Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features

Joo Hyun Seo, Jay S. Hong, Donghyuk Kim, Byung Kwan Cho, Tzu Wen Huang, Shih Feng Tsai, Bernhard O. Palsson, Pep Charusanti

研究成果: 雜誌貢獻文章

23 引文 (Scopus)

摘要

Background: The increasing number of infections caused by strains of Klebsiella pneumoniae that are resistant to multiple antibiotics has developed into a major medical problem worldwide. The development of next-generation sequencing technologies now permits rapid sequencing of many K. pneumoniae isolates, but sequence information alone does not provide important structural and operational information for its genome.Results: Here we take a systems biology approach to annotate the K. pneumoniae MGH 78578 genome at the structural and operational levels. Through the acquisition and simultaneous analysis of multiple sample-matched -omics data sets from two growth conditions, we detected 2677, 1227, and 1066 binding sites for RNA polymerase, RpoD, and RpoS, respectively, 3660 RNA polymerase-guided transcript segments, and 3585 transcription start sites throughout the genome. Moreover, analysis of the transcription start site data identified 83 probable leaderless mRNAs, while analysis of unannotated transcripts suggested the presence of 119 putative open reading frames, 15 small RNAs, and 185 antisense transcripts that are not currently annotated.Conclusions: These findings highlight the strengths of systems biology approaches to the refinement of sequence-based annotations, and to provide new insight into fundamental genome-level biology for this important human pathogen.

原文英語
文章編號679
期刊BMC Genomics
13
發行號1
DOIs
出版狀態已發佈 - 十一月 29 2012
對外發佈Yes

指紋

Klebsiella pneumoniae
Genome
Systems Biology
Transcription Initiation Site
DNA-Directed RNA Polymerases
Antisense RNA
Open Reading Frames
Binding Sites
Anti-Bacterial Agents
Technology
Messenger RNA
Growth
Infection

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

引用此文

Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. / Seo, Joo Hyun; Hong, Jay S.; Kim, Donghyuk; Cho, Byung Kwan; Huang, Tzu Wen; Tsai, Shih Feng; Palsson, Bernhard O.; Charusanti, Pep.

於: BMC Genomics, 卷 13, 編號 1, 679, 29.11.2012.

研究成果: 雜誌貢獻文章

Seo, Joo Hyun ; Hong, Jay S. ; Kim, Donghyuk ; Cho, Byung Kwan ; Huang, Tzu Wen ; Tsai, Shih Feng ; Palsson, Bernhard O. ; Charusanti, Pep. / Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features. 於: BMC Genomics. 2012 ; 卷 13, 編號 1.
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abstract = "Background: The increasing number of infections caused by strains of Klebsiella pneumoniae that are resistant to multiple antibiotics has developed into a major medical problem worldwide. The development of next-generation sequencing technologies now permits rapid sequencing of many K. pneumoniae isolates, but sequence information alone does not provide important structural and operational information for its genome.Results: Here we take a systems biology approach to annotate the K. pneumoniae MGH 78578 genome at the structural and operational levels. Through the acquisition and simultaneous analysis of multiple sample-matched -omics data sets from two growth conditions, we detected 2677, 1227, and 1066 binding sites for RNA polymerase, RpoD, and RpoS, respectively, 3660 RNA polymerase-guided transcript segments, and 3585 transcription start sites throughout the genome. Moreover, analysis of the transcription start site data identified 83 probable leaderless mRNAs, while analysis of unannotated transcripts suggested the presence of 119 putative open reading frames, 15 small RNAs, and 185 antisense transcripts that are not currently annotated.Conclusions: These findings highlight the strengths of systems biology approaches to the refinement of sequence-based annotations, and to provide new insight into fundamental genome-level biology for this important human pathogen.",
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