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Liang D, Aygün N, Matoba N, Ideraabdullah FY, Love MI, Stein JL. Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation. Hum Mol Genet 2023; 32:402-416. [PMID: 35994039 PMCID: PMC9851749 DOI: 10.1093/hmg/ddac207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/02/2022] [Accepted: 08/17/2022] [Indexed: 01/24/2023] Open
Abstract
Genomic imprinting results in gene expression bias caused by parental chromosome of origin and occurs in genes with important roles during human brain development. However, the cell-type and temporal specificity of imprinting during human neurogenesis is generally unknown. By detecting within-donor allelic biases in chromatin accessibility and gene expression that are unrelated to cross-donor genotype, we inferred imprinting in both primary human neural progenitor cells and their differentiated neuronal progeny from up to 85 donors. We identified 43/20 putatively imprinted regulatory elements (IREs) in neurons/progenitors, and 133/79 putatively imprinted genes in neurons/progenitors. Although 10 IREs and 42 genes were shared between neurons and progenitors, most putative imprinting was only detected within specific cell types. In addition to well-known imprinted genes and their promoters, we inferred novel putative IREs and imprinted genes. Consistent with both DNA methylation-based and H3K27me3-based regulation of imprinted expression, some putative IREs also overlapped with differentially methylated or histone-marked regions. Finally, we identified a progenitor-specific putatively imprinted gene overlapping with copy number variation that is associated with uniparental disomy-like phenotypes. Our results can therefore be useful in interpreting the function of variants identified in future parent-of-origin association studies.
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Affiliation(s)
- Dan Liang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Folami Y Ideraabdullah
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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2
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Jima DD, Skaar DA, Planchart A, Motsinger-Reif A, Cevik SE, Park SS, Cowley M, Wright F, House J, Liu A, Jirtle RL, Hoyo C. Genomic map of candidate human imprint control regions: the imprintome. Epigenetics 2022; 17:1920-1943. [PMID: 35786392 PMCID: PMC9665137 DOI: 10.1080/15592294.2022.2091815] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Imprinted genes – critical for growth, metabolism, and neuronal function – are expressed from one parental allele. Parent-of-origin-dependent CpG methylation regulates this expression at imprint control regions (ICRs). Since ICRs are established before tissue specification, these methylation marks are similar across cell types. Thus, they are attractive for investigating the developmental origins of adult diseases using accessible tissues, but remain unknown. We determined genome-wide candidate ICRs in humans by performing whole-genome bisulphite sequencing (WGBS) of DNA derived from the three germ layers and from gametes. We identified 1,488 hemi-methylated candidate ICRs, including 19 of 25 previously characterized ICRs (https://humanicr.org/). Gamete methylation approached 0% or 100% in 332 ICRs (178 paternally and 154 maternally methylated), supporting parent-of-origin-specific methylation, and 65% were in well-described CTCF-binding or DNaseI hypersensitive regions. This draft of the human imprintome will allow for the systematic determination of the role of early-acquired imprinting dysregulation in the pathogenesis of human diseases and developmental and behavioural disorders.
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Affiliation(s)
- Dereje D Jima
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - David A Skaar
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Antonio Planchart
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Alison Motsinger-Reif
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Sebnem E Cevik
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Sarah S Park
- Toxicology Program, North Carolina State University, Raleigh, NC, USA.,Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Michael Cowley
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Fred Wright
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - John House
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Andy Liu
- Department of Neurology, Duke University, School of Medicine, Durham, NC, USA
| | - Randy L Jirtle
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.,Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA.,Toxicology Program, North Carolina State University, Raleigh, NC, USA
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3
