Dataset Information

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

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Fusion Lumos

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

TISSUE(S): Plant Cell

SUBMITTER: Gabriela Lochmanova

LAB HEAD: Zbynek Zdrahal

PROVIDER: PXD046788 | Pride | 2024-01-26

REPOSITORIES: Pride

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Publications

Unraveling Epigenetic Changes in <i>A. thaliana</i> Calli: Impact of HDAC Inhibitors.

Pírek Pavlína P Kryštofová Karolína K Kováčová Ingrid I Kromerová Anna A Zachová Dagmar D Helia Ondřej O Panzarová Klára K Fajkus Jiří J Zdráhal Zbyněk Z Lochmanová Gabriela G Fojtová Miloslava M

Plants (Basel, Switzerland) 20231215 24

The ability for plant regeneration from dedifferentiated cells opens up the possibility for molecular bioengineering to produce crops with desirable traits. Developmental and environmental signals that control cell totipotency are regulated by gene expression via dynamic chromatin remodeling. Using a mass spectrometry-based approach, we investigated epigenetic changes to the histone proteins during callus formation from roots and shoots of <i>Arabidopsis thaliana</i> seedlings. Increased levels ...[more]

PMID: 38140504

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Project description:Propionate is a common three-carbon intermediate produced from the breakdown of propiogenic substrates, such as branched-chain amino acids and odd-numbered fatty acids, and by gut bacteria. Propionate can chemically modify proteins, and if this involves histones, it may underpin a disease-relevant link between short-chain acyls and gene expression in the heart. Here, we sought to characterize how propionate-dependent modifications to histones affect cardiac gene expression and contractile function in a mouse model producing elevated levels of propionate/propionyl-CoA. An adult mouse model of propionic acidaemia (PA) was used to investigate how propionate affects histones and gene expression in the heart, an organ strongly affected in PA patients. Mass spectrometry confirmed elevated plasma propionate in 8-week PA mice, reaching levels detected in PA patient serum. Metabolomic analyses confirmed a metabolic signature of PA, but male mice had enhanced propionate processing towards -alanine. Female PA hearts had expanded end-diastolic and end-systolic volumes, and weaker systolic contractions, without major electrocardiographic changes. Ca2+ signals were deranged in female PA mice (raised diastolic Ca2+), consistent with contractile dysfunction. Differentially-expressed genes (DEGs) included Pde9a and Mme, previously linked to cardiac dysfunction. These DEGs also responded to 48-h culture of wild-type myocytes with propionate as well as butyrate, an HDAC inhibitor, suggesting a role for increased histone acetylation alongside propionylation in inducing these genes. Indeed, histone acetylation (H3K27ac) and propionylation were elevated genome-wide in the PA heart and at the promoters of Pde9a and Mme. These propionate-associated epigenetic responses were more pronounced in female PA mice. The greater prominence of epigenetic, transcriptional, and functional responses in female PA mice, despite a mostly sex-indiscriminate overall metabolic milieu, argues that histone acylation plays a defining role in the cardiac phenotype. We conclude that perturbed propionate metabolism in vivo alters histone acylation and gene expression, which impacts cardiac contractile function.

Dataset Information

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

Publications

Unraveling Epigenetic Changes in <i>A. thaliana</i> Calli: Impact of HDAC Inhibitors.

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