Tiziana Bonaldi

Department of Experimental Oncology, European Institute of Oncology

Affiliated withEuropean Institute of Oncology European Institute of Oncology IRCCS (IEO)

Research Area

BiologyBiochemistry

Biography

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JoVE Journal Publications

ArticleTotal : 2	Year
Publication title	2014
Publication title	2022

Other Publications

Article	Year
The DNA chaperone HMGB1 facilitates ACF/CHRAC-dependent nucleosome sliding. The EMBO journal\| PubMed ID: 12486007	2002
Monocytic cells hyperacetylate chromatin protein HMGB1 to redirect it towards secretion. The EMBO journal\| PubMed ID: 14532127	2003
The use of mass spectrometry for the analysis of histone modifications. Methods in enzymology\| PubMed ID: 14979021	2004
The N-terminus of Drosophila SU(VAR)3-9 mediates dimerization and regulates its methyltransferase activity. Biochemistry\| PubMed ID: 15035645	2004
A combination of different mass spectroscopic techniques for the analysis of dynamic changes of histone modifications. Proteomics\| PubMed ID: 15188406	2004
The long acidic tail of high mobility group box 1 (HMGB1) protein forms an extended and flexible structure that interacts with specific residues within and between the HMG boxes. Biochemistry\| PubMed ID: 15379539	2004
Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nature genetics\| PubMed ID: 15765097	2005
Identification of a specific inhibitor of the histone methyltransferase SU(VAR)3-9. Nature chemical biology\| PubMed ID: 16408017	2005
"Chromatomics" the analysis of the chromatome. Molecular bioSystems\| PubMed ID: 16880972	2005
PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state. Molecular cell\| PubMed ID: 17052464	2006
Site-specific acetylation of ISWI by GCN5. BMC molecular biology\| PubMed ID: 17760996	2007
Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry. Nature methods\| PubMed ID: 18511913	2008
Quantitative proteomics as a new piece of the systems biology puzzle. Journal of proteomics\| PubMed ID: 18640294	2008
Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. Molecular cell\| PubMed ID: 18775334	2008
Systems-wide analysis of a phosphatase knock-down by quantitative proteomics and phosphoproteomics. Molecular & cellular proteomics : MCP\| PubMed ID: 19429919	2009
The HP1alpha-CAF1-SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin. EMBO reports\| PubMed ID: 19498464	2009
SILAC-based proteomic analysis to dissect the "histone modification signature" of human breast cancer cells. Amino acids\| PubMed ID: 20617350	2011
Systems biology "on-the-fly": SILAC-based quantitative proteomics and RNAi approach in Drosophila melanogaster. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 20824466	2010
Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output. PLoS biology\| PubMed ID: 21738444	2011
Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells. Nucleic acids research\| PubMed ID: 22210892	2012
Methylation of CenH3 arginine 37 regulates kinetochore integrity and chromosome segregation. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 22615363	2012
The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components. Molecular & cellular proteomics : MCP\| PubMed ID: 23319141	2013
Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells. Molecular cell\| PubMed ID: 23352454	2013
Reply to "Chaetocin is a nonspecific inhibitor of histone lysine methyltransferases". Nature chemical biology\| PubMed ID: 23416388	2013
Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics. International journal of molecular sciences\| PubMed ID: 23466885	2013
Cell reprogramming requires silencing of a core subset of polycomb targets. PLoS genetics\| PubMed ID: 23468641	2013
Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome. Molecular bioSystems\| PubMed ID: 23748837	2013
Threshold-controlled ubiquitination of the EGFR directs receptor fate. The EMBO journal\| PubMed ID: 23799367	2013
Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity. Molecular cell\| PubMed ID: 24289921	2014
Biochemical systems approaches for the analysis of histone modification readout. Biochimica et biophysica acta\| PubMed ID: 24681439	2014
Quantitative chemical proteomics identifies novel targets of the anti-cancer multi-kinase inhibitor E-3810. Molecular & cellular proteomics : MCP\| PubMed ID: 24696502	2014
Proteomics meets genetics: SILAC labeling of Drosophila melanogaster larvae and cells for in vivo functional studies. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 25059620
Improved bottom-up strategy to efficiently separate hypermodified histone peptides through ultra-HPLC separation on a bench top Orbitrap instrument. Proteomics\| PubMed ID: 25073962
ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites. Nucleic acids research\| PubMed ID: 25605800
Extracellular vesicle-mediated transfer of CLIC1 protein is a novel mechanism for the regulation of glioblastoma growth. Oncotarget\| PubMed ID: 26429879
Pathology Tissue-quantitative Mass Spectrometry Analysis to Profile Histone Post-translational Modification Patterns in Patient Samples. Molecular & cellular proteomics : MCP\| PubMed ID: 26463340
miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth. Nature communications\| PubMed ID: 26555894
The contribution of mass spectrometry-based proteomics to understanding epigenetics. Epigenomics\| PubMed ID: 26606673
Recent advances in mass spectrometry analysis of histone post-translational modifications: potential clinical impact of the PAT-H-MS approach. Expert review of proteomics\| PubMed ID: 26822344
MS-analysis of SILAC-labeled MYC-driven B lymphoma cells overexpressing miR-17-19b. Data in brief\| PubMed ID: 26977435
MYC/miR-17-92 interplay maintains B-lymphoma cell homeostasis. Cell cycle (Georgetown, Tex.)\| PubMed ID: 27097369
The EGFR-specific antibody cetuximab combined with chemotherapy triggers immunogenic cell death. Nature medicine\| PubMed ID: 27135741
Spatiotemporal plasticity of miRNAs functions: The miR-17-92 case. Molecular & cellular oncology\| PubMed ID: 27314099
Quantitative assessment of chemical artefacts produced by propionylation of histones prior to mass spectrometry analysis. Proteomics\| PubMed ID: 27373704
Mass-spectrometry analysis of histone post-translational modifications in pathology tissue using the PAT-H-MS approach. Data in brief\| PubMed ID: 27408908
SILAC-Based Quantitative Strategies for Accurate Histone Posttranslational Modification Profiling Across Multiple Biological Samples. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 27854018
High constitutive activity of a broad panel of housekeeping and tissue-specific -regulatory elements depends on a subset of ETS proteins. Genes & development\| PubMed ID: 28275002
PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples. Clinical epigenetics\| PubMed ID: 28702092
Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models. ACS medicinal chemistry letters\| PubMed ID: 28835804
Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers. Nucleic acids research\| PubMed ID: 28981749
A role for CENP-A/Cse4 phosphorylation on serine 33 in deposition at the centromere. FEMS yeast research\| PubMed ID: 29272409
Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases. Nature communications\| PubMed ID: 29317660	2018
PARP14 Controls the Nuclear Accumulation of a Subset of Type I IFN-Inducible Proteins. Journal of immunology (Baltimore, Md. : 1950)\| PubMed ID: 29500242
Zc3h10 is a novel mitochondrial regulator. EMBO reports\| PubMed ID: 29507079
Extensive and systematic rewiring of histone post-translational modifications in cancer model systems. Nucleic acids research\| PubMed ID: 29618087
The kinetochore module Okp1/Ame1 is a reader for N-terminal modifications on the centromeric histone Cse4. The EMBO journal\| PubMed ID: 30389668
Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World. Frontiers in molecular biosciences\| PubMed ID: 30467545
Alternative digestion approaches improve histone modification mapping by mass spectrometry in clinical samples. Proteomics. Clinical applications\| PubMed ID: 30471193
hmSEEKER: Identification of hmSILAC Doublets in MaxQuant Output Data. Proteomics\| PubMed ID: 30656827
Proteomics profiling of arginine methylation defines PRMT5 substrate specificity. Science signaling\| PubMed ID: 30940768
Profiling of Epigenetic Features in Clinical Samples Reveals Novel Widespread Changes in Cancer. Cancers\| PubMed ID: 31137727
Therapeutic Targeting of RNA Splicing Catalysis through Inhibition of Protein Arginine Methylation. Cancer cell\| PubMed ID: 31408619
hSWATH: Unlocking SWATH's Full Potential for an Untargeted Histone Perspective. Journal of proteome research\| PubMed ID: 31429292
Epigenetic drug target deconvolution by mass spectrometry-based technologies. Nature structural & molecular biology\| PubMed ID: 31582842
Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications. Methods (San Diego, Calif.)\| PubMed ID: 31605746
PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis. Nucleic acids research\| PubMed ID: 31777917
PRMT1 Is Recruited via DNA-PK to Chromatin Where It Sustains the Senescence-Associated Secretory Phenotype in Response to Cisplatin. Cell reports\| PubMed ID: 31995759
Targeting the scaffolding role of LSD1 (KDM1A) poises acute myeloid leukemia cells for retinoic acid-induced differentiation. Science advances\| PubMed ID: 32284990
Biochemical and Computational Approaches for the Large-Scale Analysis of Protein Arginine Methylation by Mass Spectrometry. Current protein & peptide science\| PubMed ID: 32338214
Clinical Application of Mass Spectrometry-Based Proteomics in Lung Cancer Early Diagnosis. Proteomics. Clinical applications\| PubMed ID: 32418314
Software Options for the Analysis of MS-Proteomic Data. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34236654	2021
Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples. Clinical epigenetics\| PubMed ID: 34315505	2021
Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-translational Modification (PTM) Combinatorics at Distinct Genomic Regions. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34382194	2021
Pharmacological inhibition of LSD1 triggers myeloid differentiation by targeting GSE1 oncogenic functions in AML. Oncogene\| PubMed ID: 34862459	2022

