A unified mechanism for defining introns and exons and crosslinking



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  • 1.

    Zhang, L., Vielle, A., Espinosa, S. and Zhao, R. RNAs in the spliceosome: overview of cryoEM structures. Wiley Interdiscip. Rev. RNA tene1523 (2019).

  • 2

    Wan, R., Bai, R., Yan, C., Lei, J. and Shi, Y. Structures of catalytically activated yeast spliceosome reveal the branching mechanism. Cell 177339-351 (2019).

  • 3

    From Conti, L., Baralle, M. & Buratti, E. Exon and intron definition in pre-mRNA splicing. Wiley Interdiscip. Rev. RNA 4, 49-60 (2013).

  • 4

    Berget, S. M. Exon recognition in vertebrate splicing. J. Biol. Chem. 2702411-2414 (1995).

  • 5

    Sharma, S., Kohlstaedt, L.A., Damianov, A., Rio, D.C. & Black, D.L.The polypyrimidine tract binding protein controls the transition from the definition of exon to an intronically defined spliceosome. Nat. Struct. Mol. Biol. 15, 183-191 (2008).

  • 6

    Schneider, M. et al. The exon definition complexes contain tri-snRNP and can be directly converted into precatalytic type B splice complexes. Mol. Cell 38, 223-235 (2010).

  • 7.

    Wang, P. L. et al. Circular RNA is expressed through the eukaryotic tree of life. PLoS One 9, e90859 (2014).

  • 8

    Wilusz, J. E. A. A 360 ° view of circular RNAs: from biogenesis to functions. Wiley Interdiscip. Rev. RNA 9e1478 (2018).

  • 9

    Starke, S. et al. Exon circularization requires canonical splicing signals. Cellular Representative. ten103-111 (2015).

  • ten.

    Seraphin, B., Kretzner, L. and Rosbash, M. A U1 RNA Interaction: A Pre-mRNA Base Pairing is Required at the Beginning of the Yeast Spliceosome Assembly but Does Not Only Define the Cleavage Site in 5 & # 39; EMBO J. 72533-2538 (1988).

  • 11

    Siliciano, P. G. & Guthrie, C. Selection of 5-splice site in yeast: genetic alterations in base pairing with U1 reveal additional requirements. Genes Dev. 21258-1267 (1988).

  • 12

    Ruby, S.W. & Abelson, J. A first hierarchical role of the small U1 nuclear ribonucleoprotein in spliceosome assembly. Science 2421028-1035 (1988).

  • 13

    Abovich, N. & Rosbash, M. Interlining interactions between crossed introns in the yeast commitment complex are conserved in mammals. Cell 89403-412 (1997).

  • 14

    Plaschka, C., Lin, C., Charenton, C. and Nagai, K. The structure of the prespliceosome provides insight into the assembly and regulation of spliceosomes. Nature 559419-422 (2018).

  • 15

    Bai, R., Wan, R., Yan, C., Lei, J. and Shi, Y. Fully Assembled Structures Saccharomyces cerevisiae spliceosome before activation. Science 3601423-1429 (2018).

  • 16

    Lewis, JD, Izaurralde, E., Jarmolowski, A., McGuigan, C. and Mattaj, IW A nuclear cap bonding complex facilitates the association of snRNP U1 with splice site in 5 & ## 39, of the proximal cap. Genes Dev. ten1683-1698 (1996).

  • 17

    Qiu, ZR, Chico, L., Chang, J., Shuman, S. and Schwer, B. Genetic Interactions of Hypomorphic Mutations in the M7G Capsule Binding Pocket of the Yeast Nuclear Capsule-binding Complex: A Role essential of Cbc2 in meiosis via splicing of MER3 pre-mRNA. RNA 18, 1996-2011 (2012).

  • 18

    Puig, O., Gottschalk, A., Fabrizio, P. and Seraphin, B. The interaction of the snRNP U1 with non-conserved intron sequences affects the splice site selection in 5 #. Genes Dev. 13569-580 (1999).

