Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants
Abstract
Background: Pre-mRNA splicing is a complex process requiring the identification of donor site, acceptor site, and branch point site with an adjacent polypyrimidine tract sequence. Splicing is regulated by splicing regulatory elements (SREs) with both enhancer and suppressor functions. Variants located in exonic regions can impact splicing through dysregulation of native splice sites, SREs, and cryptic splice site activation. While splicing dysregulation is considered primary disease-inducing mechanism of synonymous variants, its contribution toward disease phenotype of non-synonymous variants is underappreciated. Methods: In this study, we analyzed 415 disease-causing and 120 neutral F9 exonic point variants including both synonymous and non-synonymous for their effect on splicing using a series of in silico splice site prediction tools, SRE prediction tools, and in vitro minigene assays. Results: The use of splice site and SRE prediction tools in tandem provided better prediction but were not always in agreement with the minigene assays. The net effect of splicing dysregulation caused by variants was context dependent. Minigene assays revealed that perturbed splicing can be found. Conclusion: Synonymous variants primarily cause disease phenotype via splicing dysregulation while additional mechanisms such as translation rate also play an important role. Splicing dysregulation is likely to contribute to the diseasemore »
- Authors:
-
[1]
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation &, Research US FDA Silver Spring Maryland
- Department of Statistics University of Connecticut Storrs Connecticut
- Department of Biological, Geological and Environmental Sciences, Center for Gene Regulation in Health and Disease Cleveland State University Cleveland Ohio
- Publication Date:
- Research Org.:
- Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE; US Food and Drug Administration
- OSTI Identifier:
- 1559339
- Alternate Identifier(s):
- OSTI ID: 1559340; OSTI ID: 1623575
- Grant/Contract Number:
- SC0014664
- Resource Type:
- Published Article
- Journal Name:
- Molecular Genetics & Genomic Medicine
- Additional Journal Information:
- Journal Name: Molecular Genetics & Genomic Medicine Journal Volume: 7 Journal Issue: 8; Journal ID: ISSN 2324-9269
- Publisher:
- Wiley Blackwell (John Wiley & Sons)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Genetics & Heredity; hemophilia B; in silico splicing analysis; in vitro minigene assay; splicing dysregulation; synonymous variants
Citation Formats
Katneni, Upendra K., Liss, Aaron, Holcomb, David, Katagiri, Nobuko H., Hunt, Ryan, Bar, Haim, Ismail, Amra, Komar, Anton A., and Kimchi‐Sarfaty, Chava. Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants. United States: N. p., 2019.
Web. doi:10.1002/mgg3.840.
Katneni, Upendra K., Liss, Aaron, Holcomb, David, Katagiri, Nobuko H., Hunt, Ryan, Bar, Haim, Ismail, Amra, Komar, Anton A., & Kimchi‐Sarfaty, Chava. Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants. United States. doi:https://doi.org/10.1002/mgg3.840
Katneni, Upendra K., Liss, Aaron, Holcomb, David, Katagiri, Nobuko H., Hunt, Ryan, Bar, Haim, Ismail, Amra, Komar, Anton A., and Kimchi‐Sarfaty, Chava. Mon .
"Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants". United States. doi:https://doi.org/10.1002/mgg3.840.
@article{osti_1559339,
title = {Splicing dysregulation contributes to the pathogenicity of several F9 exonic point variants},
author = {Katneni, Upendra K. and Liss, Aaron and Holcomb, David and Katagiri, Nobuko H. and Hunt, Ryan and Bar, Haim and Ismail, Amra and Komar, Anton A. and Kimchi‐Sarfaty, Chava},
abstractNote = {Background: Pre-mRNA splicing is a complex process requiring the identification of donor site, acceptor site, and branch point site with an adjacent polypyrimidine tract sequence. Splicing is regulated by splicing regulatory elements (SREs) with both enhancer and suppressor functions. Variants located in exonic regions can impact splicing through dysregulation of native splice sites, SREs, and cryptic splice site activation. While splicing dysregulation is considered primary disease-inducing mechanism of synonymous variants, its contribution toward disease phenotype of non-synonymous variants is underappreciated. Methods: In this study, we analyzed 415 disease-causing and 120 neutral F9 exonic point variants including both synonymous and non-synonymous for their effect on splicing using a series of in silico splice site prediction tools, SRE prediction tools, and in vitro minigene assays. Results: The use of splice site and SRE prediction tools in tandem provided better prediction but were not always in agreement with the minigene assays. The net effect of splicing dysregulation caused by variants was context dependent. Minigene assays revealed that perturbed splicing can be found. Conclusion: Synonymous variants primarily cause disease phenotype via splicing dysregulation while additional mechanisms such as translation rate also play an important role. Splicing dysregulation is likely to contribute to the disease phenotype of several non=synonymous variants.},
doi = {10.1002/mgg3.840},
journal = {Molecular Genetics & Genomic Medicine},
number = 8,
volume = 7,
place = {United States},
year = {2019},
month = {6}
}
Free Publicly Available Full Text
Publisher's Version of Record
DOI: https://doi.org/10.1002/mgg3.840
DOI: https://doi.org/10.1002/mgg3.840
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 3 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Spliceosomal UsnRNP biogenesis, structure and function
journal, June 2001
- Will, Cindy L.; Lührmann, Reinhard
- Current Opinion in Cell Biology, Vol. 13, Issue 3
Nomenclature of genetic variants in hemostasis: Scientific and Standardisation Committee communication
journal, April 2011
- Goodeve, A. C.; Reitsma, P. H.; Mcvey, J. H.
