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Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane.

Moraes I, Yuan ZF, Liu S, Souza GM, Garcia BA, Casas-Mollano JA - PLoS ONE (2015)

Bottom Line: As a result, modifications, alone or in combination, are important determinants of chromatin states.Several modifications conserved in other plants, and also novel modified residues, were identified.Additionally, the sub-nuclear localization of some well-studied modifications (i.e., H3K4me3, H3K9me2, H3K27me3, H3K9ac, H3T3ph) is described and compared to other plant species.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.

ABSTRACT
Histones are the main structural components of the nucleosome, hence targets of many regulatory proteins that mediate processes involving changes in chromatin. The functional outcome of many pathways is "written" in the histones in the form of post-translational modifications that determine the final gene expression readout. As a result, modifications, alone or in combination, are important determinants of chromatin states. Histone modifications are accomplished by the addition of different chemical groups such as methyl, acetyl and phosphate. Thus, identifying and characterizing these modifications and the proteins related to them is the initial step to understanding the mechanisms of gene regulation and in the future may even provide tools for breeding programs. Several studies over the past years have contributed to increase our knowledge of epigenetic gene regulation in model organisms like Arabidopsis, yet this field remains relatively unexplored in crops. In this study we identified and initially characterized histones H3 and H4 in the monocot crop sugarcane. We discovered a number of histone genes by searching the sugarcane ESTs database. The proteins encoded correspond to canonical histones, and their variants. We also purified bulk histones and used them to map post-translational modifications in the histones H3 and H4 using mass spectrometry. Several modifications conserved in other plants, and also novel modified residues, were identified. In particular, we report O-acetylation of serine, threonine and tyrosine, a recently identified modification conserved in several eukaryotes. Additionally, the sub-nuclear localization of some well-studied modifications (i.e., H3K4me3, H3K9me2, H3K27me3, H3K9ac, H3T3ph) is described and compared to other plant species. To our knowledge, this is the first report of histones H3 and H4 as well as their post-translational modifications in sugarcane, and will provide a starting point for the study of chromatin regulation in this crop.

No MeSH data available.


Related in: MedlinePlus

Detection of H3K4 methylation in sugarcane.(A) MS/MS fragmentation pattern recorded on the [M+2H]2+ ion at m/z 415.7401 that matches the histone H3 peptide (residues 3–8) prTKme1QTAR containing monomethyl K4. (B) MS/MS spectrum of the doubly-charged ion at m/z 394.7348 corresponding to the H3 peptide prTKme2QTAR. (C) MS/MS spectrum recorded on the [M+2H]2+ ion (m/z 401.7426) that corresponds to the peptide prTKme3QTAR. Sequence of the peptide and the measured mass of the precursor ion are shown in the figure inset. N-terminal propionylation, product of the chemical derivatization, is indicated by pr.
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pone.0134586.g004: Detection of H3K4 methylation in sugarcane.(A) MS/MS fragmentation pattern recorded on the [M+2H]2+ ion at m/z 415.7401 that matches the histone H3 peptide (residues 3–8) prTKme1QTAR containing monomethyl K4. (B) MS/MS spectrum of the doubly-charged ion at m/z 394.7348 corresponding to the H3 peptide prTKme2QTAR. (C) MS/MS spectrum recorded on the [M+2H]2+ ion (m/z 401.7426) that corresponds to the peptide prTKme3QTAR. Sequence of the peptide and the measured mass of the precursor ion are shown in the figure inset. N-terminal propionylation, product of the chemical derivatization, is indicated by pr.

Mentions: Lysine and arginine methylation were also detected in several positions including the globular domain of histones H3.1 and H3.3 variant (Fig 1A). Methylation of lysines 4, 9, 14, 18, 23, 27 and 36 were found in the N-terminal tail whereas lysine 53 and 56 and arginine 42 could be detected in the globular domain. In the case of H3K4 methylation, the peptide prTKme1QTAR (H3 residues 3–8) monomethylated at H3K4 was identified from the MS/MS fragmentation pattern of the [M+2H]2+ ion at m/z 415.7401 (Fig 4A). Two other MS/MS spectra from the doubly-charged ions at m/z 394.7348 and m/z 401.7426 were also found to correspond to the peptide TKQTAR where K4 is di- and trimethylated, respectively (Fig 4B and 4C).


