transcriptionally active regions in the genome of Bacillus subtilis

The majority of all genes have so far been identified and annotated systematically through in silico gene finding. Here we report the finding of 3662 strand-specific transcriptionally active regions (TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome-wi...

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Bibliographic Details
Published in:Molecular microbiology 2009-09, Vol.73 (6), p.1043-1057
Main Authors: Rasmussen, Simon, Nielsen, Henrik Bjørn, Jarmer, Hanne
Format: Article
Language:English
Subjects:
Bacillus subtilis
Bacillus subtilis - genetics
Bacillus subtilis - growth & development
Bacillus subtilis - metabolism
Bacteriology
Base Sequence
Biological and medical sciences
Culture Media - chemistry
Fundamental and applied biological sciences. Psychology
Gene expression
Gene Expression Profiling - methods
Genes
Genomics
Membranes
Microbiology
Miscellaneous
Models, Molecular
Molecular Sequence Data
Molecular structure
Nucleic Acid Conformation
RNA, Antisense - biosynthesis
RNA, Untranslated - biosynthesis
Transcription, Genetic
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Summary:The majority of all genes have so far been identified and annotated systematically through in silico gene finding. Here we report the finding of 3662 strand-specific transcriptionally active regions (TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome-wide expression during mid-exponential growth on rich (LB) and minimal (M9) medium. The identified TARs account for 77.3% of the genes as they are currently annotated and additionally we find 84 putative non-coding RNAs (ncRNAs) and 127 antisense transcripts. One ncRNA, ncr22, is predicted to act as a translational control on cstA and an antisense transcript was observed opposite the housekeeping sigma factor sigA. Through this work we have discovered a long conserved 3' untranslated region (UTR) in a group of membrane-associated genes that is predicted to fold into a large and highly stable secondary structure. One of the genes having this tail is efeN, which encodes a target of the twin-arginine translocase (Tat) protein translocation system.
ISSN:0950-382X
1365-2958
DOI:10.1111/j.1365-2958.2009.06830.x