Re-engineered guide RNA enables DNA loops and contacts modulating repression in E. coli
No Thumbnail Available
Access rights
openAccess
URL
Journal Title
Journal ISSN
Volume Title
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
This publication is imported from Aalto University research portal.
View publication in the Research portal (opens in new window)
View/Open full text file from the Research portal (opens in new window)
Other link related to publication (opens in new window)
View publication in the Research portal (opens in new window)
View/Open full text file from the Research portal (opens in new window)
Other link related to publication (opens in new window)
Date
2024-08-27
Department
Major/Subject
Mcode
Degree programme
Language
en
Pages
12
Series
Nucleic Acids Research, Volume 52, issue 15, pp. 9328-9339
Abstract
RNA serves as information media as well as molecular scaffold in nature and synthetic systems. The single guide RNA (sgRNA) widely applied in CRISPR techniques exemplifies both functions, with a guide region bearing DNA base-pairing information, and a structural motif for Cas9 protein scaffolding. The scaffold region has been modified by fusing RNA aptamers to the tetra-stem loop. The guide region is typically not regarded as a pluggable module as it encodes the essential function of DNA sequence recognition. Here, we investigate a chimera of two sgRNAs, with distinct guide sequences joined by an RNA linker (dgRNA), regarding its DNA binding function and loop induction capability. First, we studied the sequence bi-specificity of the dgRNA and discovered that the RNA linker allows distal parts of double-stranded DNA to be brought into proximity. To test the activity of the dgRNA in organisms, we used the LacZ gene as a reporter and recapitulated the loop-mediated gene inhibition by LacI in E. coli. We found that the dgRNA can be applied to target distal genomic regions with comparable levels of inhibition. The capability of dgRNA to induce DNA contacts solely requires dCas9 and RNA, making it a minimal system to remodel chromosomal conformation in various organisms.Description
Keywords
Other note
Citation
Yang, Y, Rocamonde-Lago, I, Shen, B, Berzina, I, Zipf, J & Högberg, B 2024, ' Re-engineered guide RNA enables DNA loops and contacts modulating repression in E. coli ', Nucleic Acids Research, vol. 52, no. 15, pp. 9328-9339 . https://doi.org/10.1093/nar/gkae591