The Experts below are selected from a list of 156 Experts worldwide ranked by ideXlab platform
Walter Keller - One of the best experts on this subject based on the ideXlab platform.
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means to an end mechanisms of alteRNAtive polyadenylation of messenger RNA Precursors
Wiley Interdisciplinary Reviews - Rna, 2014Co-Authors: Andreas Gruber, Walter Keller, Georges Martin, Mihaela ZavolanAbstract:Expression of mature messenger RNAs (mRNAs) requires appropriate transcription initiation and termination, as well as pre-mRNA processing by capping, splicing, cleavage, and polyadenylation. A core 3′-end processing complex carries out the cleavage and polyadenylation reactions, but many proteins have been implicated in the selection of polyadenylation sites among the multiple alteRNAtives that eukaryotic genes typically have. In recent years, high-throughput approaches to map both the 3′-end processing sites as well as the binding sites of proteins that are involved in the selection of cleavage sites and in the processing reactions have been developed. Here, we review these approaches as well as the insights into the mechanisms of polyadenylation that emerged from genome-wide studies of polyadenylation across a range of cell types and states. WIREs RNA 2014, 5:183–196. doi: 10.1002/wRNA.1206
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editing of messenger RNA Precursors and of tRNAs by adenosine to inosine conversion
FEBS Letters, 1999Co-Authors: Walter Keller, Jeannette Wolf, Andre P GerberAbstract:The double-stranded RNA-specific adenosine deaminases ADAR1 and ADAR2 convert adenosine (A) residues to inosine (I) in messenger RNA Precursors (pre-mRNA). Their main physiological substrates are pre-mRNAs encoding subunits of ionotropic glutamate receptors or serotonin receptors in the brain. ADAR1 and ADAR2 have similar sequence features, including double-stranded RNA binding domains (dsRBDs) and a deaminase domain. The tRNA-specific adenosine deaminases Tad1p and Tad2p/Tad3p modify A 37 in tRNA-Ala1 of eukaryotes and the first nucleotide of the anticodon (A 34) of several bacterial and eukaryotic tRNAs, respectively. Tad1p is related to ADAR1 and ADAR2 throughout its sequence but lacks dsRBDs. Tad1p could be the ancestor of ADAR1 and ADAR2. The deaminase domains of ADAR1, ADAR2 and Tad1p are very similar and resemble the active site domains of cytosine/cytidine deaminases.
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purification and characterization of human cleavage factor i involved in the 3 end processing of messenger RNA Precursors
Journal of Biological Chemistry, 1996Co-Authors: Ursula Ruegsegger, Katrin Beyer, Walter KellerAbstract:Abstract Six different protein factors are required for the specific cleavage and polyadenylation of pre-mRNA in mammals. Whereas four of them have been purified and most of their components cloned, cleavage factor I (CF I) and cleavage factor II (CF II) remained poorly characterized. We report here the separation of CF I from CF II and the purification of CF I to near homogeneity. Three polypeptides of 68, 59, and 25 kDa copurify with CF I activity. All three polypeptides can be UV cross-linked to a cleavage and polyadenylation substrate in the presence of a large excess of unspecific competitor RNA, but not to a splicing-only substrate. No additional protein factor is required for the binding of CF I to pre-mRNA. Gel retardation experiments confirmed the results obtained by UV cross-linking. In addition, we could show that CF I stabilizes the binding of the cleavage and polyadenylation specificity factor (CPSF) to pre-mRNA and that CPSF and CF I together form a slower migrating complex with pre-mRNA than the single protein factors. Cleavage stimulation factor (CstF) and poly(A) polymerase (PAP) had no detectable effect on the binding of CF I to pre-mRNA. Furthermore, the CstF•CPSF•RNA as well as the CstF•CPSF• PAP•RNA complex are supershifted and stabilized upon the addition of CF I.
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3′-End Cleavage and polyadenylation of nuclear Messenger RNA Precursors
Pre-mRNA Processing, 1995Co-Authors: Walter KellerAbstract:In mammalian and probably all other eukaryotic cells, the 3′-ends of messenger RNAs are generated by post-transcriptional processing of longer Precursors (reviewed in refs. 1–4). The pre-mRNA is first cleaved endonucleolytically downstream of the coding and the 3′-untranslated region. The upstream cleavage product then receives a poly(A) tail of 200–250 nucleotides. The two steps of the 3′-processing reaction are tightly coupled and take place in the cell nucleus. After the mRNA is transported to the cytoplasm the poly(A) tail is gradually shortened throughout the lifetime of the RNA. Poly(A) tail shortening usually precedes the degradation of the rest of the molecule (reviewed in refs. 5–7). The only known exception to this pathway is the 3′-end formation occurring on Precursors to the mRNAs coding for the major histones in metazoan cells (reviewed in ref. 8). In these pre-mRNAs the mature 3′-ends are generated by an endonucleolytic cleavage, the specificity of which is determined by base pairing between a conserved sequence in the pre-mRNA and the 5′-end of the RNA moiety of the U7 snRNP. The processed histone mRNAs do not receive a poly(A) tail.
