Format

Send to

Choose Destination
Nucleic Acids Res. 2015 Apr 20;43(7):3442-53. doi: 10.1093/nar/gkv170. Epub 2015 Mar 16.

Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae.

Author information

1
EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain.
2
EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain maria.lluch@crg.es.
3
EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain luis.serrano@crg.eu.

Abstract

Distinguishing between promoter-like sequences in bacteria that belong to true or abortive promoters, or to those that do not initiate transcription at all, is one of the important challenges in transcriptomics. To address this problem, we have studied the genome-reduced bacterium Mycoplasma pneumoniae, for which the RNAs associated with transcriptional start sites have been recently experimentally identified. We determined the contribution to transcription events of different genomic features: the -10, extended -10 and -35 boxes, the UP element, the bases surrounding the -10 box and the nearest-neighbor free energy of the promoter region. Using a random forest classifier and the aforementioned features transformed into scores, we could distinguish between true, abortive promoters and non-promoters with good -10 box sequences. The methods used in this characterization of promoters can be extended to other bacteria and have important applications for promoter design in bacterial genome engineering.

PMID:
25779052
PMCID:
PMC4402517
DOI:
10.1093/nar/gkv170
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center