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Epigenetically bistable regions across neuron-specific genes govern neuron eligibility to a coding ensemble in the hippocampus

ABSTRACT: Epigenetically bistable regions across neuron-specific genes govern neuron eligibility to a coding ensemble in the hippocampus

PROVIDER: PRJNA632755 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11788900.fastq.gz	Fastqsanger.gz
	SRR11788901.fastq.gz	Fastqsanger.gz
	SRR11788902.fastq.gz	Fastqsanger.gz
	SRR11788903.fastq.gz	Fastqsanger.gz
	SRR11788904.fastq.gz	Fastqsanger.gz

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Project description:Ketone 3-hydroxybutyrate (3OHB) has been proved to be a neuroprotective endogenous molecule in multiple neurodegenerative diseases, but the detailed mechanisms of action has not been fully uncovered. Here, we employed a quantitative proteomics approach to assess the global protein expression pattern of neuron cells which were incorporated with 3OHB. While 3OHB did not derive dramatic proteome pattern fluctuation in HT22 cells, a big portion of the proteome alteration are found to be 3OHB specific responses (including: cell metabolism, protein acetylation, cognition, neurodegeneration diseases). Combining with disease related protein-protein interaction network analysis, we successfully pinpointed a hub marker, Histone lysine 27 trimethylation (H3K27me3), which has been widely studied in multiple neurodegenerative diseases, but still hasn’t been connected to 3OHB derived neuroprotective effects yet. In addition, our data suggested that the co-occurrence of H3K4me3 and H3K27me3 which was defined as chromatin bivalency referring “poised” transcriptional state could be perturbed by 3OHB, since both H3K4me3 and H3K27me3 were showing sensitive response to 3OHB. Integrative transcriptomics and epigenomics analysis highlighted bivalent transcription factors may play critical roles in 3OHB derived disease protection and alteration of neuronal development processes. To further validate and explore the possible scenario, we performed transcriptomics profiling of 3OHB perturbation upon neural differentiation process. The gene set enrichment analysis has shown that 3OHB could impair the fate decision of neural precursor cells by repressing and promoting their differentiation and proliferation related biological processes, respectively. Another interesting phenomenon is that two of relative high abundant Histone lysine hydroxybutyrylation sites (H2AK118bhb, H2BK34bhb) also responded to 3OHB fulguration. Those two sites are happen to be the most important monoubiquitylation sites that play critical role in regulating of H3K27 methylation and H3K4 (and K79) methylation, respectively. One may speculate that H2AK118bhb and H2BK34bhb involve in or even derive chromatin bivalency alteration upon 3OHB perturbation in neural systems.Taking together, our study provides a novel scenario for deciphering the 3OHB and its mechanisms of action in neural systems both in neurodegeneration disease pathogenesis and neural development process.

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Epigenetically bistable regions across neuron-specific genes govern neuron eligibility to a coding ensemble in the hippocampus

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