CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing

Li, X.; Liu, S.; Jiang, Junchen; Zhang, L.; Espinosa, Sara; Hill, Ryan C.; Hansen, Kirk C.; Zhou, Z. Hong; Zhao, Rui

doi:10.1038/s41467-017-01241-9

Cited by 60 publications

(96 citation statements)

References 75 publications

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“…Crystal structure of Prp28 and Sad1 was docked into the density of the pre-B complex according the cryo-EM structure of human tri-snRNP. 13 The cryo-EM structure of U1 snRNP 63 was docked into the bulky density lobe near the ATPase/helicase Prp28. The side chains in the protein components of the pre-B complex were removed due to lack of side chain features.…”

Section: Methodsmentioning

confidence: 99%

Structures of the human pre-catalytic spliceosome and its precursor spliceosome

et al. 2018

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The pre-catalytic spliceosome (B complex) is preceded by its precursor spliceosome (pre-B complex) and followed by the activated spliceosome (Bact complex). The pre-B-to-B and B-to-Bact transitions are driven by the ATPase/helicases Prp28 and Brr2, respectively. In this study, we report the cryo-electron microscopy structures of the human pre-B complex and the human B complex at an average resolution of 5.7 and 3.8 Å, respectively. In the pre-B complex, U1 and U2 small nuclear ribonucleoproteins (snRNPs) associate with two edges of the tetrahedron-shaped U4/U6.U5 tri-snRNP. The pre-mRNA is yet to be recognized by U5 or U6 small nuclear RNA (snRNA), and loop I of U5 snRNA remains unengaged. In the B complex, U1 snRNP and Prp28 are dissociated, the 5’-exon is anchored to loop I of U5 snRNA, and the 5′-splice site is recognized by U6 snRNA through duplex formation. In sharp contrast to S. cerevisiae, most components of U2 snRNP and tri-snRNP, exemplified by Brr2, undergo pronounced rearrangements in the human pre-B-to-B transition. Structural analysis reveals mechanistic insights into the assembly and activation of the human spliceosome.

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Section: Methodsmentioning

confidence: 99%

Structures of the human pre-catalytic spliceosome and its precursor spliceosome

et al. 2018

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“…The first high‐resolution cryoEM structure of the spliceosome was the Schizosaccharomyces pombe ILS complex determined by the Shi lab in 2015 (Yan et al, ). In the following years, high‐resolution structures of the yeast U1 snRNP (Li et al, ), tri‐snRNP (Nguyen et al, ; Wan et al, ), A (Plaschka, Lin, Charenton, & Nagai, ), pre‐B (Bai, Wan, Yan, Lei, & Shi, ), B (Bai, Wan, Yan, Lei, & Shi, 2018; Plaschka, Lin, & Nagai, ), B act (Yan, Wan, Bai, Huang, & Shi, ), C (Galej et al, ; Wan, Yan, Bai, Huang, & Shi, ), C* (Fica et al, ; Yan, Wan, Bai, Huang, & Shi, ), P (Bai, Yan, Wan, Lei, & Shi, ; Liu et al, ; Wilkinson et al, ), and ILS (Wan, Yan, Bai, Lei, & Shi, ) complexes, as well as the human B (Bertram et al, ), B act (Haselbach et al, ; Zhang et al, ), C (Zhan, Yan, Zhang, Lei, & Shi, ), and C* (Bertram et al, ; Zhang et al, ) complexes were determined. These structures provided unprecedented details on the organization of RNA and protein components in the spliceosome and their functions in the splicing reaction.…”

Section: Overviewmentioning

confidence: 99%

RNAs in the spliceosome: Insight from cryoEM structures

et al. 2019

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Pre-mRNA splicing is catalyzed by the spliceosome, a multimegadalton RNAprotein complex. The spliceosome undergoes dramatic compositional and conformational changes through the splicing cycle, forming at least 10 distinct complexes. Recent high-resolution cryoEM structures of various spliceosomal complexes revealed unprecedented details of this large molecular machine. This review highlights insight into the structure and function of the spliceosomal RNA components obtained from these new structures, with a focus on the yeast spliceosome.

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“…Wilkinson et al Embracing these advances, we (37,43,82,83,95,138) and the groups of Reinhard Lührmann/Holger Stark (2,12,13,103), Yigong Shi (6, 132-134, 144-146, 150), and Rui Zhao/Hong Zhou (66,70) have purified multiple spliceosome intermediates from yeast and human sources and have determined their three-dimensional (3D) structures at intermediate to high resolution. This body of work has revealed novel mechanistic details of pre-mRNA splicing.…”

Section: 4mentioning

confidence: 99%

Cryo-EM Studies of Pre-mRNA Splicing: From Sample Preparation to Model Visualization

Lin

Plaschka

Nagai

2018

Annu. Rev. Biophys.

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The removal of noncoding introns from pre-messenger RNA (pre-mRNA) is an essential step in eukaryotic gene expression and is catalyzed by a dynamic multi-megadalton ribonucleoprotein complex called the spliceosome. The spliceosome assembles on pre-mRNA substrates by the stepwise addition of small nuclear ribonucleoprotein particles and numerous protein factors. Extensive remodeling is required to form the RNA-based active site and to mediate the pre-mRNA branching and ligation reactions. In the past two years, cryo-electron microscopy (cryo-EM) structures of spliceosomes captured in different assembly and catalytic states have greatly advanced our understanding of its mechanism. This was made possible by long-standing efforts in the purification of spliceosome intermediates as well as recent developments in cryo-EM imaging and computational methodology. The resulting high-resolution densities allow for de novo model building in core regions of the complexes. In peripheral and less ordered regions, the combination of cross-linking, bioinformatics, biochemical, and genetic data is essential for accurate modeling. Here, we summarize these achievements and highlight the critical steps in obtaining near-atomic resolution structures of the spliceosome.

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CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing

Cited by 60 publications

References 75 publications

Structures of the human pre-catalytic spliceosome and its precursor spliceosome

Structures of the human pre-catalytic spliceosome and its precursor spliceosome

RNAs in the spliceosome: Insight from cryoEM structures

Cryo-EM Studies of Pre-mRNA Splicing: From Sample Preparation to Model Visualization

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