Research article

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

Baochen Shi^{* 1} , Xiangqian Guo^{* 1,3} , Tao Wu^{* 1} , Sitong Sheng² , Jie Wang¹ , Geir Skogerbø¹ , Xiaopeng Zhu¹ and Runsheng Chen¹

¹Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China

²Department of Molecular Physiology & Biological Physics, School of Medicine, University of Virginia, 1300 Jefferson Park Ave, Charlottesville, Virginia 22908, USA

³Graduate School of the Chinese Academy of Science, Beijing 100080, PR China

author email corresponding author email* Contributed equally

BMC Genomics 2009, 10:92doi:10.1186/1471-2164-10-92

Published:	25 February 2009

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.