mRNA recognition and packaging by the human transcription–export complex

Abstract

Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription–export complex (TREX) for nuclear export1,2. However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood3. Here we report cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNPs bound to the 2-MDa TREX complex. We show that mRNPs are recognized through multivalent interactions between the TREX subunit ALYREF and mRNP-bound exon junction complexes. Exon junction complexes can multimerize through ALYREF, which suggests a mechanism for mRNP organization. Endogenous mRNPs form compact globules that are coated by multiple TREX complexes. These results reveal how TREX may simultaneously recognize, compact and protect mRNAs to promote their packaging for nuclear export. The organization of mRNP globules provides a framework to understand how mRNP architecture facilitates mRNA biogenesis and export. Cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNA ribonucleoprotein complexes bound to the transcription–export complex reveal how mRNAs are packaged and recognized for nuclear export.

Shown for reading. Its publisher allows quoting it, not republishing it.

References 92

1. 1.

   Köhler A, Hurt E. Exporting RNA from the nucleus to the cytoplasm. Nat Rev Mol Cell Biol. 2007;8:761-773.

   Not in our library10.1038/nrm2255

2. 2.

   Singh G, Pratt G, Yeo GW, Moore MJ. The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion. Annu Rev Biochem. 2015;84:325-354.

   Not in our library10.1146/annurev-biochem-080111-092106

3. 3.

   Khong A, Parker R. The landscape of eukaryotic mRNPs. RNA. 2020;26:229-239.

   Not in our library10.1261/rna.073601.119

4. 4.
   The role of TREX in gene expression and disease · 2016

   No notice
5. 5.

   Xie Y, et al. Cryo-EM structure of the yeast TREX complex and coordination with the SR-like protein Gbp2. eLife. 2021.

   Not in our library10.7554/elife.65699

6. 6.

   Cheng H, et al. Human mRNA Export Machinery Recruited to the 5' End of mRNA. Cell. 2006;127:1389-1400.

   Not in our library10.1016/j.cell.2006.10.044

7. 7.

   Gromadzka AM, Steckelberg A-L, Singh KK, Hofmann K, Gehring NH. A short conserved motif in ALYREF directs cap- and EJC-dependent assembly of export complexes on spliced mRNAs. Nucleic Acids Res. 2016;44:2348-2361.

   Not in our library10.1093/nar/gkw009

8. 8.

   Shi M, et al. ALYREF mainly binds to the 5' and the 3' regions of the mRNA in vivo. Nucleic Acids Research. 2017;45:9640-9653.

   Not in our library10.1093/nar/gkx597

9. 9.

   Gatfield D, et al. The DExH/D box protein HEL/UAP56 is essential for mRNA nuclear export in Drosophila. Current Biology. 2001;11:1716-1721.

   Not in our library10.1016/s0960-9822(01)00532-2

10. 10.

    Sträßer K, et al. TREX is a conserved complex coupling transcription with messenger RNA export. Nature. 2002;417:304-308.

    Not in our library10.1038/nature746

11. 11.

    Zenklusen D, Vinciguerra P, Wyss J-C, Stutz F. Stable mRNP Formation and Export Require Cotranscriptional Recruitment of the mRNA Export Factors Yra1p and Sub2p by Hpr1p. Mol Cell Biol. 2002;22:8241-8253.

    Not in our library10.1128/mcb.22.23.8241-8253.2002

12. 12.

    Viphakone N, et al. TREX exposes the RNA-binding domain of Nxf1 to enable mRNA export. Nat Commun. 2012;3:1006.

    Not in our library10.1038/ncomms2005

13. 13.
    Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome · 2019

    No notice
14. 14.

    Huertas P, Aguilera A. Cotranscriptionally Formed DNA:RNA Hybrids Mediate Transcription Elongation Impairment and Transcription-Associated Recombination. Molecular Cell. 2003;12:711-721.

    Not in our library10.1016/j.molcel.2003.08.010

15. 15.

    Adivarahan S, et al. Spatial Organization of Single mRNPs at Different Stages of the Gene Expression Pathway. Molecular Cell. 2018;72:727-738.

    Not in our library10.1016/j.molcel.2018.10.010

16. 16.

    Ashkenazy-Titelman A, Atrash MK, Boocholez A, Kinor N, Shav-Tal Y. RNA export through the nuclear pore complex is directional. Nat Commun. 2022;13:5881.

    Not in our library10.1038/s41467-022-33572-7

17. 17.

