5B2J

Human nucleosome containing CpG methylated DNA

Summary for 5B2J

• Entry DOI: 10.2210/pdb5b2j/pdb
• Related: 5B2I
• Descriptor: Histone H3.1, Histone H4, Histone H2A type 1-B/E, ... (7 entities in total)
• Functional Keywords: chromatin, epigenetics, histone, transcription, transcription-dna complex, transcription/dna
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 10
• Total formula weight: 202725.49

Authors

Fujii, Y.,Wakamori, M.,Umehara, T.,Yokoyama, S. (deposition date: 2016-01-18, release date: 2016-06-15, Last modification date: 2023-11-08)

Primary citation

Fujii, Y.,Wakamori, M.,Umehara, T.,Yokoyama, S.
Crystal structure of human nucleosome core particle containing enzymatically introduced CpG methylation.
Febs Open Bio, 6:498-514, 2016

PubMed Abstract: Cytosine methylation, predominantly of the CpG sequence in vertebrates, is one of the major epigenetic modifications crucially involved in the control of gene expression. Due to the difficulty of reconstituting site-specifically methylated nucleosomal DNA at crystallization quality, most structural analyses of CpG methylation have been performed using chemically synthesized oligonucleotides, There has been just one recent study of nucleosome core particles (NCPs) reconstituted with nonpalindromic human satellite 2-derived DNAs. Through the preparation of a 146-bp palindromic α-satellite-based nucleosomal DNA containing four CpG dinucleotide sequences and its enzymatic methylation and restriction, we reconstituted a 'symmetric' human CpG-methylated nucleosome core particle (NCP). We solved the crystal structures of the CpG-methylated and unmodified NCPs at 2.6 and 3.0 Å resolution, respectively. We observed the electron densities of two methyl groups, among the eight 5-methylcytosines introduced in the CpG-fully methylated NCP. There were no obvious structural differences between the CpG-methylated 'symmetric NCP' and the unmodified NCP. The preparation of a crystallization-grade CpG-methylated NCP provides a platform for the analysis of CpG-methyl reader and eraser proteins.

PubMed: 27419055
DOI: 10.1002/2211-5463.12064

Experimental method

X-RAY DIFFRACTION (2.6 Å)