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Regulation of Mammalian Cellular Metabolism by Endogenous Cyanide Production [TST_RNA-Seq]

ABSTRACT: Regulation of Mammalian Cellular Metabolism by Endogenous Cyanide Production [TST_RNA-Seq]

PROVIDER: PRJNA1207942 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31926700.fastq.gz	Fastqsanger.gz
	SRR31926700_1.fastq.gz	Fastqsanger.gz
	SRR31926700_2.fastq.gz	Fastqsanger.gz
	SRR31926689.fastq.gz	Fastqsanger.gz
	SRR31926689_1.fastq.gz	Fastqsanger.gz

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Regulation of Mammalian Cellular Metabolism by Endogenous Cyanide Production [TST_RNA-Seq]

Project description:Small, gaseous molecules – such as nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S) are produced as signalling molecules in mammalian cells. Here, we show that low concentrations of cyanide are generated endogenously in various mammalian tissues and cells. We detect cyanide in several cellular compartments of human cells and in various tissues and the blood of mice. Cyanide production is stimulated by glycine, occurs at the low pH of lysosomes and requires peroxidase activity. When generated at a specific rate, cyanide exerts stimulatory effects on mitochondrial bioenergetics, cell metabolism, and cell proliferation, but impairs cellular bioenergetics at high concentrations. Cyanide can modify cysteine residues via protein S-cyanylation, which is detectable basally in cells and mice, and increases in response to glycine. Low-dose cyanide supplementation exhibits cytoprotective effects in hypoxia and reoxygenation models in vitro and in vivo. Conversely, pathologically elevated cyanide production in nonketotic hyperglycinemia is detrimental to cells. Our findings indicate that cyanide should be considered part of the same group of endogenous mammalian regulatory gasotransmitters as NO, CO and H2S.

2025-01-09 | GSE286106 | GEO

Regulation of Mammalian Cellular Metabolism by Endogenous Cyanide Production [Glycine_RNA-Seq]

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Regulation of Mammalian Cellular Metabolism by Endogenous Cyanide Production [Glycine_RNA-Seq]

Project description:Regulation of Mammalian Cellular Metabolism by Endogenous Cyanide Production [Glycine_RNA-Seq]

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Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development

Project description:Background. The histone variant H3.3 plays key roles in regulating chromatin states and transcription. However, the role of endogenous H3.3 in mammalian cells and during development has been less thoroughly investigated. To address this gap, we report the production and phenotypic analysis of mice and cells with targeted disruption of the H3.3-encoding gene, H3f3b. Results. H3f3b KO mice exhibit a semi-lethal phenotype traceable at least in part to defective cell division and chromosome segregation. H3f3b KO cells have widespread ectopic CENP-A protein localization suggesting one possible mechanism for defective chromosome segregation. KO cells have abnormal karyotypes and cell cycle profiles as well. The transcriptome and euchromatin-related epigenome were moderately affected by loss of H3f3b in MEFs with ontology most notably pointing to changes in chromatin regulatory and histone coding genes. Reduced numbers of H3f3b KO mice survive to maturity and almost all survivors from both sexes are infertile. Conclusions. Taken together, our studies suggest that endogenous mammalian histone H3.3 has important roles in regulating chromatin and chromosome functions that in turn are important for cell division, genome integrity, and development. Examination of H3K9Ac and H3K4me3 in wild-type and H3.3 null MEFs

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In plants, decapping prevents RDR6-dependent production of small interfering RNAs from endogenous mRNAs

Project description:Background: Cytoplasmic degradation of endogenous RNAs is an integral part of RNA quality control (RQC) and often relies on the removal of the 5' cap structure and their subsequent 5M-bM-^@M-^Y to 3M-bM-^@M-^Y degradation. In parallel, many eukaryotes degrade exogenous and selected endogenous RNAs through post-transcriptional gene silencing (PTGS). In plants, PTGS depends on small interfering (si)RNAs produced after the conversion of single-stranded RNAs to double-stranded RNAs by the cellular RNA DEPENDENT RNA POLYMERASE 6 (RDR6). PTGS and RQC compete for transgene-derived RNAs, but it is unknown whether this competition also occurs for endogenous transcripts. Results: We show that that upon decapping impairment hundreds of endogenous mRNAs give rise to a new class of siRNAs, a subset of which depends on RDR6 for their production. Conclusions: Our results suggest that the decapping of aberrant endogenous RNA in P-bodies limits their entry into the PTGS pathway and prevents the subsequent deleterious consequences arising from this entry. We anticipate that the siRNAs identified in decapping mutants represent a subset of a larger ensemble of endogenous siRNAs that we coin rqc-siRNAs because they accumulate when RQC processes are impaired. Small RNA-seq experiments performed in duplicates for each condition.

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