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  • Binds
  • The Neuroprotective Marine Compound Psammaplysene A Binds the RNA-Binding Protein HNRNPK. (harvard.edu)
  • An accessory subcomplex made of the m 1 A9 methyltransferase MRPP1 and the dehydrogenase MRPP2 binds to the metallonuclease MRPP3 that cleaves the RNA phosphodiester backbone. (springer.com)
  • yeast
  • In order to select for functional RNAs, yeast ribosomes have been used here as bait. (nih.gov)
  • The rationale for choosing yeast was the lack of the miRNA pathway, since miRNAs are very abundant in other organisms and often mask other small RNAs in transcriptomic data (4). (nih.gov)
  • In budding yeast, Cdc73 and Rtf1 are the main interfaces for the physical interaction between the PAF1 complex and RNA pol II (Nordick et al. (springer.com)
  • RNAi
  • A single-cloning-step procedure for the generation of RNAi plasmids producing long stem-loop RNA. (yale.edu)
  • Atayde, V.D., Ullu, E., Kolev, N.G. A single-cloning-step procedure for the generation of RNAi plasmids producing long stem-loop RNA. (yale.edu)
  • Nuclear
  • ① Plasmid-expressed short hairpin RNA (shRNA) requires the activity of endogenous Exportin 5 for nuclear export . (invivogen.com)
  • Dubrovsky EB, Dubrovskaya VA, Levinger L, Schiffer S, Marchfelder A (2004) Drosophila RNase Z processes mitochondrial and nuclear pre-tRNA 3′ ends in vivo . (springer.com)
  • The distribution of the injected RNAs within the nuclear and cytoplasmic oocyte compartments was determined as described in the legend to Fig. 4 B. Bar, 10 μm. (nih.gov)
  • tRNAs
  • In the nucleus, tRNA 5′-end processing is carried out by the first identified ribozyme, RNase P. In contrast, mitochondrial tRNAs are processed by a three-protein complex, mitochondrial RNase P, which does not have an RNA component. (springer.com)
  • Brzezniak LK, Bijata M, Szczesny RJ, Stepien PP (2011) Involvement of human ELAC2 gene product in 3′ end processing of mitochondrial tRNAs. (springer.com)
  • By employing the APART pipeline, we were able to detect and confirm by independent experimental methods multiple novel stable RNA molecules differentially processed from well known ncRNAs, like rRNAs, tRNAs or snoRNAs, in a stress-dependent manner. (nih.gov)
  • nucleus
  • Furthermore, by injecting U2 RNA into isolated nuclei or enucleated oocytes, we observe that U2 internal modifications occur exclusively in the nucleus. (nih.gov)
  • ribosomes
  • Following the same logic, we have generated a cDNA library enriched for small RNAs (sized 20-500 nt) that co-purified with S. cerevisiae ribosomes under 12 different growth conditions. (nih.gov)
  • Sequencing
  • Recent developments in DNA and RNA sequencing technologies have allowed for the detection of genes and mutations involved in mitochondrial function and also for the analysis of how mitochondrial genome processing varies across human individuals and populations. (findaphd.com)
  • Alan Hodgkinson's group aims to exploit both DNA and RNA sequencing to gain a better understanding of the factors that influence mitochondrial genome processing (see: Hodgkinson et al. (findaphd.com)
  • The advent of next-generation sequencing (NGS) tools has enabled the identification of RNA modifications both globally and in a substrate-specific manner. (biomedcentral.com)
  • Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. (nih.gov)
  • Up to date no methodology has been presented to distinguish stable functional RNA species from rapidly degraded side products of nucleases.Here, we present a novel automated computational pipeline, named APART, providing a complete workflow for the reliable detection of RNA processing products from next-generation-sequencing data.To disclose the potential of APART, we have analyzed a cDNA library derived from small ribosome-associated RNAs in Saccharomyces cerevisiae. (nih.gov)
  • Here, we present a novel automated computational pipeline, named APART, providing a complete workflow for the reliable detection of RNA processing products from next-generation-sequencing data. (nih.gov)
  • After deep-sequencing of the library, adaptor sequences are used to select for the reads covering the full length of the original RNA molecule (both adaptors are observed). (nih.gov)
