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

Nucleic Acids Research
Verónica Lloréns-RicoLuis Serrano

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.

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Citations

Nov 3, 2016·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Aditya Kumar, Manju Bansal
Jul 2, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Ariadna Montero-BlayLuis Serrano
Dec 19, 2019·Frontiers in Molecular Biosciences·Zane R ThornburgZaida Luthey-Schulten
Dec 18, 2020·Molecular Systems Biology·Dominick MatteauSébastien Rodrigue

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Methods Mentioned

BETA
sequence-based prediction
RNA-seq

Software Mentioned

Integrative Genomics Viewer ( IGV )
FIMO
MEME

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