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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 
TranscriptomicsRoquin promotes constitutive mRNA decay via a conserved class of stem-loop recognition motifs.
The degradation of TNFM-NM-1 mRNA is critical for restricting TNFM-NM-1 synthesis and involves a constitutive decay element (CDE) in the 3M-bM-^@M-^Y untranslated region of the mRNA. We demonstrate that the active CDE is a stem-loop RNA motif that is recognized by the RNA-binding protein Roquin. Dee...
ORGANISM(S): Mus musculus 
2013-05-15 | E-GEOD-44775 | biostudies-arrayexpress
ProteomicsMCPIP2 competes with IGF2BP1 binding to common stem-loop structure in the 3’UTRs of pro-angiogenic genes for suppressing breast tumor angiogenesis-2
This study was performed according to RNA pull-down assay using biotin-labeled WT RNA probe (with stem-loop structure) or mutant RNA probe (without stem-loop structure) and streptavidin-coated Dynabeads in human breast tumor cell MDA-MB-468, and then the pulled down proteins were isolated by SDS-PA...
ORGANISM(S): Homo Sapiens 
2024-06-05 | PXD052920 |
ProteomicsHDX-MS Studies of Dengue Virus Serotype 2 NS5 (DENV2 NS5) and Stem Loop A (SLA) Interactions
The project employs HDX-MS to study the conformational dynamics of DENV2 NS5 in its apo form and in complex with the viral promoter RNA, Stem Loop A (SLA). The conformational dynamics of the RdRp domain of DENV2 NS5 (NS5-RdRp) in its apo form and in complex with SLA was also studied.
ORGANISM(S): Escherichia coli 
2025-05-07 | PXD058297 | Pride
Dengue Sla Polymerase Hdx-ms Flavivirus Ns5 
GenomicsAging-declined RNA Exportation Impairs Hematopoietic Stem Cells by Inducing R-Loop
Aging-declined RNA Exportation Impairs Hematopoietic Stem Cells by Inducing R-Loop
PRJNA998783 | ENA
GenomicsStem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties
Stem-loop and circle-loop TADs generated by directional pairing of boundary elements have distinct physical and regulatory properties
PRJNA1096375 | ENA
GenomicsAging-declined RNA Exportation Impairs Hematopoietic Stem Cells by Inducing R-Loop
Aging-declined RNA Exportation Impairs Hematopoietic Stem Cells by Inducing R-Loop
PRJNA998782 | ENA
GenomicsAging-declined RNA Exportation Impairs Hematopoietic Stem Cells by Inducing R-Loop
Aging-declined RNA Exportation Impairs Hematopoietic Stem Cells by Inducing R-Loop
PRJNA998781 | ENA
GenomicsEffects of tRNA[Ser]Sec anticodon stem loop modifications on selenoprotein expression
Effects of tRNA[Ser]Sec anticodon stem loop modifications on selenoprotein expression
PRJNA762342 | ENA
UnknownRNA destabilization by the granulocyte colony-stimulating factor stem-loop destabilizing element involves a single stem-loop that promotes deadenylation.
Not available
S-EPMC135610 | biostudies-literature
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