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ProteomicsncRNA DUBR RAP-MS in HCT116 cells
Non-coding RNAs (ncRNAs) are finely tuned cellular regulators important for human cell growth and cancer progression. DUBR (also known as linc00883) is a nuclear ncRNA first discovered in mice for its role in regulating myoblast differentiation through interactions with chromatin and DNA methyltrans...
ORGANISM(S): Homo sapiens (Human) 
2025-05-07 | PXD057811 | Pride
Dubr Hct116 Ncrna Rap-ms 
GenomicsXist exploits three-dimensional chromosome architecture to spread across the X-chromosome
Many large noncoding RNAs (lncRNAs) regulate chromatin, but the mechanisms by which they localize to genomic targets remain unexplored. Here we investigate the localization mechanisms of Xist during X-chromosome inactivation (XCI), a paradigm of lncRNA-mediated chromatin regulation. During the maint...
ORGANISM(S): Mus musculus 
2013-05-30 | E-GEOD-46918 | biostudies-arrayexpress
GenomicsXist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing
Xist orchestrates X chromosome inactivation, a process that entails chromosome-wide silencing and remodeling of the 3-dimensional structure of the X chromosome. Yet, it remains unclear whether these changes in nuclear structure are mediated by Xist and whether they are required for silencing. Here w...
ORGANISM(S): Mus musculus 
2016-07-24 | E-GEOD-80510 | biostudies-arrayexpress
GenomicsRNA-RNA interactions enable specific targeting of noncoding RNAs to nascent pre-mRNAs and chromatin sites
We developed a general method based on RNA Antisense Purification (RAP) to identify the intermolecular RNA-RNA interactions of a target RNA (RAP-RNA). RAP-RNA identifies endogenous RNA-RNA complexes through in vivo crosslinking, RNA capture with antisense oligonucleotides, and high-throughput RNA se...
ORGANISM(S): Mus musculus 
2014-09-01 | E-GEOD-55914 | biostudies-arrayexpress
ProteomicsProteomic Analysis of RAP (RNA Antisense Purification) isolated RNPs (RiboNucleotide Particles) harboring the novel lncRNA mimi
In neurons, mRNAs and associated RNA-binding proteins assemble into ribonucleoprotein (RNP) granules essential to regulate mRNA trafficking, local translation, and turnover. Dysregulation of RNA-protein condensation can disturb synaptic plasticity. We report that the novel lncRNA mimi is a constitut...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2022-10-12 | PXD034457 | Pride
Elav  drosophila  relative lfq (label free quantification) quantitative proteomics Rap rna protein complex isolation  uv crosslinking  fly brain  neurons  lncrna mimi  fne  rbp9 
ProteomicsMudPIT analyses of the proteins co-purified with RAP01-HA, RAP21-HA, and negative controls from late asexual Plasmodium falciparum parasites
[NOTE: PF3D7_1470600 previously named RAP14 is now named RAP21]. HA-affinity purification - Purified late asexual parasites from parental and HA-tagged PF3D7_0105200 (RAP01-HA) and PF3D7_1470600 (RAP21-HA) lines were suspended in 50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 1 % Triton X-100, 1 mM ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Plasmodium Falciparum 3d7 (ncbitaxon:36329) 
2020-12-24 | MSV000086636 | MassIVE
ProteomicsProteome-wide identification lncRNA CCAT1 directly binding proteins by RAP-MS
We purify and identify CCAT1 binding proteins by RAP-MS. As a result, we identified out more than 600 CCAT1 binding proteins and more than 60% of them are RNA binding proteins recorded by RBPs database EuRBPDB. Among the identified CCAT1 binding proteins, Vimentin is a crucial protein. Additionally,...
ORGANISM(S): Homo Sapiens 
2020-11-26 | PXD022774 |
UnknownYBX1 is a modulator of MIA/CD-RAP-dependent chondrogenesis.
Not available
S-EPMC3861381 | biostudies-literature
ProteomicsRNA antisense purification with mass spectrometry (RAP-MS) experiment for identification of GRAS1 non-coding RNA interacting proteins
GRAS1 non-coding RNA is required for cell survival in A549 lung cancer cells. We identified the protein interactome of GRAS1 RNA using RAP-MS, then compared the results of the GRAS1 capture to captures of positive control U1 RNA and negative control luciferase RNA. Unique proteins binding specifical...
ORGANISM(S): Homo sapiens (Human) 
2026-09-28 | PXD042699 | Pride
Rap-ms Non-coding rna Rna-protein interactions 
UnknownThe Rice Annotation Project Database (RAP-DB): 2008 update.
Not available
S-EPMC2238920 | biostudies-literature
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