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Aoki S, Higashimoto K, Hidaka H, Ohtsuka Y, Aoki S, Mishima H, Yoshiura KI, Nakabayashi K, Hata K, Yatsuki H, Hara S, Ohba T, Katabuchi H, Soejima H. Aberrant hypomethylation at imprinted differentially methylated regions is involved in biparental placental mesenchymal dysplasia. Clin Epigenetics 2022; 14:64. [PMID: 35581658 PMCID: PMC9115938 DOI: 10.1186/s13148-022-01280-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Placental mesenchymal dysplasia (PMD) is a morphological abnormality resembling partial hydatidiform moles. It is often associated with androgenetic/biparental mosaicism (ABM) and complicated by Beckwith-Wiedemann syndrome (BWS), an imprinting disorder. These phenomena suggest an association between PMD and aberrant genomic imprinting, particularly of CDKN1C and IGF2. The existence of another type of PMD containing the biparental genome has been reported. However, the frequency and etiology of biparental PMD are not yet fully understood. RESULTS We examined 44 placental specimens from 26 patients with PMD: 19 of these were macroscopically normal and 25 exhibited macroscopic PMD. Genotyping by DNA microarray or short tandem repeat analysis revealed that approximately 35% of the macroscopic PMD specimens could be classified as biparental, while the remainder were ABM. We performed a DNA methylation analysis using bisulfite pyrosequencing of 15 placenta-specific imprinted differentially methylated regions (DMRs) and 36 ubiquitous imprinted DMRs. As expected, most DMRs in the macroscopic PMD specimens with ABM exhibited the paternal epigenotype. Importantly, the biparental macroscopic PMD specimens exhibited frequent aberrant hypomethylation at seven of the placenta-specific DMRs. Allelic expression analysis using single-nucleotide polymorphisms revealed that five imprinted genes associated with these aberrantly hypomethylated DMRs were biallelically expressed. Frequent aberrant hypomethylation was observed at five ubiquitous DMRs, including GRB10 but not ICR2 or ICR1, which regulate the expression of CDKN1C and IGF2, respectively. Whole-exome sequencing performed on four biparental macroscopic PMD specimens did not reveal any pathological genetic abnormalities. Clinical and molecular analyses of babies born from pregnancies with PMD revealed four cases with BWS, each exhibiting different molecular characteristics, and those between BWS and PMD specimens were not always the same. CONCLUSION These data clarify the prevalence of biparental PMD and ABM-PMD and strongly implicate hypomethylation of DMRs in the pathogenesis of biparental PMD, particularly placenta-specific DMRs and the ubiquitous GRB10, but not ICR2 or ICR1. Aberrant hypomethylation of DMRs was partial, indicating that it occurs after fertilization. PMD is an imprinting disorder, and it may be a missing link between imprinting disorders and placental disorders incompatible with life, such as complete hydatidiform moles and partial hydatidiform moles.
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Affiliation(s)
- Saori Aoki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan.
| | - Hidenori Hidaka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Yasufumi Ohtsuka
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Shigehisa Aoki
- Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Hitomi Yatsuki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Satoshi Hara
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Takashi Ohba
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Hidetaka Katabuchi
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan.
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4
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da Silva Francisco Junior R, Dos Santos Ferreira C, Santos E Silva JC, Terra Machado D, Côrtes Martins Y, Ramos V, Simões Carnivali G, Garcia AB, Medina-Acosta E. Pervasive Inter-Individual Variation in Allele-Specific Expression in Monozygotic Twins. Front Genet 2019; 10:1178. [PMID: 31850058 PMCID: PMC6887657 DOI: 10.3389/fgene.2019.01178] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/24/2019] [Indexed: 01/19/2023] Open
Abstract
Despite being developed from one zygote, heterokaryotypic monozygotic (MZ) co-twins exhibit discordant karyotypes. Epigenomic studies in biological samples from heterokaryotypic MZ co-twins are of the most significant value for assessing the effects on gene- and allele-specific expression of an extranumerary chromosomal copy or structural chromosomal disparities in otherwise nearly identical germline genetic contributions. Here, we use RNA-Seq data from existing repositories to establish within-pair correlations for the breadth and magnitude of allele-specific expression (ASE) in heterokaryotypic MZ co-twins discordant for trisomy 21 and maternal 21q inheritance, as well as homokaryotypic co-twins. We show that there is a genome-wide disparity at ASE sites between the heterokaryotypic MZ co-twins. Although most of the disparity corresponds to changes in the magnitude of biallelic imbalance, ASE sites switching from either strictly monoallelic to biallelic imbalance or the reverse occur in few genes that are known or predicted to be imprinted, subject to X-chromosome inactivation or A-to-I(G) RNA edited. We also uncovered comparable ASE differences between homokaryotypic MZ twins. The extent of ASE discordance in MZ twins (2.7%) was about 10-fold lower than the expected between pairs of unrelated, non-twin males or females. The results indicate that the observed within-pair dissimilarities in breadth and magnitude of ASE sites in the heterokaryotypic MZ co-twins could not solely be attributable to the aneuploidy and the missing allelic heritability at 21q.
