Crosstalk between CRISPR-Cas9 and the human transcriptome.

Aaron A Smargon, Assael A Madrigal, Brian A Yee, Kevin D Dong, Jasmine R Mueller, Gene W Yeo

Nature communications · 2022 · Vol. 13 (1) · pp. 1125

Abstract

CRISPR-Cas9 expression independent of its cognate synthetic guide RNA (gRNA) causes widespread genomic DNA damage in human cells. To investigate whether Cas9 can interact with endogenous human RNA transcripts independent of its guide, we perform eCLIP (enhanced CLIP) of Cas9 in human cells and find that Cas9 reproducibly interacts with hundreds of endogenous human RNA transcripts. This association can be partially explained by a model built on gRNA secondary structure and sequence. Critically, transcriptome-wide Cas9 binding sites do not appear to correlate with published genome-wide Cas9 DNA binding or cut-site loci under gRNA co-expression. However, even under gRNA co-expression low-affinity Cas9-human RNA interactions (which we term CRISPR crosstalk) do correlate with published elevated transcriptome-wide RNA editing. Our findings do not support the hypothesis that human RNAs can broadly guide Cas9 to bind and cleave human genomic DNA, but they illustrate a cellular and RNA impact likely inherent to CRISPR-Cas systems.

Publication Types

["Journal Article", "Research Support, N.I.H., Extramural", "Research Support, Non-U.S. Gov't"]

Keywords

[]

MeSH Terms

["CRISPR-Cas Systems", "Gene Editing", "Humans", "RNA Editing", "RNA, Guide, CRISPR-Cas Systems", "Transcriptome"]

Funding

R01 HG004659 NHGRI NIH HHS (United States)

R01 NS103172 NINDS NIH HHS (United States)

R01 EY029166 NEI NIH HHS (United States)

Linked Datasets (1)

GSE167466 GSE via ncbi_elink

GEO

Crosstalk between CRISPR-Cas9 and the human transcriptome

Homo sapiens

24 data files

File	Type	Size
Assa_2N_S60_L005_R1_001.fastq.gz	RIP-Seq	419.8 MB
Assa_2N_S60_L005_R1_001.fastq.gz	RIP-Seq	419.8 MB
Assa_2P_S61_L005_R1_001.fastq.gz	RIP-Seq	591.4 MB
Assa_2P_S61_L005_R1_001.fastq.gz	RIP-Seq	591.4 MB
FLAG_CAS9_4N_S5_L001_R1_001.fastq.gz	RIP-Seq	602.8 MB
FLAG_CAS9_4N_S5_L001_R1_001.fastq.gz	RIP-Seq	602.8 MB
FLAG_CAS9_4P_S6_L001_R1_001.fastq.gz	RIP-Seq	681.2 MB
FLAG_CAS9_4P_S6_L001_R1_001.fastq.gz	RIP-Seq	681.2 MB
FLAG_CAS9_6N_S7_L001_R1_001.fastq.gz	RIP-Seq	592.4 MB
FLAG_CAS9_6N_S7_L001_R1_001.fastq.gz	RIP-Seq	592.4 MB
FLAG_CAS9_6P_S8_L001_R1_001.fastq.gz	RIP-Seq	617.6 MB
FLAG_CAS9_6P_S8_L001_R1_001.fastq.gz	RIP-Seq	617.6 MB
FLAG_pCDNA_11P_S11_L001_R1_001.fastq.gz	RIP-Seq	610.4 MB
FLAG_pCDNA_11P_S11_L001_R1_001.fastq.gz	RIP-Seq	610.4 MB
FLAG_pCDNA_12P_S12_L001_R1_001.fastq.gz	RIP-Seq	664.2 MB
FLAG_pCDNA_12P_S12_L001_R1_001.fastq.gz	RIP-Seq	664.2 MB
V5_CAS9_1N_S1_L001_R1_001.fastq.gz	RIP-Seq	643.2 MB
V5_CAS9_1N_S1_L001_R1_001.fastq.gz	RIP-Seq	643.2 MB
V5_CAS9_1P_S2_L001_R1_001.fastq.gz	RIP-Seq	686.4 MB
V5_CAS9_1P_S2_L001_R1_001.fastq.gz	RIP-Seq	686.4 MB
V5_pCDNA_8P_S9_L001_R1_001.fastq.gz	RIP-Seq	955.2 MB
V5_pCDNA_8P_S9_L001_R1_001.fastq.gz	RIP-Seq	955.2 MB
V5_pCDNA_9P_S10_L001_R1_001.fastq.gz	RIP-Seq	644.1 MB
V5_pCDNA_9P_S10_L001_R1_001.fastq.gz	RIP-Seq	644.1 MB

Potentially Related Datasets (2)

These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.

GSE55887 GSE GEO

GEO

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

SRP050338 SRP SRA

Analysis Pipelines (2)

GSE167466 eCLIP Data Processing 18 steps

eCLIP geo_data_processing GSE167466

GSE55887 ChIP-seq Data Processing 5 steps

ChIP-seq geo_data_processing GSE55887