Describing a transcription factor dependent regulation of the micro RNA transcriptome

Uri Rozovski, Inbal Hazan-Halevy, George Calin, David Harris, Ping Li, Zhiming Liu, Michael J. Keating, Zeev Estrov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Article numbere53300
JournalJournal of Visualized Experiments
Issue number112
StatePublished - 15 Jun 2016
Externally publishedYes


  • Bioengineering
  • Data mining
  • Issue 112
  • MiR promoter
  • MiR transcriptome
  • MicroRNA (miR)
  • Transcription factor
  • Transcription regulation


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