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the biochemistry of 3 end cleavage and polyadenylation of messenger RNA Precursors
Annual Review of Biochemistry, 1992Co-Authors: Elmar Wahle, Walter KellerAbstract:AND PERSPECTIVES .... . . .... . . . . .... . . . . . .... .. . . . ..... . . . ....... . . . . .. . . . . . .... 4 1 9 POLYADENYLATION I N ANIMAL CELLS . . . . ....... . . ... ... . . . ..... . . . . . ..... . . ....... . . .. 420 Polyadenylarion Signals . .... . . . . . .... . . . ..... . . . ..... . . . ....... . . ... . . .. . . ...... . . . . ...... . . . . .. 420 3' -End Processing in vitro. . . . . .... . . . . ... . . . . . ..... . . . . .... . . . . ...... . .... ..... . . . .. .. . . . . . .... 424 Relationship Between Polyadenylation and Termination .. .. . . . . .... . . . . . 431 Regulated Polyadenylation . . . . . .. ...... . . ..... . . . . ..... . . . . . .... . . . ..... . .. . . ....... 431 POLY ADENYLA TlON IN yEAST 433 Sequences Required . ...... .. ...... . . . ..... . . . . ..... . . . .. .. . . . . ...... . . ... . . .. . . . .... .. . . ...... . . . 433 Mechanism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434 POLY ADENYLA TION IN PLANTS. 436 CONCLUDING REMARKS 436
James E Dahlberg - One of the best experts on this subject based on the ideXlab platform.
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nucleocytoplasmic transport and processing of small nuclear RNA Precursors
Molecular and Cellular Biology, 1990Co-Authors: H Neuman E De Vegvar, James E DahlbergAbstract:Abstract We have analyzed the structures and locations of small nuclear RNA (snRNA) Precursors at various stages in their synthesis and maturation. In the nuclei of pulse-labeled Xenopus laevis oocytes, we detected snRNAs that were longer than their mature forms at their 3' ends by up to 10 nucleotides. Analysis of the 5' caps of these RNAs and pulse-chase experiments showed that these nuclear snRNAs were Precursors of the cytoplasmic pre-snRNAs that have been observed in the past. Synthesis of pre-snRNAs was not abolished by wheat germ agglutinin, which inhibits export of the pre-snRNAs from the nucleus, indicating that synthesis of these RNAs is not obligatorily coupled to their export. Newly synthesized U1 RNAs could be exported from the nucleus regardless of the length of the 3' extension, but pre-U1 RNAs that were elongated at their 3' ends by more than about 10 nucleotides were poor substrates for trimming in the cytoplasm. The structure at the 3' end was critical for subsequent transport of the RNA back to the nucleus. This requirement ensures that truncated and incompletely processed U1 RNAs are excluded from the nucleus.
Sergey Y Morozov - One of the best experts on this subject based on the ideXlab platform.
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tas3 genes for small ta siarf RNAs in plants belonging to subtribe senecioninae occurrence of prematurely terminated RNA Precursors
Molecular Genetics Microbiology and Virology, 2013Co-Authors: L V Ozerova, M S Krasnikova, A V Troitsky, A G Solovyev, Sergey Y MorozovAbstract:The various classes of plant 21- to 24-nt siRNAs derive from long dsRNA Precursors that are processed by the ribonuclease Dicer-like (DCL). The species of ta-siRNA were originally discovered in Arabidopsis thaliana. Four gene families have been identified in Arabidopsis that each produces a number of ta-siRNAs: TAS1, TAS2, TAS3 and TAS4. The TAS3 genes encode ta-siR-ARF species which target the mRNA of three Auxin Response Factor (ARF) genes (ARF2, ARF3/ETT and ARF4) for subsequent degradation. The function of TAS3 precursor RNA is controlled by two miR390 target sites flanking tandem of ta-siARF sequences. In this paper, we have studied the presence of ta-siARF RNA genes in the representatives of subtribe Senecioninae. Senecioninae is the largest tribe of Asteraceae, comprised of ca. 150 genera and 3000 species which include many common succulents of greenhouses. Approximately one-third of species are placed in genus Senecio, making it one of the largest genera of flowering plants. However, there was no information on the structure of TAS genes in these plants. We revealed that the TAS3 species (TAS3-Sen1) in Senecio representatives was actively transcribed, and its homologues are distributed among many Asteracea plants and found to be similar to Arabidopsis AtTAS3a gene. We revealed several prematurely terminated transcripts of TAS3-Sen1. Finding the alteRNAtive shortened transcripts of TAS3-Sen1 lacking the 3′-terminal site cleaved by miR390 and retaining the 5′-terminal miR390 non-cleaved site suggested their using as decoys for the modulation of miR390 activity to regulate synthesis of ta-siARF RNAs in different Senecioninae species.
