title: Drosophila TRF2 is a preferential core promoter regulator.
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.
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
authors.forename: Adi
authors.initials: A
authors.lastname: Kedmi
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
authors.forename: Yonathan
authors.initials: Y
authors.lastname: Zehavi
authors.affiliation: The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
authors.forename: Yair
authors.initials: Y
authors.lastname: Glick
authors.affiliation: Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 6997801, Israel;
authors.forename: Yaron
authors.initials: Y
authors.lastname: Orenstein
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
authors.forename: Diana
authors.initials: D
authors.lastname: Ideses
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
authors.forename: Chaim
authors.initials: C
authors.lastname: Wachtel
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
authors.forename: Tirza
authors.initials: T
authors.lastname: Doniger
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
authors.forename: Hiba
authors.initials: H
authors.lastname: Waldman Ben-Asher
authors.affiliation: Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: Nemone
authors.initials: N
authors.lastname: Muster
authors.affiliation: Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: James
authors.initials: J
authors.lastname: Thompson
authors.affiliation: Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Anderson
authors.affiliation: The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
authors.forename: Dorit
authors.initials: D
authors.lastname: Avrahami
authors.affiliation: Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA.
authors.forename: John R
authors.initials: JR
authors.lastname: Yates
authors.affiliation: Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 6997801, Israel;
authors.forename: Ron
authors.initials: R
authors.lastname: Shamir
authors.affiliation: The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
authors.forename: Doron
authors.initials: D
authors.lastname: Gerber
authors.affiliation: The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel; tamar.gershon@biu.ac.il.
authors.forename: Tamar
authors.initials: T
authors.lastname: Juven-Gershon
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D002460:Cell Line; D002478:Cells, Cultured; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism*; D005786:Gene Expression Regulation; D011485:Protein Binding; D016385:TATA Box; D035341:Telomeric Repeat Binding Protein 2 / Q000235:genetics / Q000378:metabolism*
chemical_list: D029721:Drosophila Proteins; C509085:TRF2 protein, Drosophila; D035341:Telomeric Repeat Binding Protein 2
keywords: DNA binding; DPE; RNA polymerase II transcription; TRF2; core promoter