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ProteomicsA quantitative proteomic analysis of in vitro assembled chromatin
The structure of chromatin is critical for many aspects of cellular physiology and is considered to be the primary medium to store epigenetic information. It is defined by the histone molecules that constitute the nucleosome, the positioning of the nucleosomes along the DNA and the non-histone prote...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2016-01-27 | PXD002537 | Pride
Acetylation  affinity proteomics  chromatin function or biology  label-free quantification   macromolecular assemblages 
ProteomicsDissection of acetylomic profiles in T cell lymphoma following histone deacetylases inhibition
The aim was to dissect molecular changes in histone and non-histone protein acetylation dynamics following the genetic or pharmacological inhibition of HDAC activity in a model of Anaplastic Large Cell Lymphoma (ALCL), a T cell non-Hodgkin lymphoma, predominantly found in children and adolescents.
ORGANISM(S): Mus musculus (Mouse) 
2022-10-14 | PXD030503 | Pride
Acetylomics Histone deacetylase inhibitors Anaplastic large cell lymphoma Histone deacetylases Proteomics 
ProteomicsMudPIT analyses of the proteins purified by in vitro dCas9-targeted chromatin IP of the fruit fly Histone Cluster
We used a reverse chromatin immunoprecipitation (ChIP) method that takes advantage of the RNA-mediated DNA-targeting capability of Cas9 to efficiently and adaptably isolate specific genomic regions and their associated protein factors. By using purified recombinant catalytically-dead Cas9 (dCas9) co...
ORGANISM(S): Drosophila Melanogaster (ncbitaxon:7227) 
2017-10-25 | MSV000081643 | MassIVE
GenomicsChromatin Profiling by Directly Sequencing Small Quantities of Immunoprecipitated DNA
Chromatin structure and transcription factor localization can be assayed genome-wide by sequencing genomic DNA fractionated by protein occupancy or other properties. However, current technologies involve multiple steps that introduce bias and inefficiency. Here we apply a single-molecule approach to...
ORGANISM(S): Mus musculus 
2009-11-29 | E-GEOD-18699 | biostudies-arrayexpress
TranscriptomicsFactors that promote H3 chromatin integrity during transcription prevent promiscuous deposition of CENP-A(Cnp1) in fission yeast
Specialized chromatin containing CENP-A nucleosomes instead of H3 nucleosomes is found at all centromeres. However, the mechanisms that specify the locations at which CENP-A chromatin is assembled remain elusive in organisms with regional, epigenetically regulated centromeres. It is known that norma...
ORGANISM(S): Schizosaccharomyces pombe 
2015-02-19 | E-GEOD-66106 | biostudies-arrayexpress
ProteomicsUnchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1
DNA ligase I (LigI), the predominant enzyme that joins Okazaki fragments, interacts with PCNA and Pol d. LigI also interacts with UHRF1, linking Okazaki fragment joining with DNA maintenance methylation. Okazaki fragments can also be joined by a relatively poorly characterized DNA ligase IIIa (LigII...
ORGANISM(S): Mus musculus (Mouse) 
2023-04-04 | PXD039547 | Pride
Dna ligase i Anipond-ms Dna replication 
ProteomicsH2A.Z histone variants facilitate HDACi-dependent removal of H3.3K27M mutant protein in paediatric high-grade glioma cells
Diffuse intrinsic pontine gliomas (DIPG) are a deadly paediatric brain tumours, non-resectable due to brainstem localisation and diffusive growth. Patients with DIPG have a dismal prognosis of 9-12 months of survival with no effective therapy. Over 80% of DIPGs harbour a mutation in histone 3 (H3.3 ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2023-10-05 | MSV000093052 | MassIVE
ProteomicsLambert_P82_VS4_Chromatin_BioID_APMS_12JUL2014
This submission contains the mass spectrometry files for the manuscript by Lambert et al. that describes the use of BioID for chromatin associated protein complexes. A detail comparison to a chromatin optimized AP-MS protocol was also performed. This submission contains 39 IDA files for the followin...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2014-07-17 | MSV000078782 | MassIVE
TranscriptomicsArgonaute proteins couple chromatin silencing to alternative splicing (RNA IP-Seq)
While Argonaute (AGO) proteins play a major role in transcriptional gene silencing (TGS) in many organisms, their role in the nucleus of somatic mammalian cells remains elusive. Here, we have purified AGO1 and AGO2 chromatin-embedded complexes, and found these proteins associated with previously des...
ORGANISM(S): Homo sapiens 
2012-09-10 | E-GEOD-39748 | biostudies-arrayexpress
GenomicsNanoscale Chromatin Profiling of Gastric Adenocarcinoma
To identify chromatin alterations in primary gastric adenocarcionomas, we performed nano-scale chromatin immunoprecipitation-sequencing (Nano-CHiPseq) of histone modifications in 5 gastric cancers and matched normal tissues, We identified hundreds of somatically-altered promoters (marked by H3K4me3)...
ORGANISM(S): Homo sapiens 
2014-07-30 | E-GEOD-51776 | biostudies-arrayexpress
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