RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation.

Abstract

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.

• Authors: Guohua Wang, Yadong Wang, Changyu Shen, Yi-wen Huang, Kun Huang, Tim H M Huang, Kenneth P Nephew, Lang Li, Yunlong Liu
• Journal: PloS one (PLoS One) Vol. 5 Issue 11 Pg. e13798 (Nov 02 2010) ISSN: 1932-6203 [Electronic] United States
• PMID: 21072189 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)

Chemical References

• Histones
• MicroRNAs
• RNA Polymerase II
• Lysine

Topics

• Algorithms
• Cell Line, Tumor
• Chromatin Immunoprecipitation
• Computational Biology (methods)
• CpG Islands (genetics)
• Gene Expression Regulation
• Histones (metabolism)
• Humans
• Lysine (metabolism)
• Methylation
• MicroRNAs (genetics)
• Promoter Regions, Genetic (genetics)
• Protein Binding
• RNA Polymerase II (metabolism)
• Regulatory Sequences, Nucleic Acid (genetics)
• Transcription Initiation Site
• Transcription, Genetic