The Alu-Rich Genomic Architecture of SPAST Predisposes to Diverse and Functionally Distinct Disease-Associated CNV Alleles

Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and duplications in SPAST (mutations in which cause autosomal-dominant spastic paraplegia 4 [SPG4]) have been described, their origins and molecular conseq...

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Published in	American journal of human genetics Vol. 95; no. 2; pp. 143 - 161
Main Authors	Boone, Philip M., Yuan, Bo, Campbell, Ian M., Scull, Jennifer C., Withers, Marjorie A., Baggett, Brett C., Beck, Christine R., Shaw, Christine J., Stankiewicz, Pawel, Moretti, Paolo, Goodwin, Wendy E., Hein, Nichole, Fink, John K., Seong, Moon-Woo, Seo, Soo Hyun, Park, Sung Sup, Karbassi, Izabela D., Batish, Sat Dev, Ordóñez-Ugalde, Andrés, Quintáns, Beatriz, Sobrido, María-Jesús, Stemmler, Susanne, Lupski, James R.
Format	Journal Article
Language	English
Published	United States Elsevier Inc 07.08.2014 Cell Press Elsevier
Subjects	Adenosine Triphosphatases - genetics Alu Elements - genetics Alzheimer's disease Base Sequence Cation Transport Proteins - genetics Cell Line, Transformed Deoxyribonucleic acid DNA DNA Copy Number Variations - genetics Gene loci Genomics Genotype Genotype & phenotype Humans Mutation Pathogenesis Protein Isoforms - genetics Recombinant Fusion Proteins - genetics Sequence Analysis, DNA Sequence Deletion Spastic Paraplegia, Hereditary - genetics Spastin
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Abstract	Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and duplications in SPAST (mutations in which cause autosomal-dominant spastic paraplegia 4 [SPG4]) have been described, their origins and molecular consequences remain obscure. We mapped breakpoint junctions of 54 SPAST CNVs at nucleotide resolution. Diverse combinations of exons are deleted or duplicated, highlighting the importance of particular exons for spastin function. Of the 54 CNVs, 38 (70%) appear to be mediated by an Alu-based mechanism, suggesting that the Alu-rich genomic architecture of SPAST renders this locus susceptible to various genome rearrangements. Analysis of breakpoint Alus further informs a model of Alu-mediated CNV formation characterized by small CNV size and potential involvement of mechanisms other than homologous recombination. Twelve deletions (22%) overlap part of SPAST and a portion of a nearby, directly oriented gene, predicting novel chimeric genes in these subjects’ genomes. cDNA from a subject with a SPAST final exon deletion contained multiple SPAST:SLC30A6 fusion transcripts, indicating that SPAST CNVs can have transcriptional effects beyond the gene itself. SLC30A6 has been implicated in Alzheimer disease, so these fusion gene data could explain a report of spastic paraplegia and dementia cosegregating in a family with deletion of the final exon of SPAST. Our findings provide evidence that the Alu genomic architecture of SPAST predisposes to diverse CNV alleles with distinct transcriptional—and possibly phenotypic—consequences. Moreover, we provide further mechanistic insights into Alu-mediated copy-number change that are extendable to other loci.
