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  • genes
  • These RNAs are called small nuclear RNAs (snRNAs) and they're one example of a host of small RNAs produced by non-protein encoding genes. (blogspot.com)
  • Moreover, oncrasin-1 treatment suppressed the phosphorylation of the largest subunit of RNA polymerase II and the expression of intronless reporter genes in sensitive cells but not in resistant cells, suggesting that suppression of RNA transcription is a major effect of oncrasin-1 treatment. (aacrjournals.org)
  • We found that large numbers of transcripts were differentially expressed between nuclear backgrounds, and that mtDNA type altered the expression of nDNA genes, suggesting a retrograde, trans effect of mitochondrial genotype. (genetics.org)
  • Using a variety of differential expression analyses, we show the responses to mitonuclear covariation to be substantially different between the sexes, yet the mtDNA genes were consistently differentially expressed across nuclear backgrounds and sexes. (genetics.org)
  • We classify two different categories of repressed genes based on the underlying mechanism, and novel mechanisms which involve regulation through noncoding RNAs are discussed. (hindawi.com)
  • In principle, two categories of p53-repressed target genes can be classified: (I) genes that are regulated by direct interaction of p53 with target gene promoters or bound cofactors, (II) genes that are indirectly regulated by other p53 target genes. (hindawi.com)
  • Histone genes encode for pre‐mRNAs that undergo maturation through a mechanism distinct from all other RNA Pol II transcripts by substituting polyadenylation with an alternative 3′‐end formation pathway ( Marzluff et al , 2008 ). (embopress.org)
  • This study utilized RNA-Seq to identify key genes expressed in the gonads of Southern bluefin tuna ( Thunnus maccoyii , SBT) and their specific expression patterns in male and female gonad cells. (biomedcentral.com)
  • Key genes involved in the reproductive molecular pathway and specifically, germ cell development in gonads, were identified using analysis of RNA-Seq transcriptomes of male and female SBT gonad cells. (biomedcentral.com)
  • molecule
  • Many intergenic lncRNAs act in trans , and thus, by necessity, their function must be mediated by the RNA molecule itself rather than by the mere act of transcription, which seems to be the mode of function of many cis -acting RNAs ( 12 ). (asm.org)
  • In many cases, the specific context and spatial orientation of the motif within the protein molecule enables a particular mode of interaction with other biological macromolecules, leading to function ( 17 ). (asm.org)
  • We recently identified a small molecule, designated 1-[(4-chlorophenyl)methyl]-1 H -indole-3-carboxaldehyde (oncrasin-1), that can selectively kill K-Ras mutant cancer cells and induce abnormal nuclear aggregation of PKCι in sensitive cells but not in resistant cells. (aacrjournals.org)
  • The persistence length is a measure of the rigidity of a polymer, simply the average distance over which a DNA or RNA molecule behaves like a rod. (madsci.org)
  • Sequences
  • The gene is transcribed from left (5′) to right (3′) beginning at the promoter (P). The long primary RNA transcript contains both intron and exon sequences. (blogspot.com)
  • The ubiquitous presence of long noncoding RNAs (lncRNAs) in eukaryotes points to the importance of understanding how their sequences impact function. (asm.org)
  • Instead of utilizing an HDE to position the cleavage complex, sequences downstream of the stem loop in histone pre‐mRNAs were found to be complementary to endogenous small interfering RNAs (endo‐siRNAs) ( Figure 1 ). (embopress.org)
  • The novel COMRADES technique, developed by Dr. Omer Ziv at the Wellcome Trust/ Cancer Research UK Gurdon Institute with an international team of colleagues, can screen for host-virus RNA base-pairing and reveal the interacting sequences of RNA in a single experiment. (regenerativemedicine.net)
  • With the new technique, both the identity and the position of every base-pair are revealed, supplying the necessary and sufficient information for designing complementary sequences that could interfere and block each interaction, with potential clinical effects. (regenerativemedicine.net)
  • This would allow us to design short RNA or DNA sequences that can be administered to interfere with those interactions -- potentially preventing the virus' ability to replicate and infect further cells. (regenerativemedicine.net)
  • Subunit
  • This gene encodes a subunit of the transcription factor complex nuclear factor-kappa-B (NFkB). (nih.gov)
  • The putative target site for the 75/76-nt RNA is a highly conserved portion of the small subunit rRNA that contains 2′- O -ribose methylation at a conserved position (Gm1830) in L. tarentolae and in vertebrates. (asm.org)
  • The 92/94-nt RNA has the potential to form base pairs near a conserved methylation site in the large subunit rRNA, which corresponds to position Gm4141 of small rRNA 2 in T. brucei . (asm.org)