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Affiliation(s)
| | - Cristina Dos Santos Ferreira
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Juan Carlo Santos E Silva
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Douglas Terra Machado
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Yasmmin Côrtes Martins
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Victor Ramos
- Department of Genetics, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Gustavo Simões Carnivali
- Department of Computational Science, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Beatriz Garcia
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
| | - Enrique Medina-Acosta
- Laboratório de Biotecnologia, Núcleo de Diagnóstico e Investigação Molecular, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Brazil
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5
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Genetic and epigenetic pathways in Down syndrome: Insights to the brain and immune system from humans and mouse models. PROGRESS IN BRAIN RESEARCH 2019; 251:1-28. [PMID: 32057305 DOI: 10.1016/bs.pbr.2019.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The presence of an extra copy of human chromosome 21 (Hsa21) leads to a constellation of phenotypic manifestations in Down syndrome (DS), including prominent effects on the brain and immune system. Intensive efforts to unravel the molecular mechanisms underlying these phenotypes may help developing effective therapies, both in DS and in the general population. Here we review recent progress in genetic and epigenetic analysis of trisomy 21 (Ts21). New mouse models of DS based on syntenic conservation of segments of the mouse and human chromosomes are starting to clarify the contributions of chromosomal subregions and orthologous genes to specific phenotypes in DS. The expression of genes on Hsa21 is regulated by epigenetic mechanisms, and with recent findings of highly recurrent gene-specific changes in DNA methylation patterns in brain and immune system cells with Ts21, the epigenomics of DS has become an active research area. Here we highlight the value of combining human studies with mouse models for defining DS critical genes and understanding the trans-acting effects of a simple chromosomal aneuploidy on genome-wide epigenetic patterning. These genetic and epigenetic studies are starting to uncover fundamental biological mechanisms, leading to insights that may soon become therapeutically relevant.
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6
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Benton MC, Lea RA, Macartney-Coxson D, Sutherland HG, White N, Kennedy D, Mengersen K, Haupt LM, Griffiths LR. Genome-wide allele-specific methylation is enriched at gene regulatory regions in a multi-generation pedigree from the Norfolk Island isolate. Epigenetics Chromatin 2019; 12:60. [PMID: 31594537 PMCID: PMC6781349 DOI: 10.1186/s13072-019-0304-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/12/2019] [Indexed: 02/08/2023] Open
Abstract
Background Allele-specific methylation (ASM) occurs when DNA methylation patterns exhibit asymmetry among alleles. ASM occurs at imprinted loci, but its presence elsewhere across the human genome is indicative of wider importance in terms of gene regulation and disease risk. Here, we studied ASM by focusing on blood-based DNA collected from 24 subjects comprising a 3-generation pedigree from the Norfolk Island genetic isolate. We applied a genome-wide bisulphite sequencing approach with a genotype-independent ASM calling method to map ASM across the genome. Regions of ASM were then tested for enrichment at gene regulatory regions using Genomic Association Test (GAT) tool. Results In total, we identified 1.12 M CpGs of which 147,170 (13%) exhibited ASM (P ≤ 0.05). When including contiguous ASM signal spanning ≥ 2 CpGs, this condensed to 12,761 ASM regions (AMRs). These AMRs tagged 79% of known imprinting regions and most (98.1%) co-localised with known single nucleotide variants. Notably, miRNA and lncRNA showed a 3.3- and 1.8-fold enrichment of AMRs, respectively (P < 0.005). Also, the 5′ UTR and start codons each showed a 3.5-fold enrichment of AMRs (P < 0.005). There was also enrichment of AMRs observed at subtelomeric regions of many chromosomes. Five out of 11 large AMRs localised to the protocadherin cluster on chromosome 5. Conclusions This study shows ASM extends far beyond genomic imprinting in humans and that gene regulatory regions are hotspots for ASM. Future studies of ASM in pedigrees should help to clarify transgenerational inheritance patterns in relation to genotype and disease phenotypes.
