A competitive precision CRISPR method to identify the fitness effects of transcription factor binding sites

Päivi Pihlajamaa; Otto Kauko; Biswajyoti Sahu; Teemu Kivioja; Jussi Taipale

doi:10.1038/s41587-022-01444-6

A competitive precision CRISPR method to identify the fitness effects of transcription factor binding sites

Päivi Pihlajamaa, Otto Kauko, Biswajyoti Sahu, Teemu Kivioja, Jussi Taipale

Turku Bioscience

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Abstract

Here we describe a competitive genome editing method that measures the effect of mutations on molecular functions, based on precision CRISPR editing using template libraries with either the original or altered sequence, and a sequence tag, enabling direct comparison between original and mutated cells. Using the example of the MYC oncogene, we identify important transcriptional targets and show that E-box mutations at MYC target gene promoters reduce cellular fitness.

Original language	English
Pages (from-to)	197-203
Number of pages	7
Journal	Nature Biotechnology
Volume	41
Issue number	2
DOIs	https://doi.org/10.1038/s41587-022-01444-6
Publication status	Published - Feb 2023
MoE publication type	A1 Journal article-refereed

Keywords

Binding Sites/genetics
Clustered Regularly Interspaced Short Palindromic Repeats/genetics
CRISPR-Cas Systems/genetics
Gene Editing/methods
Promoter Regions, Genetic/genetics
Transcription Factors/chemistry

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10.1038/s41587-022-01444-6

s41587-022-01444-6Final published version, 11.5 MBLicence: CC BY

https://urn.fi/URN:NBN:fi-fe202402167479

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AU - Taipale, Jussi

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KW - Binding Sites/genetics

KW - Clustered Regularly Interspaced Short Palindromic Repeats/genetics

KW - CRISPR-Cas Systems/genetics

KW - Gene Editing/methods

KW - Promoter Regions, Genetic/genetics

KW - Transcription Factors/chemistry

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A competitive precision CRISPR method to identify the fitness effects of transcription factor binding sites

Abstract

Keywords

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