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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
MetabolomicsMetabolic responses induced by DNA damage and poly (ADP-ribose) polymerase (PARP) inhibition in MCF-7 cells
Genomic instability is one of the hallmarks of cancer. Several chemotherapeutic drugs and radiotherapy induce DNA damage to prevent cancer cell replication. Cells in turn activate different DNA damage response (DDR) pathways to either repair the damage or induce cell death. These DDR pathways also e...
2015-08-01 | MTBLS177 | MetaboLights
MetabolomicsPhotorespiration is linked to DNA methylation by formate as one-carbon source.
DNA methylation is a key epigenetic modification regulating genome organization, stability, and gene expression. Stable DNA methylation critically relies on methyl groups provided through folate-mediated one-carbon (C1) metabolism, yet the origin and regulation of C1 supply remain elusive. Here we d...
2026-01-06 | MTBLS13444 | MetaboLights
TranscriptomicsGenome-wide connection between DNA methylation and DNA replication timing
DNA methylation and DNA replication timing were examined across a variety of human tissues and cell lines, applying microarray-based techniques. The analyses revealed that late-replicating DNA was demethylated compared to the methylation of early-replicating regions. DNA methylation: Epstein-Barr-Vi...
ORGANISM(S): Homo sapiens 
2010-12-01 | E-GEOD-24947 | biostudies-arrayexpress
MetabolomicsCell overgrowth potentiates osmotic and replication stresses to promote p38/p53/p21-dependent senescence
Abnormal increases in cell size are associated with senescence and cell cycle exit. The mechanisms by which overgrowth primes cells to withdraw from the cell cycle remain unknown. We address this question using CDK4/6 inhibitors, which arrest cells in G0/G1 and are licensed to treat advanced HR+/HER...
2025-10-24 | MTBLS8698 | 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
MetabolomicsMulti-Omics analyses reveal dynamic interactions between DNA methylation and transcriptional regulation during black raspberry ripening
We show developmental-series transcriptome, methylome, and metabolome to reveal extensive epigenetic reprogramming during black raspberry (Rubus occidentalis) fruit ripening. Multi-omics integration reveals coordinated anthocyanin accumulation parallels expression of biosynthetic and regulatory gene...
2026-09-28 | MTBLS15819 | MetaboLights
TranscriptomicsAbnormal Developmental Control of Replication Timing Domains in Pediatric Acute Lymphoblastic Leukemia
Abnormal replication timing has been observed in cancer but no study has comprehensively evaluated this misregulation. We generated genome-wide replication timing profiles for pediatric leukemias from 17 patients and 3 cell lines, as well as normal B and T cells. Non-leukemic EBV-transformed lymphob...
ORGANISM(S): Homo sapiens 
2012-05-16 | E-GEOD-37987 | biostudies-arrayexpress
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