Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Nov 21;2(11):e1210.
doi: 10.1371/journal.pone.0001210.

Distinctive core histone post-translational modification patterns in Arabidopsis thaliana

Kangling Zhang  1 , Vaniyambadi V Sridhar, Jianhua Zhu, Avnish Kapoor, Jian-Kang Zhu
Affiliations

Distinctive core histone post-translational modification patterns in Arabidopsis thaliana

Kangling Zhang et al. PLoS One. .

Abstract

Post-translational modifications of histones play crucial roles in the genetic and epigenetic regulation of gene expression from chromatin. Studies in mammals and yeast have found conserved modifications at some residues of histones as well as non-conserved modifications at some other sites. Although plants have been excellent systems to study epigenetic regulation, and histone modifications are known to play critical roles, the histone modification sites and patterns in plants are poorly defined. In the present study we have used mass spectrometry in combination with high performance liquid chromatography (HPLC) separation and phospho-peptide enrichment to identify histone modification sites in the reference plant, Arabidopsis thaliana. We found not only modifications at many sites that are conserved in mammalian and yeast cells, but also modifications at many sites that are unique to plants. These unique modifications include H4 K20 acetylation (in contrast to H4 K20 methylation in non-plant systems), H2B K6, K11, K27 and K32 acetylation, S15 phosphorylation and K143 ubiquitination, and H2A K144 acetylation and S129, S141 and S145 phosphorylation, and H2A.X S138 phosphorylation. In addition, we found that lysine 79 of H3 which is highly conserved and modified by methylation and plays important roles in telomeric silencing in non-plant systems, is not modified in Arabidopsis. These results suggest distinctive histone modification patterns in plants and provide an invaluable foundation for future studies on histone modifications in plants.

