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Proteomic profiling of histone acetylation pattern in Arabidopsis

ABSTRACT: The levels of acetylated and non-acetylated histone peptide forms were quantified in A. thaliana plants with loss of function of HDA6, and plants exposed to HDAs inhibitors (trichostatin and sodium butyrate)during germination .

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Leaf

SUBMITTER: Gabriela Lochmanova

LAB HEAD: Zbynek Zdrahal

PROVIDER: PXD014739 | Pride | 2019-10-14

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	HistoneATh_170227.fasta	Fasta
	SB05_1L_1_Recal.pep.xml	Pepxml
	SB05_1L_1_Recal.prot.xml	Xml
	SB05_1L_1_Recal.raw	Raw
	SB05_1S_1_Recal.pep.xml	Pepxml

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Publications

Different Modes of Action of Genetic and Chemical Downregulation of Histone Deacetylases with Respect to Plant Development and Histone Modifications.

Lochmanová Gabriela G Ihnatová Ivana I Kuchaříková Hana H Brabencová Sylva S Zachová Dagmar D Fajkus Jiří J Zdráhal Zbyněk Z Fojtová Miloslava M

International journal of molecular sciences 20191014 20

A high degree of developmental plasticity enables plants to adapt to continuous, often unfavorable and unpredictable changes in their environment. At the molecular level, adaptive advantages for plants are primarily provided by epigenetic machinery including DNA methylation, histone modifications, and the activity of noncoding RNA molecules. Using a mass spectrometry-based proteomic approach, we examined the levels of acetylated histone peptide forms in Arabidopsis plants with a loss of function ...[more]

PMID: 31615119

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Sample preparation procedure for mass spectrometric analysis of plant histones

Project description:The protocol for preparing samples of plant histones prior to LC-MS/MS analysis was established, using a filter-aided sample preparation (FASP) technique to remove natural contaminants and chemical additives incompatible with MS-based procedures. The protocol consists of nuclei isolation, histone extraction into acidic solvent, protein propionylation and on-membrane digestion, then peptide propionylation in solution. Two variants of the derivatization protocol, in-solution propionylation in the vial (PROP-in-SOL) and propionylation on the filter unit (PROP-on-FILTER), were compared by efficiency of the labeling and by abundance of identified histone peptide forms.

2018-09-20 | PXD010102 | Pride

Adaptive epigenetic changes in histone variants and modifications rescue the fitness of Arabidopsis plants with dysfunctional histone chaperones

Project description:The aim was to characterize histone variants and PTMs in mutant plants with histone chaperone dysfunction using mass spectrometry-based approach. We found that the maintenance of genome stability via chromatin remodelling depends on a two-tiered process. The first level relies on a highly flexible mechanism that involves alterations in histone marks while the second adaptive level requires assistance of histone chaperones for the replacement of specific histone variants which is a more time-consuming process.

2024-08-10 | PXD046034 | Pride

Unraveling epigenetic changes in A. thaliana calli: Impact of HDAC inhibitors

Project description:The aim was to characterize epigenetic changes in histone proteins during callus formation from roots and shoots of Arabidopsis thaliana seedlings using mass spectrometry-based approach. Increased level of histone H3.3 variant was found to be the most prominent feature of 20-day-old calli, associated with chromatin relaxation. Methylation status in root- and shoot-derived calli reached the same level during long-term propagation, whereas differences in acetylation levels provided a long-lasting imprint of root and shoot origin. On the other hand, epigenetic signs of origin completely disappeared during 20 days of calli propagation in the presence of histone deacetylase inhibitors (HDACi), sodium butyrate and trichostatin A, although each HDACi affected the state of post-translational histone modifications in a specific manner.

2024-01-26 | PXD046788 | Pride

Microwave oven-assisted derivatization of histone proteoforms using trimethylacetic anhydride

Project description:We introduce a new reagent – Trimethylacetic anhydride (TMA) for highly efficient histone derivatization, which is facilitated by microwave irradiation to reduce sample preparation duration. The derivatization of unmodified NH2- groups at histone lysine residues is necessary prior LC-MS analysis using bottom-up approach. Our methodology shows high labelling efficiency and demonstrates its utilization for histone posttranslational modification abundance monitoring. Therefore, to be an alternative to conventionally used methods.

