Open AccessTissue‐specific regulatory elements in mammalian promoters
Author(s) -
Smith Andrew D,
Sumazin Pavel,
Zhang Michael Q
Publication year - 2007
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.1038/msb4100114
Subject(s) - promoter , biology , transcription factor , regulatory sequence , regulation of gene expression , gene expression , computational biology , gene , genetics , microbiology and biotechnology
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 T cells, 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.