title: Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China. shibaochen@moon.ibp.ac.cn
authors.forename: Baochen
authors.initials: B
authors.lastname: Shi
authors.forename: Xiangqian
authors.initials: X
authors.lastname: Guo
authors.forename: Tao
authors.initials: T
authors.lastname: Wu
authors.forename: Sitong
authors.initials: S
authors.lastname: Sheng
authors.forename: Jie
authors.initials: J
authors.lastname: Wang
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D002874:Chromosome Mapping; D018509:DNA, Helminth / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics*; D003850:Deoxyribonuclease I / Q000378:metabolism; D005786:Gene Expression Regulation; D049751:Genome, Helminth; D020411:Oligonucleotide Array Sequence Analysis; D012045:Regulatory Sequences, Nucleic Acid
chemical_list: D018509:DNA, Helminth; D021901:DNA, Intergenic; D003850:Deoxyribonuclease I