant to annotated coding genes. Annotated transcribed loci were generally depleted in DHSs relative to intergenic regions, but DHSs were nonetheless enriched in coding exons and UTRs, whereas introns were significantly depleted in DHSs. Many DHSs appeared to be associated with annotated non-coding RNAs and recently detected transcripts of unknown function. It has been reported that nematode highly conserved non-coding elements were associated with cis-regulatory elements, and we also found that DHSs, particularly distal intergenic DHSs, were significantly enriched in regions that were conserved between the C. elegans and C. briggsae genomes.

Conclusion: We describe the first genome-wide analysis of C. elegans DHSs, and show that the distribution of DHSs is strongly associated with functional elements in the genome.

Show MeSH