Target prediction for small, noncoding RNAs in bacteria.
Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a limited number of the corresponding mRNA targets have been identified. Here we present a program, TargetRNA, that predicts the targets of these bacterial RNA regulators. The program was evaluated by assessing whether previously known targets could be identified. The program was then used to predict targets for the Escherichia coli RNAs RyhB, OmrA, OmrB and OxyS, and the predictions were compared with changes in whole genome expression patterns observed upon expression of the sRNAs. Our results show that TargetRNA is a useful tool for finding mRNA targets of sRNAs, although its rate of success varies between sRNAs.
Tjaden
Brian
B
Computer Science Department, Wellesley College, Wellesley, MA 02481, USA. btjaden@wellesley.edu
Goodwin
Sarah S
SS
Opdyke
Jason A
JA
Guillier
Maude
M
Fu
Daniel X
DX
Gottesman
Susan
S
Storz
Gisela
G
D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D020407:Internet; D008969:Molecular Sequence Data; D012329:RNA, Bacterial / Q000737:chemistry*; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry*; D012984:Software
D012329:RNA, Bacterial; D012333:RNA, Messenger; D022661:RNA, Untranslated