High-resolution DNA-binding specificity analysis of yeast transcription factors
High-resolution DNA-binding specificity analysis of yeast transcription factors
复制标题
DOI：
10.1101/gr.090233.108
复制
发表时间：
2009-04-01
期刊：
影响因子：
7
通讯作者：
Bulyk, Martha L.
中科院分区：
文献类型：
--
作者：
Zhu, Cong;Byers, Kelsey J. R. P.;Bulyk, Martha L.
转录因子通过与DNA结合位点的序列特异性相互作用来调节基因的表达。然而，尽管最近在用微阵列读出染色质免疫沉淀(CHIP-CHIP)来鉴定体内TF结合部位方面取得了进展，但几乎一半已知的酵母TF具有未知的DNA结合特性，而且许多其他预测的TF仍未确定。为了解决我们对酵母转录因子及其顺式调控序列知识的这些空白，我们已经确定了89个已知和预测的酵母转录因子的高分辨率结合谱，超过230万个有间隙和无间隙的8-bp序列(k-MERS‘)。我们报告了50个新的或显著不同的酵母DNA结合蛋白的直接DNA结合位点基序和8种蛋白质的基序，这些基序之前只有一个共同的序列；总体而言，这相当于具有实验确定的DNA结合特异性的酵母DNA结合蛋白的数量增加了50%以上。在其他新的调节因子中，我们发现了结合PAC(聚合酶A和C)基序(GATGAG)并调节核糖体RNA(RRNA)转录和加工的蛋白质，这是核糖体生物发生的核心细胞过程。与早期的数据类型不同，这些全面的k-mer结合数据使我们能够考虑基因组序列在单个单词水平的调节潜力。这些k-mer数据使我们能够将体内TF结合靶点重新注释为直接或间接的，并在类似于1700环境和细胞条件下检查TF对基因表达的潜在影响。这些方法可用于鉴定高等真核生物中的转录因子和顺式调节元件。
Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of chromatin immunoprecipitation (ChIP-chip), nearly half of all known yeast TFs are of unknown DNA-binding specificities, and many additional predicted TFs remain uncharacterized. To address these gaps in our knowledge of yeast TFs and their cis regulatory sequences, we have determined high-resolution binding profiles for 89 known and predicted yeast TFs, over more than 2.3 million gapped and ungapped 8-bp sequences ("k-mers''). We report 50 new or significantly different direct DNA-binding site motifs for yeast DNA-binding proteins and motifs for eight proteins for which only a consensus sequence was previously known; in total, this corresponds to over a 50% increase in the number of yeast DNA-binding proteins with experimentally determined DNA-binding specificities. Among other novel regulators, we discovered proteins that bind the PAC (Polymerase A and C) motif (GATGAG) and regulate ribosomal RNA (rRNA) transcription and processing, core cellular processes that are constituent to ribosome biogenesis. In contrast to earlier data types, these comprehensive k-mer binding data permit us to consider the regulatory potential of genomic sequence at the individual word level. These k-mer data allowed us to reannotate in vivo TF binding targets as direct or indirect and to examine TFs' potential effects on gene expression in similar to 1700 environmental and cellular conditions. These approaches could be adapted to identify TFs and cis regulatory elements in higher eukaryotes.