AbstractList	Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and duplications in SPAST (mutations in which cause autosomal-dominant spastic paraplegia 4 [SPG4]) have been described, their origins and molecular consequences remain obscure. We mapped breakpoint junctions of 54 SPAST CNVs at nucleotide resolution. Diverse combinations of exons are deleted or duplicated, highlighting the importance of particular exons for spastin function. Of the 54 CNVs, 38 (70%) appear to be mediated by an Alu-based mechanism, suggesting that the Alu-rich genomic architecture of SPAST renders this locus susceptible to various genome rearrangements. Analysis of breakpoint Alus further informs a model of Alu-mediated CNV formation characterized by small CNV size and potential involvement of mechanisms other than homologous recombination. Twelve deletions (22%) overlap part of SPAST and a portion of a nearby, directly oriented gene, predicting novel chimeric genes in these subjects' genomes. cDNA from a subject with a SPAST final exon deletion contained multiple SPAST:SLC30A6 fusion transcripts, indicating that SPAST CNVs can have transcriptional effects beyond the gene itself. SLC30A6 has been implicated in Alzheimer disease, so these fusion gene data could explain a report of spastic paraplegia and dementia cosegregating in a family with deletion of the final exon of SPAST. Our findings provide evidence that the Alu genomic architecture of SPAST predisposes to diverse CNV alleles with distinct transcriptional--and possibly phenotypic--consequences. Moreover, we provide further mechanistic insights into Alu-mediated copy-number change that are extendable to other loci.Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and duplications in SPAST (mutations in which cause autosomal-dominant spastic paraplegia 4 [SPG4]) have been described, their origins and molecular consequences remain obscure. We mapped breakpoint junctions of 54 SPAST CNVs at nucleotide resolution. Diverse combinations of exons are deleted or duplicated, highlighting the importance of particular exons for spastin function. Of the 54 CNVs, 38 (70%) appear to be mediated by an Alu-based mechanism, suggesting that the Alu-rich genomic architecture of SPAST renders this locus susceptible to various genome rearrangements. Analysis of breakpoint Alus further informs a model of Alu-mediated CNV formation characterized by small CNV size and potential involvement of mechanisms other than homologous recombination. Twelve deletions (22%) overlap part of SPAST and a portion of a nearby, directly oriented gene, predicting novel chimeric genes in these subjects' genomes. cDNA from a subject with a SPAST final exon deletion contained multiple SPAST:SLC30A6 fusion transcripts, indicating that SPAST CNVs can have transcriptional effects beyond the gene itself. SLC30A6 has been implicated in Alzheimer disease, so these fusion gene data could explain a report of spastic paraplegia and dementia cosegregating in a family with deletion of the final exon of SPAST. Our findings provide evidence that the Alu genomic architecture of SPAST predisposes to diverse CNV alleles with distinct transcriptional--and possibly phenotypic--consequences. Moreover, we provide further mechanistic insights into Alu-mediated copy-number change that are extendable to other loci. Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and duplications in SPAST (mutations in which cause autosomal-dominant spastic paraplegia 4 [SPG4]) have been described, their origins and molecular consequences remain obscure. We mapped breakpoint junctions of 54 SPAST CNVs at nucleotide resolution. Diverse combinations of exons are deleted or duplicated, highlighting the importance of particular exons for spastin function. Of the 54 CNVs, 38 (70%) appear to be mediated by an Alu-based mechanism, suggesting that the Alu-rich genomic architecture of SPAST renders this locus susceptible to various genome rearrangements. Analysis of breakpoint Alus further informs a model of Alu-mediated CNV formation characterized by small CNV size and potential involvement of mechanisms other than homologous recombination. Twelve deletions (22%) overlap part of SPAST and a portion of a nearby, directly oriented gene, predicting novel chimeric genes in these subjects' genomes. cDNA from a subject with a SPAST final exon deletion contained multiple SPAST:SLC30A6 fusion transcripts, indicating that SPAST CNVs can have transcriptional effects beyond the gene itself. SLC30A6 has been implicated in Alzheimer disease, so these fusion gene data could explain a report of spastic paraplegia and dementia cosegregating in a family with deletion of the final exon of SPAST. Our findings provide evidence that the Alu genomic architecture of SPAST predisposes to diverse CNV alleles with distinct transcriptional -- and possibly phenotypic -- consequences. Moreover, we provide further mechanistic insights into Alu-mediated copy-number change that are extendable to other loci. Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and duplications in SPAST (mutations in which cause autosomal-dominant spastic paraplegia 4 [SPG4]) have been described, their origins and molecular consequences remain obscure. We mapped breakpoint junctions of 54 SPAST CNVs at nucleotide resolution. Diverse combinations of exons are deleted or duplicated, highlighting the importance of particular exons for spastin function. Of the 54 CNVs, 38 (70%) appear to be mediated by an Alu -based mechanism, suggesting that the Alu -rich genomic architecture of SPAST renders this locus susceptible to various genome rearrangements. Analysis of breakpoint Alu s further informs a model of Alu -mediated CNV formation characterized by small CNV size and potential involvement of mechanisms other than homologous recombination. Twelve deletions (22%) overlap part of SPAST and a portion of a nearby, directly oriented gene, predicting novel chimeric genes in these subjects’ genomes. cDNA from a subject with a SPAST final exon deletion contained multiple SPAST : SLC30A6 fusion transcripts, indicating that SPAST CNVs can have transcriptional effects beyond the gene itself. SLC30A6 has been implicated in Alzheimer disease, so these fusion gene data could explain a report of spastic paraplegia and dementia cosegregating in a family with deletion of the final exon of SPAST . Our findings provide evidence that the Alu genomic architecture of SPAST predisposes to diverse CNV alleles with distinct transcriptional—and possibly phenotypic—consequences. Moreover, we provide further mechanistic insights into Alu -mediated copy-number change that are extendable to other loci.
