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Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

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Interuniversity Attraction Poles IAP program, Phase VII/2012–2017, Project P7/28
Abstract
Background: Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale. Methods: RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes. Results: Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered. Conclusions: Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation.
Keywords
Small RNAs, Antisense RNA, Transcription start site, dRNA-Seq, Burkholderia cenocepacia, Biofilms, Genomic islands, GLOBAL GENE-EXPRESSION, CEPACIA COMPLEX, TRANSLATION INITIATION, SMALL RNAS, BACTERIA, IDENTIFICATION, PATHOGEN, SEQ, PERSISTENCE, RESISTANCE

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Citation

Please use this url to cite or link to this publication:

MLA
Sass, Andrea et al. “Genome-wide Transcription Start Site Profiling in Biofilm-grown Burkholderia Cenocepacia J2315.” BMC GENOMICS 16 (2015): n. pag. Print.
APA
Sass, A., Van Acker, H., Förstner, K., Van Nieuwerburgh, F., Deforce, D., Vogel, J., & Coenye, T. (2015). Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315. BMC GENOMICS, 16.
Chicago author-date
Sass, Andrea, Heleen Van Acker, Konrad Förstner, Filip Van Nieuwerburgh, Dieter Deforce, Jörg Vogel, and Tom Coenye. 2015. “Genome-wide Transcription Start Site Profiling in Biofilm-grown Burkholderia Cenocepacia J2315.” Bmc Genomics 16.
Chicago author-date (all authors)
Sass, Andrea, Heleen Van Acker, Konrad Förstner, Filip Van Nieuwerburgh, Dieter Deforce, Jörg Vogel, and Tom Coenye. 2015. “Genome-wide Transcription Start Site Profiling in Biofilm-grown Burkholderia Cenocepacia J2315.” Bmc Genomics 16.
Vancouver
1.
Sass A, Van Acker H, Förstner K, Van Nieuwerburgh F, Deforce D, Vogel J, et al. Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315. BMC GENOMICS. 2015;16.
IEEE
[1]
A. Sass et al., “Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315,” BMC GENOMICS, vol. 16, 2015.
@article{6990365,
  abstract     = {Background: Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale. 
Methods: RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes. 
Results: Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered. 
Conclusions: Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation.},
  articleno    = {775},
  author       = {Sass, Andrea and Van Acker, Heleen and Förstner, Konrad and Van Nieuwerburgh, Filip and Deforce, Dieter and Vogel, Jörg and Coenye, Tom},
  issn         = {1471-2164},
  journal      = {BMC GENOMICS},
  keywords     = {Small RNAs,Antisense RNA,Transcription start site,dRNA-Seq,Burkholderia cenocepacia,Biofilms,Genomic islands,GLOBAL GENE-EXPRESSION,CEPACIA COMPLEX,TRANSLATION INITIATION,SMALL RNAS,BACTERIA,IDENTIFICATION,PATHOGEN,SEQ,PERSISTENCE,RESISTANCE},
  language     = {eng},
  pages        = {15},
  title        = {Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315},
  url          = {http://dx.doi.org/10.1186/s12864-015-1993-3},
  volume       = {16},
  year         = {2015},
}

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