- Journal of Thrombosis and Haemostasis, Vol. 9, Issue 4
A Gene-Specific Method for Predicting Hemophilia-Causing Point Mutations
journal, November 2013
- Hamasaki-Katagiri, Nobuko; Salari, Raheleh; Wu, Andrew
- Journal of Molecular Biology, Vol. 425, Issue 21
Quantitative evaluation of all hexamers as exonic splicing elements
journal, June 2011
- Ke, Shengdong; Shang, Shulian; Kalachikov, Sergey M.
- Genome Research, Vol. 21, Issue 8
An exon-specific U1 small nuclear RNA (snRNA) strategy to correct splicing defects
journal, February 2012
- Fernandez Alanis, Eugenio; Pinotti, Mirko; Dal Mas, Andrea
- Human Molecular Genetics, Vol. 21, Issue 11
Genome-wide discovery of human splicing branchpoints
journal, January 2015
- Mercer, Tim R.; Clark, Michael B.; Andersen, Stacey B.
- Genome Research, Vol. 25, Issue 2
Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat beta -tropomyosin gene
journal, March 1999
- Chen, C. D.; Kobayashi, R.; Helfman, D. M.
- Genes & Development, Vol. 13, Issue 5
Human Splicing Finder: an online bioinformatics tool to predict splicing signals
journal, April 2009
- Desmet, François-Olivier; Hamroun, Dalil; Lalande, Marine
- Nucleic Acids Research, Vol. 37, Issue 9
Prediction of single‐nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6
journal, February 2011
- Raponi, Michela; Kralovicova, Jana; Copson, Ellen
- Human Mutation, Vol. 32, Issue 4
Definitions in Hemophilia: Recommendation of the Scientific Subcommittee on Factor VIII and Factor IX of the Scientific and Standardization Committee of the International Society on Thrombosis and Haemostasis
journal, January 2001
- White, Gilbert; Rosendaal, Frits; Aledort, Louis
- Thrombosis and Haemostasis, Vol. 85, Issue 03
Exposing synonymous mutations
journal, July 2014
- Hunt, Ryan C.; Simhadri, Vijaya L.; Iandoli, Matthew
- Trends in Genetics, Vol. 30, Issue 7
Analysis of canonical and non-canonical splice sites in mammalian genomes
journal, November 2000
- Burset, M.
- Nucleic Acids Research, Vol. 28, Issue 21
Single synonymous mutation in factor IX alters protein properties and underlies haemophilia B
journal, December 2016
- Simhadri, Vijaya L.; Hamasaki-Katagiri, Nobuko; Lin, Brian C.
- Journal of Medical Genetics, Vol. 54, Issue 5
Evaluation of Bioinformatic Programmes for the Analysis of Variants within Splice Site Consensus Regions
journal, January 2016
- Tang, Rongying; Prosser, Debra O.; Love, Donald R.
- Advances in Bioinformatics, Vol. 2016
In silico tools for splicing defect prediction: a survey from the viewpoint of end users
journal, November 2013
- Jian, Xueqiu; Boerwinkle, Eric; Liu, Xiaoming
- Genetics in Medicine, Vol. 16, Issue 7
An interactive mutation database for human coagulation factor IX provides novel insights into the phenotypes and genetics of hemophilia B
journal, July 2013
- Rallapalli, P. M.; Kemball-Cook, G.; Tuddenham, E. G.
- Journal of Thrombosis and Haemostasis, Vol. 11, Issue 7
Genomic HEXploring allows landscaping of novel potential splicing regulatory elements
journal, August 2014
- Erkelenz, Steffen; Theiss, Stephan; Otte, Marianne
- Nucleic Acids Research, Vol. 42, Issue 16
Sorting out the complexity of SR protein functions
journal, September 2000
- Graveley, Brenton R.
- RNA, Vol. 6, Issue 9
Molecular Basis and Therapeutic Strategies to Rescue Factor IX Variants That Affect Splicing and Protein Function
journal, May 2016
- Tajnik, Mojca; Rogalska, Malgorzata Ewa; Bussani, Erica
- PLOS Genetics, Vol. 12, Issue 5
Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis
journal, January 2014
- Caminsky, Natasha G.; Mucaki, Eliseos J.; Rogan, Peter K.
- F1000Research, Vol. 3
dbSNP: the NCBI database of genetic variation
journal, January 2001
- Sherry, S. T.
