TY - JOUR
T1 - Relationship between nucleosome positioning and DNA methylation
AU - Chodavarapu, Ramakrishna K.
AU - Feng, Suhua
AU - Bernatavichute, Yana V.
AU - Chen, Pao Yang
AU - Stroud, Hume
AU - Yu, Yanchun
AU - Hetzel, Jonathan A.
AU - Kuo, Frank
AU - Kim, Jin
AU - Cokus, Shawn J.
AU - Casero, David
AU - Bernal, Maria
AU - Huijser, Peter
AU - Clark, Amander T.
AU - Krämer, Ute
AU - Merchant, Sabeeha S.
AU - Zhang, Xiaoyu
AU - Jacobsen, Steven E.
AU - Pellegrini, Matteo
N1 - Funding Information:
Acknowledgements We thank members of our laboratories for input and guidance, and the Department of Energy, Institute for Genomics and Proteomics for support. R.K.C. is supported by NIH training grant GM07104. S.F. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation. P.-Y.C. is funded by Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research at UCLA. M.B. was supported by an Alexander-von-Humboldt Fellowship and U.K. by a Heisenberg Fellowship. X.Z. was supported by a Faculty Research Grant (JR-040) from the University of Georgia. Research was supported by an Innovation Award from the Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research at UCLA, NIH grants GM60398 and GM42143, and NSF Plant Genome Research Program #0701745. S.E.J. is an Investigator of the Howard Hughes Medical Institute.
PY - 2010/7/15
Y1 - 2010/7/15
N2 - Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer 1,2. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana using massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified 10-base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. These results indicate that nucleosome positioning influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA. We also observed similar trends in human nucleosomal DNA, indicating that the relationships between nucleosomes and DNA methyltransferases are conserved. Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNApolymerase II (Pol II) was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity. DNA methylation is also enriched on exons, consistent with the targeting of DNA methylation to nucleosomes, and suggesting a role forDNAmethylation in exon definition.
AB - Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer 1,2. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana using massively parallel sequencing of mononucleosomes. By combining this data with profiles of DNA methylation at single base resolution, we identified 10-base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA. These results indicate that nucleosome positioning influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA. We also observed similar trends in human nucleosomal DNA, indicating that the relationships between nucleosomes and DNA methyltransferases are conserved. Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNApolymerase II (Pol II) was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity. DNA methylation is also enriched on exons, consistent with the targeting of DNA methylation to nucleosomes, and suggesting a role forDNAmethylation in exon definition.
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U2 - 10.1038/nature09147
DO - 10.1038/nature09147
M3 - Article
C2 - 20512117
AN - SCOPUS:77954659099
SN - 0028-0836
VL - 466
SP - 388
EP - 392
JO - Nature
JF - Nature
IS - 7304
ER -