Analysis of Histones H3 and H4 Reveals Novel and Conserved Post-Translational Modifications in Sugarcane.

Moraes I, Yuan ZF, Liu S, Souza GM, Garcia BA, Casas-Mollano JA - PLoS ONE (2015)

Detection of H3K4 methylation in sugarcane.(A) MS/MS fragmentation pattern recorded on the [M+2H]2+ ion at m/z 415.7401 that matches the histone H3 peptide (residues 3–8) prTKme1QTAR containing monomethyl K4. (B) MS/MS spectrum of the doubly-charged ion at m/z 394.7348 corresponding to the H3 peptide prTKme2QTAR. (C) MS/MS spectrum recorded on the [M+2H]2+ ion (m/z 401.7426) that corresponds to the peptide prTKme3QTAR. Sequence of the peptide and the measured mass of the precursor ion are shown in the figure inset. N-terminal propionylation, product of the chemical derivatization, is indicated by pr.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4520453&req=5

pone.0134586.g004: Detection of H3K4 methylation in sugarcane.(A) MS/MS fragmentation pattern recorded on the [M+2H]2+ ion at m/z 415.7401 that matches the histone H3 peptide (residues 3–8) prTKme1QTAR containing monomethyl K4. (B) MS/MS spectrum of the doubly-charged ion at m/z 394.7348 corresponding to the H3 peptide prTKme2QTAR. (C) MS/MS spectrum recorded on the [M+2H]2+ ion (m/z 401.7426) that corresponds to the peptide prTKme3QTAR. Sequence of the peptide and the measured mass of the precursor ion are shown in the figure inset. N-terminal propionylation, product of the chemical derivatization, is indicated by pr.
Mentions: Lysine and arginine methylation were also detected in several positions including the globular domain of histones H3.1 and H3.3 variant (Fig 1A). Methylation of lysines 4, 9, 14, 18, 23, 27 and 36 were found in the N-terminal tail whereas lysine 53 and 56 and arginine 42 could be detected in the globular domain. In the case of H3K4 methylation, the peptide prTKme1QTAR (H3 residues 3–8) monomethylated at H3K4 was identified from the MS/MS fragmentation pattern of the [M+2H]2+ ion at m/z 415.7401 (Fig 4A). Two other MS/MS spectra from the doubly-charged ions at m/z 394.7348 and m/z 401.7426 were also found to correspond to the peptide TKQTAR where K4 is di- and trimethylated, respectively (Fig 4B and 4C).

Bottom Line: As a result, modifications, alone or in combination, are important determinants of chromatin states.Several modifications conserved in other plants, and also novel modified residues, were identified.Additionally, the sub-nuclear localization of some well-studied modifications (i.e., H3K4me3, H3K9me2, H3K27me3, H3K9ac, H3T3ph) is described and compared to other plant species.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.

ABSTRACT
Histones are the main structural components of the nucleosome, hence targets of many regulatory proteins that mediate processes involving changes in chromatin. The functional outcome of many pathways is "written" in the histones in the form of post-translational modifications that determine the final gene expression readout. As a result, modifications, alone or in combination, are important determinants of chromatin states. Histone modifications are accomplished by the addition of different chemical groups such as methyl, acetyl and phosphate. Thus, identifying and characterizing these modifications and the proteins related to them is the initial step to understanding the mechanisms of gene regulation and in the future may even provide tools for breeding programs. Several studies over the past years have contributed to increase our knowledge of epigenetic gene regulation in model organisms like Arabidopsis, yet this field remains relatively unexplored in crops. In this study we identified and initially characterized histones H3 and H4 in the monocot crop sugarcane. We discovered a number of histone genes by searching the sugarcane ESTs database. The proteins encoded correspond to canonical histones, and their variants. We also purified bulk histones and used them to map post-translational modifications in the histones H3 and H4 using mass spectrometry. Several modifications conserved in other plants, and also novel modified residues, were identified. In particular, we report O-acetylation of serine, threonine and tyrosine, a recently identified modification conserved in several eukaryotes. Additionally, the sub-nuclear localization of some well-studied modifications (i.e., H3K4me3, H3K9me2, H3K27me3, H3K9ac, H3T3ph) is described and compared to other plant species. To our knowledge, this is the first report of histones H3 and H4 as well as their post-translational modifications in sugarcane, and will provide a starting point for the study of chromatin regulation in this crop.

No MeSH data available.


Related in: MedlinePlus