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Gigascience. 2018 Mar 1;7(3):1-19. doi: 10.1093/gigascience/giy011.

Genome-wide determination of on-target and off-target characteristics for RNA-guided DNA methylation by dCas9 methyltransferases.

Lin L1,2, Liu Y1, Xu F3,4,5, Huang J3,4,5, Daugaard TF1, Petersen TS1, Hansen B1, Ye L3, Zhou Q3,4, Fang F3,4, Yang L3,4, Li S1,3, Fløe L1, Jensen KT1, Shrock E6, Chen F3,4,5, Yang H3,4,7, Wang J3,4, Liu X3,4, Xu X3,4, Bolund L1,2,3,4,8,9, Nielsen AL1, Luo Y1,2,3,4,8,9,10.

Author information

1
Department of Biomedicine, Aarhus University, Aarhus, Denmark.
2
Danish Regenerative Engineering Alliance for Medicine, Department of Biomedicine, Aarhus University, Aarhus, Denmark.
3
BGI-Shenzhen, Shenzhen 518083, China.
4
China National GeneBank-Shenzhen, BGI-Research, Shenzhen 518083, China.
5
Department of Biology, University of Copenhagen, Copenhagen, Denmark.
6
Department of Genetics, Harvard Medical School, Boston, MA, USA.
7
James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
8
BGI-Qingdao, 2877 Tuanjie Road, Sino-German Ecopark, Qingdao, 266000, China.
9
Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, China.
10
BrainStem - Stem Cell Center of Excellence in Neurology, Copenhagen, Denmark.

Abstract

Background:

Fusion of DNA methyltransferase domains to the nuclease-deficient clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 9 (dCas9) has been used for epigenome editing, but the specificities of these dCas9 methyltransferases have not been fully investigated.

Findings:

We generated CRISPR-guided DNA methyltransferases by fusing the catalytic domain of DNMT3A or DNMT3B to the C terminus of the dCas9 protein from Streptococcus pyogenes and validated its on-target and global off-target characteristics. Using targeted quantitative bisulfite pyrosequencing, we prove that dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B can efficiently methylate the CpG dinucleotides flanking its target sites at different genomic loci (uPA and TGFBR3) in human embryonic kidney cells (HEK293T). Furthermore, we conducted whole genome bisulfite sequencing (WGBS) to address the specificity of our dCas9 methyltransferases. WGBS revealed that although dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B did not cause global methylation changes, a substantial number (more than 1000) of the off-target differentially methylated regions (DMRs) were identified. The off-target DMRs, which were hypermethylated in cells expressing dCas9 methyltransferase and guide RNAs, were predominantly found in promoter regions, 5΄ untranslated regions, CpG islands, and DNase I hypersensitivity sites, whereas unexpected hypomethylated off-target DMRs were significantly enriched in repeated sequences. Through chromatin immunoprecipitation with massive parallel DNA sequencing analysis, we further revealed that these off-target DMRs were weakly correlated with dCas9 off-target binding sites. Using quantitative polymerase chain reaction, RNA sequencing, and fluorescence reporter cells, we also found that dCas9-BFP-DNMT3A and dCas9-BFP-DNMT3B can mediate transient inhibition of gene expression, which might be caused by dCas9-mediated de novo DNA methylation as well as interference with transcription.

Conclusion:

Our results prove that dCas9 methyltransferases cause efficient RNA-guided methylation of specific endogenous CpGs. However, there is significant off-target methylation indicating that further improvements of the specificity of CRISPR-dCas9 based DNA methylation modifiers are required.

PMID:
29635374
PMCID:
PMC5888497
DOI:
10.1093/gigascience/giy011
[Indexed for MEDLINE]
Free PMC Article

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