Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000.
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.
lant-Microbe Interactions Research Unit, Robert W. Holley Center for Agriculture and Health, Agricultural Research Service, United States Department of Agriculture, Ithaca, New York, USA. Melanie.filiatrault@ars.usda.gov
Melanie J
MJ
Filiatrault
Paul V
PV
Stodghill
Christopher R
CR
Myers
Philip A
PA
Bronstein
Bronwyn G
BG
Butcher
Hanh
H
Lam
George
G
Grills
Peter
P
Schweitzer
Wei
W
Wang
David J
DJ
Schneider
Samuel W
SW
Cartinhour
D001483:Base Sequence; D017931:DNA Primers; D018745:Genome, Plant; D018551:Solanum lycopersicum / Q000235:genetics*; D044224:Pseudomonas syringae / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D015203:Reproducibility of Results; D014158:Transcription, Genetic
D017931:DNA Primers; D018749:RNA, Plant