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Article ; Online: Cracking chromatin with proteomics: From chromatome to histone modifications.

Sigismondo, Gianluca / Papageorgiou, Dimitris N / Krijgsveld, Jeroen

2022 Volume 22, Issue 15-16, Page(s) e2100206

Abstract: Chromatin is the assembly of genomic DNA and proteins packaged in the nucleus of eukaryotic cells, which together are crucial in regulating a plethora of cellular processes. Histones may be the best known class of protein constituents in chromatin, which ...

Abstract	Chromatin is the assembly of genomic DNA and proteins packaged in the nucleus of eukaryotic cells, which together are crucial in regulating a plethora of cellular processes. Histones may be the best known class of protein constituents in chromatin, which are decorated by a range of post-translational modifications to recruit accessory proteins and protein complexes to execute specific functions, ranging from DNA compaction, repair, transcription, and duplication, all in a dynamic fashion and depending on the cellular state. The key role of chromatin in cellular fitness is emphasized by the deregulation of chromatin determinants predisposing to different diseases, including cancer. For this reason, deep investigation of chromatin composition is fundamental to better understand cellular physiology. Proteomic approaches have played a crucial role to understand critical aspects of this complex interplay, benefiting from the ability to identify and quantify proteins and their modifications in an unbiased manner. 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.
MeSH term(s)	Chromatin ; DNA/genetics ; Epigenesis, Genetic ; Histone Code ; Protein Processing, Post-Translational ; Proteomics
Chemical Substances	Chromatin ; DNA (9007-49-2)
Language	English
Publishing date	2022-06-06
Publishing country	Germany
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2032093-0
ISSN	1615-9861 ; 1615-9853
ISSN (online)	1615-9861
ISSN	1615-9853
DOI	10.1002/pmic.202100206
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Zs.A 5386: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
Zs.A 1868: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair.

Sigismondo, Gianluca / Arseni, Lavinia / Palacio-Escat, Nicolàs / Hofmann, Thomas G / Seiffert, Martina / Krijgsveld, Jeroen

Nucleic acids research

2023 Volume 51, Issue 2, Page(s) 687–711

Abstract: The DNA damage response (DDR) is essential to maintain genome stability, and its deregulation predisposes to carcinogenesis while encompassing attractive targets for cancer therapy. Chromatin governs the DDR via the concerted interplay among different ... ...

Abstract	The DNA damage response (DDR) is essential to maintain genome stability, and its deregulation predisposes to carcinogenesis while encompassing attractive targets for cancer therapy. Chromatin governs the DDR via the concerted interplay among different layers, including DNA, histone post-translational modifications (hPTMs) and chromatin-associated proteins. Here, we employ multi-layered proteomics to characterize chromatin-mediated functional interactions of repair proteins, signatures of hPTMs and the DNA-bound proteome during DNA double-strand break (DSB) repair at high temporal resolution. Our data illuminate the dynamics of known and novel DDR-associated factors both at chromatin and at DSBs. We functionally attribute novel chromatin-associated proteins to repair by non-homologous end-joining (NHEJ), homologous recombination (HR) and DSB repair pathway choice. We reveal histone reader ATAD2, microtubule organizer TPX2 and histone methyltransferase G9A as regulators of HR and involved in poly-ADP-ribose polymerase-inhibitor sensitivity. Furthermore, we distinguish hPTMs that are globally induced by DNA damage from those specifically acquired at sites flanking DSBs (γH2AX foci-specific) and profiled their dynamics during the DDR. Integration of complementary chromatin layers implicates G9A-mediated monomethylation of H3K56 in DSBs repair via HR. Our data provide a dynamic chromatin-centered view of the DDR that can be further mined to identify novel mechanistic links and cell vulnerabilities in DSB repair.
MeSH term(s)	Chromatin/genetics ; Histones/metabolism ; Proteomics ; DNA Repair ; DNA End-Joining Repair ; DNA ; Recombinational DNA Repair
Chemical Substances	Chromatin ; Histones ; DNA (9007-49-2)
Language	English
Publishing date	2023-01-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkac1264
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Article ; Online: Deposition of onco-histone H3.3-G34W leads to DNA repair deficiency and activates cGAS/STING-mediated immune responses.

