Extraction of CRISPR-targeted sequences from the metagenome

Ryota Sugimoto; Luca Nishimura; Phuong Thanh Nguyen; Ituro Inoue

doi:10.1016/j.xpro.2022.101525

Extraction of CRISPR-targeted sequences from the metagenome

STAR Protoc. 2022 Sep 16;3(3):101525. doi: 10.1016/j.xpro.2022.101525. Epub 2022 Jul 2.

Authors

Ryota Sugimoto¹, Luca Nishimura², Phuong Thanh Nguyen², Ituro Inoue³

Affiliations

¹ Human Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan. Electronic address: rsugimot@nig.ac.jp.
² Human Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan.
³ Human Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan. Electronic address: itinoue@nig.ac.jp.

Abstract

Homology-based search is commonly used to uncover mobile genetic elements (MGEs) from metagenomes, but it heavily relies on reference genomes in the database. Here we introduce a protocol to extract CRISPR-targeted sequences from the assembled human gut metagenomic sequences without using a reference database. We describe the assembling of metagenome contigs, the extraction of CRISPR direct repeats and spacers, the discovery of protospacers, and the extraction of protospacer-enriched regions using the graph-based approach. This protocol could extract numerous characterized/uncharacterized MGEs. For complete details on the use and execution of this protocol, please refer to Sugimoto et al. (2021).

Keywords: Bioinformatics; CRISPR; Genomics; Sequence analysis; Systems biology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
Clustered Regularly Interspaced Short Palindromic Repeats* / genetics
Humans
Metagenome* / genetics
Metagenomics