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      FAM111 protease activity undermines cellular fitness and is amplified by gain‐of‐function mutations in human disease

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          Abstract

          Dominant missense mutations in the human serine protease FAM111A underlie perinatally lethal gracile bone dysplasia and Kenny–Caffey syndrome, yet how FAM111A mutations lead to disease is not known. We show that FAM111A proteolytic activity suppresses DNA replication and transcription by displacing key effectors of these processes from chromatin, triggering rapid programmed cell death by Caspase‐dependent apoptosis to potently undermine cell viability. Patient‐associated point mutations in FAM111A exacerbate these phenotypes by hyperactivating its intrinsic protease activity. Moreover, FAM111A forms a complex with the uncharacterized homologous serine protease FAM111B, point mutations in which cause a hereditary fibrosing poikiloderma syndrome, and we demonstrate that disease‐associated FAM111B mutants display amplified proteolytic activity and phenocopy the cellular impact of deregulated FAM111A catalytic activity. Thus, patient‐associated FAM111A and FAM111B mutations may drive multisystem disorders via a common gain‐of‐function mechanism that relieves inhibitory constraints on their protease activities to powerfully undermine cellular fitness.

          Abstract

          This study shows that patient‐associated mutations in FAM111A and FAM111B proteases may drive multisystem human disorders via a gain‐of‐function mechanism amplifying their catalytic activity to undermine cell fitness and viability.

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          Most cited references13

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          ATR prohibits replication catastrophe by preventing global exhaustion of RPA.

          ATR, activated by replication stress, protects replication forks locally and suppresses origin firing globally. Here, we show that these functions of ATR are mechanistically coupled. Although initially stable, stalled forks in ATR-deficient cells undergo nucleus-wide breakage after unscheduled origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing induced breakage of stalled forks even in cells with active ATR. Thus, ATR-mediated suppression of dormant origins shields active forks against irreversible breakage via preventing exhaustion of nuclear RPA. This study elucidates how replicating genomes avoid destabilizing DNA damage. Because cancer cells commonly feature intrinsically high replication stress, this study also provides a molecular rationale for their hypersensitivity to ATR inhibitors. Copyright © 2013 Elsevier Inc. All rights reserved.
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            Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components.

            To maintain genome function and stability, DNA sequence and its organization into chromatin must be duplicated during cell division. Understanding how entire chromosomes are copied remains a major challenge. Here, we use nascent chromatin capture (NCC) to profile chromatin proteome dynamics during replication in human cells. NCC relies on biotin-dUTP labelling of replicating DNA, affinity purification and quantitative proteomics. Comparing nascent chromatin with mature post-replicative chromatin, we provide association dynamics for 3,995 proteins. The replication machinery and 485 chromatin factors such as CAF-1, DNMT1 and SUV39h1 are enriched in nascent chromatin, whereas 170 factors including histone H1, DNMT3, MBD1-3 and PRC1 show delayed association. This correlates with H4K5K12diAc removal and H3K9me1 accumulation, whereas H3K27me3 and H3K9me3 remain unchanged. Finally, we combine NCC enrichment with experimentally derived chromatin probabilities to predict a function in nascent chromatin for 93 uncharacterized proteins, and identify FAM111A as a replication factor required for PCNA loading. Together, this provides an extensive resource to understand genome and epigenome maintenance.
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              Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics.

              Progress in proteomics is mainly driven by advances in mass spectrometric (MS) technologies. Here we benchmarked the performance of the latest MS instrument in the benchtop Orbitrap series, the Q Exactive HF-X, against its predecessor for proteomics applications. A new peak-picking algorithm, a brighter ion source, and optimized ion transfers enable productive MS/MS acquisition above 40 Hz at 7500 resolution. The hardware and software improvements collectively resulted in improved peptide and protein identifications across all comparable conditions, with an increase of up to 50 percent at short LC-MS gradients, yielding identification rates of more than 1000 unique peptides per minute. Alternatively, the Q Exactive HF-X is capable of achieving the same proteome coverage as its predecessor in approximately half the gradient time or at 10-fold lower sample loads. The Q Exactive HF-X also enables rapid phosphoproteomics with routine analysis of more than 5000 phosphopeptides with short single-shot 15 min LC-MS/MS measurements, or 16 700 phosphopeptides quantified across ten conditions in six gradient hours using TMT10-plex and offline peptide fractionation. Finally, exciting perspectives for data-independent acquisition are highlighted with reproducible identification of 55 000 unique peptides covering 5900 proteins in half an hour of MS analysis.

                Author and article information

                Contributors
                niels.mailand@cpr.ku.dk
                Journal
                EMBO Rep
                EMBO Rep
                10.1002/(ISSN)1469-3178
                EMBR
                embor
                EMBO Reports
                John Wiley and Sons Inc. (Hoboken )
                1469-221X
                1469-3178
                09 August 2020
                05 October 2020
                09 August 2020
                : 21
                : 10 ( doiID: 10.1002/embr.v21.10 )
                : e50662
                Affiliations
                [ 1 ] Protein Signaling Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
                [ 2 ] Proteomics Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
                [ 3 ] Protein Structure and Function Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
                [ 4 ] Department of Cellular and Molecular Medicine Center for Chromosome Stability University of Copenhagen Copenhagen Denmark
                Author notes
                [*] [* ]Corresponding author. Tel: +45 35325023; E‐mail: niels.mailand@ 123456cpr.ku.dk
                Author information
                https://orcid.org/0000-0003-1292-4799
                https://orcid.org/0000-0003-0761-4921
                https://orcid.org/0000-0002-6623-709X
                Article
                EMBR202050662
                10.15252/embr.202050662
                7534640
                32776417
                bf3626de-1c49-4feb-a314-fd6a4ca0960c
                © 2020 The Author. Published under the terms of the CC BY NC ND 4.0 license

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 16 April 2020
                : 13 July 2020
                : 20 July 2020
                Page count
                Figures: 10, Tables: 0, Pages: 14, Words: 9736
                Funding
                Funded by: Novo Nordisk Fonden (NNF) , open-funder-registry 10.13039/501100009708;
                Award ID: NNF14CC0001
                Award ID: NNF18OC0030752
                Funded by: Lundbeckfonden (Lundbeck Foundation) , open-funder-registry 10.13039/501100003554;
                Award ID: R303‐2018-3212
                Funded by: EC | FP7 | FP7 Ideas: European Research Council (FP7 Ideas) , open-funder-registry 10.13039/100011199;
                Award ID: 616236
                Funded by: Kræftens Bekæmpelse (Danish Cancer Society) , open-funder-registry 10.13039/100008363;
                Award ID: R231‐A13972
                Funded by: Danmarks Grundforskningsfond (DNRF) , open-funder-registry 10.13039/501100001732;
                Award ID: DNRF115
                Categories
                Report
                Reports
                Custom metadata
                2.0
                05 October 2020
                Converter:WILEY_ML3GV2_TO_JATSPMC version:5.9.1 mode:remove_FC converted:05.10.2020

                Molecular biology
                cell fitness,chromatin,dna replication,human genetic disorders,protease,autophagy & cell death,dna replication, repair & recombination,molecular biology of disease

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