Epigenetics Program,
Department of Biochemistry and Biophysics,
Perelman School of Medicine,
Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine
Simone Sidoli is an Assistant Professor at the Albert Einstein College of Medicine, Department of Biochemistry, and Scientific Director of the Einstein Proteomics Core. Dr. Sidoli applies proteomics to identify the composition and dynamics of chromatin. This includes the development of new quantitative methods to identify histone modifications, locus-specific proteomes, and biomarkers in disease. His lab is invested in innovating new 3D cell models to reduce the necessity of animal testing, and in advancing the use of minimally invasive devices to collect biopsies.
Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells.
Cell reports Oct, 2016 | Pubmed ID: 27783950
Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry.
Journal of proteomics Jun, 2012 | Pubmed ID: 22234360
The C. elegans H3K27 demethylase UTX-1 is essential for normal development, independent of its enzymatic activity.
PLoS genetics , 2012 | Pubmed ID: 22570628
Precision mapping of coexisting modifications in histone H3 tails from embryonic stem cells by ETD-MS/MS.
Analytical chemistry Sep, 2013 | Pubmed ID: 23889513
KYSS: mass spectrometry data quality assessment for protein analysis and large-scale proteomics.
Biochemical and biophysical research communications Mar, 2014 | Pubmed ID: 24480439
Comparative proteomic analysis of histone post-translational modifications upon ischemia/reperfusion-induced retinal injury.
Journal of proteome research Apr, 2014 | Pubmed ID: 24628298
Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk.
Molecular & cellular proteomics : MCP Jul, 2014 | Pubmed ID: 24741113
Transcription factor cooperativity in early adipogenic hotspots and super-enhancers.
Cell reports Jun, 2014 | Pubmed ID: 24857652
Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones.
Proteomics Oct, 2014 | Pubmed ID: 25073878
Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2.
Genome research Jan, 2015 | Pubmed ID: 25467431
Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) Analysis for Characterization and Quantification of Histone Post-translational Modifications.
Molecular & cellular proteomics : MCP Sep, 2015 | Pubmed ID: 25636311
Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis.
Proteomics May, 2015 | Pubmed ID: 25641854
Bottom-up and middle-down proteomics have comparable accuracies in defining histone post-translational modification relative abundance and stoichiometry.
Analytical chemistry Mar, 2015 | Pubmed ID: 25719549
Two distinct modes for propagation of histone PTMs across the cell cycle.
Genes & development Mar, 2015 | Pubmed ID: 25792596
EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra.
Molecular & cellular proteomics : MCP Jun, 2015 | Pubmed ID: 25805797
Quantitative proteomics analysis of platelet-derived microparticles reveals distinct protein signatures when stimulated by different physiological agonists.
Journal of proteomics May, 2015 | Pubmed ID: 25835965
Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants.
Epigenetics & chromatin , 2015 | Pubmed ID: 25878728
Properly reading the histone code by MS-based proteomics.
Proteomics Sep, 2015 | Pubmed ID: 26223514
Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations.
Expert review of proteomics , 2015 | Pubmed ID: 26400466
Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns.
Molecular & cellular proteomics : MCP Dec, 2015 | Pubmed ID: 26424599
The PZP Domain of AF10 Senses Unmodified H3K27 to Regulate DOT1L-Mediated Methylation of H3K79.
Molecular cell Oct, 2015 | Pubmed ID: 26439302
Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals.
Cell research Nov, 2015 | Pubmed ID: 26470845
H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans.
Nucleic acids research Nov, 2015 | Pubmed ID: 26476455
Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications.
Analytical chemistry Nov, 2015 | Pubmed ID: 26505526
Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics.
Proteomics Feb, 2016 | Pubmed ID: 26508544
Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin.
Genome research Jan, 2016 | Pubmed ID: 26537359
Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation.
Proteomics Feb, 2016 | Pubmed ID: 26631989
Analyses of Histone Proteoforms Using Front-end Electron Transfer Dissociation-enabled Orbitrap Instruments.
Molecular & cellular proteomics : MCP Mar, 2016 | Pubmed ID: 26785730
Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells.
BMC genomics , 2016 | Pubmed ID: 26847871
Multiplexed data independent acquisition (MSX-DIA) applied by high resolution mass spectrometry improves quantification quality for the analysis of histone peptides.
