EU-RNA-seq for in vivo labeling and high throughput sequencing of nascent transcripts.
AuthorsPalozola KC,Donahue G,Zaret KS
JournalSTAR protocols
PubMed ID34485932
The protocol allows for labeling nascent RNA without isolating nuclei. The cell-permeable uridine analog, 5-ethynyluridine (EU), is added to media to allow in vivo labeling of nascent transcripts. Cells are lysed, total RNA is collected, and biotin is conjugated to EU-labeled RNAs. Custom biotin RNAs are added and biotinylated RNAs ... More
METTL14 is a chromatin regulator independent of its RNA N6-methyladenosine methyltransferase activity.
METTL3 and METTL14 are two components that form the core heterodimer of the main RNA m6A methyltransferase complex (MTC) that installs m6A. Surprisingly, depletion of METTL3 or METTL14 displayed distinct effects on stemness maintenance of mouse embryonic stem cell (mESC). While comparable global hypo-methylation in RNA m6A was observed in ... More
Tudor domain containing 7 (Tdrd7) is essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis.
AuthorsTanaka T, Hosokawa M, Vagin VV, Reuter M, Hayashi E, Mochizuki AL, Kitamura K, Yamanaka H, Kondoh G, Okawa K, Kuramochi-Miyagawa S, Nakano T, Sachidanandam R, Hannon GJ, Pillai RS, Nakatsuji N, Chuma S,
JournalProc Natl Acad Sci U S A
PubMed ID21670278
'In the male germline in mammals, chromatoid bodies, a specialized assembly of cytoplasmic ribonucleoprotein (RNP), are structurally evident during meiosis and haploidgenesis, but their developmental origin and regulation remain elusive. The tudor domain containing proteins constitute a conserved class of chromatoid body components. We show that tudor domain containing 7 ... More
The repression domain of the E1B 55-kilodalton protein participates in countering interferon-induced inhibition of adenovirus replication.
'To begin to investigate the mechanism by which the human adenovirus type 5 E1B 55-kDa protein protects against the antiviral effects of type 1 interferon (IFN) (J. S. Chahal, J. Qi, and S. J. Flint, PLoS Pathog. 8:e1002853, 2012 [doi:10.1371/journal.ppat.1002853]), we examined the effects of precise amino acid substitution in ... More
NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies.
AuthorsHirose T, Virnicchi G, Tanigawa A, Naganuma T, Li R, Kimura H, Yokoi T, Nakagawa S, Bénard M, Fox AH, Pierron G,
Journal
PubMed ID24173718
Paraspeckles are subnuclear structures formed around nuclear paraspeckle assembly transcript 1 (NEAT1)/MENe/ß long noncoding RNA (lncRNA). Here we show that paraspeckles become dramatically enlarged after proteasome inhibition. This enlargement is mainly caused by NEAT1 transcriptional up-regulation rather than accumulation of undegraded paraspeckle proteins. Of interest, however, using immuno-electron microscopy, we ... More
Reciprocal regulation of the basic helix-loop-helix/Per-Arnt-Sim partner proteins, Arnt and Arnt2, during neuronal differentiation.
AuthorsHao N, Bhakti VL, Peet DJ, Whitelaw ML,
JournalNucleic Acids Res
PubMed ID23599003
Basic helix-loop-helix/Per-Arnt-Sim (bHLH/PAS) transcription factors function broadly in development, homeostasis and stress response. Active bHLH/PAS heterodimers consist of a ubiquitous signal-regulated subunit (e.g., hypoxia-inducible factors, HIF-1a/2a/3a; the aryl hydrocarbon receptor, AhR) or tissue-restricted subunit (e.g., NPAS1/3/4, Single Minded 1/2), paired with a general partner protein, aryl hydrocarbon receptor nuclear translocator ... More
Inclusion bodies are a site of ebolavirus replication.
AuthorsHoenen T, Shabman RS, Groseth A, Herwig A, Weber M, Schudt G, Dolnik O, Basler CF, Becker S, Feldmann H,
JournalJ Virol
PubMed ID22915810
Inclusion bodies are a characteristic feature of ebolavirus infections in cells. They contain large numbers of preformed nucleocapsids, but their biological significance has been debated, and they have been suggested to be aggregates of viral proteins without any further biological function. However, recent data for other viruses that produce similar ... More
U7 small nuclear ribonucleoprotein represses histone gene transcription in cell cycle-arrested cells.
Histone gene expression is tightly coordinated with DNA replication, as it is activated at the onset of S phase and suppressed at the end of S phase. Replication-dependent histone gene expression is precisely controlled at both transcriptional and posttranscriptional levels. U7 small nuclear ribonucleoprotein (U7 snRNP) is involved in the ... More
Requirement of TFIIH kinase subunit Mat1 for RNA Pol II C-terminal domain Ser5 phosphorylation, transcription and mRNA turnover.
AuthorsHelenius K, Yang Y, Tselykh TV, Pessa HK, Frilander MJ, Mäkelä TP,
JournalNucleic Acids Res
PubMed ID21385826
The relevance of serine 5 phosphorylation of RNA polymerase II carboxy-terminal domain during initiation has been difficult to determine in mammalian cells as no general in vivo Ser5 kinase has been identified. Here, we demonstrate that deletion of the TFIIH kinase subunit Mat1 in mouse fibroblasts leads to dramatically reduced ... More
AP4 suppresses DNA damage, chromosomal instability and senescence via inducing MDC1/Mediator of DNA damage Checkpoint 1 and repressing MIR22HG/miR-22-3p.
Authors
JournalMol Cancer
PubMed ID35624466
Disruption of exon-bridging interactions between the minor and major spliceosomes results in alternative splicing around minor introns.
Authors
JournalNucleic Acids Res
PubMed ID33660780
Macrophage Metabolism of Apoptotic Cell-Derived Arginine Promotes Continual Efferocytosis and Resolution of Injury.
Authors
JournalCell Metab
PubMed ID32004476
Exon-Mediated Activation of Transcription Starts.
Authors
JournalCell
PubMed ID31787377
Targeting 3' and 5' untranslated regions with antisense oligonucleotides to stabilize frataxin mRNA and increase protein expression.
Authors
JournalNucleic Acids Res
PubMed ID34718736
RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells.
Authors
JournalNat Genet
PubMed ID29483655
Loss of Ataxin-1 Potentiates Alzheimer's Pathogenesis by Elevating Cerebral BACE1 Transcription.
Authors
JournalCell
PubMed ID31442405
Genome Organization Drives Chromosome Fragility.
Authors
JournalCell
PubMed ID28735753
Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse.
Authors
JournalCell
PubMed ID30078706
MOF Acetyl Transferase Regulates Transcription and Respiration in Mitochondria.