EFTUD2 missense variants disrupt protein function and splicing in mandibulofacial dysostosis Guion-Almeida type.
EFTUD2
Snu114
mandibulofacial dysostosis Guion-Almeida type
minigene
missense variants
pre-mRNA splicing
splicing variants
yeast
Journal
Human mutation
ISSN: 1098-1004
Titre abrégé: Hum Mutat
Pays: United States
ID NLM: 9215429
Informations de publication
Date de publication:
08 2020
08 2020
Historique:
received:
14
01
2020
revised:
26
03
2020
accepted:
19
04
2020
pubmed:
26
4
2020
medline:
9
11
2021
entrez:
26
4
2020
Statut:
ppublish
Résumé
Pathogenic variants in the core spliceosome U5 small nuclear ribonucleoprotein gene EFTUD2/SNU114 cause the craniofacial disorder mandibulofacial dysostosis Guion-Almeida type (MFDGA). MFDGA-associated variants in EFTUD2 comprise large deletions encompassing EFTUD2, intragenic deletions and single nucleotide truncating or missense variants. These variants are predicted to result in haploinsufficiency by loss-of-function of the variant allele. While the contribution of deletions within EFTUD2 to allele loss-of-function are self-evident, the mechanisms by which missense variants are disease-causing have not been characterized functionally. Combining bioinformatics software prediction, yeast functional growth assays, and a minigene (MG) splicing assay, we have characterized how MFDGA missense variants result in EFTUD2 loss-of-function. Only four of 19 assessed missense variants cause EFTUD2 loss-of-function through altered protein function when modeled in yeast. Of the remaining 15 missense variants, five altered the normal splicing pattern of EFTUD2 pre-messenger RNA predominantly through exon skipping or cryptic splice site activation, leading to the introduction of a premature termination codon. Comparison of bioinformatic predictors for each missense variant revealed a disparity amongst different software packages and, in many cases, an inability to correctly predict changes in splicing subsequently determined by MG interrogation. This study highlights the need for laboratory-based validation of bioinformatic predictions for EFTUD2 missense variants.
Substances chimiques
EFTUD2 protein, human
0
Peptide Elongation Factors
0
Ribonucleoprotein, U5 Small Nuclear
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1372-1382Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/N000358/1
Pays : United Kingdom
Organisme : Department of Health
ID : IS‐BRC‐1215‐20007
Pays : United Kingdom
Informations de copyright
© 2020 The Authors. Human Mutation published by Wiley Periodicals, Inc.
Références
Bartels, C., Urlaub, H., Lührmann, R., & Fabrizio, P. (2003). Mutagenesis suggests several roles of Snu114p in pre-mRNA splicing. Journal of Biological Chemistry, 278(30), 28324-28334.
Beauchamp, M. C., Djedid, A., Daupin, K., Clokie, K., Kumar, S., Majewski, J., & Jerome-Majewska, L. A. (2019). Loss of function mutation of Eftud2, the gene responsible for mandibulofacial dysostosis with microcephaly (MFDM), leads to pre-implantation arrest in mouse. PLOS One, 14(7):e0219280. https://doi.org/10.1371/journal.pone.0219280
Brenner, T. J., & Guthrie, C. (2005). Genetic analysis reveals a role for the C terminus of the Saccharomyces cerevisiae GTPase Snu114 during spliceosome activation. Genetics, 170(3), 1063-1080.
Brummer, A., & Hausser, J. (2014). MicroRNA binding sites in the coding region of mRNAs: Extending the repertoire of post-transcriptional gene regulation. BioEssays, 36(6), 617-626. https://doi.org/10.1002/bies.201300104
Buratti, E., Chivers, M., Kralovicova, J., Romano, M., Baralle, M., Krainer, A. R., & Vorechovsky, I. (2007). Aberrant 5′ splice sites in human disease genes: Mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Nucleic Acids Research, 35(13), 4250-4263. https://doi.org/10.1093/nar/gkm402
Cartegni, L., Chew, S. L., & Krainer, A. R. (2002). Listening to silence and understanding nonsense: Exonic mutations that affect splicing. Nature Reviews Genetics, 3(4), 285-298.
Deml, B., Reis, L. M., Muheisen, S., Bick, D., & Semina, E. V. (2015). EFTUD2 deficiency in vertebrates: Identification of a novel human mutation and generation of a zebrafish model. Birth defects research. Part A, Clinical and molecular teratology, 103(7), 630-640. https://doi.org/10.1002/bdra.23397
Desmet, F. O., Hamroun, D., Lalande, M., Collod-Beroud, G., Claustres, M., & Beroud, C. (2009). Human Splicing Finder: An online bioinformatics tool to predict splicing signals. Nucleic Acids Research, 37(9), e67. https://doi.org/10.1093/nar/gkp215
Fairbrother, W. G., Yeh, R. F., Sharp, P. A., & Burge, C. B. (2002). Predictive identification of exonic splicing enhancers in human genes. Science, 297(5583), 1007-1013. https://doi.org/10.1126/science.1073774
Frazer, L. N., Lovell, S. C., & O'Keefe, R. T. (2009). Analysis of synthetic lethality reveals genetic interactions between the GTPase Snu114p and snRNAs in the catalytic core of the Saccharomyces cerevisiae spliceosome. Genetics, 183, 497-515.
