과제정보
This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean Government (2020R1A2C2009382) to Y.C., J.L., and S.L. were supported by the Stadelmann-Lee Scholarship Fund, Seoul National University.
참고문헌
- Allen, G.C., Flores-Vergara, M.A., Krasynanski, S., Kumar, S., and Thompson, W.F. (2006). A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat. Protoc. 1, 2320-2325. https://doi.org/10.1038/nprot.2006.384
- Bell, C.G., Lowe, R., Adams, P.D., Baccarelli, A.A., Beck, S., Bell, J.T., Christensen, B.C., Gladyshev, V.N., Heijmans, B.T., Horvath, S., et al. (2019). DNA methylation aging clocks: challenges and recommendations. Genome Biol. 20, 249. https://doi.org/10.1186/s13059-019-1824-y
- Bouyer, D., Kramdi, A., Kassam, M., Heese, M., Schnittger, A., Roudier, F., and Colot, V. (2017). DNA methylation dynamics during early plant life. Genome Biol. 18, 179. https://doi.org/10.1186/s13059-017-1313-0
- Chatterjee, A., Stockwell, P.A., Rodger, E.J., and Morison, I.M. (2012). Comparison of alignment software for genome-wide bisulphite sequence data. Nucleic Acids Res. 40, e79. https://doi.org/10.1093/nar/gks150
- Clark, S.J., Smallwood, S.A., Lee, H.J., Krueger, F., Reik, W., and Kelsey, G. (2017). Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq). Nat. Protoc. 12, 534-547. https://doi.org/10.1038/nprot.2016.187
- Deal, R.B. and Henikoff, S. (2011). The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat. Protoc. 6, 56-68. https://doi.org/10.1038/nprot.2010.175
- Dona, F. and Houseley, J. (2014). Unexpected DNA loss mediated by the DNA binding activity of ribonuclease A. PLoS One 9, e115008. https://doi.org/10.1371/journal.pone.0115008
- Frommer, M., McDonald, L.E., Millar, D.S., Collis, C.M., Watt, F., Grigg, G.W., Molloy, P.L., and Paul, C.L. (1992). A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. U. S. A. 89, 1827-1831. https://doi.org/10.1073/pnas.89.5.1827
- Hofmeister, B.T., Lee, K., Rohr, N.A., Hall, D.W., and Schmitz, R.J. (2017). Stable inheritance of DNA methylation allows creation of epigenotype maps and the study of epiallele inheritance patterns in the absence of genetic variation. Genome Biol. 18, 155. https://doi.org/10.1186/s13059-017-1288-x
- Hsieh, T.F., Ibarra, C.A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer, R.L., and Zilberman, D. (2009). Genome-wide demethylation of Arabidopsis endosperm. Science 324, 1451-1454. https://doi.org/10.1126/science.1172417
- Ibarra, C.A., Feng, X., Schoft, V.K., Hsieh, T.F., Uzawa, R., Rodrigues, J.A., Zemach, A., Chumak, N., Machlicova, A., Nishimura, T., et al. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337, 1360-1364. https://doi.org/10.1126/science.1224839
- Karemaker, I.D. and Vermeulen, M. (2018). Single-cell DNA methylation profiling: technologies and biological applications. Trends Biotechnol. 36, 952-965. https://doi.org/10.1016/j.tibtech.2018.04.002
- Kawakatsu, T., Nery, J.R., Castanon, R., and Ecker, J.R. (2017). Dynamic DNA methylation reconfiguration during seed development and germination. Genome Biol. 18, 171. https://doi.org/10.1186/s13059-017-1251-x
- Kim, M. and Costello, J. (2017). DNA methylation: an epigenetic mark of cellular memory. Exp. Mol. Med. 49, e322. https://doi.org/10.1038/emm.2017.10
- Kim, M.J., Lee, H.J., Choi, M.Y., Kang, S.S., Kim, Y.S., Shin, J.K., and Choi, W.S. (2021). UHRF1 induces methylation of the TXNIP promoter and down-regulates gene expression in cervical cancer. Mol. Cells 44, 146-159. https://doi.org/10.14348/molcells.2021.0001
- Krueger, F., Kreck, B., Franke, A., and Andrews, S.R. (2012). DNA methylome analysis using short bisulfite sequencing data. Nat. Methods 9, 145-151. https://doi.org/10.1038/nmeth.1828
- Laux, T., Wurschum, T., and Breuninger, H. (2004). Genetic regulation of embryonic pattern formation. Plant Cell 16 Suppl, S190-S202. https://doi.org/10.1105/tpc.016014
- Levenson, V.V. (2010). DNA methylation as a universal biomarker. Expert Rev. Mol. Diagn. 10, 481-488. https://doi.org/10.1586/erm.10.17
- Li, W., Liu, H., Cheng, Z.J., Su, Y.H., Han, H.N., Zhang, Y., and Zhang, X.S. (2011). DNA methylation and histone modifications regulate de novo shoot regeneration in Arabidopsis by modulating WUSCHEL expression and auxin signaling. PLoS Genet. 7, e1002243. https://doi.org/10.1371/journal.pgen.1002243
