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MetabolomicsN6-methyladenosine modification is not a general trait of positive-sense RNA viral genomes

Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-seq, an antibody-dependent technique with...

2024-01-25 | MTBLS6978 | MetaboLights
ProteomicsLENG8 mediates nuclear retention and degradation of misprocessed mRNAs and noncoding RNAs
Incompletely processed and misprocessed mRNAs as well as numerous noncoding RNAs are retained in the nucleus and often degraded, and defects in this quality control mechanism have been linked to various diseases, including cancer and neurodegeneration. However, the underlying mechanisms remain poorl...
ORGANISM(S): Homo sapiens (Human) 
2026-03-30 | PXD065356 | Pride
Misprocessed rnas Rna nuclear retention Rna degradation Leng8 
TranscriptomicsAn Extended dsRBD with a Novel Zinc-Binding Motif Mediates Nuclear Retention of Fission Yeast Dicer
Dicer proteins function in RNA interference (RNAi) pathways by generating small RNAs (sRNAs). Here we report the solution structure of the C-terminal domain of Schizosaccharomyces pombe Dicer (Dcr1). The structure reveals an unusual double-stranded RNA binding domain (dsRBD) fold embedding a novel z...
ORGANISM(S): Schizosaccharomyces pombe 
2011-09-22 | E-GEOD-30549 | biostudies-arrayexpress
TranscriptomicsGenome-wide analysis of gene expression and intron retention during development in a U12-type splicing-deficient zebrafish mutant [RNA-seq]
To determine the global impact of the clbn mutation on gene expression and efficiency of U2- and U12-type splicing, we analyzed the transcriptome of 108hpf wt and clbn mutant larvae by microarrays and RNA sequencing. RNAseq data was used to characterize intron retention of U2-type and U12-type intro...
ORGANISM(S): Danio rerio 
2014-02-05 | E-GEOD-53758 | biostudies-arrayexpress
ProteomicsPhosphorylation of a nuclear condensate regulates cohesion and mRNA retention
Nuclear speckles are membraneless organelles that associate with active transcription sites and participate in post-transcriptional mRNA processing. During the cell cycle, nuclear speckles dissolve following phosphorylation of their protein components. Here, we identify the PP1 family as the phospha...
ORGANISM(S): Homo sapiens (Human) 
2024-11-28 | PXD055775 | Pride
Nuclear speckles Dyrk3 Phosphatase Kinase 
TranscriptomicsHP1BP3, a chromatin retention factor for co-transcriptional microRNA processing (miRNA-Seq)
Identification and characterization of HP1BP3 (a human histone H1 homologue) as a novel chromatin retention factor essential for the co-transcriptional processing of pri-miRNA. Compare global miRNA expression profile between control sample and sample depleted of HP1BP3
ORGANISM(S): Homo sapiens 
2016-07-24 | E-GEOD-77855 | biostudies-arrayexpress
TranscriptomicsAn Extended dsRBD with a Novel Zinc-Binding Motif Mediates Nuclear Retention of Fission Yeast Dicer
Dicer proteins function in RNA interference (RNAi) pathways by generating small RNAs (sRNAs). Here we report the solution structure of the C-terminal domain of Schizosaccharomyces pombe Dicer (Dcr1). The structure reveals an unusual double-stranded RNA binding domain (dsRBD) fold embedding a novel z...
ORGANISM(S): Schizosaccharomyces pombe 
2011-09-22 | E-GEOD-30586 | biostudies-arrayexpress
TranscriptomicsCoordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention
Differentiated cells acquire unique structural and functional traits through coordinated expression of lineage-specific genes. An extensive battery of genes encoding components of the synaptic transmission machinery and specialized cytoskeletal proteins is activated during neurogenesis, but the unde...
ORGANISM(S): Mus musculus 
2012-07-12 | E-GEOD-37933 | biostudies-arrayexpress
UnknownDepletion of hnRNP A2/B1 overrides the nuclear retention of the HIV-1 genomic RNA.
Not available
S-EPMC3907481 | biostudies-literature
TranscriptomicsNuclear retention of fission yeast dicer is a prerequisite for RNAi-mediated heterochromatin assembly
RNAseIII ribonucleases act at the heart of RNA silencing pathways by processing precursor RNAs into mature microRNAs and siRNAs. In the fission yeast Schizosaccharomyces pombe, siRNAs are generated by the RNAseIII enzyme Dcr1 and are required for heterochromatin formation. In this study, we have ana...
ORGANISM(S): Schizosaccharomyces pombe 
2010-02-16 | E-GEOD-18582 | biostudies-arrayexpress
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