Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor

Salim Charaniya, Sarika Mehra, Wei Lian, Karthik P. Jayapal, George Karypis, Wei Shou Hu

Research output: Contribution to journalArticlepeer-review

27 Scopus citations

Abstract

Streptomyces spp. produce a variety of valuable secondary metabolites, which are regulated in a spatio-temporal manner by a complex network of inter-connected gene products. Using a compilation of genome-scale temporal transcriptome data for the model organism, Streptomyces coelicolor, under different environmental and genetic perturbations, we have developed a supervised machine-learning method for operon prediction in this microorganism. We demonstrate that, using features dependent on transcriptome dynamics and genome sequence, a support vector machines (SVM)-based classification algorithm can accurately classify >90% of gene pairs in a set of known operons. Based on model predictions for the entire genome, we verified the co-transcription of more than 250 gene pairs by RT-PCR. These results vastly increase the database of known operons in S. coelicolor and provide valuable information for exploring gene function and regulation to harness the potential of this differentiating microorganism for synthesis of natural products.

Original languageEnglish (US)
Pages (from-to)7222-7236
Number of pages15
JournalNucleic acids research
Volume35
Issue number21
DOIs
StatePublished - Dec 2007

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