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Affiliation(s)
- Miles C Benton
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Human Genomics, Institute of Environmental Science and Research, Wellington, New Zealand
| | - Rodney A Lea
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.
| | - Donia Macartney-Coxson
- Human Genomics, Institute of Environmental Science and Research, Wellington, New Zealand
| | - Heidi G Sutherland
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Nicole White
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Daniel Kennedy
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Kerry Mengersen
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology (QUT), Brisbane, QLD, Australia
| | - Larisa M Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
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7
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Shaaban S, MacKinnon S, Andrews C, Staffieri SE, Maconachie GDE, Chan WM, Whitman MC, Morton SU, Yazar S, MacGregor S, Elder JE, Traboulsi EI, Gottlob I, Hewitt AW, Hunter DG, Mackey DA, Engle EC. Genome-Wide Association Study Identifies a Susceptibility Locus for Comitant Esotropia and Suggests a Parent-of-Origin Effect. Invest Ophthalmol Vis Sci 2019; 59:4054-4064. [PMID: 30098192 PMCID: PMC6088800 DOI: 10.1167/iovs.18-24082] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To identify genetic variants conferring susceptibility to esotropia. Esotropia is the most common form of comitant strabismus, has its highest incidence in European ancestry populations, and is believed to be inherited as a complex trait. Methods White European American discovery cohorts with nonaccommodative (826 cases and 2991 controls) or accommodative (224 cases and 749 controls) esotropia were investigated. White European Australian and United Kingdom cohorts with nonaccommodative (689 cases and 1448 controls) or accommodative (66 cases and 264 controls) esotropia were tested for replication. We performed a genome-wide case-control association study using a mixed linear additive model. Meta-analyses of discovery and replication cohorts were then conducted. Results A significant association with nonaccommodative esotropia was discovered (odds ratio [OR] = 1.41, P = 2.84 × 10-09) and replicated (OR = 1.23, P = 0.01) at rs2244352 [T] located within intron 1 of the WRB (tryptophan rich basic protein) gene on chromosome 21 (meta-analysis OR = 1.33, P = 9.58 × 10-11). This single nucleotide polymorphism (SNP) is differentially methylated, and there is a statistically significant skew toward paternal inheritance in the discovery cohort. Meta-analysis of the accommodative discovery and replication cohorts identified an association with rs912759 [T] (OR = 0.59, P = 1.89 × 10-08), an intergenic SNP on chromosome 1p31.1. Conclusions This is the first genome-wide association study (GWAS) to identify significant associations in esotropia and suggests a parent-of-origin effect. Additional cohorts will permit replication and extension of these findings. Future studies of rs2244352 and WRB should provide insight into pathophysiological mechanisms underlying comitant strabismus.
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Affiliation(s)
- Sherin Shaaban
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, United States.,Dubai Harvard Foundation for Medical Research, Boston, Massachusetts, United States
| | - Sarah MacKinnon
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Caroline Andrews
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States.,Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Sandra E Staffieri
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.,Department of Ophthalmology, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia
| | - Gail D E Maconachie
- Department of Neuroscience, The University of Leicester Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - Wai-Man Chan
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States.,Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Mary C Whitman
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - Sarah U Morton
- Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts, United States
| | - Seyhan Yazar
- Medical Research Council (MRC) Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom.,Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia
| | - Stuart MacGregor
- Stastical Genetics Laboratory, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - James E Elder
- Department of Ophthalmology, Royal Children's Hospital, University of Melbourne, Parkville, Victoria, Australia.,Department of Pediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - Elias I Traboulsi
- Department of Ophthalmology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, United States
| | - Irene Gottlob
- Department of Neuroscience, The University of Leicester Ulverscroft Eye Unit, University of Leicester, Leicester, United Kingdom
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.,Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia.,Department of Ophthalmology, School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
| | | | - David G Hunter
- Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - David A Mackey
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia.,Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia.,Department of Ophthalmology, School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Tasmania, Australia
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, United States.,F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, Massachusetts, United States.,Department of Neurology, Harvard Medical School, Boston, Massachusetts, United States.,Department of Ophthalmology, Boston Children's Hospital, Boston, Massachusetts, United States.,Howard Hughes Medical Institute, Chevy Chase, Maryland, United States.,Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, Massachusetts, United States
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8
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Hou J, Shi X, Chen C, Islam MS, Johnson AF, Kanno T, Huettel B, Yen MR, Hsu FM, Ji T, Chen PY, Matzke M, Matzke AJM, Cheng J, Birchler JA. Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa. Proc Natl Acad Sci U S A 2018; 115:E11321-E11330. [PMID: 30429332 PMCID: PMC6275517 DOI: 10.1073/pnas.1807796115] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Changes in dosage of part of the genome (aneuploidy) have long been known to produce much more severe phenotypic consequences than changes in the number of whole genomes (ploidy). To examine the basis of these differences, global gene expression in mature leaf tissue for all five trisomies and in diploids, triploids, and tetraploids of Arabidopsis thaliana was studied. The trisomies displayed a greater spread of expression modulation than the ploidy series. In general, expression of genes on the varied chromosome ranged from compensation to dosage effect, whereas genes from the remainder of the genome ranged from no effect to reduced expression approaching the inverse level of chromosomal imbalance (2/3). Genome-wide DNA methylation was examined in each genotype and found to shift most prominently with trisomy 4 but otherwise exhibited little change, indicating that genetic imbalance is generally mechanistically unrelated to DNA methylation. Independent analysis of gene functional classes demonstrated that ribosomal, proteasomal, and gene body methylated genes were less modulated compared with all classes of genes, whereas transcription factors, signal transduction components, and organelle-targeted protein genes were more tightly inversely affected. Comparing transcription factors and their targets in the trisomies and in expression networks revealed considerable discordance, illustrating that altered regulatory stoichiometry is a major contributor to genetic imbalance. Reanalysis of published data on gene expression in disomic yeast and trisomic mouse cells detected similar stoichiometric effects across broad phylogenetic taxa, and indicated that these effects reflect normal gene regulatory processes.