Author	Yuan, Bo Sobrido, María-Jesús Stemmler, Susanne Campbell, Ian M. Shaw, Christine J. Seong, Moon-Woo Karbassi, Izabela D. Goodwin, Wendy E. Stankiewicz, Pawel Beck, Christine R. Baggett, Brett C. Withers, Marjorie A. Boone, Philip M. Scull, Jennifer C. Ordóñez-Ugalde, Andrés Seo, Soo Hyun Fink, John K. Batish, Sat Dev Hein, Nichole Moretti, Paolo Lupski, James R. Quintáns, Beatriz Park, Sung Sup
AuthorAffiliation	12 Department of Human Genetics, Ruhr University, Bochum 44801, Germany 8 Veterans Affairs Medical Center, Ann Arbor, MI 48015, USA 10 Quest Diagnostics, Athena Diagnostics, Worcester, MA 01605, USA 3 Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA 1 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA 6 Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA 14 Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA 9 Department of Laboratory Medicine, Seoul National University Hospital, Seoul 110-799, Korea 7 Geriatrics Research Education and Clinical Center, Ann Arbor, MI 48105, USA 13 Texas Children’s Hospital, Houston, TX 77030, USA 4 Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA 5 Children’s Medical Center of Dallas, Dallas, TX 75207, USA 11 Fundación Pública Galega de Medicina Xenómica-SERGAS, IDIS, CIBERER, Santiago de Compostela 15706, Spain 2 Medical Genetics Laborat
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BackLink	https://www.ncbi.nlm.nih.gov/pubmed/25065914$$D View this record in MEDLINE/PubMed
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ContentType	Journal Article
Copyright	2014 The American Society of Human Genetics Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved. Copyright Cell Press Aug 7, 2014 2014 The American Society of Human Genetics. Published by Elsevier Ltd. All right reserved. 2014 The American Society of Human Genetics
Copyright_xml	– notice: 2014 The American Society of Human Genetics – notice: Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved. – notice: Copyright Cell Press Aug 7, 2014 – notice: 2014 The American Society of Human Genetics. Published by Elsevier Ltd. All right reserved. 2014 The American Society of Human Genetics
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Snippet	Intragenic copy-number variants (CNVs) contribute to the allelic spectrum of both Mendelian and complex disorders. Although pathogenic deletions and...
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SubjectTerms	Adenosine Triphosphatases - genetics Alu Elements - genetics Alzheimer's disease Base Sequence Cation Transport Proteins - genetics Cell Line, Transformed Deoxyribonucleic acid DNA DNA Copy Number Variations - genetics Gene loci Genomics Genotype Genotype & phenotype Humans Mutation Pathogenesis Protein Isoforms - genetics Recombinant Fusion Proteins - genetics Sequence Analysis, DNA Sequence Deletion Spastic Paraplegia, Hereditary - genetics Spastin
Title	The Alu-Rich Genomic Architecture of SPAST Predisposes to Diverse and Functionally Distinct Disease-Associated CNV Alleles
URI	https://dx.doi.org/10.1016/j.ajhg.2014.06.014 https://www.ncbi.nlm.nih.gov/pubmed/25065914 https://www.proquest.com/docview/1554283812 https://www.proquest.com/docview/1552374487 https://pubmed.ncbi.nlm.nih.gov/PMC4129405
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