Mancarella, Daniela / Ellinghaus, Henrik / Sigismondo, Gianluca / Veselinov, Olivera / Kühn, Alexander / Goyal, Ashish / Hartmann, Mark / Fellenberg, Jörg / Krijgsveld, Jeroen / Plass, Christoph / Popanda, Odilia / Schmezer, Peter / Bakr, Ali

International journal of cancer

2024 Volume 154, Issue 12, Page(s) 2106–2120

Abstract: Mutations in histone H3.3-encoding genes causing mutant histone tails are associated with specific cancers such as pediatric glioblastomas (H3.3-G34R/V) and giant cell tumor of the bone (H3.3-G34W). The mechanisms by which these mutations promote ... ...

Abstract	Mutations in histone H3.3-encoding genes causing mutant histone tails are associated with specific cancers such as pediatric glioblastomas (H3.3-G34R/V) and giant cell tumor of the bone (H3.3-G34W). The mechanisms by which these mutations promote malignancy are not completely understood. Here we show that cells expressing H3.3-G34W exhibit DNA double-strand breaks (DSBs) repair defects and increased cellular sensitivity to ionizing radiation (IR). Mechanistically, H3.3-G34W can be deposited to damaged chromatin, but in contrast to wild-type H3.3, does not interact with non-homologous end-joining (NHEJ) key effectors KU70/80 and XRCC4 leading to NHEJ deficiency. Together with defective cell cycle checkpoints reported previously, this DNA repair deficiency in H3.3-G34W cells led to accumulation of micronuclei and cytosolic DNA following IR, which subsequently led to activation of the cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) pathway, thereby inducing release of immune-stimulatory cytokines. These findings suggest a potential for radiotherapy for tumors expressing H3.3-G34W, which can be further improved by combination with STING agonists to induce immune-mediated therapeutic efficacy.
MeSH term(s)	Child ; Humans ; Histones/genetics ; Nucleotidyltransferases/genetics ; Immunity ; DNA ; DNA Repair-Deficiency Disorders
Chemical Substances	Histones ; Nucleotidyltransferases (EC 2.7.7.-) ; DNA (9007-49-2)
Language	English
Publishing date	2024-02-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	218257-9
ISSN	1097-0215 ; 0020-7136
ISSN (online)	1097-0215
ISSN	0020-7136
DOI	10.1002/ijc.34883
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Zs.A 478: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: ARID1A regulates DNA repair through chromatin organization and its deficiency triggers DNA damage-mediated anti-tumor immune response.

Bakr, Ali / Corte, Giuditta Della / Veselinov, Olivera / Kelekçi, Simge / Chen, Mei-Ju May / Lin, Yu-Yu / Sigismondo, Gianluca / Iacovone, Marika / Cross, Alice / Syed, Rabail / Jeong, Yunhee / Sollier, Etienne / Liu, Chun-Shan / Lutsik, Pavlo / Krijgsveld, Jeroen / Weichenhan, Dieter / Plass, Christoph / Popanda, Odilia / Schmezer, Peter

Nucleic acids research

2024

Abstract: AT-rich interaction domain protein 1A (ARID1A), a SWI/SNF chromatin remodeling complex subunit, is frequently mutated across various cancer entities. Loss of ARID1A leads to DNA repair defects. Here, we show that ARID1A plays epigenetic roles to promote ... ...

Abstract	AT-rich interaction domain protein 1A (ARID1A), a SWI/SNF chromatin remodeling complex subunit, is frequently mutated across various cancer entities. Loss of ARID1A leads to DNA repair defects. Here, we show that ARID1A plays epigenetic roles to promote both DNA double-strand breaks (DSBs) repair pathways, non-homologous end-joining (NHEJ) and homologous recombination (HR). ARID1A is accumulated at DSBs after DNA damage and regulates chromatin loops formation by recruiting RAD21 and CTCF to DSBs. Simultaneously, ARID1A facilitates transcription silencing at DSBs in transcriptionally active chromatin by recruiting HDAC1 and RSF1 to control the distribution of activating histone marks, chromatin accessibility, and eviction of RNAPII. ARID1A depletion resulted in enhanced accumulation of micronuclei, activation of cGAS-STING pathway, and an increased expression of immunomodulatory cytokines upon ionizing radiation. Furthermore, low ARID1A expression in cancer patients receiving radiotherapy was associated with higher infiltration of several immune cells. The high mutation rate of ARID1A in various cancer types highlights its clinical relevance as a promising biomarker that correlates with the level of immune regulatory cytokines and estimates the levels of tumor-infiltrating immune cells, which can predict the response to the combination of radio- and immunotherapy.
Language	English
Publishing date	2024-04-08
Publishing country	England
Document type	Journal Article
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkae233
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Zs.A 1067: Show issues