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Affiliation(s)
- Jie Hou
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Xiaowen Shi
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
| | - Chen Chen
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Md Soliman Islam
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - Adam F Johnson
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam 550000
| | - Tatsuo Kanno
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Bruno Huettel
- Max Planck Institute for Plant Breeding, Cologne, Germany 50829
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Fei-Man Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tieming Ji
- Department of Statistics, University of Missouri, Columbia, MO 65211
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529
| | - Marjori Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529;
| | - Antonius J M Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan 11529;
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211;
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9
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Moore SW. Advances in understanding the association between Down syndrome and Hirschsprung disease (DS-HSCR). Pediatr Surg Int 2018; 34:1127-1137. [PMID: 30218169 DOI: 10.1007/s00383-018-4344-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/10/2018] [Indexed: 02/07/2023]
Abstract
The clinical association between Trisomy 21 (Down syndrome) and aganglionosis (Hirschsprung disease; DS-HSCR) is well-established, being of the order of 5% and remains the most common congenital association with Hirschsprung disease. However, little consensus exists as to the possible etiologic and genetic factors influencing this association. Recent research has identified a number of levels at which development of the enteric nervous system is potentially affected in Trisomy 21. These include a decreased central pool of available neuroblasts for migration into the enteric nervous system, abnormal neuroblast type, poor synaptic nerve function and early germline gene-related influences on the migrating neuroblasts due to genetic mutations of a number of important developmental genes, and possible somatic mutations resulting from alterations in the local tissue microenvironment. In this paper, we review available evidence for this association. In addition, we provide evidence of both germline and somatic gene mutations suggesting causation. Although the picture is complex, recent associations between specific RET proto-oncogene variations have been shown to be significant in Down syndrome patients with Hirschsprung disease, as they probably interfere with vital RET functions in the development of the autonomic and enteric nervous systems, increasing the risk of disturbed normal function. In addition, we explore potential role of other facilitatory influence of other susceptibility genes as well as potential other chromosome 21 gene actions and the microenvironment on the Down syndrome gastro-intestinal tract. The various ways in which trisomy of chromosome influences the enteric nervous system are becoming clearer. The sum of these effects influences the outcome of surgery in Down syndrome patients with Hirschsprung Disease.
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Affiliation(s)
- S W Moore
- Division of Paediatric Surgery, Faculty of Medicine and Health Sciences, University of Stellenbosch, PO Box 241, Cape Town, South Africa.
