Signal Transducers and Activators of Transcription-1 (STAT1) Regulates microRNA Transcription in Interferon γ-Stimulated HeLa Cells

Guohua Wang,Denan Zhang,Yunlong Liu,Mingxiang Teng,Yadong Wang,Lang Li,Sui Huang

doi:10.1371/journal.pone.0011794

Abstract

BackgroundConstructing and modeling the gene regulatory network is one of the central themes of systems biology. With the growing understanding of the mechanism of microRNA biogenesis and its biological function, establishing a microRNA-mediated gene regulatory network is not only desirable but also achievable.MethodologyIn this study, we propose a bioinformatics strategy to construct the microRNA-mediated regulatory network using genome-wide binding patterns of transcription factor(s) and RNA polymerase II (RPol II), derived using chromatin immunoprecipitation following next generation sequencing (ChIP-seq) technology. Our strategy includes three key steps, identification of transcription start sites and promoter regions of primary microRNA transcripts using RPol II binding patterns, selection of cooperating transcription factors that collaboratively function with the transcription factors targeted by ChIP-seq assay, and construction of the network that contains regulatory cascades of both transcription factors and microRNAs.Principal FindingsUsing CAMDA (Critical Assessment of Massive Data Analysis) 2009 data set that includes ChIP-seq data on RPol II and STAT1 (signal transducers and activators of transcription 1) in HeLa S3 cells in control condition and with interferon γ stimulation, we first identified promoter regions of 83 microRNAs in HeLa cells. We then identified two potential STAT1 collaborating factors, AP-1 and C/EBP (CCAAT enhancer-binding proteins), and further established eight feedback network elements that may regulate cellular response during interferon γ stimulation.ConclusionsThis study offers a bioinformatics strategy to provide testable hypotheses on the mechanisms of microRNA-mediated transcriptional regulation, based upon genome-wide protein-DNA interaction data derived from ChIP-seq experiments.

Highlights

MicroRNAs are small non-coding RNAs known to regulate the target transcripts by promoting mRNA degradation and suppressing translation [1,2]
This study offers a bioinformatics strategy to provide testable hypotheses on the mechanisms of microRNAmediated transcriptional regulation, based upon genome-wide protein-DNA interaction data derived from ChIP-seq experiments
In order to understand the role of the microRNA-mediate regulatory network in interferon c – stimulated HeLa cells, we conducted bioinformatics analysis of the RNA polymerase II (RPol II) and Signal Transducers and Activators of Transcription-1 (STAT1) ChIP-seq data provided by the CAMDA 2009 challenging data set [11]

Summary

Introduction

MicroRNAs are small non-coding RNAs known to regulate the target transcripts by promoting mRNA degradation and suppressing translation [1,2]. Chromatin immunoprecipitation following generation sequencing technology (or ChIP-seq) has been widely used to profile the binding patterns of DNA binding proteins in a genome-wide scale, including transcription factors [11,12,13], histone marks [14,15], and RNA polymerase II [11,14,16] These provide unprecedented information in understanding complicated mechanisms of regulating gene expression. We have identified 8 potential feedback relationships involving STAT1-targeting microRNAs, interferon c gene, STAT1, or/and AP-1 binding proteins, together with many potential incoherent feed-forward loops This strategy provides important testable hypotheses for further mechanistic understanding of cellular immune response to interferon c treatment. With the growing understanding of the mechanism of microRNA biogenesis and its biological function, establishing a microRNAmediated gene regulatory network is desirable and achievable

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