A catalog of CasX genome editing sites in common model organisms

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),...

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Bibliographic Details
Published in:BMC genomics 2019-06, Vol.20 (1), p.528-528, Article 528
Main Author: Roberson, Elisha D O
Format: Article
Language:English
Subjects:
Animals
Caenorhabditis elegans
Caenorhabditis elegans - genetics
Cas12e
CasX
Databases, Genetic
DNA
Drosophila
Drosophila melanogaster
Drosophila melanogaster - genetics
Editors
Gene Editing
Genes
Genetic aspects
Genome editing
Genomes
Genomics
House mouse
Humans
Methods
Mice
Nucleases
Proteobacteria
Rats
RNA
Saccharomyces cerevisiae
Saccharomyces cerevisiae - genetics
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Summary: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.
ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-019-5924-6