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Article ; Online: BCAT1 redox function maintains mitotic fidelity.

Francois, Liliana / Boskovic, Pavle / Knerr, Julian / He, Wei / Sigismondo, Gianluca / Schwan, Carsten / More, Tushar H / Schlotter, Magdalena / Conway, Myra E / Krijgsveld, Jeroen / Hiller, Karsten / Grosse, Robert / Lichter, Peter / Radlwimmer, Bernhard

Cell reports

2023 Volume 42, Issue 3, Page(s) 112217

Language	English
Publishing date	2023-03-01
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2023.112217
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Article ; Online: SUMOylation regulates the protein network and chromatin accessibility at glucocorticoid receptor-binding sites.

Paakinaho, Ville / Lempiäinen, Joanna K / Sigismondo, Gianluca / Niskanen, Einari A / Malinen, Marjo / Jääskeläinen, Tiina / Varjosalo, Markku / Krijgsveld, Jeroen / Palvimo, Jorma J

Nucleic acids research

2021 Volume 49, Issue 4, Page(s) 1951–1971

Abstract: Glucocorticoid receptor (GR) is an essential transcription factor (TF), controlling metabolism, development and immune responses. SUMOylation regulates chromatin occupancy and target gene expression of GR in a locus-selective manner, but the mechanism of ...

Abstract	Glucocorticoid receptor (GR) is an essential transcription factor (TF), controlling metabolism, development and immune responses. SUMOylation regulates chromatin occupancy and target gene expression of GR in a locus-selective manner, but the mechanism of regulation has remained elusive. Here, we identify the protein network around chromatin-bound GR by using selective isolation of chromatin-associated proteins and show that the network is affected by receptor SUMOylation, with several nuclear receptor coregulators and chromatin modifiers preferring interaction with SUMOylation-deficient GR and proteins implicated in transcriptional repression preferring interaction with SUMOylation-competent GR. This difference is reflected in our chromatin binding, chromatin accessibility and gene expression data, showing that the SUMOylation-deficient GR is more potent in binding and opening chromatin at glucocorticoid-regulated enhancers and inducing expression of target loci. Blockage of SUMOylation by a SUMO-activating enzyme inhibitor (ML-792) phenocopied to a large extent the consequences of GR SUMOylation deficiency on chromatin binding and target gene expression. Our results thus show that SUMOylation modulates the specificity of GR by regulating its chromatin protein network and accessibility at GR-bound enhancers. We speculate that many other SUMOylated TFs utilize a similar regulatory mechanism.
MeSH term(s)	Binding Sites ; Chromatin/metabolism ; Gene Expression Regulation ; HEK293 Cells ; Humans ; Nuclear Receptor Co-Repressor 1/metabolism ; Nuclear Receptor Coactivator 1 ; Protein Interaction Mapping ; Receptors, Glucocorticoid/metabolism ; Small Ubiquitin-Related Modifier Proteins/metabolism ; Sumoylation/drug effects
Chemical Substances	Chromatin ; NCOR1 protein, human ; Nuclear Receptor Co-Repressor 1 ; Receptors, Glucocorticoid ; Small Ubiquitin-Related Modifier Proteins ; NCOA1 protein, human (EC 2.3.1.48) ; Nuclear Receptor Coactivator 1 (EC 2.3.1.48)
Language	English
Publishing date	2021-02-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkab032
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Article ; Online: The contribution of mass spectrometry-based proteomics to understanding epigenetics.