PubMed Disclaimer

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Identification of H2A modification sites.
A. MS/MS spectrum of doubly-charged precursor ion at m/z 411.72 demonstrating phosphorylation at S145 in the peptide SPVK145 pSPK of H2A.7. B. MS/MS spectrum of doubly-charged precursor ion at m/z 432.69 demonstrating phosphorylation at S145 and acetylation at K144 in peptide SPV144Kac 145 pSPK of H2A.7. C. MS/MS spectrum of doubly-charged precursor ion at m/z 582.88 demonstrating phosphorylation at S145 and acetylation at K144 in peptide ATKSPV144Kac 145 pSPK of H2A.7. D. MS/MS spectrum of doubly-charged precursor ion at m/z 601.78 demonstrating phosphorylation at S141 and S145 in peptide ATK141 pSPVK145 pSPK of H2A.7. E. MS/MS spectrum of the doubly-charged precursor ion at m/z 584.80 demonstrating phosphorylation at S129 in peptide K129 pSATKPAEEK of H2A.7. F. MS/MS spectrum of the doubly-charged precursor ion at m/z 456.24 demonstrating phosphorylation at S145 and acetylation at K144 in the peptide ASAT144Kac 145 pSPK of H2A.5. G. MS/MS spectrum of the doubly-charged precursor ion at m/z 666.81 demonstrating phosphorylation at S138 in the peptide NKGDIGSA138 pSQEF of H2AX. H. Sequence alignment of H2A isoforms (H2A.1-H2A.8). K in green color: acetylation; S in red color: phosphorylation.
Figure 2
Figure 2. Identification of H2B modification sites.
A. MS/MS spectrum of the doubly-charged precursor ion at m/z 471.69 showing H2B acetylation site at K6 in the peptide AE6KacKPAEK. B. MS/MS spectrum of the doubly-charged precursor ion at m/z 443.24 showing H2B acetylation site at K27 in the peptide AE27KacAPAEK. C. MS/MS spectrum of the doubly-charged precursor ion at m/z 550.88 for determining H2B acetylation site at K27 in the peptide SKAE27KacAPAEK. D. MS/MS spectrum of the triply-charged precursor ion at m/z 304.15 for determining H2B acetylation site at K32 in the peptide APAE32KacKPK. E. MS/MS spectrum of the quadruply-charged precursor ion at m/z 456.01 for determining H2B.1 acetylation site at K11 in the peptide KPAE11KacKPAAEKPVEEK. F. MS/MS spectrum of the quadruply-charged precursor ion at m/z 460.01 for determining H2B.2 acetylation site at K11 in the peptide KPAE11KacKPASEKPVEEK. G. MS/MS spectrum of the quadruply-charged precursor ion at m/z 552.70 for determining H2B.2 acetylation sites at K6 and K11 in the peptide AE6KacKPAE11KacKPASEKPVEEK. H. MS/MS spectrum of the doubly-charged precursor ion at m/z 661.37 for determining H2B.2 phosphorylation site in the peptide KPA14 pSEKPVEEK. I. Sequence alignment of Arabidopsis H2B (H2B.1 and H2B.2). K in green color: acetylation; S in red color: phosphorylation.
Figure 3
Figure 3. Identification of H3 methylation sites.
A. ESI mass spectrum showing mono- (m/z 465.25), di- (m/z 472.26) and tri-methylation (m/z 479.26) at K27 of H3.1. B. ESI mass spectrum showing mono- (m/z 480.25), di- (m/z 487.26) and tri-methylation (m/z 494.27) at K27 of H3.2. C. MS/MS spectrum of the doubly-charged precursor ion at m/z 479.26 for determining tri-methylation at K27 of H3.1. D. MS/MS spectrum of the doubly-charged precursor ion at m/z 494.27 for determining tri-methylation at K27 of H3.2. E. ESI-MS spectrum showing mono- (m/z 675.34), di- (m/z 682.36) and tri-methylation (m/z 689.36) at K36 in H3.2 and tri-methylation (m/z 674.33) at K36 of H3.1. F. MS/MS spectrum of the doubly-charged precursor ion at m/z 689.36 for determining tri-methylation at K36 of H3.2. G. MALDI-TOF mass spectrum showing non- (m/z 704.4) mono- (m/z 718.4), di- (m/z 732.4) and tri-methylation (746.4) at K4. H. MALDI-TOF mass spectrum showing di-methylation (m/z 929.6) at K9, acetylation at K14 or tri-methylation (m/z 943.6) at K9, acetylation at K14 and mono-methylation (m/z 957.6) at K9. I. MALDI-TOF mass spectrum showing no methylation at K79. J. Sequence alignment of H3 isoforms (H3.1 and H3.2). K in green color: acetylation; K in yellow color: methylation; K in olive color: both acetylation and methylation. Note: All peptides in A–F were released from trypsin digestion and peptides in G–I were released from Arg-C digestion.
Figure 4
Figure 4. Identification of H4 acetylation sites at K20.
A. MALDI-TOF mass spectrum of HPLC fraction of Arg_C digest containing K20 peptide. B. MALD-MS/MS spectrum of the precursor ion at m/z 1864.14 for determining acetylation at K20. C. Chromatogram of the ion at m/z 1822.10 (doubly-charged ion at m/z 911.55). D. Chromatogram of the ion at m/z 1864.11 (doubly-charged ion at m/z 932.55). E. Sequence alignment of Arabidopsis H4. K in green color: acetylation.
See this image and copyright information in PMC

References

    1. Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature. 1997;389:251–260. - PubMed
    1. Tremethick DJ. Higher-order structures of chromatin: the elusive 30 nm fiber. Cell. 2007;128:651–654. - PubMed
    1. Gilbert N, Boyle S, Fiehler H, Woodfine K, Carter NP, et al. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fiber. Mol. Cell. 2004;15:844–846. - PubMed
    1. Jiang G, Yang F, Sanchez C, Ehrlich M. Histone modification in constitutive heterochromatin versus unexpressed euchromatin in human cells. J. Cell Biochem. 2004;93:286–300. - PubMed
    1. Jenuwein T, Allis CD. Translating the histone code. Science. 2001;293:1074–1080. - PubMed

Publication types