Rational gRNA design based on transcription factor binding data
Artikel i vetenskaplig tidskrift, 2021

The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has become a standard tool in many genome engineering endeavors. The endonuclease-deficient version of Cas9 (dCas9) is also a powerful programmable tool for gene regulation. In this study, we made use of Saccharomyces cerevisiae transcription factor (TF) binding data to obtain a better understanding of the interplay between TF binding and binding of dCas9 fused to an activator domain, VPR. More specifically, we targeted dCas9-VPR toward binding sites of Gcr1-Gcr2 and Tye7 present in several promoters of genes encoding enzymes engaged in the central carbon metabolism. From our data, we observed an upregulation of gene expression when dCas9-VPR was targeted next to a TF binding motif, whereas a downregulation or no change was observed when dCas9 was bound on a TF motif. This suggests a steric competition between dCas9 and the specific TF. Integrating TF binding data, therefore, proved to be useful for designing guide RNAs for CRISPR interference or CRISPR activation applications.

glycolytic promoters

transcription factor binding

gRNA design

Saccharomyces cerevisiae



David Bergenholm

Chalmers, Biologi och bioteknik, Systembiologi

Yasaman Dabirian

Chalmers, Biologi och bioteknik, Systembiologi

Raphael Ferreira

Chalmers, Biologi och bioteknik, Systembiologi

Verena Siewers

BioInnovation Institute

Florian David

Chalmers, Biologi och bioteknik, Systembiologi

Jens B Nielsen

Chalmers, Biologi och bioteknik, Systembiologi

Synthetic Biology

19397267 (ISSN) 23977000 (eISSN)

Vol. 6 1 ysab014


Biokemi och molekylärbiologi

Medicinsk bioteknologi (med inriktning mot cellbiologi (inklusive stamcellsbiologi), molekylärbiologi, mikrobiologi, biokemi eller biofarmaci)

Bioinformatik och systembiologi





Mer information

Senast uppdaterat