Article	Year
The DNA chaperone HMGB1 facilitates ACF/CHRAC-dependent nucleosome sliding. The EMBO journal\| PubMed ID: 12486007	2002
Monocytic cells hyperacetylate chromatin protein HMGB1 to redirect it towards secretion. The EMBO journal\| PubMed ID: 14532127	2003
The use of mass spectrometry for the analysis of histone modifications. Methods in enzymology\| PubMed ID: 14979021	2004
The N-terminus of Drosophila SU(VAR)3-9 mediates dimerization and regulates its methyltransferase activity. Biochemistry\| PubMed ID: 15035645	2004
A combination of different mass spectroscopic techniques for the analysis of dynamic changes of histone modifications. Proteomics\| PubMed ID: 15188406	2004
The long acidic tail of high mobility group box 1 (HMGB1) protein forms an extended and flexible structure that interacts with specific residues within and between the HMG boxes. Biochemistry\| PubMed ID: 15379539	2004
Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nature genetics\| PubMed ID: 15765097	2005
Identification of a specific inhibitor of the histone methyltransferase SU(VAR)3-9. Nature chemical biology\| PubMed ID: 16408017	2005
"Chromatomics" the analysis of the chromatome. Molecular bioSystems\| PubMed ID: 16880972	2005
PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state. Molecular cell\| PubMed ID: 17052464	2006
Site-specific acetylation of ISWI by GCN5. BMC molecular biology\| PubMed ID: 17760996	2007
Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry. Nature methods\| PubMed ID: 18511913	2008
Quantitative proteomics as a new piece of the systems biology puzzle. Journal of proteomics\| PubMed ID: 18640294	2008
Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. Molecular cell\| PubMed ID: 18775334	2008
Systems-wide analysis of a phosphatase knock-down by quantitative proteomics and phosphoproteomics. Molecular & cellular proteomics : MCP\| PubMed ID: 19429919	2009
The HP1alpha-CAF1-SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin. EMBO reports\| PubMed ID: 19498464	2009
SILAC-based proteomic analysis to dissect the "histone modification signature" of human breast cancer cells. Amino acids\| PubMed ID: 20617350	2011
Systems biology "on-the-fly": SILAC-based quantitative proteomics and RNAi approach in Drosophila melanogaster. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 20824466	2010
Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output. PLoS biology\| PubMed ID: 21738444	2011
Yin Yang 1 extends the Myc-related transcription factors network in embryonic stem cells. Nucleic acids research\| PubMed ID: 22210892	2012
Methylation of CenH3 arginine 37 regulates kinetochore integrity and chromosome segregation. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 22615363	2012
The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components. Molecular & cellular proteomics : MCP\| PubMed ID: 23319141	2013
Tet proteins connect the O-linked N-acetylglucosamine transferase Ogt to chromatin in embryonic stem cells. Molecular cell\| PubMed ID: 23352454	2013
Reply to "Chaetocin is a nonspecific inhibitor of histone lysine methyltransferases". Nature chemical biology\| PubMed ID: 23416388	2013
Mass spectrometry-based proteomics for the analysis of chromatin structure and dynamics. International journal of molecular sciences\| PubMed ID: 23466885	2013
Cell reprogramming requires silencing of a core subset of polycomb targets. PLoS genetics\| PubMed ID: 23468641	2013
Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome. Molecular bioSystems\| PubMed ID: 23748837	2013
Threshold-controlled ubiquitination of the EGFR directs receptor fate. The EMBO journal\| PubMed ID: 23799367	2013
Polycomb-dependent H3K27me1 and H3K27me2 regulate active transcription and enhancer fidelity. Molecular cell\| PubMed ID: 24289921	2014
Biochemical systems approaches for the analysis of histone modification readout. Biochimica et biophysica acta\| PubMed ID: 24681439	2014
Quantitative chemical proteomics identifies novel targets of the anti-cancer multi-kinase inhibitor E-3810. Molecular & cellular proteomics : MCP\| PubMed ID: 24696502	2014
Proteomics meets genetics: SILAC labeling of Drosophila melanogaster larvae and cells for in vivo functional studies. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 25059620
Improved bottom-up strategy to efficiently separate hypermodified histone peptides through ultra-HPLC separation on a bench top Orbitrap instrument. Proteomics\| PubMed ID: 25073962
ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites. Nucleic acids research\| PubMed ID: 25605800
Extracellular vesicle-mediated transfer of CLIC1 protein is a novel mechanism for the regulation of glioblastoma growth. Oncotarget\| PubMed ID: 26429879
Pathology Tissue-quantitative Mass Spectrometry Analysis to Profile Histone Post-translational Modification Patterns in Patient Samples. Molecular & cellular proteomics : MCP\| PubMed ID: 26463340
miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth. Nature communications\| PubMed ID: 26555894
The contribution of mass spectrometry-based proteomics to understanding epigenetics. Epigenomics\| PubMed ID: 26606673
Recent advances in mass spectrometry analysis of histone post-translational modifications: potential clinical impact of the PAT-H-MS approach. Expert review of proteomics\| PubMed ID: 26822344
MS-analysis of SILAC-labeled MYC-driven B lymphoma cells overexpressing miR-17-19b. Data in brief\| PubMed ID: 26977435
MYC/miR-17-92 interplay maintains B-lymphoma cell homeostasis. Cell cycle (Georgetown, Tex.)\| PubMed ID: 27097369
The EGFR-specific antibody cetuximab combined with chemotherapy triggers immunogenic cell death. Nature medicine\| PubMed ID: 27135741
Spatiotemporal plasticity of miRNAs functions: The miR-17-92 case. Molecular & cellular oncology\| PubMed ID: 27314099
Quantitative assessment of chemical artefacts produced by propionylation of histones prior to mass spectrometry analysis. Proteomics\| PubMed ID: 27373704
Mass-spectrometry analysis of histone post-translational modifications in pathology tissue using the PAT-H-MS approach. Data in brief\| PubMed ID: 27408908
SILAC-Based Quantitative Strategies for Accurate Histone Posttranslational Modification Profiling Across Multiple Biological Samples. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 27854018
High constitutive activity of a broad panel of housekeeping and tissue-specific -regulatory elements depends on a subset of ETS proteins. Genes & development\| PubMed ID: 28275002
PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples. Clinical epigenetics\| PubMed ID: 28702092
Design of KDM4 Inhibitors with Antiproliferative Effects in Cancer Models. ACS medicinal chemistry letters\| PubMed ID: 28835804
