RNA-Seq analysis of Mycobacterium avium non-coding transcriptome
Deep sequencing was implemented to study the transcriptional landscape of Mycobacterium avium. High-resolution transcriptome analysis identified the transcription start points for 652 genes. One third of these genes represented leaderless transcripts, whereas the rest of the transcripts had 5'...
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| Veröffentlicht in: | PloS one 2013-09, Vol.8 (9), p.e74209-e74209 |
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| creator | Ignatov, Dmitriy Malakho, Sofia Majorov, Konstantin Skvortsov, Timofey Apt, Alexander Azhikina, Tatyana |
| description | Deep sequencing was implemented to study the transcriptional landscape of Mycobacterium avium. High-resolution transcriptome analysis identified the transcription start points for 652 genes. One third of these genes represented leaderless transcripts, whereas the rest of the transcripts had 5' UTRs with the mean length of 83 nt. In addition, the 5' UTRs of 6 genes contained SAM-IV and Ykok types of riboswitches. 87 antisense RNAs and 10 intergenic small RNAs were mapped. 6 intergenic small RNAs, including 4.5S RNA and rnpB, were transcribed at extremely high levels. Although several intergenic sRNAs are conserved in M. avium and M. tuberculosis, both of these species have unique intergenic sRNAs. Moreover, we demonstrated that even conserved small RNAs are regulated differently in these species. Different sets of intergenic sRNAs may underlie differences in physiology between conditionally pathogenic M. avium and highly specialized pathogen M. tuberculosis. |
| doi_str_mv | 10.1371/journal.pone.0074209 |
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High-resolution transcriptome analysis identified the transcription start points for 652 genes. One third of these genes represented leaderless transcripts, whereas the rest of the transcripts had 5' UTRs with the mean length of 83 nt. In addition, the 5' UTRs of 6 genes contained SAM-IV and Ykok types of riboswitches. 87 antisense RNAs and 10 intergenic small RNAs were mapped. 6 intergenic small RNAs, including 4.5S RNA and rnpB, were transcribed at extremely high levels. Although several intergenic sRNAs are conserved in M. avium and M. tuberculosis, both of these species have unique intergenic sRNAs. Moreover, we demonstrated that even conserved small RNAs are regulated differently in these species. Different sets of intergenic sRNAs may underlie differences in physiology between conditionally pathogenic M. avium and highly specialized pathogen M. tuberculosis.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0074209</identifier><identifier>PMID: 24066122</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Antisense RNA ; Bacteria ; Bioinformatics ; Cloning ; Disease ; Gene expression ; Gene Expression Regulation, Bacterial ; Gene sequencing ; Genes ; Genetic aspects ; Genomics ; Infections ; Metabolism ; Metabolites ; Mycobacterium avium ; Mycobacterium avium - genetics ; Mycobacterium tuberculosis ; Pathogens ; Proteins ; Ribonucleic acid ; Riboswitches ; RNA ; RNA sequencing ; RNA, Antisense - genetics ; RNA, Bacterial - genetics ; RNA, Small Untranslated - genetics ; Transcription ; Transcription (Genetics) ; Transcriptome - genetics ; Tuberculosis</subject><ispartof>PloS one, 2013-09, Vol.8 (9), p.e74209-e74209</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Ignatov et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2013 Ignatov et al 2013 Ignatov et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-40dc96b65edbdd3a1d6278bc17632ff6d8c42c050fcdd13e6576832619bf80383</citedby><cites>FETCH-LOGICAL-c692t-40dc96b65edbdd3a1d6278bc17632ff6d8c42c050fcdd13e6576832619bf80383</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774663/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3774663/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24066122$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Mokrousov, Igor</contributor><creatorcontrib>Ignatov, Dmitriy</creatorcontrib><creatorcontrib>Malakho, Sofia</creatorcontrib><creatorcontrib>Majorov, Konstantin</creatorcontrib><creatorcontrib>Skvortsov, Timofey</creatorcontrib><creatorcontrib>Apt, Alexander</creatorcontrib><creatorcontrib>Azhikina, Tatyana</creatorcontrib><title>RNA-Seq analysis of Mycobacterium avium non-coding transcriptome</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Deep sequencing was implemented to study the transcriptional landscape of Mycobacterium avium. High-resolution transcriptome analysis identified the transcription start points for 652 genes. One third of these genes represented leaderless transcripts, whereas the rest of the transcripts had 5' UTRs with the mean length of 83 nt. In addition, the 5' UTRs of 6 genes contained SAM-IV and Ykok types of riboswitches. 87 antisense RNAs and 10 intergenic small RNAs were mapped. 6 intergenic small RNAs, including 4.5S RNA and rnpB, were transcribed at extremely high levels. Although several intergenic sRNAs are conserved in M. avium and M. tuberculosis, both of these species have unique intergenic sRNAs. Moreover, we demonstrated that even conserved small RNAs are regulated differently in these species. Different sets of intergenic sRNAs may underlie differences in physiology between conditionally pathogenic M. avium and highly specialized pathogen M. tuberculosis.</description><subject>Analysis</subject><subject>Antisense RNA</subject><subject>Bacteria</subject><subject>Bioinformatics</subject><subject>Cloning</subject><subject>Disease</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>Gene sequencing</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomics</subject><subject>Infections</subject><subject>Metabolism</subject><subject>Metabolites</subject><subject>Mycobacterium avium</subject><subject>Mycobacterium avium - genetics</subject><subject>Mycobacterium tuberculosis</subject><subject>Pathogens</subject><subject>Proteins</subject><subject>Ribonucleic acid</subject><subject>Riboswitches</subject><subject>RNA</subject><subject>RNA sequencing</subject><subject>RNA, Antisense - genetics</subject><subject>RNA, Bacterial - 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High-resolution transcriptome analysis identified the transcription start points for 652 genes. One third of these genes represented leaderless transcripts, whereas the rest of the transcripts had 5' UTRs with the mean length of 83 nt. In addition, the 5' UTRs of 6 genes contained SAM-IV and Ykok types of riboswitches. 87 antisense RNAs and 10 intergenic small RNAs were mapped. 6 intergenic small RNAs, including 4.5S RNA and rnpB, were transcribed at extremely high levels. Although several intergenic sRNAs are conserved in M. avium and M. tuberculosis, both of these species have unique intergenic sRNAs. Moreover, we demonstrated that even conserved small RNAs are regulated differently in these species. 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| subjects | Analysis Antisense RNA Bacteria Bioinformatics Cloning Disease Gene expression Gene Expression Regulation, Bacterial Gene sequencing Genes Genetic aspects Genomics Infections Metabolism Metabolites Mycobacterium avium Mycobacterium avium - genetics Mycobacterium tuberculosis Pathogens Proteins Ribonucleic acid Riboswitches RNA RNA sequencing RNA, Antisense - genetics RNA, Bacterial - genetics RNA, Small Untranslated - genetics Transcription Transcription (Genetics) Transcriptome - genetics Tuberculosis |
| title | RNA-Seq analysis of Mycobacterium avium non-coding transcriptome |
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