Proteomics Aug, 2016 | Pubmed ID: 27193262
Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry.
Molecular bioSystems Jul, 2016 | Pubmed ID: 27301801
Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation.
Molecular & cellular proteomics : MCP Aug, 2016 | Pubmed ID: 27302890
High performance mass spectrometry based proteomics reveals enzyme and signaling pathway regulation in neutrophils during the early stage of surgical trauma.
Proteomics. Clinical applications Jan, 2017 | Pubmed ID: 27672009
Nuclear phosphoproteome analysis of 3T3-L1 preadipocyte differentiation reveals system-wide phosphorylation of transcriptional regulators.
Proteomics Mar, 2017 | Pubmed ID: 27717184
High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells.
Molecular cell Oct, 2016 | Pubmed ID: 27768875
Characterization of Individual Histone Posttranslational Modifications and Their Combinatorial Patterns by Mass Spectrometry-Based Proteomics Strategies.
Methods in molecular biology (Clifton, N.J.) , 2017 | Pubmed ID: 27854019
Why proteomics is not the new genomics and the future of mass spectrometry in cell biology.
The Journal of cell biology Jan, 2017 | Pubmed ID: 27956468
Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells.
Cell reports Jan, 2017 | Pubmed ID: 28052258
Time-resolved Global and Chromatin Proteomics during Herpes Simplex Virus Type 1 (HSV-1) Infection.
Molecular & cellular proteomics : MCP Apr, 2017 | Pubmed ID: 28179408
Multicellular Tumor Spheroids Combined with Mass Spectrometric Histone Analysis To Evaluate Epigenetic Drugs.
Analytical chemistry Mar, 2017 | Pubmed ID: 28194967
Abnormal levels of histone methylation in the retinas of diabetic rats are reversed by minocycline treatment.
Scientific reports Mar, 2017 | Pubmed ID: 28338045
Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites.
Scientific reports Apr, 2017 | Pubmed ID: 28377601
Middle-down proteomics: a still unexploited resource for chromatin biology.
Expert review of proteomics Jul, 2017 | Pubmed ID: 28649883
Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code.
Epigenetics & chromatin Jul, 2017 | Pubmed ID: 28683815
Identification of Nidogen 1 as a lung metastasis protein through secretome analysis.
Genes & development Jul, 2017 | Pubmed ID: 28827399
Proteome-wide acetylation dynamics in human cells.
Scientific reports Aug, 2017 | Pubmed ID: 28860605
Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing.
The Journal of biological chemistry Sep, 2017 | Pubmed ID: 28916722
An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides.
Nature communications Sep, 2017 | Pubmed ID: 28916805
Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails.
Journal of the American Society for Mass Spectrometry Dec, 2019 | Pubmed ID: 31512222
A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins.
Scientific reports 09, 2019 | Pubmed ID: 31541121
Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation.
Nature communications 10, 2019 | Pubmed ID: 31624313
Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis.
Methods (San Diego, Calif.) 12, 2020 | Pubmed ID: 32070774
Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy.
Nature genetics 03, 2020 | Pubmed ID: 32139906
Comprehensive Map of the Artemisia annua Proteome and Quantification of Differential Protein Expression in Chemotypes Producing High versus Low Content of Artemisinin.
Proteomics 05, 2020 | Pubmed ID: 32311217
Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function.
Nature communications 05, 2020 | Pubmed ID: 32376827
Mass Spectrometry to Study Chromatin Compaction.
Biology Jun, 2020 | Pubmed ID: 32604817
Mutant FOXL2 Hijacks SMAD4 and SMAD2/3 to Drive Adult Granulosa Cell Tumors.
Cancer research 09, 2020 | Pubmed ID: 32641411
PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination.
Genome research 08, 2020 | Pubmed ID: 32747411
nuclear RNAi factor SET-32 deposits the transgenerational histone modification, H3K23me3.
eLife 08, 2020 | Pubmed ID: 32804637
Phosphoproteomic Analysis of Rat Neutrophils Shows the Effect of Intestinal Ischemia/Reperfusion and Preconditioning on Kinases and Phosphatases.
International journal of molecular sciences Aug, 2020 | Pubmed ID: 32823483
Guide for protein fold change and p-value calculation for non-experts in proteomics.
Molecular omics 12, 2020 | Pubmed ID: 32968743
An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease.
