Click here to close
Hello! We notice that you are using Internet Explorer, which is not supported by Xenbase and may cause the site to display incorrectly.
We suggest using a current version of Chrome,
FireFox, or Safari.
J Radiat Res
2018 Mar 01;592:108-115. doi: 10.1093/jrr/rrx068.
Show Gene links
Show Anatomy links
Circular dichroism spectroscopic study on structural alterations of histones induced by post-translational modifications in DNA damage responses: lysine-9 methylation of H3.
Izumi Y
,
Matsuo K
,
Fujii K
,
Yokoya A
,
Taniguchi M
,
Namatame H
.
???displayArticle.abstract???
We report the global structural alterations in histone H3 proteins induced by lysine-9 mono-, di- and trimethylation, which are part of the critical post-translational modifications for DNA damage responses, identified using synchrotron radiation circular dichroism (CD) spectroscopy. Compared with unmodified H3, mono- and dimethylation increases the number of α-helices and decreases the numbers of β-strands, while trimethylation decreases the α-helix content and increases the β-strand content. Comparison of the secondary-structure contents of these histone H3 proteins suggests that the methylation-induced structural alterations occur at residues not only close to but also distant from the methylated sites. Such global structural alterations may regulate the interactions of methylated histones with other molecules, such as histone-binding proteins in DNA damage repair processes.
Fig. 1. (Upper panel) CD spectra of H3K9me0 (black), H3K9me1 (red), H3K9me2 (green) and H3K9me3 (blue). (Lower panel) Molar absorption coefficient (ε) of H3K9me0.
Fig. 2. Comparison of secondary-structure contents of H3K9me0 (me0), H3K9me1 (me1), H3K9me2 (me2) and H3K9me3 (me3) normalized to a total content of 100%.
Fig. 3. Sequence-based secondary structures of H3K9me0 (me0), H3K9me1 and H3K9me2 (me1/2), and H3K9me3 (me3) obtained by the VUVCD–NN combination method. The α-helix, β-strand/extended, and coil structures are shown by cylinders, arrows and lines, respectively. The symbol KCm in the sequence represents methylated aminoethylcysteine inserted instead of methylated lysine (see Materials and Methods for details). Note that the 9th and 110th residues of H3K9me0 are lysine (K) and cysteine (C), respectively, which are different from those of methylated H3 samples.
Fig. 4. Schematic view of the proposed structural alteration mechanism. The N-terminal tail region, which forms an unordered structure, is shown as curved lines. Cylinders, arrows and circles represent α-helices, β-strands and methyl groups, respectively. Secondary structures formed by M1 residues (for details, see Possible structural alteration mechanism induced by H3K9 methylation in solution) are shown in gray and the others are shown in white. Turn structures are omitted. (a) A model of H3K9me0. (b) Monomethylated H3 before structural alteration. (c) The methylated N-terminal tail interacts with M1 residues and as a result, induces structural changes from β-strands to α-helices. (d) The trimethylated N-terminal tail steps away from the M1 residues, after which the structure of the M1 residues would revert to normal (α-helices → β-strands). (e) The N-terminal tail interacts with domain(s) other than M1 residues and induces structural changes from α-helices to β-strands.
Ayrapetov,
DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin.
2014, Pubmed
Ayrapetov,
DNA double-strand breaks promote methylation of histone H3 on lysine 9 and transient formation of repressive chromatin.
2014,
Pubmed
Bannister,
Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain.
2001,
Pubmed
Barthe,
Dynamic and structural characterization of a bacterial FHA protein reveals a new autoinhibition mechanism.
2009,
Pubmed
Cao,
Histone modifications in DNA damage response.
2016,
Pubmed
D'Anna,
Conformational changes of histone ARE(F3, III).
1974,
Pubmed
D'Anna,
A histone cross-complexing pattern.
1974,
Pubmed
Davey,
Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution.
2002,
Pubmed
,
Xenbase
Gloss,
Decreasing the basicity of the active site base, Lys-258, of Escherichia coli aspartate aminotransferase by replacement with gamma-thialysine.
1995,
Pubmed
Gong,
Mammalian DNA repair: HATs and HDACs make their mark through histone acetylation.
