Simone Sidoli

Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells.

Proteomics in chromatin biology and epigenetics: Elucidation of post-translational modifications of histone proteins by mass spectrometry.

The C. elegans H3K27 demethylase UTX-1 is essential for normal development, independent of its enzymatic activity.

Precision mapping of coexisting modifications in histone H3 tails from embryonic stem cells by ETD-MS/MS.

KYSS: mass spectrometry data quality assessment for protein analysis and large-scale proteomics.

Comparative proteomic analysis of histone post-translational modifications upon ischemia/reperfusion-induced retinal injury.

Large scale analysis of co-existing post-translational modifications in histone tails reveals global fine structure of cross-talk.

Transcription factor cooperativity in early adipogenic hotspots and super-enhancers.

Middle-down hybrid chromatography/tandem mass spectrometry workflow for characterization of combinatorial post-translational modifications in histones.

Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2.

Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) Analysis for Characterization and Quantification of Histone Post-translational Modifications.

Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis.

Bottom-up and middle-down proteomics have comparable accuracies in defining histone post-translational modification relative abundance and stoichiometry.

Two distinct modes for propagation of histone PTMs across the cell cycle.

EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra.

Quantitative proteomics analysis of platelet-derived microparticles reveals distinct protein signatures when stimulated by different physiological agonists.

Proteogenomics analysis reveals specific genomic orientations of distal regulatory regions composed by non-canonical histone variants.

Properly reading the histone code by MS-based proteomics.

Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations.

Top-down and Middle-down Protein Analysis Reveals that Intact and Clipped Human Histones Differ in Post-translational Modification Patterns.

The PZP Domain of AF10 Senses Unmodified H3K27 to Regulate DOT1L-Mediated Methylation of H3K79.

Tumor suppressor ASXL1 is essential for the activation of INK4B expression in response to oncogene activity and anti-proliferative signals.

H3K23me2 is a new heterochromatic mark in Caenorhabditis elegans.

Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications.

Dynamic changes of histone H3 marks during Caenorhabditis elegans lifecycle revealed by middle-down proteomics.

Loss of HP1 causes depletion of H3K27me3 from facultative heterochromatin and gain of H3K27me2 at constitutive heterochromatin.

Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation.

Analyses of Histone Proteoforms Using Front-end Electron Transfer Dissociation-enabled Orbitrap Instruments.

Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells.

Multiplexed data independent acquisition (MSX-DIA) applied by high resolution mass spectrometry improves quantification quality for the analysis of histone peptides.

Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry.

Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation.

High performance mass spectrometry based proteomics reveals enzyme and signaling pathway regulation in neutrophils during the early stage of surgical trauma.

Nuclear phosphoproteome analysis of 3T3-L1 preadipocyte differentiation reveals system-wide phosphorylation of transcriptional regulators.

High-Resolution Mapping of RNA-Binding Regions in the Nuclear Proteome of Embryonic Stem Cells.

Characterization of Individual Histone Posttranslational Modifications and Their Combinatorial Patterns by Mass Spectrometry-Based Proteomics Strategies.

Why proteomics is not the new genomics and the future of mass spectrometry in cell biology.

Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells.

Time-resolved Global and Chromatin Proteomics during Herpes Simplex Virus Type 1 (HSV-1) Infection.

Multicellular Tumor Spheroids Combined with Mass Spectrometric Histone Analysis To Evaluate Epigenetic Drugs.

Abnormal levels of histone methylation in the retinas of diabetic rats are reversed by minocycline treatment.

Quantitative chromatin proteomics reveals a dynamic histone post-translational modification landscape that defines asexual and sexual Plasmodium falciparum parasites.

Middle-down proteomics: a still unexploited resource for chromatin biology.

Metabolic labeling in middle-down proteomics allows for investigation of the dynamics of the histone code.

Identification of Nidogen 1 as a lung metastasis protein through secretome analysis.

Proteome-wide acetylation dynamics in human cells.

Phosphoproteomics reveals that glycogen synthase kinase-3 phosphorylates multiple splicing factors and is associated with alternative splicing.

An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides.

Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails.

A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins.

Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation.

Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis.

Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy.

Comprehensive Map of the Artemisia annua Proteome and Quantification of Differential Protein Expression in Chemotypes Producing High versus Low Content of Artemisinin.

Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function.

Mass Spectrometry to Study Chromatin Compaction.

Mutant FOXL2 Hijacks SMAD4 and SMAD2/3 to Drive Adult Granulosa Cell Tumors.

PR-DUB maintains the expression of critical genes through FOXK1/2- and ASXL1/2/3-dependent recruitment to chromatin and H2AK119ub1 deubiquitination.

nuclear RNAi factor SET-32 deposits the transgenerational histone modification, H3K23me3.

Phosphoproteomic Analysis of Rat Neutrophils Shows the Effect of Intestinal Ischemia/Reperfusion and Preconditioning on Kinases and Phosphatases.