  • Deep analysis of transcriptomes via high-throughput RNA sequencing (RNA-seq) has revealed that a major fraction of all intron-containing genes from higher eukaryotes generates AS variants. (plantphysiol.org)
  • Fluorescence
  • Fluorescence in situ hybridization (FISH) and digital imaging microscopy were modified to allow detection of single RNA molecules. (umassmed.edu)
  • Computational
  • The studentship is centered on the computational analysis of large multi-omic datasets, with the aim of unravelling variation and key processes influencing mitochondrial function. (findaphd.com)
  • We propose PredRBR, an effectively computational approach to predict RNA-binding residues. (biomedcentral.com)
  • Developing computational methods to predict RNA-binding sites precisely is becoming increasingly important. (biomedcentral.com)
  • decay
  • Borowski LS, Dziembowski A, Hejnowicz MS, Stepien PP, Szczesny RJ (2013) Human mitochondrial RNA decay mediated by PNPase-hSuv3 complex takes place in distinct foci. (springer.com)
  • purification
  • RNA was extracted from the pellets obtained after purification (lanes IP) or from an amount of total extract corresponding to 1/100 of that used for purification (lanes T) and subjected to northern analysis of pre-rRNAs and mature rRNAs. (nih.gov)
  • values (below each IP lane) refer to as the percentage of each RNA recovered after purification. (nih.gov)
  • All these results are specific since no RNAs were detected upon affinity purification from extracts of the untagged strain (Figure 7).Figure 7. (nih.gov)
  • biological
  • The studies presented here expand the catalogue of cellular small RNAs and demonstrate a biological impact for at least one class of non-canonical small RNAs. (nih.gov)
  • The enormous advancement of RNA-seq now allows profiling of this diversity at high depth and spatiotemporal resolution, which is expected to provide important insight into mechanisms and biological functions of AS. (plantphysiol.org)
  • complex
  • In this review, we discuss what is known about the mitochondrial RNase P complex, the molecular mechanism of 5′-end mitochondrial tRNA processing, and how loss of this activity causes human disease. (springer.com)
  • We found that RNA levels of VPS36 , but not other ESCRT components, are positively regulated by all components of the PAF1 complex. (springer.com)
  • Our work delivers insight into the complex and compartmentalized RNA processing mechanisms that control the expression of the splicing regulator SR30 in a light-dependent manner. (plantphysiol.org)
  • small
  • Many small RNAs, including the previously described promoter-associated small RNAs, appeared to possess cap structures. (nih.gov)
  • Supplying synthetic promoter-associated small RNAs corresponding to the c-MYC transcriptional start site reduced MYC messenger RNA abundance. (nih.gov)
  • These small dsRNAs are called small interfering RNAs (siRNAs). (invivogen.com)
  • To disclose the potential of APART, we have analyzed a cDNA library derived from small ribosome-associated RNAs in Saccharomyces cerevisiae. (nih.gov)
  • ncRNA
  • ncRNA, non-coding RNA. (nih.gov)
  • The major assumption behind the construction of a cDNA library aiming at identifying stable ncRNA species is that merely functional RNAs are expected to be protected from degradation. (nih.gov)
  • transcript
  • Construction of Trypanosoma brucei Illumina RNA-Seq libraries enriched for transcript ends. (yale.edu)
  • Kolev, N.G., Ullu, E. and Tschudi, C. Construction of Trypanosoma brucei Illumina RNA-Seq libraries enriched for transcript ends. (yale.edu)
  • Chatfield KC et al (2015) Mitochondrial energy failure in HSD10 disease is due to defective mtDNA transcript processing. (springer.com)
  • However, recent studies suggest that RNA processing can be a multi-layer process leading to the generation of ncRNAs of diverse functions from a single primary transcript. (nih.gov)
  • Hybridization
  • Pulse-chase, northern hybridization and primer extension analyses show that processing of the 27SB to 7S pre-rRNAs is strongly delayed upon L35 depletion. (nih.gov)