Genomewide discovery & analysis of alternative promoters

全基因组发现

• 批准号: 7371108
• 负责人: RAMANA V DAVULURI
• 金额: $ 2.07万
• 依托单位: OHIO STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-04-27 至 2008-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7371108
• 关键词: Antibodies; Applications Grants; Automobile Driving; Biological Assay; Chromatin; Code; Computing Methodologies; DNA; Data; Databases; Development; Environment; Euchromatin; Exons; Future; Gene Expression; Gene Expression Regulation; Genes; Genetic Transcription; Genome; Genomics; Heterochromatin; Histones; Human; Human Genome; Laboratories; Length; Luciferases; Lysine; Maps; Measures; Mining; Mus; Nucleic Acid Regulatory Sequences; Orthologous Gene; Pattern; Play; Polymerase Chain Reaction; Promoter Regions; Proteins; Research; Research Personnel; Rodent; Role; Route; Sampling; Specific qualifier value; Staging; Testing; Tissue Sample; Tissues; Transcription Initiation; Transcription Initiation Site; cell type; chromatin immunoprecipitation; computerized tools; data mining; functional genomics; genome sequencing; improved; mammalian genome; mouse genome; novel; programs; promoter; prototype; tool; transcription factor

Promoters located at the 5'-ends of genes play a critical role in regulating transcriptional initiation. Emerging evidence suggests that a significant fraction of -30,000 human genes likely contain alternative promoters, which produce more elaborate regulation of gene expression in different tissues, cell-types and/or developmental stages. Despite vast information available for the human genome sequences, a comprehensive approach for identifying and characterizing alternative promoters of gene loci is still lacking. One effective approach is to analyze orthologous sequences in both mouse and human genomes. It has not been thoroughly explored as to what extent the 5'-end regulatory regions of a locus show sequence similarity between human and rodents. We hypothesize that the basal (core) promoter regions necessary for gene transcription are conserved between human and mouse. Computational approaches will be used to mine both human and mouse genomes to identify functional orthologous sequences. The derived information will be added into a prototype database for mammalian promoters, called MPromDb, developed by us. Next, these computationally derived sequences will be experimentally verified. We further hypothesize that a functional genomic sequence is in a euchromatic environment that presents an open chromatin configuration, allowing for the access of transcription factors for driving gene expression. Instead of taking the usual route to analyze gene expression, we will determine the chromatin status of a test genomic sequence as a measure for a functional promoter. The chromatin immunoprecipitation (ChIP) microarray, or the so-called ChlP-on-chip assay, previously developed in our laboratory will be extended to simultaneously assess the euchromatin status of ~1,500 putative promoters of 250 pairs of human and mouse orthologous genes. The combination of computational, statistical and highthroughput experimental approaches proposed in this grant application will help better characterize the gene regulatory regions in the human genome, one of the grand challenges of future genome research. Specifically we will: (1) Develop computational tools for annotating experimentally known alternative promoters and first exons. (2) Conduct ChlP-on-chip and luciferase assays to verify computationally annotated alternative promoter sequences of human and mouse orthologous genes, and (3) Develop computational methods to detect alternative promoters and first exons in the human and mouse genomes.

启动子位于基因的5'端，在调控转录起始中起关键作用。新兴