Abstract
Nucleosome occupancy in promoter and genic regions can severely influence the transcription levels. Few methods have been established to investigate the nucleosome occupancy along the DNA. In this chapter we describe a detailed protocol to analyze the nucleosome occupancy at a specific locus using MNase-pPCR.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A 109(32):E2183–2191. doi:10.1073/pnas.1209329109, 1209329109[pii]
Farrona S, Hurtado L, Bowman JL, Reyes JC (2004) The Arabidopsis thaliana SNF2 homolog AtBRM controls shoot development and flowering. Development 131(20):4965–4975. doi:10.1242/dev.01363
Sang Y, Silva-Ortega CO, Wu S, Yamaguchi N, Wu MF, Pfluger J, Gillmor CS, Gallagher KL, Wagner D (2012) Mutations in two non-canonical Arabidopsis SWI2/SNF2 chromatin remodeling ATPases cause embryogenesis and stem cell maintenance defects. Plant J. doi:10.1111/tpj.12009
Han SK, Sang Y, Rodrigues A, Biol F, Wu MF, Rodriguez PL, Wagner D (2012) The SWI2/SNF2 chromatin remodeling ATPase BRAHMA represses abscisic acid responses in the absence of the stress stimulus in Arabidopsis. Plant Cell 24(12):4892–4906. doi:10.1105/tpc.112.105114
Jerzmanowski A (2007) SWI/SNF chromatin remodeling and linker histones in plants. Biochim Biophys Acta 1769(5-6):330–345. doi:10.1016/j.bbaexp.2006.12.003
Zentner GE, Henikoff S (2012) Surveying the epigenomic landscape, one base at a time. Genome Biol 13(10):250. doi:10.1186/gb4051
Simon JM, Giresi PG, Davis IJ, Lieb JD (2013) A detailed protocol for formaldehyde-assisted isolation of regulatory elements (FAIRE). Current protocols in molecular biology Chapter 21:Unit21.26. doi:10.1002/0471142727.mb2126s102
Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD (2007) FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res 17(6):877–885. doi:10.1101/gr.5533506
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ (2013) Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10(12):1213–1218. doi:10.1038/nmeth.2688, nmeth.2688[pii]
Weintraub H, Groudine M (1976) Chromosomal subunits in active genes have an altered conformation. Science 193(4256):848–856
Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132(2):311–322. doi:10.1016/j.cell.2007.12.014, S0092-8674(07)01613-3[pii]
Berr A, Shafiq S, Shen WH (2011) Histone modifications in transcriptional activation during plant development. Biochim Biophys Acta 1809(10):567–576. doi:10.1016/j.bbagrm.2011.07.001
Alexander M, Heppel LA, Hurwitz J (1961) The purification and properties of micrococcal nuclease. J Biol Chem 236:3014–3019
Clark DJ, Felsenfeld G (1991) Formation of nucleosomes on positively supercoiled DNA. EMBO J 10(2):387–395
Eberharter A, Becker PB (2002) Histone acetylation: a switch between repressive and permissive chromatin—second in review series on chromatin dynamics. Embo Rep 3(3):224–229. doi:10.1093/embo-reports/kvf053
Kwon CS, Lee D, Choi G, Chung WI (2009) Histone occupancy-dependent and -independent removal of H3K27 trimethylation at cold-responsive genes in Arabidopsis. Plant J 60(1):112–121. doi:10.1111/j.1365-313X.2009.03938.x, TPJ3938[pii]
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer Science+Business Media New York
About this protocol
Cite this protocol
Kaster, M., Laubinger, S. (2016). Determining Nucleosome Position at Individual Loci After Biotic Stress Using MNase-qPCR. In: Duque, P. (eds) Environmental Responses in Plants. Methods in Molecular Biology, vol 1398. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3356-3_29
Download citation
DOI: https://doi.org/10.1007/978-1-4939-3356-3_29
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-3354-9
Online ISBN: 978-1-4939-3356-3
eBook Packages: Springer Protocols