title: Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements.
abstract: MicroRNAs (miRNAs) regulate diverse biological processes by repressing mRNAs, but their modest effects on direct targets, together with their participation in larger regulatory networks, make it challenging to delineate miRNA-mediated effects. Here, we describe an approach to characterizing miRNA-regulatory networks by systematically profiling transcriptional, post-transcriptional and epigenetic activity in a pair of isogenic murine fibroblast cell lines with and without Dicer expression. By RNA sequencing (RNA-seq) and CLIP (crosslinking followed by immunoprecipitation) sequencing (CLIP-seq), we found that most of the changes induced by global miRNA loss occur at the level of transcription. We then introduced a network modeling approach that integrated these data with epigenetic data to identify specific miRNA-regulated transcription factors that explain the impact of miRNA perturbation on gene expression. In total, we demonstrate that combining multiple genome-wide datasets spanning diverse regulatory modes enables accurate delineation of the downstream miRNA-regulated transcriptional network and establishes a model for studying similar networks in other systems.
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Sara J C
authors.initials: SJ
authors.lastname: Gosline
authors.affiliation: David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA.
authors.forename: Allan M
authors.initials: AM
authors.lastname: Gurtan
authors.affiliation: David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Courtney K
authors.initials: CK
authors.lastname: JnBaptiste
authors.affiliation: David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Bosson
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Pamela
authors.initials: P
authors.lastname: Milani
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Simona
authors.initials: S
authors.lastname: Dalin
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Bryan J
authors.initials: BJ
authors.lastname: Matthews
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
authors.forename: Yoon S
authors.initials: YS
authors.lastname: Yap
authors.affiliation: David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: sharppa@mit.edu.
authors.forename: Phillip A
authors.initials: PA
authors.lastname: Sharp
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: fraenkel-admin@mit.edu.
authors.forename: Ernest
authors.initials: E
authors.lastname: Fraenkel
mesh_terms: D053263:Gene Regulatory Networks; D042421:Histone Code / Q000235:genetics*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors