The transcriptionally active regions in the genome of Bacillus subtilis
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The transcriptionally active regions in the genome of Bacillus subtilis. / Rasmussen, Simon; Nielsen, Henrik Bjørn; Jarmer, Hanne.
In: Molecular Microbiology, Vol. 73, No. 6, 09.2009, p. 1043-57.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - The transcriptionally active regions in the genome of Bacillus subtilis
AU - Rasmussen, Simon
AU - Nielsen, Henrik Bjørn
AU - Jarmer, Hanne
PY - 2009/9
Y1 - 2009/9
N2 - 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.
AB - 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.
KW - Bacillus subtilis/genetics
KW - Base Sequence
KW - Culture Media/chemistry
KW - Gene Expression Profiling/methods
KW - Models, Molecular
KW - Molecular Sequence Data
KW - Nucleic Acid Conformation
KW - RNA, Antisense/biosynthesis
KW - RNA, Untranslated/biosynthesis
KW - Transcription, Genetic
U2 - 10.1111/j.1365-2958.2009.06830.x
DO - 10.1111/j.1365-2958.2009.06830.x
M3 - Journal article
C2 - 19682248
VL - 73
SP - 1043
EP - 1057
JO - Molecular Microbiology
JF - Molecular Microbiology
SN - 0950-382X
IS - 6
ER -
ID: 210773333