Kedmi Adi, Zehavi Yonathan, Glick Yair, Orenstein Yaron, Ideses Diana, Wachtel Chaim, Doniger Tirza, Waldman Ben-Asher Hiba, Muster Nemone, Thompson James, Anderson Scott, Avrahami Dorit, Yates John R, Shamir Ron, Gerber Doron, Juven-Gershon Tamar
The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
The Nanotechnology Institute, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel;
Genes Dev. 2014 Oct 1;28(19):2163-74. doi: 10.1101/gad.245670.114. Epub 2014 Sep 15.
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.
蛋白质编码基因的转录高度依赖于RNA聚合酶II核心启动子。核心启动子通常被定义为指导转录起始的区域，由赋予核心启动子特定特性的功能性核心启动子基序（如TATA框、起始子[Inr]和下游核心启动子元件[DPE]）组成。已知支持TATA依赖性转录的基础转录因子不足以用于DPE依赖性启动子的体外转录。为了寻找支持DPE依赖性转录的转录因子，我们采用了生化互补方法，并鉴定出果蝇TBP（TATA框结合蛋白）相关因子2（TRF2）是支持DPE依赖性转录的组分中的一种富集因子。我们证明短TRF2亚型优先激活DPE依赖性启动子。DNA微阵列分析揭示了在短TRF2上调基因中DPE启动子的富集。使用引物延伸分析和报告基因测定，我们展示了DPE在TRF2靶基因转录调控中的重要性。先前有研究表明，与TBP不同，TRF2无法结合含有TATA框的DNA。通过微流控亲和分析，我们发现与短TRF2结合的DNA寡核苷酸富含Inr和DPE基序。综上所述，我们的研究结果突出了短TRF2作为一种优先的核心启动子调节因子的作用。
