A e Patologia Cellulare e Molecolare,Universita’ di Napoli FEDERICO II. Via S. Pansini ,Napoli,Italy E-mail: Luca Cozzuto cozzutoceinge.unina.it; Mauro Petrillo petrilloceinge.unina.it; Giustina Silvestro gsilvestunina.it; Pier Paolo Di Nocera dinoceraunina.it; Giovanni Paolella paolelladbbm.unina.it Corresponding author Equal contributorsPublished: January BMC Genomics ,: doi:.: June Accepted: JanuaryThis post is available from: biomedcentral Cozzuto et al; licensee BioMed Central Ltd. This can be an Open Access short article distributed beneath the terms of your Inventive Commons Attribution License (http:creativecommons.orglicensesby.),which permits unrestricted use,distribution,and reproduction in any medium,offered the original perform is appropriately cited.AbstractBackground: Analysis of noncoding sequences in many MedChemExpress CFI-400945 (free base) bacterial genomes brought towards the identification of households of repeated sequences,capable to fold as secondary structures. These sequences have normally been claimed to become transcribed and fulfill a functional role. A earlier systematic analysis of a representative set of bacterial genomes produced a big collection of sequences,potentially capable to fold as stemloop structures (SLS). Computational analysis of those sequences was carried out by browsing for families of repetitive nucleic acid elements sharing a prevalent secondary structure. Benefits: The initial clustering process identified clusters of comparable sequences in genomes,corresponding to about of the entire population. Sequences selected within this way possess a substantially larger aptitude to fold into a steady secondary PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/21263054 structure than the initial set. Removal of redundancies and regrouping with the selected sequences resulted within a final set of households,defined by HMM evaluation. of them consist of all wellknown SLS containing repeats and others reported in literature,but not analyzed in detail. The remaining households haven’t been previously described. Two thirds in the families share a typical predicted secondary structure and are situated inside intergenic regions. Conclusion: Systematic analysis of bacterial genomes revealed a sizable number of repeated sequence families,like identified and novel ones. Their predicted structure and genomic location suggest that,even in compact bacterial genomes,a relatively huge fraction on the genome consists of nonproteincoding sequences,possibly functioning in the RNA level.BackgroundThe availability of a huge amount of sequence data stimulated indepth analyses on the organization of bacterial genomes . Even though less prominent than ineukaryotic genomes,sequence repeats are located in most bacterial species. As outlined by their sizes,sequence repeats may be roughly classified into two major classes. Significant repeats kb) are largely insertion sequencesPage of(page number not for citation purposes)BMC Genomics ,:biomedcentral(IS),and encode proteins mediating their genomic mobility. The terminal inverted repeats (TIRs) and also the nature of their gene products enable sorting ISs into precise classes . Smaller sized repeats ( bp) make up a significantly less defined and more variegate set of genomic sequences. A few of them contain palindromic sequences,demonstrated or proposed to be structured as stemloops in a position to function as regulatory elements at DNA or RNA level. For example,E. coli PUBIME elements have already been shown to interact together with the DNA gyrase and also the integration host aspect protein ,but in addition to function as mRNA stabilizers and transcriptional attenuators . Similarly.
