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.

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_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_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_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_12P_S12_L001_R1_001.fastq.gz	RIP-Seq	664.2 MB
SRR13779885_GSM5105583	RIP-Seq	643.0 MB
SRR13779886_GSM5105584	RIP-Seq	686.0 MB
SRR13779887_GSM5105585	RIP-Seq	419.0 MB
SRR13779888_GSM5105586	RIP-Seq	591.0 MB
SRR13779889_GSM5105587	RIP-Seq	955.0 MB
SRR13779890_GSM5105588	RIP-Seq	644.0 MB
SRR13779891_GSM5105589	RIP-Seq	602.0 MB
SRR13779892_GSM5105590	RIP-Seq	681.0 MB
SRR13779893_GSM5105591	RIP-Seq	592.0 MB
SRR13779894_GSM5105592	RIP-Seq	617.0 MB
SRR13779895_GSM5105593	RIP-Seq	610.0 MB
SRR13779896_GSM5105594	RIP-Seq	664.0 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_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

Potentially related datasets 3

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.

Accession	Source	Title
GSE55887	GSE · GEO GEO ↗	Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
SRP050338	SRP · SRA	No title in the index
GSE167466	GSE · GEO GEO ↗	Crosstalk between CRISPR-Cas9 and the human transcriptome

Analysis pipelines 2

Pipeline	Assay	Steps	Dataset
GSE167466 eCLIP Data Processing geo_data_processing	eCLIP	18	GSE167466
GSE55887 ChIP-seq Data Processing geo_data_processing	ChIP-seq	5	GSE55887

Funding 3 grants

Grant	Funder
R01 HG004659	NHGRI NIH HHS (United States)
R01 NS103172	NINDS NIH HHS (United States)
R01 EY029166	NEI NIH HHS (United States)