TY - JOUR
T1 - A catalog of CasX genome editing sites in common model organisms
AU - Roberson, Elisha D.O.
N1 - Funding Information:
E.D.O.R. was partially supported by NIH grant P30-AR073752. The funder had no role in the design, analysis, interpretation of data, or writing of the manuscript. Some of the computations in this paper were performed using the facilities of the Washington University Center for High Performance Computing, which were partially provided through NIH grant S10 OD018091.
Publisher Copyright:
© 2019 The Author(s).
PY - 2019/6/27
Y1 - 2019/6/27
N2 - DpbCasX, also called Cas12e, is an RNA-guided DNA endonuclease isolated from Deltaproteobacteria. In this paper I characterized the CasX-compatible genome editing sites in the reference genomes of yeast (Saccharomyces cerevisiae), flatworms (Caenorhabditis elegans), flies (Drosophila melanogaster), zebrafish (Danio rerio), mouse (Mus musculus), rats (Rattus norvegicus), and humans (Homo sapiens). Across those genomes there were > 27,000 CasX sites per megabase on average. More than 90% of genes in each genome had at least one unique site overlapping an exon, with median unique sites per gene of 6-45. I also annotated sites in the GRCm38 reference and 15 additional mouse strain genomes. The presence of specific guide sequences varied amongst the strains, with CAST/EiJ and PWK/PhJ showing the greatest divergence from the reference strain. The high density of CasX sites and number of exon overlapping sites suggests that CasX has the potential to be used as a common genome editor.
AB - DpbCasX, also called Cas12e, is an RNA-guided DNA endonuclease isolated from Deltaproteobacteria. In this paper I characterized the CasX-compatible genome editing sites in the reference genomes of yeast (Saccharomyces cerevisiae), flatworms (Caenorhabditis elegans), flies (Drosophila melanogaster), zebrafish (Danio rerio), mouse (Mus musculus), rats (Rattus norvegicus), and humans (Homo sapiens). Across those genomes there were > 27,000 CasX sites per megabase on average. More than 90% of genes in each genome had at least one unique site overlapping an exon, with median unique sites per gene of 6-45. I also annotated sites in the GRCm38 reference and 15 additional mouse strain genomes. The presence of specific guide sequences varied amongst the strains, with CAST/EiJ and PWK/PhJ showing the greatest divergence from the reference strain. The high density of CasX sites and number of exon overlapping sites suggests that CasX has the potential to be used as a common genome editor.
KW - Caenorhabditis elegans
KW - Cas12e
KW - CasX
KW - Danio rerio
KW - Drosophila melanogaster
KW - Genome editing
KW - Homo sapiens
KW - Mus musculus
KW - Rattus norvegicus
KW - Saccharomyces cerevisiae
UR - http://www.scopus.com/inward/record.url?scp=85068267462&partnerID=8YFLogxK
U2 - 10.1186/s12864-019-5924-6
DO - 10.1186/s12864-019-5924-6
M3 - Article
C2 - 31248380
AN - SCOPUS:85068267462
SN - 1471-2164
VL - 20
JO - BMC Genomics
JF - BMC Genomics
IS - 1
M1 - 528
ER -