Frazer, L. N., Nancollis, V., & O'Keefe, R. T. (2008). The role of Snu114p during pre-mRNA splicing. Biochemical Society Transactions, 36(Pt 3), 551-553.
Gibson, D. G. (2011). Enzymatic assembly of overlapping DNA fragments. Method Enzymol, 498, 349-361. https://doi.org/10.1016/B978-0-12-385120-8.00015-2
Gordon, C. T., Petit, F., Oufadem, M., Decaestecker, C., Jourdain, A. S., Andrieux, J., … Amiel, J. (2012). EFTUD2 haploinsufficiency leads to syndromic oesophageal atresia. Journal of Medical Genetics, 49(12), 737-746. https://doi.org/10.1136/jmedgenet-2012-101173
Huang, L. J., Vanstone, M. R., Hartley, T., Osmond, M., Barrowman, N., Allanson, J., … Consortium, C. R. C. (2016). Mandibulofacial dysostosis with microcephaly: Mutation and database update. Human Mutation, 37(2), 148-154. https://doi.org/10.1002/humu.22924
Kishore, S., Khanna, A., & Stamm, S. (2008). Rapid generation of splicing reporters with pSpliceExpress. Gene, 427(1-2), 104-110. https://doi.org/10.1016/j.gene.2008.09.021
Kunkel, T. A. (1985). Rapid and efficient site-specific mutagenesis without phenotypic selection. Proceedings of the National Academy of Sciences of the United States of America, 82, 488-492.
Lacour, J. C., McBride, L., St Hilaire, H., Mundinger, G. S., Moses, M., Koon, J., … Lacassie, Y. (2019). Novel de novo EFTUD2 mutations in 2 cases with MFDM, initially suspected to have alternative craniofacial diagnoses. Cleft Palate-Craniofacial Journal, 56(5), 674-678. https://doi.org/10.1177/1055665618806379
Lehalle, D., Gordon, C. T., Oufadem, M., Goudefroye, G., Boutaud, L., Alessandri, J. L., … Amiel, J. (2014). Delineation of EFTUD2 haploinsufficiency-related phenotypes through a series of 36 patients. Human Mutation, 35(4), 478-485. https://doi.org/10.1002/humu.22517
Lehalle, D., Wieczorek, D., Zechi-Ceide, R. M., Passos-Bueno, M. R., Lyonnet, S., Amiel, J., & Gordon, C. T. (2015). A review of craniofacial disorders caused by spliceosomal defects. Clinical Genetics, 88(5), 405-415. https://doi.org/10.1111/cge.12596
Lei, L., Yan, S. Y., Yang, R., Chen, J. Y., Li, Y. M., Bu, Y., … Xiong, J. W. (2017). Spliceosomal protein eftud2 mutation leads to p53-dependent apoptosis in zebrafish neural progenitors. Nucleic Acids Research, 45(6), 3422-3436. https://doi.org/10.1093/nar/gkw1043
Lim, K. H., & Fairbrother, W. G. (2012). Spliceman-a computational web server that predicts sequence variations in pre-mRNA splicing. Bioinformatics, 28(7), 1031-1032. https://doi.org/10.1093/bioinformatics/bts074
Lines, M. A., Huang, L., Schwartzentruber, J., Douglas, S. L., Lynch, D. C., Beaulieu, C., … Boycott, K. M. (2012). Haploinsufficiency of a spliceosomal GTPase encoded by EFTUD2 causes mandibulofacial dysostosis with microcephaly. American Journal of Human Genetics, 90(2), 369-377. https://doi.org/10.1016/j.ajhg.2011.12.023
Luquetti, D. V., Hing, A. V., Rieder, M. J., Nickerson, D. A., Turner, E. H., Smith, J., … Cunningham, M. L. (2013). "Mandibulofacial dysostosis with microcephaly" caused by EFTUD2 mutations: Expanding the phenotype. American Journal of Medical Genetics, 161A(1), 108-113. https://doi.org/10.1002/ajmg.a.35696
Matsuo, M., Yamauchi, A., Ito, Y., Sakauchi, M., Yamamoto, T., Okamoto, N., … Saito, K. (2017). Mandibulofacial dysostosis with microcephaly: A case presenting with seizures. Brain and Development, 39(2), 177-181. https://doi.org/10.1016/j.braindev.2016.08.008
Mort, M., Sterne-Weiler, T., Li, B., Ball, E. V., Cooper, D. N., Radivojac, P., … Mooney, S. D. (2014). MutPred splice: Machine learning-based prediction of exonic variants that disrupt splicing. Genome Biology, 15(1), R19. https://doi.org/10.1186/gb-2014-15-1-r19