  • 19

    Lesser, C. F. & Guthrie, C. Mutational Analysis of Pre-mRNA Splicing at Saccharomyces cerevisiae using a new sensitive reporter gene, CUP1. Genetic 133851-863 (1993).

  • 20

    Liu, S. et al. Structure of the post-catalytic P-spliceosomal yeast complex. Science 358, 1278-1283 (2017).

  • 21

    Lu, M. et al. Crystal structure of the three FF domains in tandem of the CA150 transcription elongation regulator. J. Mol. Biol. 393397-408 (2009).

  • 22

    Liu, J., Fan, S., CJ, Greenleaf, AL and Zhou, P. The specific interaction of TCERG1 transcriptional elongation regulator with RNA polymerase II requires simultaneous phosphorylation at Ser2 level, Ser5 and Ser7 in the carboxy-terminal domain repeat. J. Biol. Chem. 28810890-10901 (2013).

  • 23

    Li, X. et al. CryoEM structure Saccharomyces cerevisiae U1 snRNP provides an overview of alternative splicing. Nat. Common. 81035 (2017).

  • 24

    Görnemann, J. et al. The assembly and splicing of cotranscriptional spliceosomes are independent of the WW domain of Prp40p. RNA 172119-2129 (2011).

  • 25

    Ester, C. & Uetz, P. The FF domains of the u1 snRNP protein Prp40 U1 induce interactions with Luc7 and Snu71. BMC Biochem. 929 (2008).

  • 26

    Wiesner, S., G. Stier, M. Sattler and M. Macias, J. Solution structure and ligand recognition of the WW domain pair of Prp40 yeast splicing factor. J. Mol. Biol. 324807 to 822 (2002).

  • 27

    Jacewicz, A., Chico, L., Smith, P., Schwer, B. and Shuman, S. Structural basis for RNA recognition of intron branching by Ms15 yeast and selective effects of interfacial mutations on the cell. splicing of the yeast pre-mRNA. RNA 21, 401-414 (2015).

  • 28

    Kappel, K. & Das, R. Sampling of native-type structures of RNA-protein complexes by folding and docking Rosetta. Structure 27140-151e145 (2019).

  • 29

    Howe, K.J., Kane, C.M. and Ares, M., Jr. The disturbance of transcriptional elongation influences the fidelity of the inclusion of the inner exon in Saccharomyces cerevisiae. RNA 9993-1006 (2003).

  • 30

    Campodonico, E. & Schwer, B. ATP-dependent spliceosome remodeling: intragenic suppressors of mutants of the Saccharomyces cerevisiae Prp22. Genetic 160407-415 (2002).

  • 31.

    Liang, D. et al. The production of protein coding genes shifts to circular RNAs when the pre-mRNA processing mechanism is limiting. Mol. Cell. 68940-954e943 (2017).

  • 32

    Ragan, C., Goodall, G.J., Shirokikh, N.E. & Preiss, T. Overview of the biogenesis and potential functions of circular exonic RNA. Sci. Representative. 92048 (2019).

  • 33

    Liang, D. & Wilusz, J. E. Short intronic repetitive sequences facilitate circular RNA production. Genes Dev. 28, 2233-2247 (2014).

  • 34

    Jeck, W. R. et al. Circular RNAs are abundant, conserved and associated with ALU repeats. RNA 19141-157 (2013).

  • 35

    Mokry, M. et al. Accurate detection of SNPs and mutations by targeted genomic enrichment, based on a DNA chip, of short fragment sequencing libraries. Nucleic Acids Res. 38, e116 (2010).

  • 36

    Spingola, M., L. Grate, D. Haussler, and M. Ares, M., Jr. Bioinformatics and molecular-scale genome-wide analysis of introns in Saccharomyces cerevisiae. RNA 5221-234 (1999).

  • 37

    Li, X. et al. Comprehensive in vivo analyzes of RNA binding sites reveal the role of Prp8 in the splice assembly. Nucleic Acids Res. 413805-3818 (2013).

  • 38

    Abelson, J. et al. Conformational dynamics of single molecules of pre-mRNA during in vitro splicing. Nat. Struct. Mol. Biol. 17504-512 (2010).

