Reprogrammable CRISPR/Cas9-based system for inducing sitespecific DNA methylation

Biology Open

Volumn 5, Issue 6, 2016, Pages 866-874

  McDonald, James I ^a   Celik, Hamza ^b   Rois, Lisa E ^a   Fishberger, Gregory ^a   Fowler, Tolison ^a   Rees, Ryan ^a   Kramer, Ashley ^a   Martens, Andrew ^a   Edwardsand, John R ^a   Challen, Grant A ^a  

^a WASHINGTON UNIVERSITY   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

CpG dinucleotides; CRISPR Cas9 based system; DNA methylation

Indexed keywords

5 METHYLCYTOSINE; CPG OLIGODEOXYNUCLEOTIDE; CYCLIN DEPENDENT KINASE INHIBITOR 1B; CYCLIN DEPENDENT KINASE INHIBITOR 2A; CYCLIN DEPENDENT KINASE INHIBITOR 2D; DNA METHYLTRANSFERASE 3A; DOXYCYCLINE; GUIDE RNA; HYBRID PROTEIN;

ALLELE; ARTICLE; BINDING SITE; CHROMOSOME 17; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONTROLLED STUDY; CPG ISLAND; CRISPR CAS SYSTEM; DNA METHYLATION; ENZYME ACTIVE SITE; GENE EXPRESSION; GENE SILENCING; HUMAN; HUMAN CELL; NUCLEAR REPROGRAMMING; PROMOTER REGION; REAL TIME POLYMERASE CHAIN REACTION;

EID: 84978376788     PISSN: None     EISSN: 20466390     Source Type: Journal    
DOI: 10.1242/bio.019067     Document Type: Article

References (26)