Nguyen, T. H. D., Galej, W. P., Bai, X. C., Oubridge, C., Newman, A. J., Scheres, S. H. W., & Nagai, K. (2016). Cryo-EM structure of the yeast U4/U6.U5 tri-snRNP at 3.7 angstrom resolution. Nature, 530(7590), 298-302. https://doi.org/10.1038/nature16940
Ni, W. J., & Leng, X. M. (2015). Dynamic miRNA-mRNA paradigms: New faces of miRNAs. Biochemistry and Biophysics Reports, 4, 337-341. https://doi.org/10.1016/j.bbrep.2015.10.011
Reese, M. G., Eeckman, F. H., Kulp, D., & Haussler, D. (1997). Improved splice site detection in Genie. Journal of Computational Biology, 4(3), 311-323. https://doi.org/10.1089/cmb.1997.4.311
Sarkar, A., Emrick, L. T., Smith, E. M., Austin, E. G., Yang, Y. P., Hunter, J. V., … Lalani, S. R. (2015). Novel de novo mutations in EFTUD2 detected by exome sequencing in mandibulofacial dysostosis with microcephaly syndrome. American Journal of Medical Genetics, 167(4), 914-918. https://doi.org/10.1002/ajmg.a.36948
Schwarz, J. M., Cooper, D. N., Schuelke, M., & Seelow, D. (2014). MutationTaster2: Mutation prediction for the deep-sequencing age. Nature Methods, 11(4), 361-362. https://doi.org/10.1038/nmeth.2890
Shapiro, M. B., & Senapathy, P. (1987). RNA splice junctions of different classes of eukaryotes: Sequence statistics and functional implications in gene expression. Nucleic Acids Research, 15(17), 7155-7174. https://doi.org/10.1093/nar/15.17.7155
Smigiel, R., Bezniakow, N., Jakubiak, A., Bloch, M., Patkowski, D., Obersztyn, E., & Sasiadek, M. M. (2015). Phenotype analysis of Polish patients with mandibulofacial dysostosis type Guion-Almeida associated with esophageal atresia and choanal atresia caused by EFTUD2 gene mutations. Journal of Applied Genetics, 56(2), 199-204. https://doi.org/10.1007/s13353-014-0255-4
Soukarieh, O., Gaildrat, P., Hamieh, M., Drouet, A., Baert-Desurmont, S., Frebourg, T., … Martins, A. (2016). Exonic splicing mutations are more prevalent than currently estimated and can be predicted by using in silico tools. PLOS Genetics, 12(1):e1005756. https://doi.org/10.1371/journal.pgen.1005756
Sterne-Weiler, T., & Sanford, J. R. (2014). Exon identity crisis: Disease-causing mutations that disrupt the splicing code. Genome Biology, 15(1), 1-8. https://doi.org/10.1186/Gb4150. Artn 201.
Vincent, M., Genevieve, D., Ostertag, A., Marlin, S., Lacombe, D., Martin-Coignard, D., … Collet, C. (2016). Treacher Collins syndrome: A clinical and molecular study based on a large series of patients. Genetics in Medicine, 18(1), 49-56. https://doi.org/10.1038/gim.2015.29
Voigt, C., Megarbane, A., Neveling, K., Czeschik, J. C., Albrecht, B., Callewaert, B., … Wieczorek, D. (2013). Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies-Expanding the phenotypes associated with EFTUD2 mutations. Orphanet Journal of Rare Diseases, 8, 110. https://doi.org/10.1186/1750-1172-8-110
Wahl, M. C., Will, C. L., & Lührmann, R. (2009). The spliceosome: Design principles of a dynamic RNP machine. Cell, 136(4), 701-718.
Will, C. L., & Lührmann, R. (2011). Spliceosome structure and function. Cold Spring Harbor Perspectives in Biology, 3(7), a003707. https://doi.org/10.1101/cshperspect.a003707
Wood, K. A., Rowlands, C. F., Qureshi, W. M. S., Thomas, H. B., Buczek, W. A., Briggs, T. A., … O'Keefe, R. T. (2019). Disease modelling of core pre-mRNA splicing factor haploinsufficiency. Human Molecular Genetics, 28, 3704-3723. https://doi.org/10.1093/hmg/ddz169
Xiong, H. Y., Alipanahi, B., Lee, L. J., Bretschneider, H., Merico, D., Yuen, R. K., … Frey, B. J. (2015). RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science, 347(6218):1254806. https://doi.org/10.1126/science.1254806
Yeo, G., & Burge, C. B. (2004). Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. Journal of Computational Biology, 11(2-3), 377-394. https://doi.org/10.1089/1066527041410418