- Lin, J.Y., Le, B.H., Chen, M., Henry, K.F., Hur, J., Hsieh, T.F., Chen, P.Y., Pelletier, J.M., Pellegrini, M., Fischer, R.L., et al. (2017). Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development. Proc. Natl. Acad. Sci. U. S. A. 114, E9730-E9739. https://doi.org/10.1073/pnas.1716758114
- Locke, W.J., Guanzon, D., Ma, C., Liew, Y.J., Duesing, K.R., Fung, K.Y.C., and Ross, J.P. (2019). DNA methylation cancer biomarkers: translation to the clinic. Front. Genet. 10, 1150. https://doi.org/10.3389/fgene.2019.01150
- Luo, C., Rivkin, A., Zhou, J., Sandoval, J.P., Kurihara, L., Lucero, J., Castanon, R., Nery, J.R., Pinto-Duarte, A., Bui, B., et al. (2018). Robust single-cell DNA methylome profiling with snmC-seq2. Nat. Commun. 9, 3824. https://doi.org/10.1038/s41467-018-06355-2
- Miura, F. and Ito, T. (2015). Highly sensitive targeted methylome sequencing by post-bisulfite adaptor tagging. DNA Res. 22, 13-18. https://doi.org/10.1093/dnares/dsu034
- Papareddy, R.K., Paldi, K., Paulraj, S., Kao, P., Lutzmayer, S., and Nodine, M.D. (2020). Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis. Genome Biol. 21, 251. https://doi.org/10.1186/s13059-020-02163-4
- Park, K., Frost, J.M., Adair, A.J., Kim, D.M., Yun, H., Brooks, J.S., Fischer, R.L., and Choi, Y. (2016). Optimized methods for the isolation of Arabidopsis female central cells and their nuclei. Mol. Cells 39, 768-775. https://doi.org/10.14348/molcells.2016.0209
- Parry, A., Rulands, S., and Reik, W. (2021). Active turnover of DNA methylation during cell fate decisions. Nat. Rev. Genet. 22, 59-66. https://doi.org/10.1038/s41576-020-00287-8
- Picard, C.L. and Gehring, M. (2017). Proximal methylation features associated with nonrandom changes in gene body methylation. Genome Biol. 18, 73. https://doi.org/10.1186/s13059-017-1206-2
- Raissig, M.T., Gagliardini, V., Jaenisch, J., Grossniklaus, U., and Baroux, C. (2013). Efficient and rapid isolation of early-stage embryos from Arabidopsis thaliana seeds. J. Vis. Exp. (76), 50371.
- Rich-Griffin, C., Stechemesser, A., Finch, J., Lucas, E., Ott, S., and Schafer, P. (2020). Single-cell transcriptomics: a high-resolution avenue for plant functional genomics. Trends Plant Sci. 25, 186-197. https://doi.org/10.1016/j.tplants.2019.10.008
- Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015). Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330. https://doi.org/10.1038/nature14248
- Salas, L.A., Wiencke, J.K., Koestler, D.C., Zhang, Z., Christensen, B.C., and Kelsey, K.T. (2018). Tracing human stem cell lineage during development using DNA methylation. Genome Res. 28, 1285-1295. https://doi.org/10.1101/gr.233213.117
- Smallwood, S.A., Lee, H.J., Angermueller, C., Krueger, F., Saadeh, H., Peat, J., Andrews, S.R., Stegle, O., Reik, W., and Kelsey, G. (2014). Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat. Methods 11, 817-820. https://doi.org/10.1038/nmeth.3035
- Stuart, T. and Satija, R. (2019). Integrative single-cell analysis. Nat. Rev. Genet. 20, 257-272. https://doi.org/10.1038/s41576-019-0093-7
- Xiang, D., Venglat, P., Tibiche, C., Yang, H., Risseeuw, E., Cao, Y., Babic, V., Cloutier, M., Keller, W., Wang, E., et al. (2011). Genome-wide analysis reveals gene expression and metabolic network dynamics during embryo development in Arabidopsis. Plant Physiol. 156, 346-356. https://doi.org/10.1104/pp.110.171702
- Yu, B., Dong, X., Gravina, S., Kartal, O., Schimmel, T., Cohen, J., Tortoriello, D., Zody, R., Hawkins, R.D., and Vijg, J. (2017). Genome-wide, single-cell DNA methylomics reveals increased non-CpG methylation during human oocyte maturation. Stem Cell Rep. 9, 397-407. https://doi.org/10.1016/j.stemcr.2017.05.026
- Zeng, Y. and Chen, T. (2019). DNA methylation reprogramming during mammalian development. Genes (Basel) 10, 257. https://doi.org/10.3390/genes10040257
피인용 문헌
- MET1-Dependent DNA Methylation Represses Light Signaling and Influences Plant Regeneration in Arabidopsis vol.44, pp.10, 2021, https://doi.org/10.14348/molcells.2021.0160