title: Global transcription of CRISPR loci in the human oral cavity.
abstract: BACKGROUND
  Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are active in acquired resistance against bacteriophage and plasmids in a number of environments. In the human mouth, CRISPR loci evolve to counteract oral phage, but the expression of these CRISPR loci has not previously been investigated. We sequenced cDNA from CRISPR loci found in numerous different oral bacteria and compared with oral phage communities to determine whether the transcription of CRISPR loci is specifically targeted towards highly abundant phage present in the oral environment.
  
  
  RESULTS
  We found that of the 529,027 CRISPR spacer groups studied, 88 % could be identified in transcripts, indicating that the vast majority of CRISPR loci in the oral cavity were transcribed. There were no strong associations between CRISPR spacer repertoires and oral health status or nucleic acid type. We also compared CRISPR repertoires with oral bacteriophage communities, and found that there was no significant association between CRISPR transcripts and oral phage, regardless of the CRISPR type being evaluated. We characterized highly expressed CRISPR spacers and found that they were no more likely than other spacers to match oral phage. By reassembling the CRISPR-bearing reads into longer CRISPR loci, we found that the majority of the loci did not have spacers matching viruses found in the oral cavities of the subjects studied. For some CRISPR types, loci containing spacers matching oral phage were significantly more likely to have multiple spacers rather than a single spacer matching oral phage.
  
  
  CONCLUSIONS
  These data suggest that the transcription of oral CRISPR loci is relatively ubiquitous and that highly expressed CRISPR spacers do not necessarily target the most abundant oral phage.
authors.affiliation: Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. lumandrewg@gmail.com.
authors.forename: Andrew G
authors.initials: AG
authors.lastname: Lum
authors.affiliation: Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. lymelcc@gmail.com.
authors.forename: Melissa
authors.initials: M
authors.lastname: Ly
authors.affiliation: Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. tmsantiagorodriguez@ucsd.edu.
authors.forename: Tasha M
authors.initials: TM
authors.lastname: Santiago-Rodriguez
authors.affiliation: Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. mayuri.naidu@gmail.com.
authors.forename: Mayuri
authors.initials: M
authors.lastname: Naidu
authors.affiliation: College of Dental Medicine, Western University of Health Sciences, 309 E Second Street, Pomona, CA, 91766, USA. tboehm@westernu.edu.
authors.forename: Tobias K
authors.initials: TK
authors.lastname: Boehm
authors.affiliation: Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. dpride@ucsd.edu.|Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA, 92093-0612, USA. dpride@ucsd.edu.
authors.forename: David T
authors.initials: DT
authors.lastname: Pride
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000821:virology; D001435:Bacteriophages / Q000235:genetics*; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D020869:Gene Expression Profiling; D006801:Humans; D009055:Mouth / Q000382:microbiology* / Q000821:virology; D012329:RNA, Bacterial / Q000032:analysis; D012367:RNA, Viral / Q000032:analysis; D017423:Sequence Analysis, RNA
chemical_list: D012329:RNA, Bacterial; D012367:RNA, Viral