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tas3 genes for small ta siarf RNAs in plants belonging to subtribe senecioninae occurrence of prematurely terminated RNA Precursors
Molekuliarnaia genetika mikrobiologiia i virusologiia, 2013Co-Authors: L V Ozerova, M S Krasnikova, A V Troitsky, A G Solovyev, Sergey Y MorozovAbstract:: The various classes of plant 21 - to 24-nt siRNAs derive from long dsRNA Precursors that are processed by the ribonuclease Dicer-like (DCL). The species of ta-siRNA were originally discovered in Arabidopsis thaliana. Four gene families have been identified in Arabidopsis that each produces a number of ta-siRNAs: TAS1, TAS2, TAS3 and TAS4. The TAS3 genes encode tasiR-ARF species which target the mRNA of three Auxin Response Factor (ARF) genes (ARF2, ARF3/ETT and ARF4) for subsequent degradation. The function of TAS3 precursor RNA is controlled by two miR390 target sites flanking tandem of ta-siARF sequences. In this paper, we have studied the presence ofta-siARF RNA genes in the representatives of subtribe Senecioninae. Senecioneae is the largest tribe of Asteraceae, comprised of ca. 150 genera and 3,000 species which include many common succulents of greenhouses. Approximately one-third of species are placed in genus Senecio, making it one of the largest genera of flowering plants. However, there was no information on the structure of TAS genes in these plants. We revealed that the TAS3 species (TAS3-Sen1) in Senecio representatives was actively transcribed, and its homologues are distributed among many Asteracea plants and found to be similar to Arabidopsis AtTAS3a gene. We revealed several prematurely terminated transcripts of TAS3-Sen1. Finding the alteRNAtive shortened transcripts of TAS3-Sen1 lacking the 3'-terminal site cleaved by miR390 and retaining the 5'-terminal miR390 non-cleaved site suggested their using as decoys for the modulation of miR390 activity to regulate synthesis of ta-siARF RNAs in different Senecioninae species.
H Neuman E De Vegvar - One of the best experts on this subject based on the ideXlab platform.
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nucleocytoplasmic transport and processing of small nuclear RNA Precursors
Molecular and Cellular Biology, 1990Co-Authors: H Neuman E De Vegvar, James E DahlbergAbstract:Abstract We have analyzed the structures and locations of small nuclear RNA (snRNA) Precursors at various stages in their synthesis and maturation. In the nuclei of pulse-labeled Xenopus laevis oocytes, we detected snRNAs that were longer than their mature forms at their 3' ends by up to 10 nucleotides. Analysis of the 5' caps of these RNAs and pulse-chase experiments showed that these nuclear snRNAs were Precursors of the cytoplasmic pre-snRNAs that have been observed in the past. Synthesis of pre-snRNAs was not abolished by wheat germ agglutinin, which inhibits export of the pre-snRNAs from the nucleus, indicating that synthesis of these RNAs is not obligatorily coupled to their export. Newly synthesized U1 RNAs could be exported from the nucleus regardless of the length of the 3' extension, but pre-U1 RNAs that were elongated at their 3' ends by more than about 10 nucleotides were poor substrates for trimming in the cytoplasm. The structure at the 3' end was critical for subsequent transport of the RNA back to the nucleus. This requirement ensures that truncated and incompletely processed U1 RNAs are excluded from the nucleus.
Elmar Wahle - One of the best experts on this subject based on the ideXlab platform.
