Alternative Promoter Usage in Tissue-specific Gene Expr*

描述：（由申请人提供）转录调控在人类中极其重要且高度复杂。在这个项目中，我们以组织特异性的方式关注替代第一外显子的转录调控。在真核生物基因组中，第一外显子的特征往往很差。此外，备选第一外显子可能位于彼此相距很远的基因组位置，从而导致近端启动子的不同使用。在文献中有许多关于广泛分离的替代启动子的例子，它们负责组织特异性表达。该建议的中心假设是，第一外显子的选择性剪接表明了近端启动子的选择性使用，这将是我们鉴定调节差异组织特异性基因表达的功能顺式元件簇的重要因素。

DESCRIPTION: (provided by applicant) Transcriptional regulation is extremely important and highly complex in humans. In this project, we focus on the transcriptional regulation of alternative first exons in a tissue specific manner. First exons are often poorly characterized in eukaryotic genomes. Furthermore, alternative first exons can reside in genomic locations that are far apart from each other, leading to distinct usage of proximal promoters. There are numerous examples in the literature on widely separated alternative promoters that are responsible for tissue specific expression. The central hypothesis of this proposal is that alternative splicing of first exons is indicative of alternative proximal promoter usage, which will be an important factor in our identification of functional cis-element clusters that regulate differential tissue-specific gene expressions. The project tightly couples the computational expertise in Weng's laboratory with the extremely sensitive and quantitative gene expression technique recently developed by Ding and Cantor at Boston University. We will computationally characterize all genes in the 30 Mb of human sequence selected by the ENCODE project, identify ~ 100 genes with alternative first exon splicing, study the expression levels of splicing variants in major tissue types, and investigate the cis-elements in the promoters of these genes that could account for their transcriptional regulation. The project has four specific aims: 1) Computationally analyze the ENCODE sequences and select ~100 genes that exhibit both alternative first exon usage and tissue specific expression patterns; 2) Experimentally validate first exon usage for all genes identified in Aim 1 and measure their expression levels in ten major tissue types; 3) Computationally predict cis-element clusters in the alternative proximal promoters of the genes and select ~40 most confident predictions that may account for tissue-specific expressions; and 4) Experimentally test the ~40 computational predictions using transfection assays in five cell lines.