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ProteomicsFluctuations in histone H4 isoforms during cellular reprogramming monitored by middle-down proteomics
Cellular reprogramming remodels the gene expression program by re-setting the epigenome of somatic cells into an embryonic-like state. Post-translational modifications of histones play an important role in this process. We previously used ChIP-seq to profile the distribution of specific histone H3 m...
ORGANISM(S): Mus musculus (Mouse) 
2015-08-17 | PXD002062 | Pride
Proteomics Middle-down Histone h4 Cellular reprogramming Post translational modifications 
ProteomicsTop Down Histone H4 - SUM159 Butyrate
Proteins physiologically exist and function as ‘proteoforms’ that arise from one gene but acquire additional function by further variation such as post-translational modification (PTM). When multiple PTMs coexist on single protein molecules top down proteomics becomes the only feasible method; howev...
ORGANISM(S): Homo sapiens (Human) 
2019-11-22 | PXD013766 | Pride
Top-down Histone h4 
ProteomicsForebrain Hindbrain histone H4 Mus musculus P25 P47
Quantitative top down analysis of histone H4 proteoforms in the mouse forebrain and hindbrain at 25 and 47 days of age.
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
MSV000090249 | MassIVE
ProteomicsGlutamate methylation on histones H4 and H2B
Glutamate methylation is a novel histone modification discovered on histones H4 (E52/E53, E63, E74) and histone H2B (E96)
ORGANISM(S): Homo sapiens (Human) Drosophila melanogaster (Fruit fly) Phaeodactylum tricornutum Caenorhabditis elegans Thalassiosira pseudonana 
2025-02-10 | PXD053679 | Pride
Diatoms Transcriptional regulation Glutamate methylation Histones structure Nucleosome stability 
ProteomicsTwo DOT1 enzymes cooperatively mediate efficient ubiquitin-independent histone H3 lysine 76 tri-methylation in kinetoplastids
In higher eukaryotes, a single DOT1 histone H3 lysine 79 (H3K79) methyltransferase processively produces H3K79me2/me3 from me0 through histone H2B mono-ubiquitin interaction. The early-branched kinetoplastid Trypanosoma brucei harbors the essential H3K76 di-methyltransferase DOT1A and the non-essent...
ORGANISM(S): Trypanosoma Brucei (ncbitaxon:5691) 
2022-11-09 | MSV000090680 | MassIVE
TranscriptomicsDNA methylation and expression profiling study for prostate cancer
Microarray-based DNA methylation and gene expression profiling was carried out using a panel of prostate cancer cell lines (LNCaP-FGC, DU-145, and PC-3) and the control normal prostate RWPE1 cell line. The identification of prostate cancer-specific methylation markers was based on the following crit...
ORGANISM(S): Homo sapiens 
2011-07-24 | E-GEOD-23388 | biostudies-arrayexpress
ProteomicsMiddle-Down Characterization of the Cell Cycle Dependence of Histone H4 PTMs and Proteoforms
In the present study, a middle-down approach is employed for the identification, characterization, and quantitation of the PTMs and proteoforms of histone H4 in two breast cancer cell lines. Our experimental strategy not only preserves the combinatorial attributes of existing PTMs, but also enhances...
ORGANISM(S): Homo sapiens (Human) 
2018-07-05 | PXD008296 | Pride
Hilic Ft-icr Ptm Mass spectrometry Etd 
TranscriptomicsIDH1 mutation defines methylation class and survival in human glioma
Astrocytoma, oligodendroglioma, oligoastrocytoma, and ependymoma are the main histologic subtypes of glioma. The molecular character of these subtypes has profound implications for understanding their causes and treatment. We describe the epigenetic landscape of these tumor types using novel DNA met...
ORGANISM(S): Homo sapiens 
2010-12-20 | E-GEOD-20395 | biostudies-arrayexpress
GenomicsmethylSig: a whole genome DNA methylation analysis pipeline
DNA methylation plays critical roles in gene regulation and cellular specification without altering DNA sequences. The wide application of reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing (bis-seq) opens the door to study DNA methylation at single CpG site re...
ORGANISM(S): Homo sapiens 
2014-08-22 | E-GEOD-55569 | biostudies-arrayexpress
GenomicsGenome-wide DNA methylation aberrations in human atherosclerosis (sequencing)
Epigenetics may help understanding the molecular mechanisms of atherosclerosis as genetic predisposition explains only part of cardiovascular disease risk. In particular, DNA methylation, a reversible and highly regulative DNA modification could contribute to disease onset and progression as it func...
ORGANISM(S): Homo sapiens 
2014-08-12 | E-GEOD-46327 | biostudies-arrayexpress
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