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Dastsooz H, Anselmi F, Lauria A, Cicconetti C, Proserpio V, Mohammadisoleimani E, Firoozi Z, Mansoori Y, Haghi-Aminjan H, Caizzi L, Oliviero S. Involvement of N4BP2L1, PLEKHA4, and BEGAIN genes in breast cancer and muscle cell development. Front Cell Dev Biol 2024; 12:1295403. [PMID: 38859961 PMCID: PMC11163233 DOI: 10.3389/fcell.2024.1295403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 04/22/2024] [Indexed: 06/12/2024] Open
Abstract
Patients with breast cancer show altered expression of genes within the pectoralis major skeletal muscle cells of the breast. Through analyses of The Cancer Genome Atlas (TCGA)-breast cancer (BRCA), we identified three previously uncharacterized putative novel tumor suppressor genes expressed in normal muscle cells, whose expression was downregulated in breast tumors. We found that NEDD4 binding protein 2-like 1 (N4BP2L1), pleckstrin homology domain-containing family A member 4 (PLEKHA4), and brain-enriched guanylate kinase-associated protein (BEGAIN) that are normally highly expressed in breast myoepithelial cells and smooth muscle cells were significantly downregulated in breast tumor tissues of a cohort of 50 patients with this cancer. Our data revealed that the low expression of PLEKHA4 in patients with menopause below 50 years correlated with a higher risk of breast cancer. Moreover, we identified N4BP2L1 and BEGAIN as potential biomarkers of HER2-positive breast cancer. Furthermore, low BEGAIN expression in breast cancer patients with blood fat, heart problems, and diabetes correlated with a higher risk of this cancer. In addition, protein and RNA expression analysis of TCGA-BRCA revealed N4BP2L1 as a promising diagnostic protein biomarker in breast cancer. In addition, the in silico data of scRNA-seq showed high expression of these genes in several cell types of normal breast tissue, including breast myoepithelial cells and smooth muscle cells. Thus, our results suggest their possible tumor-suppressive function in breast cancer and muscle development.
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Affiliation(s)
- Hassan Dastsooz
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- IIGM-Italian Institute for Genomic Medicine, IRCCS, Candiolo, TO, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo Cancer (IT), Torino, Italy
| | - Francesca Anselmi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Andrea Lauria
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Chiara Cicconetti
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Valentina Proserpio
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | | | - Zahra Firoozi
- Department of Medical Genetics, Fasa University of Medical Sciences, Fasa, Iran
| | - Yaser Mansoori
- Department of Medical Genetics, Fasa University of Medical Sciences, Fasa, Iran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Hamed Haghi-Aminjan
- Pharmaceutical Sciences Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Livia Caizzi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- IIGM-Italian Institute for Genomic Medicine, IRCCS, Candiolo, TO, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo Cancer (IT), Torino, Italy
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2
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Potabattula R, Prell A, Dittrich M, Nava C, Depienne C, Bejaoui Y, El Hajj N, Hahn T, Schorsch M, Haaf T. Effects of paternal and chronological age on BEGAIN methylation and its possible role in autism. Aging (Albany NY) 2023; 15:12763-12779. [PMID: 38019471 DOI: 10.18632/aging.205275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/23/2023] [Indexed: 11/30/2023]
Abstract
Children from old fathers carry an increased risk for autism spectrum (ASD) and other neurodevelopmental disorders, which may at least partially be mediated by paternal age effects on the sperm epigenome. The brain enriched guanylate kinase associated (BEGAIN) protein is involved in protein-protein interactions at and transmission across synapses. Since several epigenome-wide methylation screens reported a paternal age effect on sperm BEGAIN methylation, here we confirmed a significant negative correlation between BEGAIN promoter methylation and paternal age, using more sensitive bisulfite pyrosequencing and a larger number of sperm samples. Paternal age-associated BEGAIN hypomethylation was also observed in fetal cord blood (FCB) of male but not of female offspring. There was no comparable maternal age effect on FCB methylation. In addition, we found a significant negative correlation between BEGAIN methylation and chronological age (ranging from 1 to 70 years) in peripheral blood samples of male but not of female donors. BEGAIN hypomethylation was more pronounced in male children, adolescents and adults suffering from ASD compared to controls. Both genetic variation (CC genotype of SNP rs7141087) and epigenetic factors may contribute to BEGAIN promoter hypomethylation. The age- and sex-specific BEGAIN methylation trajectories in the male germ line and somatic tissues, in particular the brain, support a role of this gene in ASD development.
