The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA
Open accessAbstract
The maize genome, with its large complement of transposons and repeats, is a paradigm for the study of epigenetic mechanisms such as paramutation and imprinting. Here, we present the genome-wide map of cytosine methylation for two maize inbred lines, B73 and Mo17. CG (65%) and CHG (50%) methylation (where H = A, C, or T) is highest in transposons, while CHH (5%) methylation is likely guided by 24-nt, but not 21-nt, small interfering RNAs (siRNAs). Correlations with methylation patterns suggest that CG methylation in exons (8%) may deter insertion of Mutator transposon insertion, while CHG methylation at splice acceptor sites may inhibit RNA splicing. Using the methylation map as a guide, we used low-coverage sequencing to show that parental methylation differences are inherited by recombinant inbred lines. However, frequent methylation switches, guided by siRNA, persist for up to eight generations, suggesting that epigenetic inheritance resembling paramutation is much more common than previously supposed. The methylation map will provide an invaluable resource for epigenetic studies in maize.
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Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Transposable elements and the epigenetic regulation of the genome
Slotkin, R. K., & Martienssen, R. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2072 · Cited by 2,044
Self-citationCTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
Shukla, S., Kavak, E., Gregory, M., Imashimizu, M., Shutinoski, B., Kashlev, M., Oberdoerffer, P., Sandberg, R., & Oberdoerffer, S. (2011) · Nature · doi:10.1038/nature10442 · Cited by 973
A Role for RNAi in the Selective Correction of DNA Methylation Defects
Teixeira, F. K., Heredia, F., Sarazin, A., Roudier, F., Boccara, M., Ciaudo, C., Cruaud, C., Poulain, J., Berdasco, M., Fraga, M. F., et al. (2009) · Science · doi:10.1126/science.1165313 · Cited by 358
Epigenomic consequences of immortalized plant cell suspension culture
Tanurdzic, M., Vaughn, M. W., Jiang, H., Lee, T.-J., Slotkin, R. K., Sosinski, B., Thompson, W. F., Doerge, R. W., & Martienssen, R. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060302 · Cited by 218
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Transgenerational epigenetic inheritance: myths and mechanisms
Heard, E., & Martienssen, R. A. (2014) · Cell · doi:10.1016/j.cell.2014.02.045 · Cited by 1,864
Self-citationWidespread natural variation of DNA methylation within angiosperms
Niederhuth, C. E., Bewick, A. J., Ji, L., Alabady, M. S., Kim, K. D., Li, Q., Rohr, N. A., Rambani, A., Burke, J. M., Udall, J. A., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-1059-0 · Cited by 566
Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm
Ong-Abdullah, M., Ordway, J. M., Jiang, N., Ooi, S.-E., Kok, S.-Y., Sarpan, N., Azimi, N., Hashim, A. T., Ishak, Z., Rosli, S. K., et al. (2015) · Nature · doi:10.1038/nature15365 · Cited by 521
Self-citationGene body DNA methylation in plants
Bewick, A. J., & Schmitz, R. J. (2017) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2016.12.007 · Cited by 409
Profiling genome-wide DNA methylation
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Metadata
- Authors
- Regulski, M., Lu, Z., Kendall, J., Donoghue, M. T. A., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., McCombie, W. R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., & Martienssen, R. A.
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2013-06-05
- Volume
- 23
- Issue
- 10
- Pages
- 1651-1662
- ISSN
- 1088-9051 (ISSN-L)
- OpenAlex
- W2104618447
- Cited by
- 268
- References
- 6
- Type
- posted content
- Language
- en
- Open access
- bronze
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- Regulski, M., Lu, Z., Kendall, J., Donoghue, M. T. A., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., McCombie, W. R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., & Martienssen, R. A. (2013). The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research. https://doi.org/10.1101/gr.153510.112
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