Nature genetics 10, 2020 | Pubmed ID: 32989324
Author Correction: An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease.
Nature genetics Nov, 2020 | Pubmed ID: 33033384
White adipose remodeling during browning in mice involves YBX1 to drive thermogenic commitment.
Molecular metabolism 02, 2021 | Pubmed ID: 33285300
H1 histones control the epigenetic landscape by local chromatin compaction.
Nature 01, 2021 | Pubmed ID: 33299182
Toxoplasma gondii PPM3C, a secreted protein phosphatase, affects parasitophorous vacuole effector export.
PLoS pathogens 12, 2020 | Pubmed ID: 33370417
One-shot analysis of translated mammalian lncRNAs with AHARIBO.
eLife 02, 2021 | Pubmed ID: 33594971
A Workflow for Ultra-rapid Analysis of Histone Post-translational Modifications with Direct-injection Mass Spectrometry.
Bio-protocol Sep, 2020 | Pubmed ID: 33659415
Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons.
Nature neuroscience 05, 2021 | Pubmed ID: 33723435
QSER1 protects DNA methylation valleys from de novo methylation.
Science (New York, N.Y.) 04, 2021 | Pubmed ID: 33833093
Author Correction: Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons.
Nature neuroscience May, 2021 | Pubmed ID: 33833436
Protective neutralizing antibodies from human survivors of Crimean-Congo hemorrhagic fever.
Cell 06, 2021 | Pubmed ID: 34077751
VAL genes regulate vegetative phase change via miR156-dependent and independent mechanisms.
PLoS genetics 06, 2021 | Pubmed ID: 34181637
The Polycomb protein RING1B enables estrogen-mediated gene expression by promoting enhancer-promoter interaction and R-loop formation.
Nucleic acids research 09, 2021 | Pubmed ID: 34428304
Independent transcriptomic and proteomic regulation by type I and II protein arginine methyltransferases.
iScience Sep, 2021 | Pubmed ID: 34505004
High throughput and low bias DNA methylation and hydroxymethylation analysis by direct injection mass spectrometry.
Analytica chimica acta Oct, 2021 | Pubmed ID: 34538324
A Key Silencing Histone Mark on Chromatin Is Lost When Colorectal Adenocarcinoma Cells Are Depleted of Methionine by Methionine γ-Lyase.
Frontiers in molecular biosciences , 2021 | Pubmed ID: 34660696
Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation.
Molecular cell 01, 2022 | Pubmed ID: 34856123
Pipecolic Acid, a Putative Mediator of the Encephalopathy of Cerebral Malaria and the Experimental Model of Cerebral Malaria.
The Journal of infectious diseases Feb, 2022 | Pubmed ID: 34932816
Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation.
eLife 01, 2022 | Pubmed ID: 34984976
Genotype-specific features reduce the susceptibility of South American yellow fever virus strains to vaccine-induced antibodies.
Cell host & microbe 02, 2022 | Pubmed ID: 34998466
DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform.
MethodsX , 2021 | Pubmed ID: 35004218
Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation.
Molecular omics Jan, 2022 | Pubmed ID: 35044400
A Dynamic and Combinatorial Histone Code Drives Malaria Parasite Asexual and Sexual Development.
Molecular & cellular proteomics : MCP Mar, 2022 | Pubmed ID: 35051657
CpG island reconfiguration for the establishment and synchronization of polycomb functions upon exit from naive pluripotency.
Molecular cell 03, 2022 | Pubmed ID: 35202573
Synthesis and Characterization of Transition-State Analogue Inhibitors against Human DNA Methyltransferase 1.
Journal of medicinal chemistry Apr, 2022 | Pubmed ID: 35324190
Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution.
Nature metabolism Apr, 2022 | Pubmed ID: 35361955
Altered abundances of human immunoglobulin M and immunoglobulin G subclasses in Alzheimer's disease frontal cortex.
Scientific reports Apr, 2022 | Pubmed ID: 35484384
The transcription factor PAX8 promotes angiogenesis in ovarian cancer through interaction with SOX17.
Science signaling Apr, 2022 | Pubmed ID: 35380877
Dense Granule Protein GRA64 Interacts with Host Cell ESCRT Proteins during Infection.
mBio Aug, 2022 | Pubmed ID: 35730903
Methamphetamine Dysregulates Macrophage Functions and Autophagy to Mediate HIV Neuropathogenesis.
