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| Status |
Public on Jan 27, 2016 |
| Title |
Mapping of internal monophosphate 5’ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains |
| Organism |
Bacillus subtilis |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The narrow-specificity endoribonuclease RNase III and the 5’ exonuclease RNase J1 have been recently found to be not essential in the Gram-positive model organism, Bacillus subtilis. In this study, we performed a global analysis of internal 5’ ends that are generated or acted upon by these enzymes. An RNA-Seq protocol known as PARE (Parallel Analysis of RNA Ends) was used to capture 5’ monophosphorylated RNA ends in ribonuclease wild-type and mutant strains. Comparison of PARE peaks in strains with RNase III present or absent showed that, in addition to its well-known role in ribosomal (rRNA) processing, many coding sequences and intergenic regions were direct targets of RNase III. A set of regular RNA-seq experiments were performed to investigate RNA profiles in these strains and used to account for the changes in RNA abundance indirectly caused by the loss of RNase III in PARE. The PARE analysis also revealed an accumulation of 3’-proximal peaks that correlated with the absence of RNase J1, confirming the importance of RNase J1 in degrading RNA fragments that contain the transcription terminator structure. In addition, an endonuclease cleavage just two nucleotides downstream of the 16S rRNA 3’ end was discovered with PARE analysis. This latter observation begins to answer, at least for B. subtilis, a long-standing question on the exonucleolytic vs. endonucleolytic nature of 16S rRNA maturation
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| Overall design |
Examination of 5' monophosphate ends of Bacillus sutbtilis RNAs in wild-type and ribonucleases-mutant strains by PARE (Parallel Analysis of RNA Ends)
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| Contributor(s) |
Liu B, DiChiara JM, Bechhofer DH |
| Citation(s) |
26883633 |
| |
| Submission date |
Jan 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
David H Bechhofer |
| E-mail(s) |
[email protected]
|
| Phone |
212-241-5628
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Department of Pharmacology and Systems Therapeutics
|
| Street address |
One Gustave L. Levy Place, Box 1603
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platforms (2) |
| GPL18561 |
Illumina HiSeq 2000 (Bacillus subtilis) |
| GPL21373 |
Illumina MiSeq (Bacillus subtilis) |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA309763 |
| SRA |
SRP068910 |
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