  • 39

    Carragher, B. et al. Leginon: an automated system for acquiring images from vitreous ice samples. J. Struct. Biol. 132, 33-45 (2000).

  • 40

    Zheng, S.Q., Palovcak, E., Armache, J.-P., Cheng, Y. and Agard, D.A. MotionCor2: anisotropic correction of beam-induced motion to improve cryoelectronic microscopy. Nat. The methods
    14, 331 to 332 (2017).

  • 41

    Rohou, A. & Grigorieff, N. CTFFIND4: Rapid and accurate estimation of defocusing with the aid of electronic micrographs. J. Struct. Biol. 192216-221 (2015).

  • 42

    Scheres, S.H. and Chen, S. Prevention of overadjustment in the determination of cryo-EM structure. Nat. The methods 9853-854 (2012).

  • 43

    Chen, S. et al. High-resolution noise substitution to measure over-adjustment and validate resolution in 3D single-particle electron cryomicroscopy structure determination. ultramicroscopy 135, 24-35 (2013).

  • 44

    Rosenthal, P. B. & Henderson, R. Optimum determination of particle orientation, absolute hand loss and contrast in single-particle electron cryomicroscopy. J. Mol. Biol. 333721-745 (2003).

  • 45

    Kucukelbir, A., Sigworth, F.J. and Tagare, H.D. Quantify the local resolution of cryo-EM density maps. Nat. The methods 11, 63-65 (2014).

  • 46

    Pettersen, E.F. et al. UCSF Chimera – a visualization system for exploratory research and analysis. J. Comput. Chem. 251605-1612 (2004).

  • 47

    Emsley, P., Lohkamp, ​​B., Scott, W. G. and Cowtan, K. Characteristics and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501 (2010).

  • 48.

    Keating, K. S. & Pyle, A. M. RCrane: Construction of Semi-Automated RNA Models. Acta Crystallogr. D Biol. Crystallogr. 68, 985-995 (2012).

  • 49

    Cabbage, F.C., Sripakdeevong, P., Dibrov, S.M., Hermann, T. & Das, R. Correction of ubiquitous errors in RNA crystallography by the prediction of enumerative structures. Nat. The methods ten, 74-76 (2013).

  • 50

    Kappel, K. et al. De novo modeling of computer RNA in cryo-EM maps of large ribonucleoprotein complexes. Nat. The methods 15947-954 (2018).

  • 51.

    Adams, P.D. et al. PHENIX: a complete system based on Python for a solution with a macromolecular structure. Acta Crystallogr. D Biol. Crystallogr. 66213-221 (2010).

  • 52.

    Chen, V.B. et al. MolProbity: validation of the structure any atom for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12-21 (2010).

  • 53

    Goddard, T. D. et al. UCSF ChimeraX: Meeting Modern Challenges in Visualization and Analysis. Protein Sci. 27, 14-25 (2018).

  • 54

    Wiśniewski, J.R., Zougman, A., Nagaraj, N. and Mann, M. Universal sample preparation method for the analysis of the proteome. Nat. The methods 6359-362 (2009).

  • 55

    Grimm, M., Zimniak, T., Kahraman, A. & Herzog, F. xVis: a web server for schematic visualization and interpretation of spatial constraints derived from crosslinks. Nucleic Acids Res. 43, W362 to W369 (2015).

  • 56.

    Seraphin, B. & Rosbash, M. Identification of U1 functional snRNA-pre-mRNA complexes involved in spliceosome assembly and splicing. Cell 59349-358 (1989).

  • 57

    Qin, D., Huang, L., Wlodaver, A., Andrade, J. and Staley, J. P. Sequencing of termini lariat in S. cerevisiae reveals 5 'splice sites, branching points and new splicing events. RNA 22, 237-253 (2016).

  • 58.

    Li, Z. & Brow, D. A. A rapid test for the quantitative detection of specific RNA. Nucleic Acids Res. 214645-4646 (1993).

  • 59

    Kozlowski, L. P. & Bujnicki, J. MetaDisorder M.: a meta-server for the prediction of intrinsic protein disorder. BMC Bioinformatics 13111 (2012).

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