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The Biochemistry of 3′-End Cleavage and Polyadenylation of Messenger RNA Precursors
Annual Review of Biochemistry, 1992Co-Authors: Elmar Wahle, Walter KellerAbstract:AND PERSPECTIVES .... . . .... . . . . .... . . . . . .... .. . . . ..... . . . ....... . . . . .. . . . . . .... 4 1 9 POLYADENYLATION I N ANIMAL CELLS . . . . ....... . . ... ... . . . ..... . . . . . ..... . . ....... . . .. 420 Polyadenylarion Signals . .... . . . . . .... . . . ..... . . . ..... . . . ....... . . ... . . .. . . ...... . . . . ...... . . . . .. 420 3' -End Processing in vitro. . . . . .... . . . . ... . . . . . ..... . . . . .... . . . . ...... . .... ..... . . . .. .. . . . . . .... 424 Relationship Between Polyadenylation and Termination .. .. . . . . .... . . . . . 431 Regulated Polyadenylation . . . . . .. ...... . . ..... . . . . ..... . . . . . .... . . . ..... . .. . . ....... 431 POLY ADENYLA TlON IN yEAST 433 Sequences Required . ...... .. ...... . . . ..... . . . . ..... . . . .. .. . . . . ...... . . ... . . .. . . . .... .. . . ...... . . . 433 Mechanism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434 POLY ADENYLA TION IN PLANTS. 436 CONCLUDING REMARKS 436
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the biochemistry of 3 end cleavage and polyadenylation of messenger RNA Precursors
Annual Review of Biochemistry, 1992Co-Authors: Elmar Wahle, Walter KellerAbstract:AND PERSPECTIVES .... . . .... . . . . .... . . . . . .... .. . . . ..... . . . ....... . . . . .. . . . . . .... 4 1 9 POLYADENYLATION I N ANIMAL CELLS . . . . ....... . . ... ... . . . ..... . . . . . ..... . . ....... . . .. 420 Polyadenylarion Signals . .... . . . . . .... . . . ..... . . . ..... . . . ....... . . ... . . .. . . ...... . . . . ...... . . . . .. 420 3' -End Processing in vitro. . . . . .... . . . . ... . . . . . ..... . . . . .... . . . . ...... . .... ..... . . . .. .. . . . . . .... 424 Relationship Between Polyadenylation and Termination .. .. . . . . .... . . . . . 431 Regulated Polyadenylation . . . . . .. ...... . . ..... . . . . ..... . . . . . .... . . . ..... . .. . . ....... 431 POLY ADENYLA TlON IN yEAST 433 Sequences Required . ...... .. ...... . . . ..... . . . . ..... . . . .. .. . . . . ...... . . ... . . .. . . . .... .. . . ...... . . . 433 Mechanism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434 POLY ADENYLA TION IN PLANTS. 436 CONCLUDING REMARKS 436
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purification of the cleavage and polyadenylation factor involved in the 3 processing of messenger RNA Precursors
Journal of Biological Chemistry, 1991Co-Authors: S Bienroth, Elmar Wahle, C Sutercrazzolara, Walter KellerAbstract:Abstract Polyadenylation of messenger RNA Precursors requires the nucleotide sequence AAUAAA and two factors: poly(A) polymerase and a specificity factor termed cleavage and polyadenylation factor (CPF). We have purified CPF from calf thymus and from HeLa cells to near homogeneity. Four polypeptides with molecular masses of 160, 100, 73, and 30 kDa cofractionate with CPF activity. Glycerol gradient centrifugation and gel filtration indicate that these four proteins form one large complex with a sedimentation constant of 12 S, a Stokes radius near 100 A, and a native molecular mass near 500 kDa. Purified CPF binds specifically to an RNA that contains the AAUAAA sequence. Mutation of the AAUAAA sequence inhibits CPF binding as well as polyadenylation. Purified CPF contains only trace amounts of RNA and does not react with antibodies against common epitopes of small nuclear ribonucleoprotein particles. Thus, contrary to previous indications, CPF does not appear to be a small nuclear ribonucleoprotein particle.
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purification and characterization of a mammalian polyadenylate polymerase involved in the 3 end processing of messenger RNA Precursors
Journal of Biological Chemistry, 1991Co-Authors: Elmar WahleAbstract:Abstract A polyadenylate polymerase involved in the polyadenylation of pre-mRNA has been purified 6,000-fold to apparent homogeneity from extracts of calf thymus. In the last purification step, anion exchange chromatography separates the enzyme into three major peaks that are indistinguishable by other physical or functional criteria. On denaturing polyacrylamide gels, the two predominant forms of poly(A) polymerase have molecular weights of 57,000 and 60,000. In solution, the enzyme is a monomer. It polymerizes exclusively ATP. The reaction is distributive and proceeds linearly without any lag phase. The requirement for a primer can be satisfied by any of a number of polyribonucleotides. A significantly higher activity in the presence of Mn2+ as opposed to Mg2+ is due to a hundredfold higher affinity for the primer terminus. In the presence of mg2+ and of a specificity factor partially purified from HeLa cells, the enzyme specifically polyadenylates an RNA that ends at the natural adenovirus L3 polyadenylation site. This reaction depends on the AAUAAA polyadenylation signal.
