Fig. 2

Analysis of the transcription start sites of miRNAs. a Transcription start sites mapped by 5′ RACE. Based on the data from 5′ RACE, the transcription start sites of pri-miRNAs (GRCh37/hg19) were annotated. The 5′ end positions of pre-miRNAs were identified by manual inspection of sequencing data of mature miRNAs from HCT116 cells [18]. Distances between the transcription start sites and miRNA hairpin sequences were calculated and shown as a bar graph. b and c Distribution of Pol II, TBP, CpG islands, CAGE tags, H3K4me3, and H2A.Z, near the transcription start sites of (b) mRNAs and (c) miRNAs. The ChIP-seq data of Pol II, TBP, H3K4me3, and H2A.Z, and the information of CAGE tags were obtained from the ENCODE project [21]. In the case that the data for HCT116 cell line is not available, the data for other solid cancer cell lines, including A549, HepG2, and MCF7, were mixed and used for analysis. The information of CpG islands was obtained from The UCSC Genome Browser [30]. The distribution of these factors near the 5′ ends of mRNAs was analyzed using the information of 5′ end positions of RefSeq mRNAs from The UCSC Genome Browser [30]. The graph has been depicted with a bin of 200 nts