RNA Polymerase II Binding Patterns Reveal Genomic Regions Involved in MicroRNA Gene Regulation

University of Calgary, Canada
PLoS ONE (Impact Factor: 3.23). 11/2010; 5(11):e13798. DOI: 10.1371/journal.pone.0013798
Source: PubMed


MicroRNAs are small non-coding RNAs involved in post-transcriptional regulation of gene expression. Due to the poor annotation of primary microRNA (pri-microRNA) transcripts, the precise location of promoter regions driving expression of many microRNA genes is enigmatic. This deficiency hinders our understanding of microRNA-mediated regulatory networks. In this study, we develop a computational approach to identify the promoter region and transcription start site (TSS) of pri-microRNAs actively transcribed using genome-wide RNA Polymerase II (RPol II) binding patterns derived from ChIP-seq data. Based upon the assumption that the distribution of RPol II binding patterns around the TSS of microRNA and protein coding genes are similar, we designed a statistical model to mimic RPol II binding patterns around the TSS of highly expressed, well-annotated promoter regions of protein coding genes. We used this model to systematically scan the regions upstream of all intergenic microRNAs for RPol II binding patterns similar to those of TSS from protein coding genes. We validated our findings by examining the conservation, CpG content, and activating histone marks in the identified promoter regions. We applied our model to assess changes in microRNA transcription in steroid hormone-treated breast cancer cells. The results demonstrate many microRNA genes have lost hormone-dependent regulation in tamoxifen-resistant breast cancer cells. MicroRNA promoter identification based upon RPol II binding patterns provides important temporal and spatial measurements regarding the initiation of transcription, and therefore allows comparison of transcription activities between different conditions, such as normal and disease states.

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    • "It is also not certain whether the same mechanism is responsible for the increase of all five miRNAs. MicroRNA precursors are transcribed by the same machinery that transcribes mRNA (Wang et al. 2010). Some such as hsa-miR-92a are expressed as a miRNA cluster from a polycistronic gene coding for multiple miRNAs (Olive et al. 2010). "
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    • "However, RNA polymerase II transcribes miRNA like mRNA and the same transcription factors are involved in miRNA transcription as that of mRNA transcription (Wang et al., 2010a,b). The chromosomes having high number of miRNA genes are more crucial for several cellular processes including different diseases . "
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    • "This led to the identification of another 274 MIR TSSs. We also predicted the promoter regions and TSSs of MIRs using genome-wide RNAPII binding peaks derived from ChIA-PET data (22), which is based on the previous observation that RNAPII binding peaks are proximal to the TSS of MIRs (38). The nearest RNAPII peak within 50 kb upstream of pre-miRNA was assigned to the TSS of that MIR. "
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