Relationship between nucleosome positioning and DNA methylation

被引：532

作者：

Chodavarapu, Ramakrishna K. ^{[1
]}

Feng, Suhua ^{[1
,2
]}

Bernatavichute, Yana V. ^{[1
,3
]}

Chen, Pao-Yang ^{[1
]}

Stroud, Hume ^{[1
]}

Yu, Yanchun ^{[4
]}

Hetzel, Jonathan A. ^{[1
]}

Kuo, Frank ^{[1
]}

Kim, Jin ^{[1
]}

Cokus, Shawn J. ^{[1
]}

Casero, David ^{[1
]}

Bernal, Maria ^{[5
]}

Huijser, Peter ^{[6
]}

Clark, Amander T. ^{[1
,7
]}

Kraemer, Ute ^{[5
]}

Merchant, Sabeeha S. ^{[3
,8
]}

Zhang, Xiaoyu ^{[4
]}

Jacobsen, Steven E. ^{[1
,2
,3
]}

Pellegrini, Matteo ^{[1
,3
]}

机构：

[1] Univ Calif Los Angeles, Dept Mol Cell & Dev Biol, Los Angeles, CA 90095 USA

[2] Univ Calif Los Angeles, Howard Hughes Med Inst, Los Angeles, CA 90095 USA

[3] Univ Calif Los Angeles, Inst Mol Biol, Los Angeles, CA 90095 USA

[4] Univ Georgia, Dept Plant Biol, Athens, GA 30602 USA

[5] Univ Heidelberg, D-69120 Heidelberg, Germany

[6] Max Planck Inst Plant Breeding Res, Dept Mol Plant Genet, D-50829 Cologne, Germany

[7] Univ Calif Los Angeles, Eli & Edythe Broad Ctr Regenerat Med & Stem Cell, Los Angeles, CA 90095 USA

[8] Univ Calif Los Angeles, Dept Chem & Biochem, Los Angeles, CA 90095 USA

来源：

NATURE | 2010年 / 466卷 / 7304期

关键词：

GENOME; ORGANIZATION; PLANTS; RESOLUTION; SEQUENCE; PARTICLE; ANIMALS; REVEALS; H2A.Z; MARKS;

D O I：

10.1038/nature09147

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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. RNA polymerase 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 for DNA methylation in exon definition.

引用

页码：388 / 392

页数：5

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