2013,
Pubmed
Greenfield,
Computed circular dichroism spectra for the evaluation of protein conformation.
1969,
Pubmed
Göransson,
The conserved glu in the cyclotide cycloviolacin O2 has a key structural role.
2009,
Pubmed
Hunt,
Histone modifications and DNA double-strand break repair after exposure to ionizing radiations.
2013,
Pubmed
Izumi,
Secondary Structure Alterations of Histones H2A and H2B in X-Irradiated Human Cancer Cells: Altered Histones Persist in Cells for at Least 24 Hours.
2015,
Pubmed
Izumi,
Structure Change from β-Strand and Turn to α-Helix in Histone H2A-H2B Induced by DNA Damage Response.
2016,
Pubmed
Izumi,
DNA damage response induces structural alterations in histone H3-H4.
2017,
Pubmed
Jacobs,
Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3.
2001,
Pubmed
Jones,
Protein secondary structure prediction based on position-specific scoring matrices.
1999,
Pubmed
Kern,
Structure of a transiently phosphorylated switch in bacterial signal transduction.
,
Pubmed
Lachner,
Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins.
2001,
Pubmed
Lu,
The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure.
2008,
Pubmed
Luger,
Crystal structure of the nucleosome core particle at 2.8 A resolution.
1997,
Pubmed
Matsuo,
Improved estimation of the secondary structures of proteins by vacuum-ultraviolet circular dichroism spectroscopy.
2005,
Pubmed
Matsuo,
Optical cell with a temperature-control unit for a vacuum-ultraviolet circular dichroism spectrophotometer.
2003,
Pubmed
Matsuo,
Improved sequence-based prediction of protein secondary structures by combining vacuum-ultraviolet circular dichroism spectroscopy with neural network.
2008,
Pubmed
Matsuo,
Secondary-structure analysis of proteins by vacuum-ultraviolet circular dichroism spectroscopy.
2004,
Pubmed
McPhie,
Circular dichroism studies on proteins in films and in solution: estimation of secondary structure by g-factor analysis.
2001,
Pubmed
Miles,
Synchrotron radiation circular dichroism spectroscopy of proteins and applications in structural and functional genomics.
2006,
Pubmed
Nakayama,
Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly.
2001,
Pubmed
Nielsen,
Rb targets histone H3 methylation and HP1 to promoters.
2001,
Pubmed
Pandita,
Chromatin remodeling finds its place in the DNA double-strand break response.
2009,
Pubmed
Pinheiro,
Prdm3 and Prdm16 are H3K9me1 methyltransferases required for mammalian heterochromatin integrity.
2012,
Pubmed
Polo,
Reshaping chromatin after DNA damage: the choreography of histone proteins.
2015,
Pubmed
Price,
Chromatin remodeling at DNA double-strand breaks.
2013,
Pubmed
Sasaki,
Heterochromatin controls γH2A localization in Neurospora crassa.
2014,
Pubmed
Simon,
The site-specific installation of methyl-lysine analogs into recombinant histones.
2007,
Pubmed
,
Xenbase
Smerdon,
DNA repair and the role of chromatin structure.
1991,
Pubmed
Soria,
Prime, repair, restore: the active role of chromatin in the DNA damage response.
2012,
Pubmed
Sreerama,
Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy.
1999,
Pubmed
Sreerama,
Estimation of protein secondary structure from circular dichroism spectra: comparison of CONTIN, SELCON, and CDSSTR methods with an expanded reference set.
2000,
Pubmed
Tachibana,
G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis.
2002,
Pubmed
Tian,
Mitochondrial Stress Induces Chromatin Reorganization to Promote Longevity and UPR(mt).
2016,
Pubmed
Timms,
Structural insights into the recovery of aldolase activity in N-acetylneuraminic acid lyase by replacement of the catalytically active lysine with γ-thialysine by using a chemical mutagenesis strategy.
2013,
Pubmed
Voigt,
Histone tails: ideal motifs for probing epigenetics through chemical biology approaches.
2011,
Pubmed
Wu,
Interaction of BARD1 and HP1 Is Required for BRCA1 Retention at Sites of DNA Damage.
2015,
Pubmed
van Attikum,
Crosstalk between histone modifications during the DNA damage response.
2009,
Pubmed
