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- Title
Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000.
- Authors
Filiatrault, Melanie J; Stodghill, Paul V; Myers, Christopher R; Bronstein, Philip A; Butcher, Bronwyn G; Lam, Hanh; Grills, George; Schweitzer, Peter; Wang, Wei; Schneider, David J; Cartinhour, Samuel W
- Abstract
RNA-Seq has provided valuable insights into global gene expression in a wide variety of organisms. Using a modified RNA-Seq approach and Illumina's high-throughput sequencing technology, we globally identified 5'-ends of transcripts for the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. A substantial fraction of 5'-ends obtained by this method were consistent with results obtained using global RNA-Seq and 5'RACE. As expected, many 5'-ends were positioned a short distance upstream of annotated genes. We also captured 5'-ends within intergenic regions, providing evidence for the expression of un-annotated genes and non-coding RNAs, and detected numerous examples of antisense transcription, suggesting additional levels of complexity in gene regulation in DC3000. Importantly, targeted searches for sequence patterns in the vicinity of 5'-ends revealed over 1200 putative promoters and other regulatory motifs, establishing a broad foundation for future investigations of regulation at the genomic and single gene levels.
- Publication
PloS one, 2011, Vol 6, Issue 12, pe29335
- ISSN
1932-6203
- Publication type
Journal Article
- DOI
10.1371/journal.pone.0029335