Biomedicines May, 2022 | Pubmed ID: 35740279
CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction.
Nature cell biology Jul, 2022 | Pubmed ID: 35787684
Reduced endosomal microautophagy activity in aging associates with enhanced exocyst-mediated protein secretion.
Aging cell Oct, 2022 | Pubmed ID: 36116133
Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium.
EMBO reports Nov, 2022 | Pubmed ID: 36120829
Morphine disrupts macrophage functions even during HIV infection.
Journal of leukocyte biology Nov, 2022 | Pubmed ID: 36205434
Endocrine resistance and breast cancer plasticity are controlled by CoREST.
Nature structural & molecular biology Nov, 2022 | Pubmed ID: 36344844
Investigation of reversible histone acetylation and dynamics in gene expression regulation using 3D liver spheroid model.
Epigenetics & chromatin Nov, 2022 | Pubmed ID: 36411440
Post-Translational Modifications of Histone Variants in the Absence and Presence of a Methionine-Depleting Enzyme in Normal and Cancer Cells.
Cancers Jan, 2023 | Pubmed ID: 36672476
Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5.
Epigenetics & chromatin Feb, 2023 | Pubmed ID: 36803422
Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography.
Analytical chemistry Mar, 2023 | Pubmed ID: 36916610
MAT Gain of Activity Mutation in Is Associated with Resistance to MTAN Transition State Analogues.
ACS infectious diseases Apr, 2023 | Pubmed ID: 36920074
PROTAC-Mediated Selective Degradation of Cytosolic Soluble Epoxide Hydrolase Enhances ER Stress Reduction.
ACS chemical biology Apr, 2023 | Pubmed ID: 36947831
HSV-2 triggers upregulation of MALAT1 in CD4+ T cells and promotes HIV latency reversal.
The Journal of clinical investigation Jun, 2023 | Pubmed ID: 37079384
DPP4 inhibition impairs senohemostasis to improve plaque stability in atherosclerotic mice.
The Journal of clinical investigation Jun, 2023 | Pubmed ID: 37097759
Orally administered sodium nitrite prevents the increased α-1 adrenergic vasoconstriction induced by hypertension and promotes the S-nitrosylation of calcium/calmodulin-dependent protein kinase II.
Biochemical pharmacology Jun, 2023 | Pubmed ID: 37127250
Epigenetic dysregulation from chromosomal transit in micronuclei.
Nature Jul, 2023 | Pubmed ID: 37286593
The role of histone H3 lysine demethylases in glioblastoma.
Cancer metastasis reviews Jun, 2023 | Pubmed ID: 37286866
Structural and mechanistic basis of neutralization by a pan-hantavirus protective antibody.
Science translational medicine Jun, 2023 | Pubmed ID: 37315110
mTORC2-NDRG1-CDC42 axis couples fasting to mitochondrial fission.
Nature cell biology Jul, 2023 | Pubmed ID: 37386153
Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability.
Nature cell biology Jul, 2023 | Pubmed ID: 37414849
TMEM106B Puncta Is Increased in Multiple Sclerosis Plaques, and Reduced Protein in Mice Results in Delayed Lipid Clearance Following CNS Injury.
Cells Jun, 2023 | Pubmed ID: 37443768
Tet2 regulates Sin3a recruitment at active enhancers in embryonic stem cells.
iScience Jul, 2023 | Pubmed ID: 37456851
Proteomics and phosphoproteomics profiling in glutamatergic neurons and microglia in an iPSC model of Jansen de Vries Syndrome.
bioRxiv : the preprint server for biology Jul, 2023 | Pubmed ID: 37461463
Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.
Nature genetics Aug, 2023 | Pubmed ID: 37488417
Prophylactic effect of chronic immunosuppression in a mouse model of CSF-1 receptor-related leukoencephalopathy.
Glia Jul, 2023 | Pubmed ID: 37519044
Robert Warneford-Thomson1,4,
Chongsheng He1,2,
Simone Sidoli1,3,
Benjamin A. Garcia1,3,
Roberto Bonasio1,2
1Epigenetics Institute, University of Pennsylvania Perelman School of Medicine,
2Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine,
3Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine,
4Graduate Group in Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine