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Open AccessJournal ArticleDOI

Proteome dynamics at broken replication forks reveal a distinct ATM-directed repair response suppressing DNA double-strand break ubiquitination

TLDR
In this article, the authors used nascent chromatin capture (NCC) proteomics to characterize the repair of replication-associated DNA double-strand breaks (DSBs) triggered by topoisomerase 1 (TOP1) inhibitors.
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This article is published in Molecular Cell.The article was published on 2021-03-04 and is currently open access. It has received 37 citations till now. The article focuses on the topics: DNA repair & DNA replication.

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Arginine shortage induces replication stress and confers genotoxic resistance by inhibiting histone H4 translation and promoting PCNA ubiquitination.

TL;DR: In this paper , the impact of arginine availability on DNA replication and genotoxicity resistance was examined using DNA combing assays, and it was shown that limiting extracellular arginines results in the arrest of cancer cells at S phase and a slowing or stalling of DNA replication.
References
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Journal ArticleDOI

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks

TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.

TL;DR: By following this protocol, investigators are able to gain an in-depth understanding of the biological themes in lists of genes that are enriched in genome-scale studies.
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Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

TL;DR: The survey will help tool designers/developers and experienced end users understand the underlying algorithms and pertinent details of particular tool categories/tools, enabling them to make the best choices for their particular research interests.
Journal ArticleDOI

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.

TL;DR: MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data, detects peaks, isotope clusters and stable amino acid isotope–labeled (SILAC) peptide pairs as three-dimensional objects in m/z, elution time and signal intensity space and achieves mass accuracy in the p.p.b. range.
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