Journal Article

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

Shen, Changyu, Liu, Yunlong, Huang, Yi-wen, Nephew, Kenneth P., Huang, Tim H. M., Wang, Guohua, Li, Lang, Wang, Yadong, Huang, Kun

2010

Overview

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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Algorithms / Analysis / Annotations / Binding / Binding sites / Bioinformatics / Biology / Biosynthesis / Breast cancer / Cancer / Cell cycle / Cell Line, Tumor / Chromatin Immunoprecipitation / Computational Biology / Computational Biology - methods / Computational Biology/Genomics / Computational Biology/Systems Biology / Computational Biology/Transcriptional Regulation / Computer applications / Computer science / Conservation / Conserved sequence / CpG islands / CpG Islands - genetics / Deoxyribonucleic acid / DNA / DNA-directed RNA polymerase / Gene expression / Gene Expression Regulation / Gene regulation / Genes / Genetic aspects / Genomes / Genomics / Histones - metabolism / Humans / Immunology / Lysine - metabolism / Mathematical models / Medicine / Methylation / MicroRNA / MicroRNAs / MicroRNAs - genetics / miRNA / Post-transcription / Promoter Regions, Genetic - genetics / Protein Binding / Proteins / Regulatory Sequences, Nucleic Acid - genetics / Ribonucleic acid / RNA / RNA polymerase II / RNA Polymerase II - metabolism / Spatial distribution / Statistical models / Steroid hormones / Tamoxifen / Transcription (Genetics) / Transcription factors / Transcription initiation / Transcription Initiation Site / Transcription, Genetic / Trends / Virology