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Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Andreas Prell
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Caroline Nava
- U.F. de Neurogénétique Moléculaire et Cellulaire, Dpt. de Génétique et Cytogénétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Yosra Bejaoui
- College of Health and Life Sciences and College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Nady El Hajj
- College of Health and Life Sciences and College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | | | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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3
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Beard DC, Zhang X, Wu DY, Martin JR, Hamagami N, Swift RG, McCullough KB, Ge X, Bell-Hensley A, Zheng H, Lawrence AB, Hill CA, Papouin T, McAlinden A, Garbow JR, Dougherty JD, Maloney SE, Gabel HW. Distinct disease mutations in DNMT3A result in a spectrum of behavioral, epigenetic, and transcriptional deficits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530041. [PMID: 36909558 PMCID: PMC10002657 DOI: 10.1101/2023.02.27.530041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Phenotypic heterogeneity is a common feature of monogenic neurodevelopmental disorders that can arise from differential severity of missense variants underlying disease, but how distinct alleles impact molecular mechanisms to drive variable disease presentation is not well understood. Here, we investigate missense mutations in the DNA methyltransferase DNMT3A associated with variable overgrowth, intellectual disability, and autism, to uncover molecular correlates of phenotypic heterogeneity in neurodevelopmental disease. We generate a DNMT3A P900L/+ mouse model mimicking a disease mutation with mild-to-moderate severity and compare phenotypic and epigenomic effects with a severe R878H mutation. We show that the P900L mutation leads to disease-relevant overgrowth, obesity, and social deficits shared across DNMT3A disorder models, while the R878H mutation causes more extensive epigenomic disruption leading to differential dysregulation of enhancers elements. We identify distinct gene sets disrupted in each mutant which may contribute to mild or severe disease, and detect shared transcriptomic disruption that likely drives common phenotypes across affected individuals. Finally, we demonstrate that core gene dysregulation detected in DNMT3A mutant mice overlaps effects in other developmental disorder models, highlighting the importance of DNMT3A-deposited methylation in neurodevelopment. Together, these findings define central drivers of DNMT3A disorders and illustrate how variable disruption of transcriptional mechanisms can drive the spectrum of phenotypes in neurodevelopmental disease.
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Affiliation(s)
- Diana C. Beard
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xiyun Zhang
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dennis Y. Wu
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jenna R. Martin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Raylynn G. Swift
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Katherine B. McCullough
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xia Ge
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin Bell-Hensley
- Department of Biomedical Engineering, Washington University, St. Louis, MO 63110, USA
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hongjun Zheng
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Austin B. Lawrence
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Cheryl A. Hill
- Department of Pathology and Anatomical Science, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Thomas Papouin
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Audrey McAlinden
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joel R. Garbow
- Department of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joseph D. Dougherty
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan E. Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Harrison W. Gabel
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO 63110, USA
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4
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Xie J, Ji T, Ferreira MAR, Li Y, Patel BN, Rivera RM. Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model. BMC Bioinformatics 2019; 20:530. [PMID: 31660858 PMCID: PMC6819473 DOI: 10.1186/s12859-019-3141-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/09/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND High-throughput sequencing experiments, which can determine allele origins, have been used to assess genome-wide allele-specific expression. Despite the amount of data generated from high-throughput experiments, statistical methods are often too simplistic to understand the complexity of gene expression. Specifically, existing methods do not test allele-specific expression (ASE) of a gene as a whole and variation in ASE within a gene across exons separately and simultaneously. RESULTS We propose a generalized linear mixed model to close these gaps, incorporating variations due to genes, single nucleotide polymorphisms (SNPs), and biological replicates. To improve reliability of statistical inferences, we assign priors on each effect in the model so that information is shared across genes in the entire genome. We utilize Bayesian model selection to test the hypothesis of ASE for each gene and variations across SNPs within a gene. We apply our method to four tissue types in a bovine study to de novo detect ASE genes in the bovine genome, and uncover intriguing predictions of regulatory ASEs across gene exons and across tissue types. We compared our method to competing approaches through simulation studies that mimicked the real datasets. The R package, BLMRM, that implements our proposed algorithm, is publicly available for download at https://github.com/JingXieMIZZOU/BLMRM . CONCLUSIONS We will show that the proposed method exhibits improved control of the false discovery rate and improved power over existing methods when SNP variation and biological variation are present. Besides, our method also maintains low computational requirements that allows for whole genome analysis.
