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ProteomicsA fold switch regulates conformation of an alphavirus virus RNA-dependent RNA polymerase
Alphaviruses are mosquito-vectored, positive-strand RNA viruses causing rheumatic and neurological diseases. Like all RNA viruses, they encode an RNA-dependent RNA polymerase (RdRp, nsP4). Purification of an nsP4 derivative capable of processive RNA synthesis from a heteropolymeric template has been...
ORGANISM(S): Alphavirus 
2026-01-06 | PXD071261 | Pride
Fold switching Hdxms Alphavirus Rna-dependent rna polymerase Rna virus 
ProteomicsThe concept of "RNA dependence" - Proteome-wide and quantitative identification of protein interactions dependent on RNA
The general role of RNA in the cell beyond protein biosynthesis is only beginning to emerge with little knowledge about the structural or organizational functions of RNA. In turn, functional non-coding RNAs (ncRNAs) are often identified by their regulation or impact on cellular phenotypes. However, ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-06-13 | MSV000082468 | MassIVE
GenomicsGenomic Study of RNA Polymerase II and III SNAPc-Bound Promoters Reveals a Gene Transcribed by both Enzymes and a Broad Use of Common Activators
SNAPc-dependent promoters are unique among cellular promoters in being very similar to each other, even though some of them recruit RNA polymerase II and other RNA polymerase III. We have examined all SNAPc-bound promoters present in the human genome. We find that there is a surprisingly small numbe...
ORGANISM(S): Homo sapiens 
2012-11-22 | E-GEOD-38303 | biostudies-arrayexpress
TranscriptomicsArgonaute-bound small RNAs from promoter-proximal RNA Polymerase II
Argonaute (Ago) proteins mediate post-transcriptional gene repression by binding guide microRNAs (miRNAs) to regulate targeted RNAs. To confidently assess Agobound small RNAs, we adapted a mouse embryonic stem cell system to express a single inducible epitope-tagged Ago protein. Here, we report t...
ORGANISM(S): Mus musculus 
2014-03-13 | E-GEOD-50595 | biostudies-arrayexpress
ProteomicsStructure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex, and the Regulation of Transcription
MedPIC: Crosslinking-MS of 54 subunit pre-initiation complex from yeast. MedPolII: Crosslinking-MS of 33 subunit Mediator + polII complex from yeast.
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) 
2016-08-02 | MSV000080013 | MassIVE
TranscriptomicsCharacterization of small RNA-generating regions targeted by RNA polymerase V in Arabidopsis
In plants, heterochromatin is maintained by a small RNA-based gene silencing mechanism known as RNA-directed DNA methylation (RdDM). RdDM requires the non-redundant functions of two plant-specific DNA-dependent RNA polymerases (Pol) Pol IV and Pol V. Pol IV plays a major role in siRNA biogenesis, w...
ORGANISM(S): Arabidopsis thaliana 
2012-06-11 | E-GEOD-36424 | biostudies-arrayexpress
ProteomicsProteins co-localized with RNA Pol2 in ALS patient-derived neural precursors
Deficiency of proteostasis and RNA metabolism are increasingly recognized as critical drivers of neurodegenerative diseases. In this study, we focused on RNA polymerase II (Pol2) as the converging point of these two elements to understand how transcriptional machinery is affected by ALS-associated V...
ORGANISM(S): Homo Sapiens (human) 
2023-03-02 | PXD034483 | JPOST Repository
ProteomicsDengue Virus type 3 RNA-dependent RNA polymerase versus inhibitors
Dengue Virus type 3 RNA-dependent RNA polymerase versus inhibitors
ORGANISM(S): Dengue Virus Type 3 
2025-10-21 | PXD057011 | JPOST Repository
MetabolomicsSmall auxin-up RNA promotes GmMYB176 gene transcription to modulate soybean isoflavone content

Isoflavones have been widely studied because of their potential health benefits, including antioxidant, anti-inflammatory, and anticancer properties. Soybeans (Glycine max (L.) Merr) are an effective source of natural isoflavones in humans. Therefore, it is important to cultivate varieties showin...

2025-06-23 | MTBLS12627 | MetaboLights
TranscriptomicsDSIF and RNA polymerase II CTD Phosphorylation Coordinate the Recruitment of Rpd3S to Actively Transcribed Genes
Histone deacetylase Rpd3 is part of two distinct complexes: the large (Rpd3L) and small (Rpd3S) complexes. While Rpd3L targets specific promoters for gene repression, Rpd3S is recruited to ORFs to deacetylate histones in the wake of RNA polymerase II, to prevent cryptic initiation within genes. Meth...
ORGANISM(S): Saccharomyces cerevisiae 
2010-11-28 | E-GEOD-22636 | biostudies-arrayexpress
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