    Davidson IF, Peters J-M. Genome folding through loop extrusion by SMC complexes. Nat Rev Mol Cell Biol. 2021;22:445-464.

    Not in our library10.1038/s41580-021-00349-7

18. 18.

    Metkar M, et al. Higher-Order Organization Principles of Pre-translational mRNPs. Molecular Cell. 2018;72:715-726.

    Not in our library10.1016/j.molcel.2018.09.012

19. 19.
    Human protein-coding genes and gene feature statistics in 2019 · 2019

    No notice
20. 20.

    Le Hir H, Izaurralde E, Maquat LE, Moore MJ. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 2000;19:6860-6869.

    Not in our library10.1093/emboj/19.24.6860

21. 21.

    Singh G, et al. The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus. Cell. 2012;151:750-764.

    Not in our library10.1016/j.cell.2012.10.007

22. 22.

    Zhou Z, et al. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans. Nature. 2000;407:401-405.

    Not in our library10.1038/35030160

23. 23.

    Bono F, Ebert J, Lorentzen E, Conti E. The Crystal Structure of the Exon Junction Complex Reveals How It Maintains a Stable Grip onmRNA. Cell. 2006;126:713-725.

    Not in our library10.1016/j.cell.2006.08.006

24. 24.

    Andersen CBF, et al. Structure of the Exon Junction Core Complex with a Trapped DEAD-Box ATPase Bound to RNA. Science. 2006;313:1968-1972.

    Not in our library10.1126/science.1131981

25. 25.
    REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus · 2001

    Not checked
26. 26.

    Portman DS, O’Connor JP, Dreyfuss G. YRA1, an essential Saccharomyces cerevisiae gene, encodes a novel nuclear protein with RNA annealing activity. RNA. 1997;3:527-537.

    Not in our library

27. 27.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

28. 28.

    Pühringer T, et al. Structure of the human core transcription-export complex reveals a hub for multivalent interactions. eLife. 2020;9:e61503.

    Not in our library10.7554/elife.61503

29. 29.
    UIF, a New mRNA Export Adaptor that Works Together with REF/ALY, Requires FACT for Recruitment to mRNA · 2009

    No notice
30. 30.

    Dufu K, et al. ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex. Genes Dev. 2010;24:2043-2053.

    Not in our library10.1101/gad.1898610

31. 31.

    Schuller SK, et al. Structural insights into the nucleic acid remodeling mechanisms of the yeast THO-Sub2 complex. eLife. 2020;9:e61467.

    Not in our library10.7554/elife.61467

32. 32.

    Luo M-J, et al. Pre-mRNA splicing and mRNA export linked by direct interactions between UAP56 and Aly. Nature. 2001;413:644-647.

    Not in our library10.1038/35098106

33. 33.

    Fica SM, Oubridge C, Wilkinson ME, Newman AJ, Nagai K. A human postcatalytic spliceosome structure reveals essential roles of metazoan factors for exon ligation. Science. 2019;363:710-714.

    Not in our library10.1126/science.aaw5569

34. 34.

    Tunnicliffe RB, Tian X, Storer J, Sandri-Goldin RM, Golovanov AP. Overlapping motifs on the herpes viral proteins ICP27 and ORF57 mediate interactions with the mRNA export adaptors ALYREF and UIF. Sci Rep. 2018;8:15005.

    Not in our library10.1038/s41598-018-33379-x

35. 35.

    Viphakone N, et al. Luzp4 defines a new mRNA export pathway in cancer cells. Nucleic Acids Research. 2015;43:2353-2366.

    Not in our library10.1093/nar/gkv070

36. 36.

    Chang C-T, et al. Chtop is a component of the dynamic TREX mRNA export complex. EMBO J. 2013;32:473-486.

    Not in our library10.1038/emboj.2012.342

37. 37.

    Merz C, Urlaub H, Will CL, Lührmann R. Protein composition of human mRNPs spliced in vitro and differential requirements for mRNP protein recruitment. RNA. 2007;13:116-128.

    Not in our library10.1261/rna.336807

38. 38.

    Huang Y, Yario TA, Steitz JA. A molecular link between SR protein dephosphorylation and mRNA export. Proc Natl Acad Sci U S A. 2004;101:9666-9670.

    Not in our library10.1073/pnas.0403533101

39. 39.

    Batisse J, Batisse C, Budd A, Böttcher B, Hurt E. Purification of Nuclear Poly(A)-binding Protein Nab2 Reveals Association with the Yeast Transcriptome and a Messenger Ribonucleoprotein Core Structure. J Biol Chem. 2009;284:34911-34917.

