Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: a synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer

Karsten Bork Nielsen, Suzette Sørensen, Luca Cartegni, Thomas Juhl Corydon, Thomas Koed Doktor, Lisbeth Dahl Schroeder, Line Sinnathamby Reinert, Orly Elpeleg, Adrian R Krainer, Niels Gregersen, Jørgen Kjems, Brage Storstein Andresen

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

The idea that point mutations in exons may affect splicing is intriguing and adds an additional layer of complexity when evaluating their possible effects. Even in the best-studied examples, the molecular mechanisms are not fully understood. Here, we use patient cells, model minigenes, and in vitro assays to show that a missense mutation in exon 5 of the medium-chain acyl-CoA dehydrogenase (MCAD) gene primarily causes exon skipping by inactivating a crucial exonic splicing enhancer (ESE), thus leading to loss of a functional protein and to MCAD deficiency. This ESE functions by antagonizing a juxtaposed exonic splicing silencer (ESS) and is necessary to define a suboptimal 3' splice site. Remarkably, a synonymous polymorphic variation in MCAD exon 5 inactivates the ESS, and, although this has no effect on splicing by itself, it makes splicing immune to deleterious mutations in the ESE. Furthermore, the region of MCAD exon 5 that harbors these elements is nearly identical to the exon 7 region of the survival of motor neuron (SMN) genes that contains the deleterious silent mutation in SMN2, indicating a very similar and finely tuned interplay between regulatory elements in these two genes. Our findings illustrate a mechanism for dramatic context-dependent effects of single-nucleotide polymorphisms on gene-expression regulation and show that it is essential that potential deleterious effects of mutations on splicing be evaluated in the context of the relevant haplotype.
OriginalsprogEngelsk
TidsskriftAmerican Journal of Human Genetics
Vol/bind80
Udgave nummer3
Sider (fra-til)416-32
Antal sider17
ISSN0002-9297
DOI
StatusUdgivet - 2007

Fingeraftryk

Single Nucleotide Polymorphism
Mutation
RNA Splice Sites
Motor Neurons
Missense Mutation
Point Mutation
Haplotypes
Silent Mutation
Proteins

Citer dette

Nielsen, Karsten Bork ; Sørensen, Suzette ; Cartegni, Luca ; Corydon, Thomas Juhl ; Doktor, Thomas Koed ; Schroeder, Lisbeth Dahl ; Reinert, Line Sinnathamby ; Elpeleg, Orly ; Krainer, Adrian R ; Gregersen, Niels ; Kjems, Jørgen ; Andresen, Brage Storstein. / Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: a synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer. I: American Journal of Human Genetics. 2007 ; Bind 80, Nr. 3. s. 416-32.
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title = "Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: a synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer",
abstract = "The idea that point mutations in exons may affect splicing is intriguing and adds an additional layer of complexity when evaluating their possible effects. Even in the best-studied examples, the molecular mechanisms are not fully understood. Here, we use patient cells, model minigenes, and in vitro assays to show that a missense mutation in exon 5 of the medium-chain acyl-CoA dehydrogenase (MCAD) gene primarily causes exon skipping by inactivating a crucial exonic splicing enhancer (ESE), thus leading to loss of a functional protein and to MCAD deficiency. This ESE functions by antagonizing a juxtaposed exonic splicing silencer (ESS) and is necessary to define a suboptimal 3' splice site. Remarkably, a synonymous polymorphic variation in MCAD exon 5 inactivates the ESS, and, although this has no effect on splicing by itself, it makes splicing immune to deleterious mutations in the ESE. Furthermore, the region of MCAD exon 5 that harbors these elements is nearly identical to the exon 7 region of the survival of motor neuron (SMN) genes that contains the deleterious silent mutation in SMN2, indicating a very similar and finely tuned interplay between regulatory elements in these two genes. Our findings illustrate a mechanism for dramatic context-dependent effects of single-nucleotide polymorphisms on gene-expression regulation and show that it is essential that potential deleterious effects of mutations on splicing be evaluated in the context of the relevant haplotype.",
keywords = "Acyl-CoA Dehydrogenase, Cyclic AMP Response Element-Binding Protein, DNA Primers, Enhancer Elements, Genetic, Exons, Female, Genes, BRCA1, Humans, Immunity, Infant, Infant, Newborn, Lipid Metabolism, Inborn Errors, Molecular Sequence Data, Muscular Atrophy, Spinal, Mutation, Missense, Nerve Tissue Proteins, Polymorphism, Single Nucleotide, RNA Splicing, RNA Stability, RNA-Binding Proteins, SMN Complex Proteins, Sequence Homology, Nucleic Acid, Silencer Elements, Transcriptional, Survival of Motor Neuron 2 Protein, Transcription, Genetic",
author = "Nielsen, {Karsten Bork} and Suzette S{\o}rensen and Luca Cartegni and Corydon, {Thomas Juhl} and Doktor, {Thomas Koed} and Schroeder, {Lisbeth Dahl} and Reinert, {Line Sinnathamby} and Orly Elpeleg and Krainer, {Adrian R} and Niels Gregersen and J{\o}rgen Kjems and Andresen, {Brage Storstein}",
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doi = "10.1086/511992",
language = "English",
volume = "80",
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Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: a synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer. / Nielsen, Karsten Bork; Sørensen, Suzette; Cartegni, Luca; Corydon, Thomas Juhl; Doktor, Thomas Koed; Schroeder, Lisbeth Dahl; Reinert, Line Sinnathamby; Elpeleg, Orly; Krainer, Adrian R; Gregersen, Niels; Kjems, Jørgen; Andresen, Brage Storstein.

