title: CRISPR-Cas9 nuclear dynamics and target recognition in living cells.
abstract: The bacterial CRISPR-Cas9 system has been repurposed for genome engineering, transcription modulation, and chromosome imaging in eukaryotic cells. However, the nuclear dynamics of clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) guide RNAs and target interrogation are not well defined in living cells. Here, we deployed a dual-color CRISPR system to directly measure the stability of both Cas9 and guide RNA. We found that Cas9 is essential for guide RNA stability and that the nuclear Cas9-guide RNA complex levels limit the targeting efficiency. Fluorescence recovery after photobleaching measurements revealed that single mismatches in the guide RNA seed sequence reduce the target residence time from >3 h to as low as <2 min in a nucleotide identity- and position-dependent manner. We further show that the duration of target residence correlates with cleavage activity. These results reveal that CRISPR discriminates between genuine versus mismatched targets for genome editing via radical alterations in residence time.
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605.
authors.forename: Hanhui
authors.initials: H
authors.lastname: Ma
authors.affiliation: RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605.
authors.forename: Li-Chun
authors.initials: LC
authors.lastname: Tu
authors.affiliation: Department of Computer Science, University of Central Florida, Orlando, FL 32816.
authors.forename: Ardalan
authors.identifier: 0000-0002-2747-2193
authors.initials: A
authors.lastname: Naseri
authors.affiliation: RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605.
authors.forename: Maximiliaan
authors.identifier: 0000-0003-3363-8791
authors.initials: M
authors.lastname: Huisman
authors.affiliation: Department of Computer Science, University of Central Florida, Orlando, FL 32816.
authors.forename: Shaojie
authors.initials: S
authors.lastname: Zhang
authors.affiliation: RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605.
authors.forename: David
authors.initials: D
authors.lastname: Grunwald
authors.affiliation: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605 thoru.pederson@umassmed.edu.
authors.forename: Thoru
authors.identifier: 0000-0002-3703-7806
authors.initials: T
authors.lastname: Pederson
mesh_terms: D001483:Base Sequence; D064113:CRISPR-Cas Systems / Q000235:genetics*; D045744:Cell Line, Tumor; D002467:Cell Nucleus / Q000378:metabolism*; D002470:Cell Survival; D004247:DNA / Q000378:metabolism; D006801:Humans; D008954:Models, Biological; D020871:RNA Stability; D000094704:RNA, Guide, CRISPR-Cas Systems; D013997:Time Factors
chemical_list: D000094704:RNA, Guide, CRISPR-Cas Systems; D004247:DNA