Record Details

Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor

DSpace at IIT Bombay

View Archive Info
 
 
Field Value
 
Title Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor
 
Creator CHARANIYA, S
MEHRA, S
LIAN, W
JAYAPAL, KP
KARYPIS, G
HU, WS
 
Subject sigma-factor sigma(h)
antibiotic biosynthetic pathways
gene-expression
escherichia-coli
growth-phase
dependent transcription
microbial genomes
2 promoters
a3(2)
classification
 
Description 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.
 
Publisher OXFORD UNIV PRESS
 
Date 2011-08-22T07:31:04Z
2011-12-26T12:56:15Z
2011-12-27T05:44:40Z
2011-08-22T07:31:04Z
2011-12-26T12:56:15Z
2011-12-27T05:44:40Z
2007
 
Type Article
 
Identifier NUCLEIC ACIDS RESEARCH, 35(21), 7222-7236
0305-1048
http://dx.doi.org/10.1093/nar/gkm501
http://dspace.library.iitb.ac.in/xmlui/handle/10054/10358
http://hdl.handle.net/10054/10358
 
Language en