I: American Journal of Human Genetics, Bind 80, Nr. 3, 2007, s. 416-32.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - Seemingly neutral polymorphic variants may confer immunity to splicing-inactivating mutations: a synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer

AU - Nielsen, Karsten Bork

AU - Sørensen, Suzette

AU - Cartegni, Luca

AU - Corydon, Thomas Juhl

AU - Doktor, Thomas Koed

AU - Schroeder, Lisbeth Dahl

AU - Reinert, Line Sinnathamby

AU - Elpeleg, Orly

AU - Krainer, Adrian R

AU - Gregersen, Niels

AU - Kjems, Jørgen

AU - Andresen, Brage Storstein

PY - 2007

Y1 - 2007

N2 - The idea that point mutations in exons may affect splicing is intriguing and adds an additional layer of complexity when evaluating their possible effects. Even in the best-studied examples, the molecular mechanisms are not fully understood. Here, we use patient cells, model minigenes, and in vitro assays to show that a missense mutation in exon 5 of the medium-chain acyl-CoA dehydrogenase (MCAD) gene primarily causes exon skipping by inactivating a crucial exonic splicing enhancer (ESE), thus leading to loss of a functional protein and to MCAD deficiency. This ESE functions by antagonizing a juxtaposed exonic splicing silencer (ESS) and is necessary to define a suboptimal 3' splice site. Remarkably, a synonymous polymorphic variation in MCAD exon 5 inactivates the ESS, and, although this has no effect on splicing by itself, it makes splicing immune to deleterious mutations in the ESE. Furthermore, the region of MCAD exon 5 that harbors these elements is nearly identical to the exon 7 region of the survival of motor neuron (SMN) genes that contains the deleterious silent mutation in SMN2, indicating a very similar and finely tuned interplay between regulatory elements in these two genes. Our findings illustrate a mechanism for dramatic context-dependent effects of single-nucleotide polymorphisms on gene-expression regulation and show that it is essential that potential deleterious effects of mutations on splicing be evaluated in the context of the relevant haplotype.

AB - The idea that point mutations in exons may affect splicing is intriguing and adds an additional layer of complexity when evaluating their possible effects. Even in the best-studied examples, the molecular mechanisms are not fully understood. Here, we use patient cells, model minigenes, and in vitro assays to show that a missense mutation in exon 5 of the medium-chain acyl-CoA dehydrogenase (MCAD) gene primarily causes exon skipping by inactivating a crucial exonic splicing enhancer (ESE), thus leading to loss of a functional protein and to MCAD deficiency. This ESE functions by antagonizing a juxtaposed exonic splicing silencer (ESS) and is necessary to define a suboptimal 3' splice site. Remarkably, a synonymous polymorphic variation in MCAD exon 5 inactivates the ESS, and, although this has no effect on splicing by itself, it makes splicing immune to deleterious mutations in the ESE. Furthermore, the region of MCAD exon 5 that harbors these elements is nearly identical to the exon 7 region of the survival of motor neuron (SMN) genes that contains the deleterious silent mutation in SMN2, indicating a very similar and finely tuned interplay between regulatory elements in these two genes. Our findings illustrate a mechanism for dramatic context-dependent effects of single-nucleotide polymorphisms on gene-expression regulation and show that it is essential that potential deleterious effects of mutations on splicing be evaluated in the context of the relevant haplotype.

KW - Acyl-CoA Dehydrogenase

KW - Cyclic AMP Response Element-Binding Protein

KW - DNA Primers

KW - Enhancer Elements, Genetic

KW - Exons

KW - Female

KW - Genes, BRCA1

KW - Humans

KW - Immunity

KW - Infant

KW - Infant, Newborn

KW - Lipid Metabolism, Inborn Errors

KW - Molecular Sequence Data

KW - Muscular Atrophy, Spinal

KW - Mutation, Missense

KW - Nerve Tissue Proteins

KW - Polymorphism, Single Nucleotide

KW - RNA Splicing

KW - RNA Stability

KW - RNA-Binding Proteins

KW - SMN Complex Proteins

KW - Sequence Homology, Nucleic Acid

KW - Silencer Elements, Transcriptional

KW - Survival of Motor Neuron 2 Protein

KW - Transcription, Genetic

U2 - 10.1086/511992

DO - 10.1086/511992

M3 - Journal article

VL - 80

SP - 416

EP - 432

JO - American Journal of Human Genetics

JF - American Journal of Human Genetics

SN - 0002-9297

IS - 3

ER -