  • motif
  • The Sm domain is an ancient RNA-binding motif with oligo(U) specificity. (ebi.ac.uk)
  • Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ACA-motif snoRNPs and constitute a common bipartite structure. (nih.gov)
  • Mutational analyses indicated that nuclear localization of BORG was mediated through a novel RNA motif consisting of the pentamer sequence AGCCC with sequence restrictions at positions −8 (T or A) and −3 (G or C) relative to the first nucleotide of the pentamer. (asm.org)
  • Mutation of the motif to a scrambled sequence resulted in complete loss of nuclear localization, while addition of even a single copy of the motif to a cytoplasmically localized RNA was sufficient to impart nuclear localization. (asm.org)
  • Further, the presence of this motif in other cellular RNAs showed a direct correlation with nuclear localization, suggesting that the motif may act as a general nuclear localization signal for cellular RNAs. (asm.org)
  • intron
  • The cell must cleave the primary transcript at each end of the intron while holding on to the flanking exons so the chopped RNA transcript does not come apart. (blogspot.com)
  • nucleotide
  • A mistake in even a single nucleotide can be devastating to the cell, and a reliable, repeatable method of RNA processing is necessary to ensure cell survival. (wikipedia.org)
  • chromatin
  • Increasing evidence suggests that many lncRNAs are tissue specific and developmentally regulated and play important functional roles in diverse aspects of cellular function, with regulation of chromatin states and other nuclear events emerging as a major function of this class of transcripts ( 2 , 7 - 10 ). (asm.org)
  • localization
  • As many lncRNAs regulate nuclear events and thus must localize to nuclei, we analyzed the sequence requirements for nuclear localization in an intergenic lncRNA named BORG (BMP2-OP1-responsive gene), which is both spliced and polyadenylated but is strictly localized in nuclei. (asm.org)
  • Linker segment aa 155 to 196 contains a nuclear localization signal rich in basic amino acids that is necessary for RRM2 activity in mud1 ∆ complementation. (g3journal.org)
  • Phage Display
  • Both cell-based and biochemical interactions have been monitored, and applications such as phage display, ELISA, and EMSA (electrophoretic mobility shift assay) have been adapted to Alpha. (perkinelmer.com)
  • viral
  • Small interfering RNA (siRNA)-mediated knockdown of hnRNP A2 resulted in a 90% reduction of viral RNA replication in cells infected with JEV, and the reduction was cancelled by the expression of an siRNA-resistant hnRNP A2 mutant. (asm.org)
  • The detailed information derived from COMRADES offers the potential to design a new generation of medicines that work by blocking virus-host RNA interactions or interfering with essential structures in the viral genome. (regenerativemedicine.net)
  • These interactions offer potential targets for anti-viral therapies, and indeed an anti-hepatitis C virus drug that targets such host-virus RNA interaction, Miraversen, is currently in advanced clinical trials. (regenerativemedicine.net)
  • Given the wide applicability of this technique to any RNA virus and any host cell, both human and animal RNA viral diseases can be a target for such research. (regenerativemedicine.net)
  • duplex
  • C3'-endo versus C2'-endo conformations dominate duplex RNA and DNA, respectively (Note that single deoxy- or ribonucleotides generally have a C2'-endo conformation, though there is distribution of sugar conformations for isolated nucleotides). (madsci.org)
  • In general, the 2'-OH is involved in hydrogen-bonding interactions with water, in duplex RNA regions, so this does not directly impact the structure or distribution of structures on its own. (madsci.org)
  • In terms of thermodynamic stability, it is known that duplex RNA is more stable than duplex DNA. (madsci.org)
  • duplex regions of RNA are short and interrupted. (madsci.org)
  • The structural differences between duplex RNA and DNA should give you a clue why this pattern is observed. (madsci.org)
  • biomolecular interactions
  • This remarkable success has often overlooked the importance of the molecular motions that are required for function, with structural biologists tending to focus their attention on highly stable, high affinity biomolecular interactions. (frontiersin.org)
  • AlphaScreen® and AlphaLISA® are bead-based assay technologies used to study biomolecular interactions in a microplate format. (perkinelmer.com)
  • synthesis
  • During one-step growth, synthesis of both positive- and negative-strand JEV RNAs was delayed by the knockdown of hnRNP A2. (asm.org)
  • function
  • Their primary function is in the processing of pre-messenger RNA (hnRNA) in the nucleus. (wikipedia.org)
  • Investigation of structure-function interaction of polyhedron of Bombyx mori Nuclear Polyhedrosis Virus (NPV) with polyhedra protease and RNA. (org.ua)