Tissue-specific regulatory elements in mammalian promoters

Smith, A. D., Sumazin, P., Zhang, M. Q. (2007) Tissue-specific regulatory elements in mammalian promoters. Molecular Systems Biology, 3. ISSN 1744-4292

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URL: https://www.ncbi.nlm.nih.gov/pubmed/17224917
DOI: 10.1038/msb4100114

Abstract

Transcription factor-binding sites and the cis-regulatory modules they compose are central determinants of gene expression. We previously showed that binding site motifs and modules in proximal promoters can be used to predict a significant portion of mammalian tissue-specific transcription. Here, we report on a systematic analysis of promoters controlling tissue-specific expression in heart, kidney, liver, pancreas, skeletal muscle, testis and CD4 Tcells, for both human and mouse. We integrated multiple sources of expression data to compile sets of transcripts with strong evidence for tissue-specific regulation. The analysis of the promoters corresponding to these sets produced a catalog of predicted tissue-specific motifs and modules, and cis-regulatory elements. Predicted regulatory interactions are supported by statistical evidence, and provide a foundation for targeted experiments that will improve our understanding of tissue-specific regulatory networks. In a broader context, methods used to construct the catalog provide a model for the analysis of genomic regions that regulate differentially expressed genes.

Item Type: Paper
Uncontrolled Keywords: cis-regulatory modules tissue-specific regulation BINDING PROTEIN HUMAN GENOME START SITES GENE DISCOVERY DATABASE MOUSE EXPRESSION SEQUENCES ENHANCER
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > transcription
bioinformatics > genomics and proteomics > databases > database optimization
bioinformatics > genomics and proteomics > databases > databases
organism description > animal > mammal > primates > hominids > human
organism description > animal > mammal > rodent > mouse
organs, tissues, organelles, cell types and functions > organs types and functions
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date Deposited: 02 Nov 2011 14:18
Last Modified: 10 Apr 2018 16:22
PMCID: PMC1800356
Related URLs:
URI: http://repository.cshl.edu/id/eprint/23141

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