- Nucleic Acids Research, Vol. 29, Issue 1
Correction: Exonic Splicing Mutations Are More Prevalent than Currently Estimated and Can Be Predicted by Using In Silico Tools
journal, April 2016
- Soukarieh, Omar; Gaildrat, Pascaline; Hamieh, Mohamad
- PLOS Genetics, Vol. 12, Issue 4
Improved Splice Site Detection in Genie
journal, January 1997
- Reese, Martin G.; Eeckman, Frank H.; Kulp, David
- Journal of Computational Biology, Vol. 4, Issue 3
RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression
journal, January 1987
- Shapiro, Marvin B.; Senapathy, Periannan
- Nucleic Acids Research, Vol. 15, Issue 17
A Synonymous Single Nucleotide Polymorphism in ΔF508 CFTR Alters the Secondary Structure of the mRNA and the Expression of the Mutant Protein
journal, July 2010
- Bartoszewski, Rafal A.; Jablonsky, Michael; Bartoszewska, Sylwia
- Journal of Biological Chemistry, Vol. 285, Issue 37
Pick one, but be quick: 5' splice sites and the problems of too many choices
journal, January 2013
- Roca, X.; Krainer, A. R.; Eperon, I. C.
- Genes & Development, Vol. 27, Issue 2
Maximum Entropy Modeling of Short Sequence Motifs with Applications to RNA Splicing Signals
journal, March 2004
- Yeo, Gene; Burge, Christopher B.
- Journal of Computational Biology, Vol. 11, Issue 2-3
New type of disease causing mutations: the example of the composite exonic regulatory elements of splicing in CFTR exon 12
journal, May 2003
- Pagani, F.
- Human Molecular Genetics, Vol. 12, Issue 10
Unusual expression of the F9 gene in peripheral lymphocytes hinders investigation of F9 mRNA in hemophilia B patients
journal, December 2003
- Green, P. M.; Rowley, G.; Giannelli, F.
- Journal of Thrombosis and Haemostasis, Vol. 1, Issue 12
Listening to silence and understanding nonsense: exonic mutations that affect splicing
journal, April 2002
- Cartegni, Luca; Chew, Shern L.; Krainer, Adrian R.
- Nature Reviews Genetics, Vol. 3, Issue 4
The gene structure of human anti-haemophilic factor IX.
journal, May 1984
- Anson, D. S.; Choo, K. H.; Rees, D. J.
- The EMBO Journal, Vol. 3, Issue 5
Haemophilia A and haemophilia B: molecular insights
journal, April 2002
- Bowen, D. J.
- Molecular Pathology, Vol. 55, Issue 2
miRNAs in the spotlight: Making 'silent' mutations speak up
journal, August 2011
- Salzman, David W.; Weidhaas, Joanne B.
- Nature Medicine, Vol. 17, Issue 8
Loss of exon identity is a common mechanism of human inherited disease
journal, July 2011
- Sterne-Weiler, T.; Howard, J.; Mort, M.
- Genome Research, Vol. 21, Issue 10
An Exon-Specific U1snRNA Induces a Robust Factor IX Activity in Mice Expressing Multiple Human FIX Splicing Mutants
journal, January 2016
- Balestra, Dario; Scalet, Daniela; Pagani, Franco
- Molecular Therapy - Nucleic Acids, Vol. 5
The CDC Hemophilia B mutation project mutation list: a new online resource
journal, August 2013
- Li, Tengguo; Miller, Connie H.; Payne, Amanda B.
- Molecular Genetics & Genomic Medicine, Vol. 1, Issue 4
A new and updated resource for codon usage tables
journal, September 2017
- Athey, John; Alexaki, Aikaterini; Osipova, Ekaterina
- BMC Bioinformatics, Vol. 18, Issue 1
Mutations of Pre-mRNA Splicing Regulatory Elements: Are Predictions Moving Forward to Clinical Diagnostics?
journal, July 2017
- Grodecká, Lucie; Buratti, Emanuele; Freiberger, Tomáš
- International Journal of Molecular Sciences, Vol. 18, Issue 8
A "Silent" Polymorphism in the MDR1 Gene Changes Substrate Specificity
journal, January 2007
- Kimchi-Sarfaty, C.; Oh, J. M.; Kim, I.-W.
- Science, Vol. 315, Issue 5811, p. 525-528
Improved splice site detection in Genie
conference, January 1997
- Reese, Martin G.; Eeckman, Frank H.; Kulp, David
- Proceedings of the first annual international conference on Computational molecular biology - RECOMB '97
Works referencing / citing this record:
Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies
journal, October 2019
- Alexaki, Aikaterini; Hettiarachchi, Gaya K.; Athey, John C.
- Scientific Reports, Vol. 9, Issue 1
A Single Synonymous Variant (c.354G>A [p.P118P]) in ADAMTS13 Confers Enhanced Specific Activity
journal, November 2019
- Hunt, Ryan; Hettiarachchi, Gaya; Katneni, Upendra
- International Journal of Molecular Sciences, Vol. 20, Issue 22