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      The conserved AU dinucleotide at the 5′ end of nascent U1 snRNA is optimized for the interaction with nuclear cap-binding-complex

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          Abstract

          Splicing is initiated by a productive interaction between the pre-mRNA and the U1 snRNP, in which a short RNA duplex is established between the 5′ splice site of a pre-mRNA and the 5′ end of the U1 snRNA. A long-standing puzzle has been why the AU dincucleotide at the 5′-end of the U1 snRNA is highly conserved, despite the absence of an apparent role in the formation of the duplex. To explore this conundrum, we varied this AU dinucleotide into all possible permutations and analyzed the resulting molecular consequences. This led to the unexpected findings that the AU dinucleotide dictates the optimal binding of cap-binding complex (CBC) to the 5′ end of the nascent U1 snRNA, which ultimately influences the utilization of U1 snRNP in splicing. Our data also provide a structural interpretation as to why the AU dinucleotide is conserved during evolution.

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          Most cited references 77

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          How did alternative splicing evolve?

           Gil Ast (2004)
          Alternative splicing creates transcriptome diversification, possibly leading to speciation. A large fraction of the protein-coding genes of multicellular organisms are alternatively spliced, although no regulated splicing has been detected in unicellular eukaryotes such as yeasts. A comparative analysis of unicellular and multicellular eukaryotic 5' splice sites has revealed important differences - the plasticity of the 5' splice sites of multicellular eukaryotes means that these sites can be used in both constitutive and alternative splicing, and for the regulation of the inclusion/skipping ratio in alternative splicing. So, alternative splicing might have originated as a result of relaxation of the 5' splice site recognition in organisms that originally could support only constitutive splicing.
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            Synthetic genetic array analysis in Saccharomyces cerevisiae.

            Synthetic lethality occurs when the combination of two mutations leads to an inviable organism. Screens for synthetic lethal genetic interactions have been used extensively to identify genes whose products buffer one another or impinge on the same essential pathway. For the yeast Saccharomyces cerevisiae, we developed a method termed Synthetic Genetic Array (SGA) analysis, which offers an efficient approach for the systematic construction of double mutants and enables a global analysis of synthetic lethal genetic interactions. In a typical SGA screen, a query mutation is crossed to an ordered array of approx 5000 viable gene deletion mutants (representing approximately 80% of all yeast genes) such that meiotic progeny harboring both mutations can be scored for fitness defects. This array-based approach automates yeast genetic analysis in general and can be easily adapted for a number of different screens, including genetic suppression, plasmid shuffling, dosage lethality, or suppression.
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              Spliceosomal UsnRNP biogenesis, structure and function.

              Significant advances have been made in elucidating the biogenesis pathway and three-dimensional structure of the UsnRNPs, the building blocks of the spliceosome. U2 and U4/U6*U5 tri-snRNPs functionally associate with the pre-mRNA at an earlier stage of spliceosome assembly than previously thought, and additional evidence supporting UsnRNA-mediated catalysis of pre-mRNA splicing has been presented.
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                Author and article information

                Journal
                Nucleic Acids Res
                Nucleic Acids Res
                nar
                Nucleic Acids Research
                Oxford University Press
                0305-1048
                1362-4962
                19 September 2017
                13 July 2017
                13 July 2017
                : 45
                : 16
                : 9679-9693
                Affiliations
                [1 ]Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
                [2 ]Genomics Research Center, Academia Sinica, Taipei, Taiwan
                [3 ]Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
                [4 ]Institute of Chemistry, Academia Sinica, Taipei, Taiwan
                [5 ]Chemical Biology and Molecular Biophysics program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
                [6 ]Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
                Author notes
                [* ]To whom correspondence should be addressed. Tel: +886 2 2787 1242; Fax: +886 2 2789 9931; Email: chang108@ 123456gate.sinica.edu.tw
                Article
                gkx608
                10.1093/nar/gkx608
                5766165
                28934473
                © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                Page count
                Pages: 15
                Product
                Categories
                RNA and RNA-protein complexes

                Genetics

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