Drosophila TRF2 is a preferential core promoter regulator
- Adi Kedmi1,5,
- Yonathan Zehavi1,5,
- Yair Glick2,
- Yaron Orenstein3,
- Diana Ideses1,
- Chaim Wachtel1,
- Tirza Doniger1,
- Hiba Waldman Ben-Asher1,
- Nemone Muster4,
- James Thompson4,
- Scott Anderson4,
- Dorit Avrahami2,
- John R. Yates III4,
- Ron Shamir3,
- Doron Gerber2 and
- Tamar Juven-Gershon1
- 1The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
- 2The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
- 3Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 6997801, Israel;
- 4Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
- Corresponding author: tamar.gershon{at}biu.ac.il
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↵5 These authors contributed equally to this work.
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.
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Footnotes
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Supplemental material is available for this article.
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Article published online ahead of print. Article and publication date are online at http://www.genesdev.org/cgi/doi/10.1101/gad.245670.114.
- Received May 18, 2014.
- Accepted August 25, 2014.
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