@article{Neuhaus_Landstorfer_Simon-Diffe_ncRNA_from-2017,
author = {Neuhaus, Klaus and Landstorfer, Richard and Simon, Svenja 
          and Schober, Steffen and Wright, Patrick R. and Smith, 
          Cameron and Backofen, Rolf and Wecko, Romy and Keim, Daniel 
          A. and Scherer, Siegfried},
title = {Differentiation of {ncRNAs} from small {mRNAs} in 
         {Escherichia} coli {O157}:{H7} {EDL933} ({EHEC}) by combined 
         {RNAseq} and {RIBOseq} - {ryhB} encodes the regulatory {RNA} 
         {RyhB} and a peptide, {RyhP}},
journal = {BMC Genomics},
year = {2017},
doi = {10.1186/s12864-017-3586-9},
volume = {18},
user = {wrightp},
pmid = {28245801},
pages = {216},
number = {1},
issn = {1471-2164},
abstract = {BACKGROUND: While NGS allows rapid global detection of 
            transcripts, it remains difficult to distinguish ncRNAs from 
            short mRNAs. To detect potentially translated RNAs, we 
            developed an improved protocol for bacterial ribosomal 
            footprinting (RIBOseq). This allowed distinguishing ncRNA 
            from mRNA in EHEC. A high ratio of ribosomal footprints per 
            transcript (ribosomal coverage value, RCV) is expected to 
            indicate a translated RNA, while a low RCV should point to a 
            non-translated RNA. RESULTS: Based on their low RCV, 150 
            novel non-translated EHEC transcripts were identified as 
            putative ncRNAs, representing both antisense and intergenic 
            transcripts, 74 of which had expressed homologs in E. coli 
            MG1655. Bioinformatics analysis predicted statistically 
            significant target regulons for 15 of the intergenic 
            transcripts; experimental analysis revealed 4-fold or higher 
            differential expression of 46 novel ncRNA in different 
            growth media. Out of 329 annotated EHEC ncRNAs, 52 showed an 
            RCV similar to protein-coding genes, of those, 16 had 
            RIBOseq patterns matching annotated genes in other 
            enterobacteriaceae, and 11 seem to possess a Shine-Dalgarno 
            sequence, suggesting that such ncRNAs may encode small 
            proteins instead of being solely non-coding. To support that 
            the RIBOseq signals are reflecting translation, we tested 
            the ribosomal-footprint covered ORF of ryhB and found a 
            phenotype for the encoded peptide in iron-limiting 
            condition. CONCLUSION: Determination of the RCV is a useful 
            approach for a rapid first-step differentiation between 
            bacterial ncRNAs and small mRNAs. Further, many known ncRNAs 
            may encode proteins as well.}
}