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ProteomicsIdentification of DNA methylation reader proteins of Arabidopsis thaliana by DNA-affinity pull-down MS and their characterization by IP-MS.
In plants, cytosine DNA methylation (mC) is largely associated with transcriptional repression of transposable elements, but it can also be found in the body of expressed genes, referred to as gene body methylation (GbM). GbM is correlated with ubiquitously expressed genes, however its function, or ...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2025-06-09 | PXD050777 | Pride
Mbd Arabidopsis Plants Dna affinity pull-down Dna methylation Epigenetics Suvh Ap Lc-ms/ms 
ProteomicsA quantitative proteomics tool to identify DNA-protein interactions in primary cells or blood
The interaction between transcription factors and genomic DNA forms the basis for spatio-temporal control of gene expression. Therefore, these interactions and their impact on disease and cellular fate are extensively studied on a global level, mainly using techniques based on next-generation sequen...
ORGANISM(S): Homo sapiens (Human) 
2015-01-05 | PXD000782 | Pride
Blood Pbmcs Dna pull-down Primary cells 
ProteomicsPull-down affinity purifications using di-nucleosomes decorated with enhancer-associated modifications and incorporating 200bp linker DNA
Characteristic features of chromatin states are not limited to particular epigenetic modifications but include other regulatory cues, such as linker DNA length, typically ranging from around 35-55 bp in most eu- and heterochromatin domains (Valouev et al, 2011; Voong et al., 2016, Cell) to over 200 ...
ORGANISM(S): Homo sapiens (Human) 
2023-12-12 | PXD041443 | Pride
Ndrs H3k4me1 H3k27ac Pull-down 
TranscriptomicsTcRBP40 pull-down ribonomics
RNA pull-down assay.
For the recombinant protein pull-down assays, 50 M-5g of recombinant His-tag TcRBP40 protein were bound to 100 uL of Ni-NTA resin (Qiagen) overnight at 4M-0C. 100 M-5g of total RNA from epimastigotes were incubated with the bound protein in 500 M-5l EMSA buffer at 4M-0C for 2...
ORGANISM(S): Trypanosoma cruzi 
2012-06-30 | E-MEXP-3057 | biostudies-arrayexpress
ProteomicsIdentifying Specific Protein Interactors of Nucleosomes Carrying Methylated Histones using Quantitative Mass Spectrometry
Chemical modification of histone proteins by methylation plays a central role in chromatin regulation by recruiting epigenetic ‘readers’ via specialized binding domains. Depending on the degree of methylation, the exact modified amino acid, and the associated reader proteins histone methylations are...
ORGANISM(S): Homo sapiens (Human) 
2022-08-11 | PXD027238 | Pride
H3k4me3 Nucleosome pull-down affinity purification H3k9me3 Histone ptms 
ProteomicsDNA-protein affinity precipitation to identify proteins interacting with the atpT promoter in Synechocystis sp. PCC 6803
The small protein AtpΘ (encoded by gene atpT) identified in cyanobacteria becomes maximum expressed during low-energy conditions such as during darkness. In the model cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis 6803), AtpΘ was demonstrated to inhibit the ATP hydrolysis activity of the F...
ORGANISM(S): Synechocystis sp. PCC 6803 
2022-04-14 | PXD027801 | Pride
Dna-protein affinity precipitation  atpt promoter  synechocystis sp. pcc 6803  cyabrb 
ProteomicsIdentification of potential Rsf1 promoter-interacting proteins in rice (Oryza sativa Nipponbare) roots during nematode infection
We performed DNA-pull down experiments using biotin-labeled and unlabeled promoter sequences of Rsf1, a susceptibility factor in rice against root-knot nematode infection, to capture interacting nuclear proteins from rice roots at different time points post-infection (0, 1, and 3 days). Captured pro...
ORGANISM(S): Oryza sativa (Rice) 
2025-12-07 | PXD071646 | Pride
Lc-ms/ms Nuclear proteins. Promoter pull-down Root-knot nematode Dna-protein interaction Rice 
ProteomicsPT-modified B12 probe and Non-PT-modified B34 probe pull-down with Salmonella enterica serovar Cerro 87 cell lysate
To capture proteins that exhibit differential binding with PT- and non-PT-modified DNA in vivo, we performed pull-down assays using biotinylated DNA probes and the cell lysate of S. enterica serovar Cerro 87 that contains the dndBCDE-dndFGH module. For these experiments, we used two 30 bp DNA probes...
ORGANISM(S): Salmonella enterica subsp. enterica serovar Cerro 
2022-02-26 | PXD031869 | Pride
Salmonella，q exactive Phosphorothioation modification 
ProteomicsIdentification of cellular protein interacting with HBV genome by protein mass spectrometry
: Hepatitis B virus (HBV) remains a major public health threat with more than 296 million people chronically infected worldwide at high risk to develop hepatocellular carcinoma. Current therapies are effective in suppressing HBV replication but rarely lead to cure. The fundamental limitation rests o...
ORGANISM(S): Homo sapiens (Human) 
2024-06-16 | PXD042733 | Pride
Hbv cccdna Mini-chromosome Transcription Therapy 
ProteomicsExamining the effect of the linker DNA length on protein binding to di-nucleosomes decorated with H3K9me3 and H3K27me3
Characteristic features of chromatin states are not limited to particular epigenetic modifications but include other regulatory cues, such as linker DNA length, typically ranging from between 35-55 bp (Valouev et al, 2011; Voong et al., 2016, Cell) to over 200 bp in nucleosome-depleted regions (NDRs...
ORGANISM(S): Homo sapiens (Human) 
2023-12-10 | PXD042368 | Pride
Nucleosome pull-down Linker dna H3k27me3 H3k9me3 
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