Proteome dynamics at broken replication forks reveal a distinct ATM-directed repair response suppressing DNA double-strand break ubiquitination
Kyosuke Nakamura,Georg Kustatscher,Constance Alabert,Martina Hödl,Ignasi Forné,Moritz Völker-Albert,Shankha Satpathy,Tracey E. Beyer,Niels Mailand,Chunaram Choudhary,Axel Imhof,Juri Rappsilber,Juri Rappsilber,Anja Groth +13 more
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.About:
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.read more
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Cracking chromatin with proteomics: From chromatome to histone modifications
TL;DR: This review gives an overview of the proteomic approaches that have been developed by combining mass spectrometry‐based with tailored biochemical and genetic methods to examine overall protein make‐up of chromatin, to characterize chromatin domains, to determine protein interactions, and to decipher the broad spectrum of histone modifications that represent the quintessence of Chromatin function.
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A systemic cell cycle block impacts stage-specific histone modification profiles during Xenopus embryogenesis.
TL;DR: In this article, the authors investigated the possible relationship between the propagation of epigenetic information and the developmental cell proliferation during Xenopus embryogenesis and showed that the inhibition of cell proliferation is principally compatible with embryo survival and cellular differentiation.
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Higher‐order modular regulation of the human proteome
Georg Kustatscher,Martina Hödl,Edward Rullmann,Piotr Grabowski,E. Fiagbedzi,Anja Groth,Juri Rappsilber +6 more
TL;DR: ProgulonFinder as mentioned in this paper is a web application that enables the targeted search for progulons of specific cellular processes and reveal multiple new replication factors, validated by extensive phenotyping of siRNA-induced knockdown.
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Genetic requirements for repair of lesions caused by single genomic ribonucleotides in S phase
Natalie Schindler,Matthias Tonn,Vanessa Kellner,Jia Jun Fung,Arianna Lockhart,Olga Vydzhak,Thomas Juretschke,Stefan Möckel,Petra Beli,Anton Khmelinskii,Brian Luke +10 more
TL;DR: In this article , a cell cycle phase restricted allele of RNase H2 was used to nick at rNMPs in S phase and study their repair. But, the results were limited to single-ended double-strand breaks (DSBs).
References
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Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
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MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.
Jiirgen Cox,Matthias Mann +1 more
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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The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Yasset Perez-Riverol,Attila Csordas,Jingwen Bai,Manuel Bernal-Llinares,Suresh Hewapathirana,Deepti J. Kundu,Avinash Inuganti,Johannes Griss,Johannes Griss,Gerhard Mayer,Martin Eisenacher,Enrique Perez,Julian Uszkoreit,Julianus Pfeuffer,Timo Sachsenberg,Şule Yılmaz,Shivani Tiwary,Juergen Cox,Enrique Audain,Mathias Walzer,Andrew F. Jarnuczak,Tobias Ternent,Alvis Brazma,Juan Antonio Vizcaíno +23 more
TL;DR: Key statistics on the current data contents and volume of downloads are outlined, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas are outlined.
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