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ProteomicsMeCP2 requires interactions with nucleosome linker DNA to read chromatin DNA methylation
ethyl-CpG-binding protein 2 (MeCP2) is an epigenetic reader essential for neuronal function, but how it binds DNA methylation within chromatin is still unclear. Using designer nucleosomes we observe that MeCP2 preferentially binds DNA methylation positioned at multiple sites around the nucleosome. S...
ORGANISM(S): Homo sapiens (Human) 
2026-06-29 | PXD064826 | Pride
Mecp2 Cross-linking mass spectrometry Dna methylation Nucleosomes Chromatin 
GenomicsGenomic distribution of linker histone varinat H1T
We report genome-wide distribution of germ cell-specific linker histone variant H1T in cancer cell line AGS, MDA-MB-231, and mouse embryonic stem cells (mESCs). We found that H1T expressed not only testis but also non-germ cells such as cancer cells and pluripotent stem cells and showed the biased d...
ORGANISM(S): Homo sapiens 
2016-03-30 | E-GEOD-75287 | biostudies-arrayexpress
ProteomicsProteome analysis of i-motif DNA binding proteins
Non-canonical DNA structures such as G-quadruplex (G4) and i-motif (iM) are formed at the guanine- and cytosine-rich sequences, respectively, and prohibit DNA replication and transcription. The formation and resolution of these non-canonical structures are therefore required to be dynamically regula...
ORGANISM(S): Homo Sapiens (human) 
2024-10-15 | PXD051188 | JPOST Repository
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 
ProteomicsIdentification and analysis of phosphorylation within Xenopus laevis linker histone H1.0
As a key structural component of the chromatin of higher eukaryotes, linker histones (H1s) are involved in stabilizing the folding of extended nucleosome arrays into higher-order chromatin structures and function as a gene-specific regulators of transcription in vivo. The H1 C-terminal domain (CTD) ...
ORGANISM(S): Xenopus laevis (African clawed frog) 
2022-08-12 | PXD032292 | Pride
Identification and analysis of phosphorylation within xenopus laevis linker histone h1.0 
GenomicsMapping of somatic linker histone H1 variants in T47D-MTVL cells
At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the di...
ORGANISM(S): Homo sapiens 
2014-02-04 | E-GEOD-49334 | biostudies-arrayexpress
GenomicsNovel nucleosomal particles containing core histones and linker DNA but no histone H1
Novel nucleosomal particles containing core histones and linker DNA but no histone H1
PRJNA275314 | ENA
TranscriptomicsMapping of somatic linker histone H1 variants in T47D-MTVL and HeLa cells
At least six histone H1 variants exist in mammalian somatic cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction. In addition, H1 seems to be involved in the active regulation of gene expression. It is not well known whether the di...
ORGANISM(S): Homo sapiens 
2014-02-04 | E-GEOD-49333 | biostudies-arrayexpress
ProteomicsAnalysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry
Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of protei...
ORGANISM(S): Homo sapiens (Human) Xenopus laevis (African clawed frog) 
2020-10-20 | PXD020290 | Pride
Mass spectrometry Protein-dna interactions Uv-cross-linking 
GenomicsNovel nucleosomal particles containing core histones and linker DNA but no histone H1
The nucleosome plays a central role in genome regulation. Traditional methods for mapping nucleosomes depend on the resistance of the nucleosome core to micrococcal nuclease (MNase). However, the lengths of the protected DNA fragments are heterogeneous, limiting the accuracy of nucleosome position i...
ORGANISM(S): Synthetic plasmid 
2015-09-23 | E-GEOD-65889 | biostudies-arrayexpress
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