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ProteomicsDegradation of G-Quadruplex Binding Proteins in Chromatin Using G4-Ligand-Based PROTACs
Targeted protein degradation can intervene with the function of disease-related proteins, but most current approaches rely on direct ligand engagement of a protein target, limiting their applicability to proteins that are difficult to bind selectively. We present a conceptually unique approach to de...
ORGANISM(S): Homo sapiens (Human) 
2026-01-27 | PXD073248 | Pride
G‑quadruplex  g4l‑protacs  chromatin  targeted protein degradation 
GenomicsG-Quadruplex structures are stable and detectable in human genomic DNA.
The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome. Herein, we address the hypothesis that G-quadruplex structures can exist within double-stranded genomic DNA using a G-quadruplex-specific probe. An engineered antibody is ...
ORGANISM(S): Homo sapiens 
2013-05-08 | E-GEOD-45241 | biostudies-arrayexpress
ProteomicsInteracting proteins of the NRAS RNA G-quadruplex
Biotinylated RNA oligos were used as baits for affinity enrichments from cytoplasmic cell extracts.
ORGANISM(S): Homo sapiens (Human) 
2019-11-12 | PXD010860 | Pride
Hela Rna Proteomics G4 Rna binding proteins 
ProteomicsDNA G-quadruplex structures act as functional elements in - and -globin enhancers
Enhancer elements interact with target genes at a distance to modulate their expression, but the molecular details of enhancer-promoter interaction are incompletely understood. G-quadruplex DNA secondary structures (G4s) have recently been shown to co-occur with 3D chromatin interactions, however, t...
ORGANISM(S): Homo sapiens (Human) 
2025-06-05 | PXD063882 | Pride
G-quadruplex structures Enhancers Epigenetics 3d chromatin interactions 
GenomicsSystematic identification of G-quadruplex sensitive lethality by genome-wide genetic screening
A375 and HT1080 cells are treated with G-quadruplex ligands PDS or PhenDC3 following genome-wide shRNA knockdown. This enables the identification of genes that when silenced, specifically compromises cell growth in the presence of the ligand. First, a pilot screen was performed to determine a ligand...
ORGANISM(S): Homo sapiens 
2019-06-22 | E-MTAB-6367 | biostudies-arrayexpress
TranscriptomicsSequence preference of DNMT3A/B dictates genome-wide DNA methylation signature
Exploring the sequence specificity of methylation by DNMT3A and DNMT3B using bisulfite sequencing in E.coli and publicly available mouse and human datasets
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2020-06-22 | E-MTAB-8406 | biostudies-arrayexpress
GenomicsGenome-wide distribution of 5-formylcytosine in ES cells is associated with transcription and depends on TDG
Methylation of cytosine in DNA (5mC) is an important epigenetic mark that is involved in the regulation of genome function. During early embryonic development in mammals, the DNA methylation landscape is dynamically reprogrammed in part through active demethylation. Recent advances have identified k...
ORGANISM(S): Mus musculus 
2012-08-17 | E-GEOD-40148 | biostudies-arrayexpress
TranscriptomicsrG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome
RNA structures are of crucial importance for biological function and gene regulation. Guanine (G)-rich sequences in RNA can assemble to form RNA G-quadruplex (rG4) structures; specific rG4s have been shown to regulate gene expression, and are associated with human diseases. However, no transcriptome...
ORGANISM(S): Homo sapiens 
2016-08-10 | E-GEOD-77282 | biostudies-arrayexpress
GenomicsEnhanced methylome sequencing by recovery of unsequenceable fragments
Bisulfite sequencing is a valuable tool for mapping the position of 5-methylcytosine in the genome at single base resolution. However, the associated chemistry renders the majority of DNA fragments unsequenceable, thus necessitating PCR amplification. Furthermore, bisulfite conversion generates an A...
ORGANISM(S): Plasmodium berghei ANKA 
2016-03-16 | E-GEOD-65116 | biostudies-arrayexpress
GenomicsQuantitative sequencing of 5-formylcytosine in DNA at single-base resolution
Cytosine base modifications 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) are present in mammalian DNA. Here, reduced bisulfite sequencing is developed for quantitatively sequencing 5fC at single-base resolution. This method is then applied with oxidative bisulfit...
ORGANISM(S): Mus musculus 
2014-04-08 | E-GEOD-56572 | biostudies-arrayexpress
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