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Affiliation(s)
- Jing Xie
- Department of Statistics, University of Missouri at Columbia, Columbia, 65211 MO USA
| | - Tieming Ji
- Department of Statistics, University of Missouri at Columbia, Columbia, 65211 MO USA
| | | | - Yahan Li
- Division of Animal Science, University of Missouri at Columbia, Columbia, 65211 MO USA
| | - Bhaumik N. Patel
- Division of Animal Science, University of Missouri at Columbia, Columbia, 65211 MO USA
| | - Rocio M. Rivera
- Division of Animal Science, University of Missouri at Columbia, Columbia, 65211 MO USA
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5
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Duan J(E, Zhang M, Flock K, Seesi SA, Mandoiu I, Jones A, Johnson E, Pillai S, Hoffman M, McFadden K, Jiang H, Reed S, Govoni K, Zinn S, Jiang Z, Tian X(C. Effects of maternal nutrition on the expression of genomic imprinted genes in ovine fetuses. Epigenetics 2018; 13:793-807. [PMID: 30051747 PMCID: PMC6224220 DOI: 10.1080/15592294.2018.1503489] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/04/2018] [Accepted: 07/15/2018] [Indexed: 12/27/2022] Open
Abstract
Genomic imprinting is an epigenetic phenomenon of differential allelic expression based on parental origin. To date, 263 imprinted genes have been identified among all investigated mammalian species. However, only 21 have been described in sheep, of which 11 are annotated in the current ovine genome. Here, we aim to i) use DNA/RNA high throughput sequencing to identify new monoallelically expressed and imprinted genes in day 135 ovine fetuses and ii) determine whether maternal diet (100%, 60%, or 140% of National Research Council Total Digestible Nutrients) influences expression of imprinted genes. We also reported strategies to solve technical challenges in the data analysis pipeline. We identified 80 monoallelically expressed, 13 new putative imprinted genes, and five known imprinted genes in sheep using the 263 genes stated above as a guide. Sanger sequencing confirmed allelic expression of seven genes, CASD1, COPG2, DIRAS3, INPP5F, PLAGL1, PPP1R9A, and SLC22A18. Among the 13 putative imprinted genes, five were localized in the known sheep imprinting domains of MEST on chromosome 4, DLK1/GTL2 on chromosome 18 and KCNQ1 on chromosome 21, and three were in a novel sheep imprinted cluster on chromosome 4, known in other species as PEG10/SGCE. The expression of DIRAS3, IGF2, PHLDA2, and SLC22A18 was altered by maternal diet, albeit without allelic expression reversal. Together, our results expanded the list of sheep imprinted genes to 34 and demonstrated that while the expression levels of four imprinted genes were changed by maternal diet, the allelic expression patterns were un-changed for all imprinted genes studied.
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Affiliation(s)
| | - Mingyuan Zhang
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Kaleigh Flock
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Sahar Al Seesi
- Department of Computer Science, University of Connecticut, Storrs, CT, USA
| | - Ion Mandoiu
- Department of Computer Science, University of Connecticut, Storrs, CT, USA
| | - Amanda Jones
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Elizabeth Johnson
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Sambhu Pillai
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Maria Hoffman
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Katelyn McFadden
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Hesheng Jiang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Sarah Reed
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Kristen Govoni
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Steve Zinn
- Department of Animal Science, University of Connecticut, Storrs, CT, USA
| | - Zongliang Jiang
- School of Animal Science, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
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6
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Soares ML, Edwards CA, Dearden FL, Ferrón SR, Curran S, Corish JA, Rancourt RC, Allen SE, Charalambous M, Ferguson-Smith MA, Rens W, Adams DJ, Ferguson-Smith AC. Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control. Genome Res 2018; 28:345-356. [PMID: 29367313 PMCID: PMC5848613 DOI: 10.1101/gr.221366.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022]
Abstract
Approximately half the mammalian genome is composed of repetitive sequences, and accumulating evidence suggests that some may have an impact on genome function. Here, we characterized a large array class of repeats of long-interspersed elements (LINE-1). Although widely distributed in mammals, locations of such arrays are species specific. Using targeted deletion, we asked whether a 170-kb LINE-1 array located at a mouse imprinted domain might function as a modulator of local transcriptional control. The LINE-1 array is lamina associated in differentiated ES cells consistent with its AT-richness, and although imprinting occurs both proximally and distally to the array, active LINE-1 transcripts within the tract are biallelically expressed. Upon deletion of the array, no perturbation of imprinting was observed, and abnormal phenotypes were not detected in maternal or paternal heterozygous or homozygous mutant mice. The array does not shield nonimprinted genes in the vicinity from local imprinting control. Reduced neural expression of protein-coding genes observed upon paternal transmission of the deletion is likely due to the removal of a brain-specific enhancer embedded within the LINE array. Our findings suggest that presence of a 170-kb LINE-1 array reflects the tolerance of the site for repeat insertion rather than an important genomic function in normal development.
