RT Journal Article
SR Electronic
T1 DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 080531
DO 10.1101/080531
A1 Ling Zhang
A1 Wen Jun Xie
A1 Sirui Liu
A1 Luming Meng
A1 Chan Gu
A1 Yi Qin Gao
YR 2016
UL http://biorxiv.org/content/early/2016/10/13/080531.abstract
AB It has been thought that DNA methylation can remodel chromatin structure, and modulate the transcriptional level of genes by altering chromatin density and accessibility of DNA to cellular machinery, which is still largely unknown. Here we report that both the long-range and local correlations in DNA methylation reflect the spatial organization of chromatin. We discover a long-range power law correlation that implies a scale-free property of DNA methylation and the cell-class-specific scaling exponents reflect the global change of DNA methylation landscape during cellular differentiation or oncogenesis which can be further related with chromatin structure. By analyzing on the local correlation which correlates with nucleosome positioning, Hi-C data and molecular modeling, we show that partially methylated domain (PMD) prefers a compact structure. We further demonstrate that chromatin structures reflect the DNA sequence property and are intimately related to gene expression. Our study therefore provides a novel view of the spatial organization of chromatin structure from a perspective of DNA methylation.