Exploiting transcription factor binding site clustering to identify 利用转录因子结合位点的聚类识别.pptVIP

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2018-04-12 发布于江西
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Exploiting transcription factor binding site clustering to identify 利用转录因子结合位点的聚类识别.ppt

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Exploiting transcription factor binding site clustering to identify 利用转录因子结合位点的聚类识别.ppt

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome ECS289A Presentation By Hua Chen 2003-3-3 Background Knowledge A significant character of cis-regulatory sites: the multiple binding sites for different transcriptional factors tend to cluster together in one region around the gene, forming the Cis-Regulatory Modules (CRM). The searching of cis-regulatory sites gives out too many candidate positions, which make it difficult to tell the true ones; The character of CRM provides a feasible method to identify the cis-regulatory sites in the genome. One example of CRM in Drosophila:eve gene Targets: Adopt the clustering of cis-regulatory modules as a method to identify the functional motifs; Test the method with some known real CRM regions; Search the genome to discover CRMs and confirm the results by experiments. Methods: Collecting Transcription Factor Binding Sequences in preceding lab works and doing Alignment; Construction of Position Weight Matrices (PWM) for the conserved motifs. Test the method with the known CRMs; Genome-wide Searching for unknown regulatory regions; mRNA Hybridization and Microarray hybridization to test whether the predicted regions are near to genes under regulation of the Transcription Factors; One special case: giant gene, further investigated by Transgenics and Mutant Embryo. Step1: Collection and Alignment of TF Binding Sites Bcd, Cad, Hb, Kr, Kni binding sequences are determined by in vitro DNAse protection assays; The sequences are aligned with MEME. Step 2: Construction of PWMs and Searching: Patser is used to construct the Position Weight Matrix; Cis-Analyst is used to identify the potential binding sites matching to the PWM in the Drosophila genome. A user-defined cutoff parameter (site_p) to eliminate predicted low-affinity sites; Search the sequence with a specified window length; Retain the windows that contain at least min_sites bindin