Guide for protein fold change and p-value calculation for non-experts in proteomics.

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease.

Author Correction: An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease.

White adipose remodeling during browning in mice involves YBX1 to drive thermogenic commitment.

H1 histones control the epigenetic landscape by local chromatin compaction.

Toxoplasma gondii PPM3C, a secreted protein phosphatase, affects parasitophorous vacuole effector export.

One-shot analysis of translated mammalian lncRNAs with AHARIBO.

A Workflow for Ultra-rapid Analysis of Histone Post-translational Modifications with Direct-injection Mass Spectrometry.

Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons.

QSER1 protects DNA methylation valleys from de novo methylation.

Author Correction: Long-term behavioral and cell-type-specific molecular effects of early life stress are mediated by H3K79me2 dynamics in medium spiny neurons.

Protective neutralizing antibodies from human survivors of Crimean-Congo hemorrhagic fever.

VAL genes regulate vegetative phase change via miR156-dependent and independent mechanisms.

The Polycomb protein RING1B enables estrogen-mediated gene expression by promoting enhancer-promoter interaction and R-loop formation.

Independent transcriptomic and proteomic regulation by type I and II protein arginine methyltransferases.

High throughput and low bias DNA methylation and hydroxymethylation analysis by direct injection mass spectrometry.

A Key Silencing Histone Mark on Chromatin Is Lost When Colorectal Adenocarcinoma Cells Are Depleted of Methionine by Methionine γ-Lyase.

Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation.

Pipecolic Acid, a Putative Mediator of the Encephalopathy of Cerebral Malaria and the Experimental Model of Cerebral Malaria.

Type I and II PRMTs inversely regulate post-transcriptional intron detention through Sm and CHTOP methylation.

Genotype-specific features reduce the susceptibility of South American yellow fever virus strains to vaccine-induced antibodies.

DNA methylation and hydroxymethylation analysis using a high throughput and low bias direct injection mass spectrometry platform.

Multi-omic profiling of histone variant H3.3 lysine 27 methylation reveals a distinct role from canonical H3 in stem cell differentiation.

A Dynamic and Combinatorial Histone Code Drives Malaria Parasite Asexual and Sexual Development.

CpG island reconfiguration for the establishment and synchronization of polycomb functions upon exit from naive pluripotency.

Synthesis and Characterization of Transition-State Analogue Inhibitors against Human DNA Methyltransferase 1.

Macrophages use apoptotic cell-derived methionine and DNMT3A during efferocytosis to promote tissue resolution.

Altered abundances of human immunoglobulin M and immunoglobulin G subclasses in Alzheimer's disease frontal cortex.

The transcription factor PAX8 promotes angiogenesis in ovarian cancer through interaction with SOX17.

Dense Granule Protein GRA64 Interacts with Host Cell ESCRT Proteins during Infection.

Methamphetamine Dysregulates Macrophage Functions and Autophagy to Mediate HIV Neuropathogenesis.

CRISPR screening uncovers a central requirement for HHEX in pancreatic lineage commitment and plasticity restriction.

Reduced endosomal microautophagy activity in aging associates with enhanced exocyst-mediated protein secretion.

Autophagic state prospectively identifies facultative stem cells in the intestinal epithelium.

Morphine disrupts macrophage functions even during HIV infection.

Endocrine resistance and breast cancer plasticity are controlled by CoREST.

Investigation of reversible histone acetylation and dynamics in gene expression regulation using 3D liver spheroid model.

Post-Translational Modifications of Histone Variants in the Absence and Presence of a Methionine-Depleting Enzyme in Normal and Cancer Cells.

Proximity labeling reveals a new in vivo network of interactors for the histone demethylase KDM5.

Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography.

MAT Gain of Activity Mutation in Is Associated with Resistance to MTAN Transition State Analogues.

PROTAC-Mediated Selective Degradation of Cytosolic Soluble Epoxide Hydrolase Enhances ER Stress Reduction.

HSV-2 triggers upregulation of MALAT1 in CD4+ T cells and promotes HIV latency reversal.

DPP4 inhibition impairs senohemostasis to improve plaque stability in atherosclerotic mice.

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.

Epigenetic dysregulation from chromosomal transit in micronuclei.

The role of histone H3 lysine demethylases in glioblastoma.

Structural and mechanistic basis of neutralization by a pan-hantavirus protective antibody.

mTORC2-NDRG1-CDC42 axis couples fasting to mitochondrial fission.

Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability.

TMEM106B Puncta Is Increased in Multiple Sclerosis Plaques, and Reduced Protein in Mice Results in Delayed Lipid Clearance Following CNS Injury.

Tet2 regulates Sin3a recruitment at active enhancers in embryonic stem cells.

Proteomics and phosphoproteomics profiling in glutamatergic neurons and microglia in an iPSC model of Jansen de Vries Syndrome.

Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.

Prophylactic effect of chronic immunosuppression in a mouse model of CSF-1 receptor-related leukoencephalopathy.