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Affiliation(s)
- Miguel L Soares
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Departamento de Biomedicina, Unidade de Biologia Experimental, Faculdade de Medicina da Universidade do Porto, Porto; and i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-319 Porto, Portugal
| | - Carol A Edwards
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Frances L Dearden
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Sacri R Ferrón
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Scott Curran
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Jennifer A Corish
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Rebecca C Rancourt
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Sarah E Allen
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Marika Charalambous
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | | | - Willem Rens
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
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7
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Xu X, Ectors F, Davis EE, Pirottin D, Cheng H, Farnir F, Hadfield T, Cockett N, Charlier C, Georges M, Takeda H. Ectopic Expression of Retrotransposon-Derived PEG11/RTL1 Contributes to the Callipyge Muscular Hypertrophy. PLoS One 2015; 10:e0140594. [PMID: 26474044 PMCID: PMC4608697 DOI: 10.1371/journal.pone.0140594] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 09/27/2015] [Indexed: 11/18/2022] Open
Abstract
The callipyge phenotype is an ovine muscular hypertrophy characterized by polar overdominance: only heterozygous +Mat/CLPGPat animals receiving the CLPG mutation from their father express the phenotype. +Mat/CLPGPat animals are characterized by postnatal, ectopic expression of Delta-like 1 homologue (DLK1) and Paternally expressed gene 11/Retrotransposon-like 1 (PEG11/RTL1) proteins in skeletal muscle. We showed previously in transgenic mice that ectopic expression of DLK1 alone induces a muscular hypertrophy, hence demonstrating a role for DLK1 in determining the callipyge hypertrophy. We herein describe newly generated transgenic mice that ectopically express PEG11 in skeletal muscle, and show that they also exhibit a muscular hypertrophy phenotype. Our data suggest that both DLK1 and PEG11 act together in causing the muscular hypertrophy of callipyge sheep.
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Affiliation(s)
- Xuewen Xu
- Unit of Animal Genomics, GIGA Research Center and Faculty of Veterinary Medicine, University of Liège, 1 Avenue de l’Hôpital, Liège, Belgium
| | - Fabien Ectors
- Transgenic platform, FARAH and GIGA Research Center, University of Liège, 1 Avenue de l’Hôpital, Liège, Belgium
| | - Erica E. Davis
- Unit of Animal Genomics, GIGA Research Center and Faculty of Veterinary Medicine, University of Liège, 1 Avenue de l’Hôpital, Liège, Belgium
| | - Dimitri Pirottin
- Unit of Animal Genomics, GIGA Research Center and Faculty of Veterinary Medicine, University of Liège, 1 Avenue de l’Hôpital, Liège, Belgium
| | - Huijun Cheng
- Unit of Animal Genomics, GIGA Research Center and Faculty of Veterinary Medicine, University of Liège, 1 Avenue de l’Hôpital, Liège, Belgium
| | - Frédéric Farnir
- Unit of Biostatistics, FARAH and Faculty of Veterinary Medicine, University of Liège, Boulevard de Colonster, Liège, Belgium
| | - Tracy Hadfield
- Department of Animal, Dairy and Veterinary sciences, Utah State University, Logan, Utah, United States of America
| | - Noelle Cockett
- Department of Animal, Dairy and Veterinary sciences, Utah State University, Logan, Utah, United States of America
| | - Carole Charlier
- Unit of Animal Genomics, GIGA Research Center and Faculty of Veterinary Medicine, University of Liège, 1 Avenue de l’Hôpital, Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA Research Center and Faculty of Veterinary Medicine, University of Liège, 1 Avenue de l’Hôpital, Liège, Belgium
| | - Haruko Takeda
- Unit of Animal Genomics, GIGA Research Center and Faculty of Veterinary Medicine, University of Liège, 1 Avenue de l’Hôpital, Liège, Belgium
- * E-mail:
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8
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Magee DA, Spillane C, Berkowicz EW, Sikora KM, MacHugh DE. Imprinted loci in domestic livestock species as epigenomic targets for artificial selection of complex traits. Anim Genet 2014; 45 Suppl 1:25-39. [PMID: 24990393 DOI: 10.1111/age.12168] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2014] [Indexed: 12/30/2022]
Abstract
The phenomenon of genomic imprinting, whereby a subset of mammalian genes display parent-of-origin-specific monoallelic expression, is one of the most active areas of epigenetics research. Over the past two decades, more than 100 imprinted mammalian genes have been identified, while considerable advances have been made in elucidating the molecular mechanisms governing imprinting. These studies have helped to unravel the epigenome--a separate layer of regulatory information contained in eukaryotic chromosomes that influences gene expression and phenotypes without involving changes to the underlying DNA sequence. Although most studies of genomic imprinting in mammals have focussed on mouse models or human biomedical disorders, there is burgeoning interest in the phenotypic effects of imprinted genes in domestic livestock species. In particular, research has focused on imprinted genes influencing foetal growth and development, which are associated with economically important production traits in cattle, sheep and pigs. These findings, when coupled with the data emerging from the various different livestock genome projects, have major implications for the future of animal breeding, health and management. Here, we review current scientific knowledge regarding genomic imprinting in livestock species and evaluate how this information can be used in modern livestock improvement programmes.
