Abstract:
:To fully exploit the microbial genome resources, a high-throughput experimental platform is needed to associate genes with phenotypes at the genome level. We present here a novel method that enables investigation of the cellular consequences of repressing individual transcripts based on the CRISPR interference (CRISPRi) pooled screening in bacteria. We identify rules for guide RNA library design to handle the unique structure of prokaryotic genomes by tiling screening and construct an E. coli genome-scale guide RNA library (~60,000 members) accordingly. We show that CRISPRi outperforms transposon sequencing, the benchmark method in the microbial functional genomics field, when similar library sizes are used or gene length is short. This tool is also effective for mapping phenotypes to non-coding RNAs (ncRNAs), as elucidated by a comprehensive tRNA-fitness map constructed here. Our results establish CRISPRi pooled screening as a powerful tool for mapping complex prokaryotic genetic networks in a precise and high-throughput manner.
journal_name
Nat Communjournal_title
Nature communicationsauthors
Wang T,Guan C,Guo J,Liu B,Wu Y,Xie Z,Zhang C,Xing XHdoi
10.1038/s41467-018-04899-xsubject
Has Abstractpub_date
2018-06-26 00:00:00pages
2475issue
1issn
2041-1723pii
10.1038/s41467-018-04899-xjournal_volume
9pub_type
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