Noberini, Roberta / Sigismondo, Gianluca / Bonaldi, Tiziana

Epigenomics

2016 Volume 8, Issue 3, Page(s) 429–445

Abstract: Chromatin is a macromolecular complex composed of DNA and histones that regulate gene expression and nuclear architecture. The concerted action of DNA methylation, histone post-translational modifications and chromatin-associated proteins control the ... ...

Abstract	Chromatin is a macromolecular complex composed of DNA and histones that regulate gene expression and nuclear architecture. The concerted action of DNA methylation, histone post-translational modifications and chromatin-associated proteins control the epigenetic regulation of the genome, ultimately determining cell fate and the transcriptional outputs of differentiated cells. Deregulation of this complex machinery leads to disease states, and exploiting epigenetic drugs is becoming increasingly attractive for therapeutic intervention. Mass spectrometry (MS)-based proteomics emerged as a powerful tool complementary to genomic approaches for epigenetic research, allowing the unbiased and comprehensive analysis of histone post-translational modifications and the characterization of chromatin constituents and chromatin-associated proteins. Furthermore, MS holds great promise for epigenetic biomarker discovery and represents a useful tool for deconvolution of epigenetic drug targets. Here, we will provide an overview of the applications of MS-based proteomics in various areas of chromatin biology.
MeSH term(s)	Biomarkers/analysis ; Biomarkers/chemistry ; Chromatin/metabolism ; Epigenesis, Genetic ; Histones/analysis ; Histones/metabolism ; Humans ; Mass Spectrometry/methods ; Protein Processing, Post-Translational ; Proteomics/methods
Chemical Substances	Biomarkers ; Chromatin ; Histones
Language	English
Publishing date	2016-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1750-192X
ISSN (online)	1750-192X
DOI	10.2217/epi.15.108
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Article ; Online: BCAT1 redox function maintains mitotic fidelity.

Cell reports

2022 Volume 41, Issue 3, Page(s) 111524

Abstract: The metabolic enzyme branched-chain amino acid transaminase 1 (BCAT1) drives cell proliferation in aggressive cancers such as glioblastoma. Here, we show that BCAT1 localizes to mitotic structures and has a non-metabolic function as a mitotic regulator. ... ...

Abstract	The metabolic enzyme branched-chain amino acid transaminase 1 (BCAT1) drives cell proliferation in aggressive cancers such as glioblastoma. Here, we show that BCAT1 localizes to mitotic structures and has a non-metabolic function as a mitotic regulator. Furthermore, BCAT1 is required for chromosome segregation in cancer and induced pluripotent stem cells and tumor growth in human cerebral organoid and mouse syngraft models. Applying gene knockout and rescue strategies, we show that the BCAT1 CXXC redox motif is crucial for controlling cysteine sulfenylation specifically in mitotic cells, promoting Aurora kinase B localization to centromeres, and securing accurate chromosome segregation. These findings offer an explanation for the well-established role of BCAT1 in promoting cancer cell proliferation. In summary, our data establish BCAT1 as a component of the mitotic apparatus that safeguards mitotic fidelity through a moonlighting redox functionality.
MeSH term(s)	Animals ; Humans ; Mice ; Amino Acids, Branched-Chain ; Aurora Kinase B ; Cysteine ; Disease Models, Animal ; Oxidation-Reduction ; Transaminases
Chemical Substances	Amino Acids, Branched-Chain ; Aurora Kinase B (EC 2.7.11.1) ; BCAT1 protein, human (EC 2.6.1.) ; Cysteine (K848JZ4886) ; Transaminases (EC 2.6.1.-) ; Bcat1 protein, mouse (EC 2.6.1.)
Language	English
Publishing date	2022-11-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.111524
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Article: Human SLFN5 and its Xenopus Laevis ortholog regulate entry into mitosis and oocyte meiotic resumption.

Vit, Gianmatteo / Hirth, Alexander / Neugebauer, Nicolas / Kraft, Bianca N / Sigismondo, Gianluca / Cazzola, Anna / Tessmer, Claudia / Duro, Joana / Krijgsveld, Jeroen / Hofmann, Ilse / Berger, Michael / Klüter, Harald / Niehrs, Christof / Nilsson, Jakob / Krämer, Alwin

Cell death discovery

2022 Volume 8, Issue 1, Page(s) 484

Abstract: The Schlafen gene family was first described in mice as a regulator of thymocyte development. Further studies showed involvement of human orthologs in different processes related with viral replication, cellular proliferation, and differentiation. In ... ...

