title: Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome.
abstract: While the transcription regulation of protein coding genes was extensively studied, little is known on how transcription factors are involved in transcription of non-coding RNAs, specifically of microRNAs. Here, we propose a strategy to study the potential role of transcription factor in regulating transcription of microRNAs using publically available data, computational resources and high throughput data. We use the H3K4me3 epigenetic signature to identify microRNA promoters and chromatin immunoprecipitation (ChIP)-sequencing data from the ENCODE project to identify microRNA promoters that are enriched with transcription factor binding sites. By transfecting cells of interest with shRNA targeting a transcription factor of interest and subjecting the cells to microRNA array, we study the effect of this transcription factor on the microRNA transcriptome. As an illustrative example we use our study on the effect of STAT3 on the microRNA transcriptome of chronic lymphocytic leukemia (CLL) cells.
authors.affiliation: Division of Hematology, Davidoff Cancer Center, Rabin Medical Center.
authors.forename: Uri
authors.initials: U
authors.lastname: Rozovski
authors.affiliation: The Center of Nanoscience and Nanotechnology, Tel Aviv University.
authors.forename: Inbal
authors.initials: I
authors.lastname: Hazan-Halevy
authors.affiliation: Experimental Therapeutics, The University of Texas MD Anderson Cancer Center.
authors.forename: George
authors.initials: G
authors.lastname: Calin
authors.affiliation: Department of Leukemia, The University of Texas MD Anderson Cancer Center.
authors.forename: David
authors.initials: D
authors.lastname: Harris
authors.affiliation: Department of Leukemia, The University of Texas MD Anderson Cancer Center.
authors.forename: Ping
authors.initials: P
authors.lastname: Li
authors.affiliation: Department of Leukemia, The University of Texas MD Anderson Cancer Center.
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Department of Leukemia, The University of Texas MD Anderson Cancer Center.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Keating
authors.affiliation: Department of Leukemia, The University of Texas MD Anderson Cancer Center; zestrov@mdanderson.org.
authors.forename: Zeev
authors.initials: Z
authors.lastname: Estrov
mesh_terms: D057225:Data Mining; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D015451:Leukemia, Lymphocytic, Chronic, B-Cell / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics*; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D034741:RNA, Small Interfering / Q000008:administration & dosage / Q000235:genetics; D050796:STAT3 Transcription Factor / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics*; D059467:Transcriptome; D014162:Transfection
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering; D050796:STAT3 Transcription Factor; C494086:STAT3 protein, human; D014157:Transcription Factors