title: Genome-wide detection of predicted non-coding RNAs in Rhizobium etli expressed during free-living and host-associated growth using a high-resolution tiling array.
abstract: BACKGROUND
  Non-coding RNAs (ncRNAs) play a crucial role in the intricate regulation of bacterial gene expression, allowing bacteria to quickly adapt to changing environments. In the past few years, a growing number of regulatory RNA elements have been predicted by computational methods, mostly in well-studied gamma-proteobacteria but lately in several alpha-proteobacteria as well. Here, we have compared an extensive compilation of these non-coding RNA predictions to intergenic expression data of a whole-genome high-resolution tiling array in the soil-dwelling alpha-proteobacterium Rhizobium etli.
  
  
  RESULTS
  Expression of 89 candidate ncRNAs was detected, both on the chromosome and on the six megaplasmids encompassing the R. etli genome. Of these, 11 correspond to functionally well characterized ncRNAs, 12 were previously identified in other alpha-proteobacteria but are as yet uncharacterized and 66 were computationally predicted earlier but had not been experimentally identified and were therefore classified as novel ncRNAs. The latter comprise 17 putative sRNAs and 49 putative cis-regulatory ncRNAs. A selection of these candidate ncRNAs was validated by RT-qPCR, Northern blotting and 5' RACE, confirming the existence of 4 ncRNAs. Interestingly, individual transcript levels of numerous ncRNAs varied during free-living growth and during interaction with the eukaryotic host plant, pointing to possible ncRNA-dependent regulation of these specialized processes.
  
  
  CONCLUSIONS
  Our data support the practical value of previous ncRNA prediction algorithms and significantly expand the list of candidate ncRNAs encoded in the intergenic regions of R. etli and, by extension, of alpha-proteobacteria. Moreover, we show high-resolution tiling arrays to be suitable tools for studying intergenic ncRNA transcription profiles across the genome. The differential expression levels of some of these ncRNAs may indicate a role in adaptation to changing environmental conditions.
authors.affiliation: Centre of Microbial and Plant Genetics, Katholieke Universiteit Leuven, Heverlee, Belgium.
authors.forename: Maarten
authors.initials: M
authors.lastname: Vercruysse
authors.forename: Maarten
authors.initials: M
authors.lastname: Fauvart
authors.forename: Lore
authors.initials: L
authors.lastname: Cloots
authors.forename: Kristof
authors.initials: K
authors.lastname: Engelen
authors.forename: Inge M
authors.initials: IM
authors.lastname: Thijs
authors.forename: Kathleen
authors.initials: K
authors.lastname: Marchal
authors.forename: Jan
authors.initials: J
authors.lastname: Michiels
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D016680:Genome, Bacterial; D020411:Oligonucleotide Array Sequence Analysis; D012329:RNA, Bacterial / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D042163:Rhizobium etli / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D012329:RNA, Bacterial; D022661:RNA, Untranslated