Abstract	The Schlafen gene family was first described in mice as a regulator of thymocyte development. Further studies showed involvement of human orthologs in different processes related with viral replication, cellular proliferation, and differentiation. In recent years, a new role for human Slfn11 in DNA replication and chromatin remodeling was described. As commonly observed in many gene families, Slfn paralogs show a tissue-specific expression. This made it difficult to reach conclusions which can be valid in different biological models regarding the function of the different Schlafen proteins. In the present study, we investigate the involvement of SLFN5 in cell-cycle regulation and cell proliferation. A careful analysis of SLFN5 expression revealed that SLFN5 is highly expressed in proliferating tissues and that the protein is ubiquitously present in all the tissues and cell line models we analyzed. Very interestingly, SLFN5 expression oscillates during cell cycle, peaking during S phase. The fact that SLFN5 interacts with protein phosphatase 2A and that SLFN5 depletion causes cell cycle arrest and cellular apoptosis, suggests a direct involvement of this human paralog in cell cycle progression and cellular proliferation. We substantiated our in vitro and in cellulo results using Xenopus laevis oocytes to show that mRNA depletion of the unique Slfn gene present in Xenopus, whose protein sequence shares 80% of homology with SLFN5, recapitulates the phenotype observed in human cells preventing the resumption of meiosis during oocyte development.
Language	English
Publishing date	2022-12-08
Publishing country	United States
Document type	Journal Article
ISSN	2058-7716
ISSN	2058-7716
DOI	10.1038/s41420-022-01274-0
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Article ; Online: Multi-level and lineage-specific interactomes of the Hox transcription factor Ubx contribute to its functional specificity.

Carnesecchi, Julie / Sigismondo, Gianluca / Domsch, Katrin / Baader, Clara Eva Paula / Rafiee, Mahmoud-Reza / Krijgsveld, Jeroen / Lohmann, Ingrid

Nature communications

2020 Volume 11, Issue 1, Page(s) 1388

Abstract: Transcription factors (TFs) control cell fates by precisely orchestrating gene expression. However, how individual TFs promote transcriptional diversity remains unclear. Here, we use the Hox TF Ultrabithorax (Ubx) as a model to explore how a single TF ... ...

Abstract	Transcription factors (TFs) control cell fates by precisely orchestrating gene expression. However, how individual TFs promote transcriptional diversity remains unclear. Here, we use the Hox TF Ultrabithorax (Ubx) as a model to explore how a single TF specifies multiple cell types. Using proximity-dependent Biotin IDentification in Drosophila, we identify Ubx interactomes in three embryonic tissues. We find that Ubx interacts with largely non-overlapping sets of proteins with few having tissue-specific RNA expression. Instead most interactors are active in many cell types, controlling gene expression from chromatin regulation to the initiation of translation. Genetic interaction assays in vivo confirm that they act strictly lineage- and process-specific. Thus, functional specificity of Ubx seems to play out at several regulatory levels and to result from the controlled restriction of the interaction potential by the cellular environment. Thereby, it challenges long-standing assumptions such as differential RNA expression as determinant for protein complexes.
MeSH term(s)	Animals ; Cell Lineage/physiology ; Chromatin/metabolism ; Drosophila/embryology ; Drosophila/genetics ; Drosophila/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Female ; Gene Expression Regulation, Developmental ; Genes, Insect ; Homeodomain Proteins/genetics ; Homeodomain Proteins/metabolism ; Male ; Mesoderm/cytology ; Mesoderm/metabolism ; Protein Interaction Domains and Motifs ; Protein Interaction Maps ; RNA/metabolism ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Chromatin ; Drosophila Proteins ; Homeodomain Proteins ; Transcription Factors ; Ubx protein, Drosophila ; RNA (63231-63-0)
Language	English
Publishing date	2020-03-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-15223-x
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