1. Bell, J. T., Pai, A. A., Pickrell, J. K., Gaffney, D. J., Pique-Regi, R., Degner, J. F., Gilad, Y. and Pritchard, J. K. (2011). DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 12, R10.
2. Bernstein, D. L., Le Lay, J. E., Ruano, E. G. and Kaestner, K. H. (2015). TALEmediated epigenetic suppression of CDKN2A increases replication in human fibroblasts. J. Clin. Invest. 125, 1998-2006.
3. Bestor, T. H., Edwards, J. R. and Boulard, M. (2015). Notes on the role of dynamic DNA methylation in mammalian development. Proc. Natl. Acad. Sci. USA 112, 6796-6799.
4. Bock, C., Reither, S., Mikeska, T., Paulsen, M., Walter, J. and Lengauer, T. (2005). BiQ analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics 21, 4067-4068.
5. Bock, C., Beerman, I., Lien, W.-H., Smith, Z. D., Gu, H., Boyle, P., Gnirke, A., Fuchs, E., Rossi, D. J. and Meissner, A. (2012). DNA methylation dynamics during in vivo differentiation of blood and skin stem cells. Mol. Cell 47, 633-647.
6. Busslinger, M., Hurst, J. and Flavell, R. A. (1983). DNA methylation and the regulation of globin gene expression. Cell 34, 197-206.
7. Ciriello, G., Miller, M. L., Aksoy, B. A., Senbabaoglu, Y., Schultz, N. and Sander, C. (2013). Emerging landscape of oncogenic signatures across human cancers. Nat. Genet. 45, 1127-1133.
8. Cui, C., Gan, Y., Gu, L., Wilson, J., Liu, Z., Zhang, B. and Deng, D. (2015). P16-specific DNA methylation by engineered zinc finger methyltransferase inactivates gene transcription and promotes cancer metastasis. Genome Biol. 16, 252.
9. Doench, J. G., Hartenian, E., Graham, D. B., Tothova, Z., Hegde, M., Smith, I., Sullender, M., Ebert, B. L., Xavier, R. J. and Root, D. E. (2014). Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat. Biotechnol. 32, 1262-1267.
10. Egger, G., Liang, G., Aparicio, A. and Jones, P. A. (2004). Epigenetics in human disease and prospects for epigenetic therapy. Nature 429, 457-463.
11. Hellemans, J., Mortier, G., De Paepe, A., Speleman, F. and Vandesompele, J. (2007). qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 8,R19.
12. Hinshelwood, R. A., Melki, J. R., Huschtscha, L. I., Paul, C., Song, J. Z., Stirzaker, C., Reddel, R. R. and Clark, S. J. (2009). Aberrant de novo methylation of the p16INK4A CpG island is initiated post gene silencing in association with chromatin remodelling and mimics nucleosome positioning. Hum. Mol. Genet. 18, 3098-3109.
13. Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A. and Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821.
14. Krueger, F. and Andrews, S. R. (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572.
15. Liggett, W. H. and Sidransky, D. (1998). Role of the p16 tumor suppressor gene in cancer. J. Clin. Oncol. 16, 1197-1206.
16. Lou, S., Lee, H.-M., Qin, H., Li, J.-W., Gao, Z., Liu, X., Chan, L. L., Kl Lam, V., So, W.-Y., Wang, Y. et al. (2014). Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. Genome Biol. 15, 6.
17. Lund, K., Cole, J. J., VanderKraats, N. D., McBryan, T., Pchelintsev, N. A., Clark, W., Copland, M., Edwards, J. R. and Adams, P. D. (2014). DNMT inhibitors reverse a specific signature of aberrant promoter DNA methylation and associated gene silencing in AML. Genome Biol. 15, 406.
18. Maeder, M. L., Linder, S. J., Cascio, V. M., Fu, Y., Ho, Q. H. and Joung, J. K. (2013). CRISPR RNA-guided activation of endogenous human genes. Nat. Methods 10, 977-979.
19. Mali, P., Aach, J., Stranges, P. B., Esvelt, K. M., Moosburner, M., Kosuri, S., Yang, L. and Church, G. M. (2013). CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833-838.
20. Perez-Pinera, P., Kocak, D. D., Vockley, C. M., Adler, A. F., Kabadi, A. M., Polstein, L. R., Thakore, P. I., Glass, K. A., Ousterout, D. G., Leong, K. W. et al. (2013a). RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat. Methods 10, 973-976.
21. Perez-Pinera, P., Ousterout, D. G., Brunger, J. M., Farin, A. M., Glass, K. A., Guilak, F., Crawford, G. E., Hartemink, A. J. and Gersbach, C. A. (2013b). Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat. Methods 10, 239-242.
22. Reither, S., Li, F., Gowher, H. and Jeltsch, A. (2003). Catalytic mechanism of DNA-(cytosine-C5)-methyltransferases revisited: covalent intermediate formation is not essential for methyl group transfer by the murine Dnmt3a enzyme. J. Mol. Biol. 329, 675-684.
23. Shima, K., Nosho, K., Baba, Y., Cantor, M., Meyerhardt, J. A., Giovannucci, E. L., Fuchs, C. S. and Ogino, S. (2011). Prognostic significance of CDKN2A Biology Open (p16) promoter methylation and loss of expression in 902 colorectal cancers: cohort study and literature review. Int. J. Cancer 128, 1080-1094.
24. Siddique, A. N., Nunna, S., Rajavelu, A., Zhang, Y., Jurkowska, R. Z., Reinhardt, R., Rots, M. G., Ragozin, S., Jurkowski, T. P. and Jeltsch, A. (2013). Targeted methylation and gene silencing of VEGF-A in human cells by using a designed Dnmt3a-Dnmt3L single-chain fusion protein with increased DNA methylation activity. J. Mol. Biol. 425, 479-491.
25. VanderKraats, N. D., Hiken, J. F., Decker, K. F. and Edwards, J. R. (2013). Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes. Nucleic Acids Res. 41, 6816-6827.
26. Xie, S., Shen, B., Zhang, C., Huang, X. and Zhang, Y. (2014). sgRNAcas9: a software package for designing CRISPR sgRNA and evaluating potential offtarget cleavage sites. PLoS ONE 9, e100448.