A universal framework for regulatory element discovery across all genomes and data types.

TitleA universal framework for regulatory element discovery across all genomes and data types.
Publication TypeJournal Article
Year of Publication2007
AuthorsElemento O, Slonim N, Tavazoie S
JournalMol Cell
Date Published2007 Oct 26
KeywordsAnimals, Cluster Analysis, Databases, Genetic, DNA, Fungal, DNA, Protozoan, Gene Expression Profiling, Gene Expression Regulation, Gene Expression Regulation, Fungal, Humans, Mice, MicroRNAs, Nucleic Acid Conformation, Oligonucleotide Array Sequence Analysis, Plasmodium falciparum, Regulatory Elements, Transcriptional, Regulatory Sequences, Nucleic Acid, Reproducibility of Results, RNA, Fungal, RNA, Protozoan, Saccharomyces cerevisiae, Sequence Analysis, DNA, Sequence Analysis, RNA, Sequence Homology, Nucleic Acid, Software, Time Factors, Transcription Factors, Untranslated Regions

Deciphering the noncoding regulatory genome has proved a formidable challenge. Despite the wealth of available gene expression data, there currently exists no broadly applicable method for characterizing the regulatory elements that shape the rich underlying dynamics. We present a general framework for detecting such regulatory DNA and RNA motifs that relies on directly assessing the mutual information between sequence and gene expression measurements. Our approach makes minimal assumptions about the background sequence model and the mechanisms by which elements affect gene expression. This provides a versatile motif discovery framework, across all data types and genomes, with exceptional sensitivity and near-zero false-positive rates. Applications from yeast to human uncover putative and established transcription-factor binding and miRNA target sites, revealing rich diversity in their spatial configurations, pervasive co-occurrences of DNA and RNA motifs, context-dependent selection for motif avoidance, and the strong impact of posttranscriptional processes on eukaryotic transcriptomes.

Alternate JournalMol. Cell
PubMed ID17964271
PubMed Central IDPMC2900317
Grant ListR01 HG003219 / HG / NHGRI NIH HHS / United States
R01 HG003219-04 / HG / NHGRI NIH HHS / United States
P50 GM071508 / GM / NIGMS NIH HHS / United States