Allele-specific expression analysis by RNA-FISH demonstrates preferential maternal expression of UBE3A and imprint maintenance within 15q11- q13 duplications

Herzing, L. B.K.

doi:10.1093/hmg/11.15.1707

Cited by 109Genetic Syndromes and ImprintingGenomic variations and chromosomal abnormalitiesGenetics and Neurodevelopmental Disorders

Allele-specific expression analysis by RNA-FISH demonstrates preferential maternal expression of UBE3A and imprint maintenance within 15q11- q13 duplications

Herzing, L. B.K.·2002·Human Molecular Genetics

DOI 10.1093/hmg/11.15.1707

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Abstract

15q11- q13 contains many imprinted genes, and undergoes duplicon-mediated rearrangements, including deletions, duplications and triplications, and generation of marker chromosomes. Abnormal phenotypes, including language delays and autism spectrum disorders, are primarily observed with maternal 15q11- q13 duplication. To determine possible epigenetic effects on expression within duplicated 15q11- q13 regions, we utilized RNA-FISH to directly observe gene expression. RNA-FISH, unlike RT-PCR, is polymorphism-independent, and it also detects relative levels of expression at each allele. Unamplified, gene-specific RNA signals were detected using cDNA probes. Subsequent DNA-FISH confirmed RNA signals and assigned parental origin by colocalization of genomic probes. SNRPN and NDN expression was detected primarily from paternal alleles. Control Dystrobrevin transcripts were detected equally from both alleles; however, maternal-UBE3A signals were consistently larger than paternal signals in normal fibroblasts and in neural-precursor cells. Larger UBE3A signals were also observed on one or both maternal alleles in a cell line carrying a maternal interstitial duplication, on both alleles of a maternally derived marker(15) chromosome, and occasionally on a paternal allele in a cell line carrying a paternal interstitial duplication. Expression of NDNL2, just distal to the duplicated region, was not markedly altered but paralleled changes in UBE3A expression. Excess total maternal-UBE3A RNA was confirmed by Northern blot analysis of cell lines carrying 15q11- q13 duplications or triplications. These results demonstrate that: (1) UBE3A is imprinted in fibroblasts, lymphoblasts and neural-precursor cells; (2) allelic imprint status is maintained in the majority of cells upon duplication both in cis and in trans; and (3) alleles on specific types of duplications may exhibit an increase in expression levels/loss of expression constraints.

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Maternal duplications of the 15q11-13 locus lead to increased expression of UBE3A and epigenetic silencing of the paternal antisense transcript, UBE3A-ATS.
“Maternal duplications of the 15q11–13 locus lead to increased expression of UBE3A and epigenetic silencing of the paternal antisense transcript, UBE3A-ATS121–124.”
From Rhythms of life: circadian disruption and brain disorders across the lifespan (2019) · cites this paper as [122]

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Authors: Herzing, L. B. K.
Affiliations: University of Chicago (US)
Corresponding author: Herzing, L. B.K.
ORCID: Herzing, L. B.K.
Venue: Human Molecular Genetics
Publisher: Oxford University Press (OUP)
Published: 2002-07-15
Volume: 11
Issue: 15
Pages: 1707-1718
ISSN: 0964-6906 (ISSN-L)
1460-2083
DOI: 10.1093/hmg/11.15.1707
OpenAlex: W2113463790
Cited by: 109
References: 62
Citations by year: 2026: 1 · 2025: 1 · 2024: 1 · 2023: 1 · 2020: 1 · 2019: 1 · 2018: 1 · 2017: 1 · 2016: 2 · 2014: 4 · 2013: 6 · 2012: 5
FWCI: 3.55
Type: journal article
Language: en
Open access: closed
Locations: Human Molecular Genetics (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health (5r01hd036111-03, 5k02mh001389-03, 5r01mh052223-05, NOI-HD-8-3284)
National Institute of Mental Health (R01 MH52223, K02MH01389)
Eunice Kennedy Shriver National Institute of Child Health and Human Development (N01-HD-8-3284, R01 HD36111)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Syndromes and Imprinting
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
Keywords: UBE3A, genomic imprinting, allele-specific expression, maternal expression, SNRPN, NDN, neural progenitor cells, fibroblasts, autism spectrum disorder, language delay
MeSH terms: Autoantigens, Chromosomes, Human, Pair 15, Female, Fibroblasts, Humans, Ligases, Male, RNA, Blotting, Northern, Gene Expression, In Situ Hybridization, Fluorescence, Ribonucleoproteins, Small Nuclear, Genomic Imprinting, Gene Duplication, Ubiquitin-Protein Ligases, snRNP Core Proteins

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Allele-specific expression analysis by RNA-FISH demonstrates preferential maternal expression of UBE3A and imprint maintenance within 15q11- q13 duplications

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