title: Chromatin structure characteristics of pre-miRNA genomic sequences.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are non-coding RNAs with important roles in regulating gene expression. Recent studies indicate that transcription and cleavage of miRNA are coupled, and that chromatin structure may influence miRNA transcription. However, little is known about the relationship between the chromatin structure and cleavage of pre-miRNA from pri-miRNA.
  
  
  RESULTS
  By analysis of genome-wide nucleosome positioning data sets from human and Caenorhabditis elegans (C. elegans), we found an enrichment of positioned nucleosome on pre-miRNA genomic sequences, which is highly correlated with GC content within pre-miRNA. In addition, obvious enrichments of three histone modifications (H2BK5me1, H3K36me3 and H4K20me1) as well as RNA Polymerase II (RNAPII) were observed on pre-miRNA genomic sequences corresponding to the active-promoter miRNAs and expressed miRNAs.
  
  
  CONCLUSIONS
  Our results revealed the chromatin structure characteristics of pre-miRNA genomic sequences, and implied potential mechanisms that can recognize these characteristics, thus improving pre-miRNA cleavage.
authors.affiliation: Center for Biomedical Informatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China.
authors.forename: Shijia
authors.initials: S
authors.lastname: Zhu
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Jiang
authors.forename: Guohua
authors.initials: G
authors.lastname: Wang
authors.forename: Bo
authors.initials: B
authors.lastname: Liu
authors.forename: Mingxiang
authors.initials: M
authors.lastname: Teng
authors.forename: Yadong
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D002843:Chromatin / Q000737:chemistry*; D020869:Gene Expression Profiling; D016678:Genome; D006657:Histones / Q000235:genetics; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D009707:Nucleosomes / Q000235:genetics; D012319:RNA Polymerase II / Q000235:genetics; D012322:RNA Precursors / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D006657:Histones; D035683:MicroRNAs; D009707:Nucleosomes; D012322:RNA Precursors; D012319:RNA Polymerase II