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MetabolomicsThe pyruvate kinase, a metabolic sensor powering glycolysis, drives the metabolic control of DNA replication

BACKGROUND: In all living organisms, DNA replication is exquisitely regulated in a wide range of growth conditions to achieve timely and accurate genome duplication prior to cell division. Failures in this regulation cause DNA damage with potentially disastrous consequences ...

2022-04-19 | MTBLS4415 | MetaboLights
MetabolomicsA synthetic cell with integrated DNA self-replication and lipid biosynthesis

The emergence, organization, and persistence of cellular life are the result of the functional integration of metabolic and genetic networks. Here, we engineer phospholipid vesicles that can operate three essential functions, namely transcription-translation of a partial genome, self-replication ...

2026-02-02 | MTBLS13437 | MetaboLights
MetabolomicsDNA nanomachines reveal an adaptive energy mode in confinement-induced amoeboid migration powered by polarized mitochondrial distribution

Energy metabolism is highly interdependent with adaptive cell migration in vivo. Mechanical confinement is a critical physical cue that induces switchable migration modes of the mesenchymal-to-amoeboid transition (MAT). However, the energy states in distinct migration modes, especially a...

2024-03-25 | MTBLS9657 | MetaboLights
ProteomicsProteome-wide analysis of SUMO2 targets in response to pathological DNA replication stress in human cells
SUMOylation is a form of post-translational modification involving covalent attachment of SUMO (Small Ubiquitin-like Modifier) polypeptides to specific lysine residues in the target protein. In human cells, there are four SUMO proteins, SUMO1–4, with SUMO2 and SUMO3 forming a closely related subfami...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-28 | MSV000080699 | MassIVE
ProteomicsMetalloprotease SPRTN/DVC1 Orchestrates Replication-Coupled DNA-Protein Crosslink Removal
Cytotoxicity of DNA-protein crosslinks (DPCs) is ascribed largely to their ability to block the progression of DNA replication fork. DPCs are frequently occurring in cells, either as a consequence of metabolism or exogenous agents. The mechanism of DPCs removal is not completely understood. Here, we...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2017-03-29 | MSV000080743 | MassIVE
ProteomicsProteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links part 2 of 2: AP-MS DATA (QUBIC)
DNA interstrand crosslinks (ICLs) block replication fork progression by inhibiting DNA strand separation. Repair of ICLs requires sequential incisions, translesion DNA synthesis, and homologous recombination, but the full set of factors involved in these transactions remains unknown. Here we establi...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-03-13 | MSV000079577 | MassIVE
TranscriptomicsInvolvement of a chromatin remodeling complex in damage tolerance during DNA replication
ATP-dependent chromatin remodeling complexes have been shown to participate in DNA replication in addition to transcription and DNA repair. However, the mechanisms of their involvement in DNA replication remain unclear. Here, we reveal a specific function of the yeast INO80 chromatin remodeling comp...
ORGANISM(S): Saccharomyces cerevisiae 
2010-06-20 | E-GEOD-18570 | biostudies-arrayexpress
TranscriptomicsAccumulation of sumoylated Rad52 in checkpoint mutants perturbed in DNA replication
Checkpoints are cellular surveillance and signaling pathways that regulate responses to DNA damage and perturbations of DNA replication. Here we show that high levels of sumoylated Rad52 are present in the mec1 sml1 and rad53 sml1 checkpoint mutants exposed to DNA damaging agents such as methyl meth...
ORGANISM(S): Saccharomyces cerevisiae 
2010-05-18 | E-GEOD-14761 | biostudies-arrayexpress
TranscriptomicsA unique epigenetic signature is associated with active DNA replication loci in human embryonic stem cells
The cellular epigenetic landscape changes as pluripotent stem cells differentiate to somatic cells or when differentiated cells transform to a cancerous state. These epigenetic changes are commonly correlated with differences in gene expression. Whether active DNA replication is also associated with...
ORGANISM(S): Homo sapiens 
2013-11-05 | E-GEOD-43152 | biostudies-arrayexpress
TranscriptomicsRole of Tet3 and DNA replication in zygotic demethylation of both paternal and maternal genomes [RNA-seq]
With the exception of imprinted genes and certain repeats, DNA methylation is globally erased during pre-implantation development. Recent studies have suggested that Tet3-mediated oxidation of 5-methylcytosine (5mC) and DNA replication-dependent dilution both contribute to global paternal DNA demeth...
ORGANISM(S): Mus musculus 
2014-10-21 | E-GEOD-61329 | biostudies-arrayexpress
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