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10
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Henneman P, Bouman A, Mul A, Knegt L, van der Kevie-Kersemaekers AM, Zwaveling-Soonawala N, Meijers-Heijboer HEJ, van Trotsenburg ASP, Mannens MM. Widespread domain-like perturbations of DNA methylation in whole blood of Down syndrome neonates. PLoS One 2018; 13:e0194938. [PMID: 29601581 PMCID: PMC5877863 DOI: 10.1371/journal.pone.0194938] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/13/2018] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Down syndrome (DS) is the most frequent genetic cause of intellectual disability. Despite the fact that more than 50 years have passed since the discovery of its genetic aberrations, the exact pathogenesis of the DS phenotype has remained largely unexplained. It was recently hypothesized that the DS pathogenesis involves complex (epi)genetic, molecular and cellular determinants. To date, many reports have addressed epigenetic aberrations associated with DS at different developmental stages/ages and tissue types, but to our best knowledge not in DS newborns. This study aimed to investigate genome-wide methylation patterns in DS newborns compared to non-trisomic newborns. METHOD We analyzed blood samples obtained from ten newborns with DS and five age-matched non-trisomic newborns. Epigenetic profiles were obtained from extracted DNA using the Illumina Infinium 450K array. Since aberrant blood cell distribution is known to be present in DS, we applied two distinct models: with and without correction for estimated blood cell distribution. RESULTS Differentially methylated position (DMP) analysis of the uncorrected model detected 19525 significant hits (51,2% hypomethylated). In the corrected model, we found 121953 significant DMPs (49,8% hypomethylated). Independent of the used model we observed a chromosome 21 dosage effect. Moreover, we detected 46 and 145 differentially methylated regions in the uncorrected and corrected model respectively, both showing hypomethylation overrepresentation. Replication analyses of DMPs and DMRs found by Bacalini et al. (2015) showed a large overlap. CONCLUSION In this study, we found methylation profile differences between DS newborns and controls reflecting a systematically affected epigenetic profile. The observed chromosome 21 dosage effect suggests the involvement of affected essential regulatory factors/regions or altered expression of chromatin modeling enzymes located on chromosome 21. Additional research is necessary to substantiate these hypotheses.
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Affiliation(s)
- Peter Henneman
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Arjan Bouman
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Adri Mul
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Lia Knegt
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | | | - Nitash Zwaveling-Soonawala
- Department of Pediatric Endocrinology, Emma Children’s Hospital, Academic Medical Center, Amsterdam, The Netherlands
| | | | - A. S. Paul van Trotsenburg
- Department of Pediatrics and Translational Genetics, Emma Children’s Hospital, Academic Medical Center, Amsterdam, The Netherlands
| | - Marcel M. Mannens
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
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11
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de Sá Machado Araújo G, da Silva Francisco Junior R, Dos Santos Ferreira C, Mozer Rodrigues PT, Terra Machado D, Louvain de Souza T, Teixeira de Souza J, Figueiredo Osorio da Silva C, Alves da Silva AF, Andrade CCF, da Silva AT, Ramos V, Garcia AB, Machado FB, Medina-Acosta E. Maternal 5 mCpG Imprints at the PARD6G-AS1 and GCSAML Differentially Methylated Regions Are Decoupled From Parent-of-Origin Expression Effects in Multiple Human Tissues. Front Genet 2018; 9:36. [PMID: 29545821 PMCID: PMC5838017 DOI: 10.3389/fgene.2018.00036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/29/2018] [Indexed: 11/13/2022] Open
Abstract
A hallmark of imprinted genes in mammals is the occurrence of parent-of-origin-dependent asymmetry of DNA cytosine methylation (5mC) of alleles at CpG islands (CGIs) in their promoter regions. This 5mCpG asymmetry between the parental alleles creates allele-specific imprinted differentially methylated regions (iDMRs). iDMRs are often coupled to the transcriptional repression of the methylated allele and the activation of the unmethylated allele in a tissue-specific, developmental-stage-specific and/or isoform-specific fashion. iDMRs function as regulatory platforms, built through the recruitment of chemical modifications to histones to achieve differential, parent-of-origin-dependent chromatin segmentation states. Here, we used a comparative computational data mining approach to identify 125 novel constitutive candidate iDMRs that integrate the maximal number of allele-specific methylation region records overlapping CGIs in human methylomes. Twenty-nine candidate iDMRs display gametic 5mCpG asymmetry, and another 96 are candidate secondary iDMRs. We established the maternal origin of the 5mCpG imprints of one gametic (PARD6G-AS1) and one secondary (GCSAML) iDMRs. We also found a constitutively hemimethylated, nonimprinted domain at the PWWP2AP1 promoter CGI with oocyte-derived methylation asymmetry. Given that the 5mCpG level at the iDMRs is not a sufficient criterion to predict active or silent locus states and that iDMRs can regulate genes from a distance of more than 1 Mb, we used RNA-Seq experiments from the Genotype-Tissue Expression project and public archives to assess the transcriptional expression profiles of SNPs across 4.6 Mb spans around the novel maternal iDMRs. We showed that PARD6G-AS1 and GCSAML are expressed biallelically in multiple tissues. We found evidence of tissue-specific monoallelic expression of ZNF124 and OR2L13, located 363 kb upstream and 419 kb downstream, respectively, of the GCSAML iDMR. We hypothesize that the GCSAML iDMR regulates the tissue-specific, monoallelic expression of ZNF124 but not of OR2L13. We annotated the non-coding epigenomic marks in the two maternal iDMRs using data from the Roadmap Epigenomics project and showed that the PARD6G-AS1 and GCSAML iDMRs achieve contrasting activation and repression chromatin segmentations. Lastly, we found that the maternal 5mCpG imprints are perturbed in several hematopoietic cancers. We conclude that the maternal 5mCpG imprints at PARD6G-AS1 and GCSAML iDMRs are decoupled from parent-of-origin transcriptional expression effects in multiple tissues.
