title: CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems.
abstract: Central to Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas systems are repeated RNA sequences that serve as Cas-protein-binding templates. Classification is based on the architectural composition of associated Cas proteins, considering repeat evolution is essential to complete the picture. We compiled the largest data set of CRISPRs to date, performed comprehensive, independent clustering analyses and identified a novel set of 40 conserved sequence families and 33 potential structure motifs for Cas-endoribonucleases with some distinct conservation patterns. Evolutionary relationships are presented as a hierarchical map of sequence and structure similarities for both a quick and detailed insight into the diversity of CRISPR-Cas systems. In a comparison with Cas-subtypes, I-C, I-E, I-F and type II were strongly coupled and the remaining type I and type III subtypes were loosely coupled to repeat and Cas1 evolution, respectively. Subtypes with a strong link to CRISPR evolution were almost exclusive to bacteria; nevertheless, we identified rare examples of potential horizontal transfer of I-C and I-E systems into archaeal organisms. Our easy-to-use web server provides an automated assignment of newly sequenced CRISPRs to our classification system and enables more informed choices on future hypotheses in CRISPR-Cas research: http://rna.informatik.uni-freiburg.de/CRISPRmap.
authors.affiliation: Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany, ZBSA Centre for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstr. 49, 79104 Freiburg, Germany, BIOSS Centre for Biological Signalling Studies, Cluster of Excellence, Albert-Ludwigs-University Freiburg, Germany and Center for non-coding RNA in Technology and Health, University of Copenhagen, Gronnegardsvej 3, DK-1870 Frederiksberg C, Denmark.
authors.forename: Sita J
authors.initials: SJ
authors.lastname: Lange
authors.forename: Omer S
authors.initials: OS
authors.lastname: Alkhnbashi
authors.forename: Dominic
authors.initials: D
authors.lastname: Rose
authors.forename: Sebastian
authors.initials: S
authors.lastname: Will
authors.forename: Rolf
authors.initials: R
authors.lastname: Backofen
mesh_terms: D056704:Adaptive Immunity / Q000235:genetics; D001105:Archaea / Q000235:genetics / Q000276:immunology; D019843:Archaeal Proteins / Q000737:chemistry / Q000145:classification; D001419:Bacteria / Q000235:genetics / Q000276:immunology; D001426:Bacterial Proteins / Q000737:chemistry / Q000145:classification; D016000:Cluster Analysis; D017124:Conserved Sequence; D019615:Crenarchaeota / Q000235:genetics; D019605:Euryarchaeota / Q000235:genetics; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D020407:Internet; D055029:Inverted Repeat Sequences; D059372:Nucleotide Motifs; D059367:RNA Cleavage; D019642:RNA, Archaeal / Q000737:chemistry* / Q000145:classification; D012329:RNA, Bacterial / Q000737:chemistry* / Q000145:classification; D012984:Software
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D019642:RNA, Archaeal; D012329:RNA, Bacterial