    Not in our library10.1074/jbc.m109.062034

40. 40.

    Skoglund U, Andersson K, Strandberg B, Daneholt B. Three-dimensional structure of a specific pre-messenger RNP particle established by electronmicroscope tomography. Nature. 1986;319:560-564.

    Not in our library10.1038/319560a0

41. 41.
    Structural and biochemical analyses of the DEAD-box ATPase Sub2 in association with THO or Yra1 · 2017

    Not checked
42. 42.

    Montpetit B, et al. A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export. Nature. 2011;472:238-242.

    Not in our library10.1038/nature09862

43. 43.

    Sträßer K, Hurt E. Splicing factor Sub2p is required for nuclear mRNA export through its interaction with Yra1p. Nature. 2001;413:648-652.

    Not in our library10.1038/35098113

44. 44.

    Zenklusen D, Vinciguerra P, Strahm Y, Stutz F. The Yeast hnRNP-Like Proteins Yra1p and Yra2p Participate in mRNA Export through Interactionwith Mex67p. Mol Cell Biol. 2001;21:4219-4232.

    Not in our library10.1128/mcb.21.13.4219-4232.2001

45. 45.

    Blazquez L, et al. Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing. Mol Cell. 2018;72:496-509.

    Not in our library10.1016/j.molcel.2018.09.033

46. 46.

    Boehm V, et al. Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity. Mol Cell. 2018;72:482-495.

    Not in our library10.1016/j.molcel.2018.08.030

47. 47.

    Murachelli AG, Ebert J, Basquin C, Le Hir H, Conti E. The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex. Nat Struct Mol Biol. 2012;19:378-386.

    Not in our library10.1038/nsmb.2242

48. 48.

    Mazza C, Ohno M, Segref A, Mattaj IW, Cusack S. Crystal structure of the human nuclear cap binding complex. Mol Cell. 2001;8:383-396.

    Not in our library10.1016/s1097-2765(01)00299-4

49. 49.

    Tegunov D. High-resolution in situ imaging of biological samples with Warp and M. Acta Crystallographica Section A Foundations and Advances. 2020;76.

    Not in our library

50. 50.

    Krijthe Jesse H. T-Distributed Stochastic Neighbor Embedding using Barnes-Hut. 2015.

    Not in our library

51. 51.

    Baejen C, et al. Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition. Mol Cell. 2014;55:745-757.

    Not in our library10.1016/j.molcel.2014.08.005

52. 52.

    Schwanhäusser B, et al. Global quantification of mammalian gene expression control. Nature. 2011;473:337-342.

    Not in our library10.1038/nature10098

53. 53.

    Taniguchi I, Ohno M. ATP-Dependent Recruitment of Export Factor Aly/REF onto Intronless mRNAs by RNA Helicase UAP56. Mol Cell Biol. 2008;28:601-608.

    Not in our library10.1128/mcb.01341-07

54. 54.

    Yan Q, et al. Proximity labeling identifies a repertoire of site-specific R-loop modulators. Nat Commun. 2022;13:53.

    Not in our library10.1038/s41467-021-27722-6

55. 55.

    Fan J, et al. Exosome cofactor hMTR4 competes with export adaptor ALYREF to ensure balanced nuclear RNA pools for degradation and export. EMBO J. 2017;36:2870-2886.

    Not in our library10.15252/embj.201696139

56. 56.

    Silla T, Karadoulama E, Mqkosa D, Lubas M, Jensen TH. The RNA Exosome Adaptor ZFC3H1 Functionally Competes with Nuclear Export Activity to Retain Target Transcripts. Cell Reports. 2018;23:2199-2210.

    Not in our library10.1016/j.celrep.2018.04.061

57. 57.
    Viscoelasticity and advective flow of RNA underlies nucleolar form and function · 2023

    No notice
58. 58.
    The cellular environment shapes the nuclear pore complex architecture · 2021

    No notice
59. 59.

    Schmidt U, et al. Assembly and mobility of exon-exon junction complexes in living cells. Rna. 2009;15:862-876.

    Not in our library10.1261/rna.1387009

60. 60.

    Derrer CP, et al. The RNA export factor Mex67 functions as a mobile nucleoporin. J Cell Biol. 2019;218:3967-3976.

    Not in our library10.1083/jcb.201909028

61. 61.

