Drosophila TRF2 is a preferential core promoter regulator

Adi Kedmi, Yonathan Zehavi, Yair Glick, Yaron Orenstein, Diana Ideses, Chaim Wachtel, Tirza Doniger, Hiba Waldman Ben-Asher, Nemone Muster, James Thompson, Scott Anderson, Dorit Avrahami, John R. Yates, Ron Shamir, Doron Gerber, Tamar Juven-Gershon

Research output: Contribution to journalArticlepeer-review

36 Scopus citations

Abstract

Transcription of protein-coding genes is highly dependent on the RNA polymerase II core promoter. Core promoters, generally defined as the regions that direct transcription initiation, consist of functional core promoter motifs (such as the TATA-box, initiator [Inr], and downstream core promoter element [DPE]) that confer specific properties to the core promoter. The known basal transcription factors that support TATA-dependent transcription are insufficient for in vitro transcription of DPE-dependent promoters. In search of a transcription factor that supports DPE-dependent transcription, we used a biochemical complementation approach and identified the Drosophila TBP (TATA-box-binding protein)-related factor 2 (TRF2) as an enriched factor in the fractions that support DPE-dependent transcription. We demonstrate that the short TRF2 isoform preferentially activates DPE-dependent promoters. DNA microarray analysis reveals the enrichment of DPE promoters among short TRF2 up-regulated genes. Using primer extension analysis and reporter assays, we show the importance of the DPE in transcriptional regulation of TRF2 target genes. It was previously shown that, unlike TBP, TRF2 fails to bind DNA containing TATA-boxes. Using microfluidic affinity analysis, we discovered that short TRF2-bound DNA oligos are enriched for Inr and DPE motifs. Taken together, our findings highlight the role of short TRF2 as a preferential core promoter regulator.

Original languageEnglish
Pages (from-to)2163-2174
Number of pages12
JournalGenes and Development
Volume28
Issue number19
DOIs
StatePublished - 1 Oct 2014

Bibliographical note

Publisher Copyright:
© 2014, Kedmi et al.

Keywords

  • Core promoter
  • DNA binding
  • DPE
  • RNA polymerase II transcription
  • TRF2

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