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Affiliation(s)
- Graziela de Sá Machado Araújo
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Ronaldo da Silva Francisco Junior
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Cristina Dos Santos Ferreira
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Pedro Thyago Mozer Rodrigues
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Douglas Terra Machado
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Thais Louvain de Souza
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Faculdade de Medicina de Campos, Campos dos Goytacazes, Brazil
| | - Jozimara Teixeira de Souza
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Cleiton Figueiredo Osorio da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Antônio Francisco Alves da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Claudia Caixeta Franco Andrade
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil.,Faculdade Metropolitana São Carlos, Bom Jesus do Itabapoana, Brazil
| | - Alan Tardin da Silva
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Victor Ramos
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Ana Beatriz Garcia
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Filipe Brum Machado
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
| | - Enrique Medina-Acosta
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Brazil
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12
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A Pair of Maternal Chromosomes Derived from Meiotic Nondisjunction in Trisomy 21 Affects Nuclear Architecture and Transcriptional Regulation. Sci Rep 2017; 7:764. [PMID: 28396582 PMCID: PMC5429678 DOI: 10.1038/s41598-017-00714-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 03/10/2017] [Indexed: 12/22/2022] Open
Abstract
Eukaryotic genomes are organised into complex higher-order structures within the nucleus, and the three-dimensional arrangement of chromosomes is functionally important for global gene regulation. The existence of supernumerary chromosome 21 in Down syndrome may perturb the nuclear architecture at different levels, which is normally optimised to maintain the physiological balance of gene expression. However, it has not been clearly elucidated whether and how aberrant configuration of chromosomes affects gene activities. To investigate the effects of trisomy 21 on nuclear organisation and gene expression, we performed three-dimensional fluorescent imaging analysis of chromosome-edited human induced pluripotent stem cells (iPSCs), which enabled identification of the parental origin of the three copies of chromosome 21. We found that two copies of maternal chromosomes resulting from meiotic nondisjunction had a higher tendency to form an adjacent pair and were located relatively distant from the nuclear membrane, suggesting the conserved interaction between these homologous chromosomes. Transcriptional profiling of parental-origin-specific corrected disomy 21 iPSC lines indicated upregulated expression of the maternal alleles for a group of genes, which was accompanied by a fluctuating expression pattern. These results suggest the unique effects of a pair of maternal chromosomes in trisomy 21, which may contribute to the pathological phenotype.
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13
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Do C, Xing Z, Yu YE, Tycko B. Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models. Epigenomics 2016; 9:189-207. [PMID: 27911079 PMCID: PMC5549717 DOI: 10.2217/epi-2016-0138] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
An important line of postgenomic research seeks to understand how genetic factors can influence epigenetic patterning. Here we review epigenetic effects of chromosomal aneuploidies, focusing on findings in Down syndrome (DS, trisomy 21). Recent work in human DS and mouse models has shown that the extra chromosome 21 acts in trans to produce epigenetic changes, including differential CpG methylation (DS-DM), in specific sets of downstream target genes, mostly on other chromosomes. Mechanistic hypotheses emerging from these data include roles of chromosome 21-linked methylation pathway genes (DNMT3L and others) and transcription factor genes (RUNX1, OLIG2, GABPA, ERG and ETS2) in shaping the patterns of DS-DM. The findings may have broader implications for trans-acting epigenetic effects of chromosomal and subchromosomal aneuploidies in other human developmental and neuropsychiatric disorders, and in cancers.
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Affiliation(s)
- Catherine Do
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program & Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics Program & Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Columbia University, New York, NY 10032, USA.,Taub Institute for Research on Alzheimer's disease & the Aging Brain, Columbia University, New York, NY 10032, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Pathology & Cell Biology, Columbia University, New York, NY 10032, USA
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