Chromatin proteomics reveals novel combinatorial histone modification signatures that mark distinct subpopulations of macrophage enhancers. Nucleic acids research\| PubMed ID: 28981749
A role for CENP-A/Cse4 phosphorylation on serine 33 in deposition at the centromere. FEMS yeast research\| PubMed ID: 29272409
Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases. Nature communications\| PubMed ID: 29317660	2018
PARP14 Controls the Nuclear Accumulation of a Subset of Type I IFN-Inducible Proteins. Journal of immunology (Baltimore, Md. : 1950)\| PubMed ID: 29500242
Zc3h10 is a novel mitochondrial regulator. EMBO reports\| PubMed ID: 29507079
Extensive and systematic rewiring of histone post-translational modifications in cancer model systems. Nucleic acids research\| PubMed ID: 29618087
The kinetochore module Okp1/Ame1 is a reader for N-terminal modifications on the centromeric histone Cse4. The EMBO journal\| PubMed ID: 30389668
Mass Spectrometry-Based Proteomics to Unveil the Non-coding RNA World. Frontiers in molecular biosciences\| PubMed ID: 30467545
Alternative digestion approaches improve histone modification mapping by mass spectrometry in clinical samples. Proteomics. Clinical applications\| PubMed ID: 30471193
hmSEEKER: Identification of hmSILAC Doublets in MaxQuant Output Data. Proteomics\| PubMed ID: 30656827
Proteomics profiling of arginine methylation defines PRMT5 substrate specificity. Science signaling\| PubMed ID: 30940768
Profiling of Epigenetic Features in Clinical Samples Reveals Novel Widespread Changes in Cancer. Cancers\| PubMed ID: 31137727
Therapeutic Targeting of RNA Splicing Catalysis through Inhibition of Protein Arginine Methylation. Cancer cell\| PubMed ID: 31408619
hSWATH: Unlocking SWATH's Full Potential for an Untargeted Histone Perspective. Journal of proteome research\| PubMed ID: 31429292
Epigenetic drug target deconvolution by mass spectrometry-based technologies. Nature structural & molecular biology\| PubMed ID: 31582842
Enrichment of histones from patient samples for mass spectrometry-based analysis of post-translational modifications. Methods (San Diego, Calif.)\| PubMed ID: 31605746
PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis. Nucleic acids research\| PubMed ID: 31777917
PRMT1 Is Recruited via DNA-PK to Chromatin Where It Sustains the Senescence-Associated Secretory Phenotype in Response to Cisplatin. Cell reports\| PubMed ID: 31995759
Targeting the scaffolding role of LSD1 (KDM1A) poises acute myeloid leukemia cells for retinoic acid-induced differentiation. Science advances\| PubMed ID: 32284990
Biochemical and Computational Approaches for the Large-Scale Analysis of Protein Arginine Methylation by Mass Spectrometry. Current protein & peptide science\| PubMed ID: 32338214
Clinical Application of Mass Spectrometry-Based Proteomics in Lung Cancer Early Diagnosis. Proteomics. Clinical applications\| PubMed ID: 32418314
Software Options for the Analysis of MS-Proteomic Data. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34236654	2021
Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples. Clinical epigenetics\| PubMed ID: 34315505	2021
Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-translational Modification (PTM) Combinatorics at Distinct Genomic Regions. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 34382194	2021
Pharmacological inhibition of LSD1 triggers myeloid differentiation by targeting GSE1 oncogenic functions in AML. Oncogene\| PubMed ID: 34862459	2022