Parallel genetics of regulatory sequences using scalable genome editing in vivo

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Item Type:

Article

Title:

Parallel genetics of regulatory sequences using scalable genome editing in vivo

Creators Name:

Froehlich, J.J. and Uyar, B. and Herzog, M. and Theil, K. and Glažar, P. and Akalin, A. and Rajewsky, N.

Abstract:

How regulatory sequences control gene expression is fundamental for explaining phenotypes in health and disease. Regulatory elements must ultimately be understood within their genomic environment and development- or tissue-specific contexts. Because this is technically challenging, few regulatory elements have been characterized in vivo. Here, we use inducible Cas9 and multiplexed guide RNAs to create hundreds of mutations in enhancers/promoters and 3' UTRs of 16 genes in C. elegans. Our software crispr-DART analyzes indel mutations in targeted DNA sequencing. We quantify the impact of mutations on expression and fitness by targeted RNA sequencing and DNA sampling. When applying our approach to the lin-41 3' UTR, generating hundreds of mutants, we find that the two adjacent binding sites for the miRNA let-7 can regulate lin-41 expression independently of each other. Finally, we map regulatory genotypes to phenotypic traits for several genes. Our approach enables parallel analysis of regulatory sequences directly in animals.

Keywords:

Gene Regulation, Gene-Regulatory Elements, Animal Phenotype, Caenorhabditis elegans, In Vivo, CRISPR-Cas9, Parallel Genetics, Indel Mutations, lin-41 3′ UTR, let-7 microRNA, Animals, Caenorhabditis elegans

Source:

Cell Reports

ISSN:

2211-1247

Publisher:

Cell Press / Elsevier

Volume:

Number:

Page Range:

108988

Date:

13 April 2021