Genomic and functional profiling of duplicated chromosome 15 cell lines reveal regulatory alterations in UBE3A-associated ubiquitin-proteasome pathway processes

Colin A. Baron, Clifford G. Tepper, Stephenie Y. Liu, Ryan R. Davis, Nicholas J. Wang, N. Carolyn Schanen, Jeffrey P. Gregg

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

Autism is a complex neurodevelopmental disorder having both genetic and epigenetic etiological elements. Isodicentric chromosome 15 (Idic15), characterized by duplications of the multi-disorder critical region of 15q11-q14, is a relatively common cytogenetic event. When the duplication involves maternally derived content, this abnormality is strongly correlated with autism disorder. However, the mechanistic links between Idic15 and autism are ill-defined. To gain insight into the potential role of these duplications, we performed a comprehensive, genomics-based characterization of an in vitro model system consisting of lymphoblast cell lines derived from individuals with both autism and Idic15. Array-based comparative genomic hybridization using commercial single nucleotide polymorphism arrays was conducted and found to be capable of sub-classifying Idic15 samples by virtue of the lengths of the duplicated chromosomal region. In further analysis, whole-genome expression profiling revealed that 112 transcripts were significantly dysregulated in samples harboring duplications. Paramount among changing genes was ubiquitin protein ligase E3A (UBE3A; 15q11-q13), which was found to be nearly 1.5-2.0-fold up-regulated in duplicated samples at both the RNA and protein levels. Other key findings from gene expression analysis included two down-regulated genes, APP and ESUMO1, with well-characterized roles in the process of apoptosis. We further demonstrate in this lymphoblast model that the gene-dosage directed increases in UBE3A levels can lead to dysregulation of the process of ubiquitination in response to genotoxic insult. This study provides insight into the direct and indirect effects of copy number gains in chromosome 15 and provides a framework for the study of these effects in neuronal systems.

Original languageEnglish (US)
Pages (from-to)853-869
Number of pages17
JournalHuman Molecular Genetics
Volume15
Issue number6
DOIs
StatePublished - Mar 2006
Externally publishedYes

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Chromosomes, Human, Pair 15
Proteasome Endopeptidase Complex
Autistic Disorder
Ubiquitin
Cell Line
Ubiquitin-Protein Ligases
Comparative Genomic Hybridization
Gene Dosage
Ubiquitination
Genomics
Epigenomics
Cytogenetics
Genes
Single Nucleotide Polymorphism
Genome
RNA
Apoptosis
Gene Expression
Isodicentric Chromosome 15 Syndrome
Proteins

ASJC Scopus subject areas

  • Genetics

Cite this

Genomic and functional profiling of duplicated chromosome 15 cell lines reveal regulatory alterations in UBE3A-associated ubiquitin-proteasome pathway processes. / Baron, Colin A.; Tepper, Clifford G.; Liu, Stephenie Y.; Davis, Ryan R.; Wang, Nicholas J.; Schanen, N. Carolyn; Gregg, Jeffrey P.

In: Human Molecular Genetics, Vol. 15, No. 6, 03.2006, p. 853-869.

Research output: Contribution to journalArticle

Baron, Colin A. ; Tepper, Clifford G. ; Liu, Stephenie Y. ; Davis, Ryan R. ; Wang, Nicholas J. ; Schanen, N. Carolyn ; Gregg, Jeffrey P. / Genomic and functional profiling of duplicated chromosome 15 cell lines reveal regulatory alterations in UBE3A-associated ubiquitin-proteasome pathway processes. In: Human Molecular Genetics. 2006 ; Vol. 15, No. 6. pp. 853-869.
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