Dataset Information

Quantitiave analysis of protein methylome reveals the cellular response to ionizing radiation

ABSTRACT: Protein methylation plays important roles in DNA damage signaling. To date, there is still a lack of global profiling of whole-cell methylation changes during the DNA damage response and repair. In this study, using HILIC affinity enrichment combined with MS analysis, we conducted a quantitative analysis of the methylated proteins in HEK293T cells in response to IR-induced DNA damage. In total, 235 distinct methylation sites responding to IR treatment were identified, and 38% of them were previously unknown. Multiple RNA-binding proteins were differentially methylated upon DNA damage stress. Furthermore, we identified 14 novel methylations in DNA damage response-related proteins. Moreover, we validated the function of PARP1 K23 methylation in repairing IR-induced DNA lesions.

ORGANISM(S): Homo Sapiens

SUBMITTER: Yali Chen

PROVIDER: PXD031655 | iProX | Mon Feb 14 00:00:00 GMT 2022

REPOSITORIES: iProX

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Quantitative Analysis of the Protein Methylome Reveals PARP1 Methylation is involved in DNA Damage Response.

Wang Xinzhu X Mi Shaojie S Zhao Mingxin M Lu Chen C Jia Chenxi C Chen Yali Y

Frontiers in molecular biosciences 20220629

Protein methylation plays important roles in DNA damage response. To date, proteome-wide profiling of protein methylation upon DNA damage has been not reported yet. In this study, using HILIC affinity enrichment combined with MS analysis, we conducted a quantitative analysis of the methylated proteins in HEK293T cells in response to IR treatment. In total, 235 distinct methylation sites responding to IR treatment were identified, and 38% of them were previously unknown. Multiple RNA-binding prot ...[more]

PMID: 35847980

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Project description:Previous studies have shown that exposure to ionising radiation (IR) results in DNA methylation changes in plants. However, to the best of our knowledge, this phenomenon is yet to be studied across multiple generations. Furthermore, the exact role of these changes in the IR-induced plant response is still far from understood. Here, we study the effect of gamma radiation on DNA methylation and its effect across generations in young Arabidopsis plant. A multigenerational set-up was used in which three generations of seven-day old Arabidopsis thaliana plants were exposed to either of the different radiation treatments (30 mGy h-1, 60 mGy h-1, 110 mGy h-1, or 430 mGy h-1) or to natural background radiation (control condition) for 14 days. The parental generation consisted of previously non-exposed plants, whereas generation 1 and generation 2 plants had already received a similar irradiation in the previous one or two generations, respectively. Directly after exposure the entire methylomes were analysed with UPLC-MS to measure whole genome methylation levels. Whole genome bisulphite sequencing (WGBS) was used to identify differentially methylated regions (DMRs), including their methylation context in the three generations in three different radiation conditions (control, 30 mGy/h, and 110 mGy/h). Both intra- and intergenerational comparisons of the genes and transposable elements (TEs) associated with the DMRs were made across the gamma radiation exposure conditions. It was apparent that there was a higher number of changes in CpG methylation, whereas only limited changes in CHG methylation occurred and no changes in CHH methylation were observed. A clear increase in IR-induced DMRs was seen over the three generations that were exposed to the lowest dose rate, where Gen 2 had a markedly higher number of DMRs than the previous two generations (Parent and Gen 1). Counterintuitively, we did not see significant differences in the plants exposed to the higher dose rate. In addition, a large number of DMRs associated with TEs were found, the majority of them being hyper methylated, likely leading to more genetic stability. Next to that, a significant number of DMRs were associated with genes (either in their promoter associated region or gene body). A functional analysis of these genes (not included in with this data) showed an enrichment for genes related to development as well as various stress responses, including DNA repair, RNA splicing, and (a)biotic stress responses. These observations indicate a role of DNA methylation in the regulation of these genes in response to IR exposure and shows a possible role for epigenetics in adaptation to IR in plants.

Dataset Information

Quantitiave analysis of protein methylome reveals the cellular response to ionizing radiation

Publications

Quantitative Analysis of the Protein Methylome Reveals PARP1 Methylation is involved in DNA Damage Response.

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