Mapping of small RNAs in the human ENCODE regions.

ABSTRACT: The elucidation of the largely unknown transcriptome of small RNAs is crucial for the understanding of genome and cellular function. We report here the results of the analysis of small RNAs (< 50 nt) in the ENCODE regions of the human genome. Size-fractionated RNAs from four different cell lines (HepG2, HelaS3, GM06990, SK-N-SH) were mapped with the forward and reverse ENCODE high-density resolution tiling arrays. The top 1% of hybridization signals are termed SmRfrags (Small RNA fragments). Eight percent of SmRfrags overlap the GENCODE genes (CDS), given that the majority map to intergenic regions (34%), intronic regions (53%), and untranslated regions (UTRs) (5%). In addition, 9.6% and 16.8% of SmRfrags in the 5' UTR regions overlap significantly with His/Pol II/TAF250 binding sites and

SUBMITTER: Borel C 

PROVIDER: S-EPMC2427294 | biostudies-literature | 2008 Apr

REPOSITORIES: biostudies-literature