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Detection of Histone Modifications Associated with miRNAs

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1932))

Abstract

The posttranslational modifications of histones and miRNAs are key epigenetic mechanisms participating in the development, growth, and reproduction of plants. Recently, coordination between these two mechanisms has been demonstrated; each mechanism can be controlled by the other for the regulation of several biological processes. For example, the acetylation of histone H3, a key modification for chromatin remodeling and gene activation, has been linked to the actions of miRNA. In this work, we describe a method for the isolation and immunodetection of two posttranslational modifications in the residues of lysine 9 and 27 of H3, which have been associated with long miRNAs in plants.

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References

  1. Baubec T, Dinh HQ, Pecinka A, Rakic B, Rozhon W, Wohlrab B, von Haeseler A, Scheid OM (2010) Cooperation of multiple chromatin modifications can generate unanticipated stability of epigenetic states in Arabidopsis. Plant Cell 22:34–47

    Article  CAS  Google Scholar 

  2. Pikaard CS, Mittelsten Scheid O (2014) Epigenetic regulation in plants. Cold Spring Harb Perspect Biol 6:a019315

    Article  Google Scholar 

  3. De-la-Peña C, Nic-Can GI, Galaz-Ávalos RM, Avilez-Montalvo RN, Loyola-Vargas VM (2015) The role of chromatin modifications in somatic embryogenesis in plants. Front Plant Sci 6:635

    Article  Google Scholar 

  4. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233

    Article  CAS  Google Scholar 

  5. Djami-Tchatchou AT, Sanan-Mishra N, Ntushelo K, Dubery IA (2017) Functional roles of microRNAs in agronomically important plants—potential as targets for crop improvement and protection. Front Plant Sci 8:378

    Article  Google Scholar 

  6. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57:19–53

    Article  CAS  Google Scholar 

  7. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  CAS  Google Scholar 

  8. Zhao Y, Wang F, Juan L (2015) MicroRNA promoter identification in Arabidopsis using multiple histone markers. Biomed Res Int 2015:10

    Google Scholar 

  9. Baumberger N, Baulcombe DC (2005) Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci U S A 102:11928–11933

    Article  CAS  Google Scholar 

  10. Chen X, Lu L, Qian S, Scalf M, Smith LM, Zhong X (2018) Canonical and noncanonical actions of Arabidopsis histone deacetylases in ribosomal RNA processing. Plant Cell 30:134–152

    Article  CAS  Google Scholar 

  11. Wu L, Zhou H, Zhang Q, Zhang J, Ni F, Liu C, Qi Y (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38:465–475

    Article  CAS  Google Scholar 

  12. Jia X, Yan J, Tang G (2011) MicroRNA-mediated DNA methylation in plants. Front Biol 6:133–139

    Article  CAS  Google Scholar 

  13. Kim W, Benhamed M, Servet C, Latrasse D, Zhang W, Delarue M, Zhou D-X (2009) Histone acetyltransferase GCN5 interferes with the miRNA pathway in Arabidopsis. Cell Res 19:899

    Article  CAS  Google Scholar 

  14. Chen ZJ, Tian L (2007) Roles of dynamic and reversible histone acetylation in plant development and polyploidy. Biochim Biophys Acta 1769:295–307

    Article  CAS  Google Scholar 

  15. Wang X, Zheng G, Dong D (2015) Coordinated action of histone modification and microRNA regulations in human genome. Gene 570:277–281

    Article  CAS  Google Scholar 

  16. Jenuwein T, Allis CD (2001) Translating the histone code. Science 293:1074–1080

    Article  CAS  Google Scholar 

  17. Horn PJ, Peterson CL (2006) Heterochromatin assembly: a new twist on an old model. Chromosom Res 14:83–94

    Article  CAS  Google Scholar 

  18. Kuo M-H, Allis CD (1998) Roles of histone acetyltransferases and deacetylases in gene regulation. BioEssays 20:615–626

    Article  CAS  Google Scholar 

  19. Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci U S A 51:786–794

    Article  CAS  Google Scholar 

  20. Almeida MI, Reis RM, Calin GA (2011) MicroRNA history: discovery, recent applications, and next frontiers. Mutat Res 717:1–8

    Article  CAS  Google Scholar 

  21. Gosline SJC, Gurtan AM, JnBaptiste CK, Bosson A, Milani P, Dalin S, Matthews BJ, Yap YS, Sharp PA, Fraenkel E (2016) Elucidating MicroRNA regulatory networks using transcriptional, post-transcriptional, and histone modification measurements. Cell Rep 14:310–319

    Article  CAS  Google Scholar 

  22. Murashige T, Skoog F (1962) A revised medium for rapid growth and bio assays with tobacco tissue cultures. Physiol Plant 15:473–497

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by grants from Consejo Nacional de Ciencia y Tecnología (CONACYT) to CD (CB2016-285898 and FC2016-1515) and a CONACYT scholarship to SHC (271240).

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Correspondence to Clelia De-la-Peña .

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Hernández-Castellano, S., De-la-Peña, C. (2019). Detection of Histone Modifications Associated with miRNAs. In: de Folter, S. (eds) Plant MicroRNAs. Methods in Molecular Biology, vol 1932. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9042-9_25

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  • DOI: https://doi.org/10.1007/978-1-4939-9042-9_25

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9041-2

  • Online ISBN: 978-1-4939-9042-9

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