Abstract
BackgroundThe interest in non-coding RNAs (ncRNAs) constantly rose during the past few years because of the wide spectrum of biological processes in which they are involved. This led to the discovery of numerous ncRNA genes across many species. However, for most organisms the non-coding transcriptome still remains unexplored to a great extent. Various experimental techniques for the identification of ncRNA transcripts are available, but as these methods are costly and time-consuming, there is a need for computational methods that allow the detection of functional RNAs in complete genomes in order to suggest elements for further experiments. Several programs for the genome-wide prediction of functional RNAs have been developed but most of them predict a genomic locus with no indication whether the element is transcribed or not.ResultsWe present NOCORNAc, a program for the genome-wide prediction of ncRNA transcripts in bacteria. NOCORNAc incorporates various procedures for the detection of transcriptional features which are then integrated with functional ncRNA loci to determine the transcript coordinates. We applied RNAz and NOCORNAc to the genome of Streptomyces coelicolor and detected more than 800 putative ncRNA transcripts most of them located antisense to protein-coding regions. Using a custom design microarray we profiled the expression of about 400 of these elements and found more than 300 to be transcribed, 38 of them are predicted novel ncRNA genes in intergenic regions. The expression patterns of many ncRNAs are similarly complex as those of the protein-coding genes, in particular many antisense ncRNAs show a high expression correlation with their protein-coding partner.ConclusionsWe have developed NOCORNAc, a framework that facilitates the automated characterization of functional ncRNAs. NOCORNAc increases the confidence of predicted ncRNA loci, especially if they contain transcribed ncRNAs. NOCORNAc is not restricted to intergenic regions, but it is applicable to the prediction of ncRNA transcripts in whole microbial genomes. The software as well as a user guide and example data is available at http://www.zbit.uni-tuebingen.de/pas/nocornac.htm.
Highlights
The interest in non-coding RNAs constantly rose during the past few years because of the wide spectrum of biological processes in which they are involved
Genome-wide detection and classification of ncRNAs The alignment of the genomes of S. coelicolor, S. avermitilis and S. griseus produced by Mauve after preprocessing by rnazWindow covered 34.6% of S. coelicolor’s genomic sequence
RNAz predicted 4,707 ncRNA loci (P-value ≥ 0.5) for the reference organism S. coelicolor. Of these loci NOCORNAc annotated 2,358 with a Rho-independent terminator signal and 2,237 with a SIDD site. Combining these annotations NOCORNAc predicted 843 ncRNA transcripts of which 653 are located antisense to a protein-coding region. 10 predicted transcripts are partially overlapping a coding region in sense direction. 180 predicted transcripts are located in an intergenic region
Summary
The interest in non-coding RNAs (ncRNAs) constantly rose during the past few years because of the wide spectrum of biological processes in which they are involved. This led to the discovery of numerous ncRNA genes across many species. In the past few years non-coding RNAs (ncRNAs) have been increasingly recognized to be involved in a variety of biological functions, especially gene regulation [1,2,3,4]. Several experimental techniques are used to identify bacterial ncRNAs [14,15,16] These methods are laborious and expensive, especially if a large number of elements is analysed. NcRNAs that are not expressed under the specific conditions of the experiment will not be detected
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