2021-06-14 | PXD019502 | Pride

Dissection of acetylomic profiles in T cell lymphoma following histone deacetylases inhibition

Project description:The aim was to dissect molecular changes in histone and non-histone protein acetylation dynamics following the genetic or pharmacological inhibition of HDAC activity in a model of Anaplastic Large Cell Lymphoma (ALCL), a T cell non-Hodgkin lymphoma, predominantly found in children and adolescents.

2022-10-14 | PXD030503 | Pride

Alternative digestion approaches improve histone modification mapping by mass spectrometry in clinical samples

Project description:Profiling histone post-translational modifications (PTMs) in clinical samples holds great potential for the identification of epigenetic biomarkers and the discovery of novel epigenetic targets. We have recently developed a battery of mass spectrometry (MS)-based approaches to analyze histone PTMs in different types of primary samples. However, most of these protocols rely on SDS-PAGE separation following histone enrichment in order to eliminate detergents and isolate histones from other proteins present in the sample. As a consequence, many proteolytic enzymes, whose performance is poor in gel, cannot be used, limiting the digestions options for clinical samples, and hence the modification coverage. In this study, we used a simple procedure involving acetone protein precipitation followed by histone enrichment through a C18 StageTip column to obtain histone preparations suitable for various in solution digestion protocols.

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Comparison of in-gel digestion methods for histone PTM analysis

Project description:In order to optimize the histone digestion procedure for low-abundance clinical samples, we compared different in-gel digestion protocols. Histones are usually digested in-gel using “Arg-C-like” strategies, which involve chemical acylation of lysines followed by trypsin digestion (17). Acylated lysines are not recognized by trypsin, which -as a consequence- cuts only at the C-terminus of arginines and generates peptides of suitable length for MS analysis. We compared four Arg-C-like protocols: 1) D3 protocol (deuterated acetic anhydride as acylating agent); 2) PRO protocol (propionic anhydride as acylating agent); 3) PRO-PRO protocol (propionic anhydride as acylating agent and peptide N-terminal derivatization); 4) PRO-PIC protocol (propionic anhydride as acylating agent and phenyl-isocyanate as peptide N-terminal derivatization). We also used an Arg-C in solution digestion as a reference, and tested the performance of the methods with decreasing sample amounts.

2021-09-09 | PXD024745 | Pride

Analysis of HUVEC secretome and histone N-terminal acetylation after Notch activation

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2023-02-15 | PXD032978 | Pride

Epigenetic and transcriptional control of adipocyte function by centenarian-associated SIRT6 N308K/A313S mutant

Project description:Obesity is a major health burden. Adipogenesis, the proliferation and differentiation of pree-adipocytes in mature adipocytes, could be a potential therapeutic approach for obesity. Deficiency of SIRT6, a member of the sirtuin family of nicotinamide adenine dinucleotide (NAD)+-dependent protein deacetylases, blocks adipogenesis. New allelic variants of SIRT6 (N308K/A313S) were recently associated with the longevity in Ashkenazi Jews. In this study, we aimed to clarify how these new centenarian-associated SIRT6 genetic variants affect adipogenesis at the transcriptional and epigenetic level. Overexpression of centenarian-associated SIRT6 mutant increased adipogenic differentiation to a similar extent compared to the WT form. However, it triggered distinct histone PTM profiles in mature adipocytes, with significantly higher acetylation levels, and activated divergent transcriptional programs, including those dependent on signaling related to the sympathetic innervation and to PI3K pathway. 3T3-L1 mature adipocytes overexpressing SIRT6 N308K/A313S displayed increased insulin sensitivity in a neuropeptide Y (NPY)-dependent manner.

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Phosphorylation of methyltransferase Set2p and demethylase Jhd1p and its association with histone H3K36 methylation and stress response pathways in Saccharomyces cerevisiae

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