Please use this identifier to cite or link to this item: https://hdl.handle.net/2440/79262
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Type: Journal article
Title: Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders
Author: Nguyen, L.
Kim, H.
Rosenfeld, J.
Shen, Y.
Gusella, J.
Lacassie, Y.
Layman, L.
Shaffer, L.
Gecz, J.
Citation: Human Molecular Genetics, 2013; 22(9):1816-1825
Publisher: Oxford Univ Press
Issue Date: 2013
ISSN: 0964-6906
1460-2083
Statement of
Responsibility: 
Lam S. Nguyen, Hyung-Goo Kim, Jill A. Rosenfeld, Yiping Shen, James F. Gusella, Yves Lacassie, Lawrence C. Layman, Lisa G. Shaffer and Jozef Gécz
Abstract: The nonsense-mediated mRNA decay (NMD) pathway functions not only to degrade transcripts containing premature termination codons (PTC), but also to regulate the transcriptome. UPF3B and RBM8A, important components of NMD, have been implicated in various forms of intellectual disability (ID) and Thrombocytopenia with Absent Radius (TAR) syndrome, which is also associated with ID. To gauge the contribution of other NMD factors to ID, we performed a comprehensive search for copy number variants (CNVs) of 18 NMD genes among individuals with ID and/or congenital anomalies. We identified 11 cases with heterozygous deletions of the genomic region encompassing UPF2, which encodes for a direct interacting protein of UPF3B. Using RNA-Seq, we showed that the genome-wide consequence of reduced expression of UPF2 is similar to that seen in patients with UPF3B mutations. Out of the 1009 genes found deregulated in patients with UPF2 deletions by at least 2-fold, majority (95%) were deregulated similarly in patients with UPF3B mutations. This supports the major role of deletion of UPF2 in ID. Furthermore, we found that four other NMD genes, UPF3A, SMG6, EIF4A3 and RNPS1 are frequently deleted and/or duplicated in the patients. We postulate that dosage imbalances of these NMD genes are likely to be the causes or act as predisposing factors for neuro-developmental disorders. Our findings further emphasize the importance of NMD pathway(s) in learning and memory.
Keywords: Neurons
Humans
Genetic Predisposition to Disease
Telomerase
Eukaryotic Initiation Factor-4A
RNA-Binding Proteins
Ribonucleoproteins
Transcription Factors
RNA, Messenger
Codon, Nonsense
Case-Control Studies
Sequence Analysis, RNA
Developmental Disabilities
Computational Biology
Gene Deletion
Gene Dosage
Adolescent
Child
Female
Male
DEAD-box RNA Helicases
DNA Copy Number Variations
Intellectual Disability
Transcriptome
Nonsense Mediated mRNA Decay
Rights: © The Author 2013
DOI: 10.1093/hmg/ddt035
Appears in Collections:Aurora harvest 4
Genetics publications

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