    Ben-Yishay R, et al. Imaging within single NPCs reveals NXF1’s role in mRNA export on the cytoplasmic side of the pore. J Cell Biol. 2019;218:2962-2981.

    Not in our library10.1083/jcb.201901127

62. 62.
    Highly accurate protein structure prediction with AlphaFold · 2021

    No notice
63. 63.
    AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models · 2021

    No notice
64. 64.

    Punjani A, Rubinstein JL, Fleet DJ, Brubaker MA. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat Methods. 2017;14:290-296.

    Not in our library10.1038/nmeth.4169

65. 65.
    REAP: A two minute cell fractionation method · 2010

    No notice
66. 66.
    RELION: Implementation of a Bayesian approach to cryo-EM structure determination · 2012

    No notice
67. 67.
    Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION -3.1 · 2020

    No notice
68. 68.

    Tegunov D, Cramer P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat Methods. 2019;16:1146-1152.

    Not in our library10.1038/s41592-019-0580-y

69. 69.

    Mastronarde DN, Held SR. Automated tilt series alignment and tomographic reconstruction in IMOD. Journal of Structural Biology. 2017;197.

    Not in our library10.1016/j.jsb.2016.07.011

70. 70.

    Schindelin J, et al. Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012;9:676-682.

    Not in our library10.1038/nmeth.2019

71. 71.

    Koch B, et al. Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing. Nat Protoc. 2018;13:1465-1487.

    Not in our library10.1038/nprot.2018.042

72. 72.

    Muhar M, et al. SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. Science. 2018;360:800-805.

    Not in our library10.1126/science.aao2793

73. 73.

    Kastner B, et al. GraFix: sample preparation for single-particle electron cryomicroscopy. Nat Methods. 2008;5:53-55.

    Not in our library10.1038/nmeth1139

74. 74.

    Mastronarde DN. Automated electron microscope tomography using robust prediction of specimen movements. Journal of Structural Biology. 2005;152.

    Not in our library10.1016/j.jsb.2005.07.007

75. 75.
    Features and development of Coot · 2010

    No notice
76. 76.

    Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 2004;60:2126-2132.

    Not in our library10.1107/s0907444904019158

77. 77.
    ISOLDE : a physically realistic environment for model building into low-resolution electron-density maps · 2018

    No notice
78. 78.
    PHENIX : a comprehensive Python-based system for macromolecular structure solution · 2010

    No notice
79. 79.
    Real-space refinement in PHENIX for cryo-EM and crystallography · 2018

    No notice
80. 80.

    Goddard TD, et al. UCSF ChimeraX: Meeting modern challenges in visualization and analysis: UCSF ChimeraX Visualization System. Protein Science. 2018;27:14-25.

    Not in our library10.1002/pro.3235

81. 81.

    Pettersen EF, et al. UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Protein Science. 2021;30.

    Not in our library10.1002/pro.3943

82. 82.

    Webb B, Sali A, Kaufmann M, Klinger C, Savelsbergh A. Functional Genomics. 2017;1654:39-54.

    Not in our library

83. 83.
    Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging · 2017

    No notice
84. 84.

    Nicastro D, et al. The molecular architecture of axonemes revealed by cryoelectron tomography. Science. 2006;313:944-948.

    Not in our library10.1126/science.1128618

85. 85.

    Heumann JM, Hoenger A, Mastronarde DN. Clustering and variance maps for cryo-electron tomography using wedge-masked differences. Journal of Structural Biology. 2011;175.

    Not in our library10.1016/j.jsb.2011.05.011

86. 86.

    Krijthe JH. Rtsne: T-Distributed Stochastic Neighbor Embedding using Barnes-Hut Implementation. 2015.

    Not in our library

87. 87.

    R: A Language and Environment for Statistical Computing. 2021.

    Not in our library

88. 88.

    Wickham H. ggplot2: Elegant Graphics for Data Analysis. 2016.

    Not in our library

89. 89.
    An integrated workflow for crosslinking mass spectrometry · 2019

    No notice
90. 90.
    Reliable identification of protein-protein interactions by crosslinking mass spectrometry · 2021

    No notice
91. 91.

    Piovesan A, Caracausi M, Antonaros F, Pelleri MC, Vitale L. GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics. Database (Oxford). 2016;baw153.

    Not in our library10.1093/database/baw153

92. 92.

    Abràmoff MD, Hospitals I, Magalhães PJ, Abràmoff M. Image Processing with ImageJ. Biophotonics International. 2004.

    Not in our library

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.