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ProteomicsCharacterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression
Chromatin-associated RNAs have diverse roles in the nucleus. However, their mechanisms of action are poorly understood, in part due to the inability to identify proteins that specifically associate with chromatin-bound RNAs. Here, we address this problem for a subset of chromatin-associated RNAs tha...
ORGANISM(S): Mus musculus (Mouse) 
2021-09-17 | PXD022697 | Pride
R-loop-interacting proteins Immunoprecipitation/mass spectrometry approach Rna-protein crosslinking 
ProteomicsCRISPR-assisted RNA-protein interaction detection (CARPID) combined with quantitative mass spectrometry was used to identify proteins interacting with the long non-coding RNA (lncRNA) Taurine Up-regulated 1 (TUG1) in HEK293T cells under physiological conditions and after Camptothecin (CPT) treatment.
This project utilized CRISPR-assisted RNA-protein interaction detection (CARPID) combined with mass spectrometry to identify proteins interacting with the long non-coding RNA (lncRNA) TUG1 in HEK293T cells. TUG1 preferentially interacts with known R-loop-associated proteins, particularly under Campt...
ORGANISM(S): Homo Sapiens (human) 
2025-07-17 | PXD049137 | JPOST Repository
UnknownComprehensive identification of proteins interacting with long non-coding RNA TUG1 in R-loop regulation.
Not available
S-EPMC12480733 | biostudies-literature
UnknownCharacterization of R-Loop-Interacting Proteins in Embryonic Stem Cells Reveals Roles in rRNA Processing and Gene Expression.
Not available
S-EPMC8461376 | biostudies-literature
GenomicsCharacterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression
Characterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression
PRJNA679790 | ENA
TranscriptomicsCharacterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression
We performed mRNA-seq on mouse embryonic stem cells, with four DEAD-box family proteins, DDX10, DDX24, DDX27, DDX54 being partially depleted using RNA interference. Knockdown of EGFP was carried out as a control. By comparing all four knockdowns, we observed misregulation of a highly-overlapping set...
ORGANISM(S): Mus musculus 
2021-08-25 | GSE161890 | GEO
ProteomicsProximity labeling identifies a repertoire of site-specific R-loop modulators
R-loops are three stranded nucleic acid structures that accumulate on chromatin in neurological diseases and cancers and that contribute to genome instability. Using a proximity-dependent labeling system, we identified distinct classes of proteins that regulate R-loops in vivo through different mech...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2021-06-03 | MSV000087568 | MassIVE
OtherDRIP-sequencing U2OS
Here, we identify that a human DNA helicase RTEL1, which is known to play a role in the maintenance of telomeres by interacting with proteins in the shelterin complex by resolving G4 quadruplexes, is essential for prevention of R-loop accumulation during replication and for MiDAS in mitosis at both ...
ORGANISM(S): Homo sapiens 
2020-02-12 | GSE129907 | GEO
UnknownProximity labeling identifies a repertoire of site-specific R-loop modulators.
Not available
S-EPMC8748879 | biostudies-literature
UnknownATAD5 restricts R-loop formation through PCNA unloading and RNA helicase maintenance at the replication fork.
Not available
S-EPMC7367208 | biostudies-literature
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