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TranscriptomicsSmall RNA accumulation in Transposable Element-silent and Transposable Element-active epigenomes
Background: The small RNAs that Transposable Elements generate are vastly different when they are transcriptionally silenced compared to when they are transcriptionally activated. We performed the deep sequencing of small RNAs in a number of small RNA biogenesis mutants in both Transposable Element-...
ORGANISM(S): Arabidopsis thaliana 
2014-11-14 | E-GEOD-57191 | biostudies-arrayexpress
TranscriptomicsIncorporation of transposable element small RNAs into the Arabidopsis AGO1 protein
Background: Transposable element 24 nucleotide small RNAs are not efficiently incorporated into the AGO1 protein, which is involved in endogenous RNAi and gene regulation through the microRNA and tasiRNA pathways. Results: The AGO1 protein incorporates large quantities of transposable element siRNA...
ORGANISM(S): Arabidopsis thaliana 
2014-04-07 | E-GEOD-45990 | biostudies-arrayexpress
ProteomicsA viral pan-end RNA element and host complex define a SARS-CoV-2 regulon
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, generates multiple protein-coding, subgenomic RNAs (sgRNAs) from a longer genomic RNA, all bearing identical termini with poorly understood roles in regulating viral gene expression. Insulin and interferon...
ORGANISM(S): Homo sapiens (Human) 
2023-06-12 | PXD042148 | Pride
Sars-cov-2  covid-19  translational control  rna element  rna-binding protein  eprs1  aminoacyl-trna synthetase  multi-trna synthetase complex  post-transcriptional regulon  3’ untranslated region  obesity  insulin  interferon-gamma  spike protein  subgenomic rna  programmed ribosomal frameshifting  spear element  orf10  3’end  sars-cov-2 replicon  ppmo 
ProteomicsCoV 3'UTR cis-acting element interactome
Comparison of CoV 3'UTR cis-acting element interactome to link the cis-acting element to coronavirus replication by LC-MS/MS. The study is performed by in vitro-transcribed RNA followed by RNA-protein pull-down assay. In addition, the concluded results are decided by comparison between the biologica...
ORGANISM(S): Coronavirus Bcov/pb675/art_lit/pan/2011 (ncbitaxon:1269292) 
2024-08-07 | MSV000095535 | MassIVE
ProteomicsCoV 3'UTR cis-acting element interactome
Comparison of CoV 3'UTR cis-acting element interactome to link the cis-acting element to coronavirus replication by LC-MS/MS. The study is performed by in vitro-transcribed RNA followed by RNA-protein pull-down assay. In addition, the concluded results are decided by comparison between the biologica...
ORGANISM(S): Coronavirus Bcov/pb675/art_lit/pan/2011 (ncbitaxon:1269292) 
2024-08-06 | MSV000095522 | MassIVE
TranscriptomicsTranscription profiling of human neuroblastoma cell line IMR-32 overexpressiong SQSTM1 and DPP3 to identify activators for the antioxidant response element
The antioxidant response element (ARE) is a cis-acting regulatory enhancer element found in the 5’ flanking region of many phase II detoxification enzymes. Upregulation of ARE-dependent target genes is known to have neuroprotective effects; yet, the mechanism of activation is largely unknown. By scr...
ORGANISM(S): Homo sapiens 
2007-11-01 | E-GEOD-6451 | biostudies-arrayexpress
TranscriptomicsProbing Xist RNA structure in cells using Targeted Structure-Seq
The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bas...
ORGANISM(S): Mus musculus 
2016-02-09 | E-GEOD-67667 | biostudies-arrayexpress
ProteomicsPrediction and experimental validation of a new salinity-responsive cis-regulatory element (CRE) in tilapia
Quantitative DIA proteomics in combination with the transcription inhibitor actinomycin D was performed on the tilapia OmB cell line to identify proteins that are upregulated by transcriptional regulation during hyperosmotic stress. This analysis revealed proteins that are transcriptionally up-regul...
ORGANISM(S): Oreochromis Mossambicus 
2022-09-25 | PXD032181 | panorama
ProteomicsStructural requirements for photo-induced RNA-protein cross-linking
Cross-linking of isotope-labelled RNA coupled with mass spectrometry (CLIR-MS) was used to study the UV cross-linking behavior of in vitro reconstituted FOX1 RRM in complex with its cognate RNA sequence, the Fox binding element (FBE), (U)GCAUGU. The FBE heptanucleotide was subsequently mutated, and ...
ORGANISM(S): Homo sapiens (Human) 
2022-06-09 | PXD031381 | Pride
Uv cross-linking  mbnl1  fox1  ptbp1  sf3a1  u1  u2  cross-linking  xl-ms  structural proteomics  protein-rna  rna-protein  protein-rna complex  rna-protein complex  clir-ms 
TranscriptomicsUnlinking a lncRNA from its associated cis element [Capture-C]
Capture-C using probes at the Cdkn1b promoter and the Lockd promoter Many long non-coding (lnc) RNAs are reported to regulate gene expression and protein functions. However, the proportion of lncRNAs with biological activities among the thousands expressed in mammalian cells is controversial. We stu...
ORGANISM(S): Mus musculus 
2016-06-01 | E-GEOD-75880 | biostudies-arrayexpress
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