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Affiliation(s)
- D A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, 4, Ireland
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9
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Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, Haig D, Dulac C. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 2010; 329:643-8. [PMID: 20616232 PMCID: PMC3005244 DOI: 10.1126/science.1190830] [Citation(s) in RCA: 448] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Genomic imprinting results in preferential expression of the paternal or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain. This approach uncovered parent-of-origin allelic effects of more than 1300 loci. We identified parental bias in the expression of individual genes and of specific transcript isoforms, with differences between brain regions. Many imprinted genes are expressed in neural systems associated with feeding and motivated behaviors, and parental biases preferentially target genetic pathways governing metabolism and cell adhesion. We observed a preferential maternal contribution to gene expression in the developing brain and a major paternal contribution in the adult brain. Thus, parental expression bias emerges as a major mode of epigenetic regulation in the brain.
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Affiliation(s)
- Christopher Gregg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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10
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Byrne K, Colgrave ML, Vuocolo T, Pearson R, Bidwell CA, Cockett NE, Lynn DJ, Fleming-Waddell JN, Tellam RL. The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep. PLoS One 2010; 5:e8638. [PMID: 20072617 PMCID: PMC2799525 DOI: 10.1371/journal.pone.0008638] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 12/15/2009] [Indexed: 01/22/2023] Open
Abstract
Members of the Ty3-Gypsy retrotransposon family are rare in mammalian genomes despite their abundance in invertebrates and some vertebrates. These elements contain a gag-pol-like structure characteristic of retroviruses but have lost their ability to retrotranspose into the mammalian genome and are thought to be inactive relics of ancient retrotransposition events. One of these retrotransposon-like elements, PEG11 (also called RTL1) is located at the distal end of ovine chromosome 18 within an imprinted gene cluster that is highly conserved in placental mammals. The region contains several conserved imprinted genes including BEGAIN, DLK1, DAT, GTL2 (MEG3), PEG11 (RTL1), PEG11as, MEG8, MIRG and DIO3. An intergenic point mutation between DLK1 and GTL2 causes muscle hypertrophy in callipyge sheep and is associated with large changes in expression of the genes linked in cis between DLK1 and MEG8. It has been suggested that over-expression of DLK1 is the effector of the callipyge phenotype; however, PEG11 gene expression is also strongly correlated with the emergence of the muscling phenotype as a function of genotype, muscle type and developmental stage. To date, there has been no direct evidence that PEG11 encodes a protein, especially as its anti-sense transcript (PEG11as) contains six miRNA that cause cleavage of the PEG11 transcript. Using immunological and mass spectrometry approaches we have directly identified the full-length PEG11 protein from postnatal nuclear preparations of callipyge skeletal muscle and conclude that its over-expression may be involved in inducing muscle hypertrophy. The developmental expression pattern of the PEG11 gene is consistent with the callipyge mutation causing recapitulation of the normal fetal-like gene expression program during postnatal development. Analysis of the PEG11 sequence indicates strong conservation of the regions encoding the antisense microRNA and in at least two cases these correspond with structural or functional domains of the protein suggesting co-evolution of the sense and antisense genes.
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Affiliation(s)
- Keren Byrne
- CSIRO Livestock Industries, St Lucia, Queensland, Australia
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Colosimo A, Di Rocco G, Curini V, Russo V, Capacchietti G, Berardinelli P, Mattioli M, Barboni B. Characterization of the methylation status of five imprinted genes in sheep gametes. Anim Genet 2009; 40:900-8. [PMID: 19694650 DOI: 10.1111/j.1365-2052.2009.01939.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Genomic imprinting is a mammalian developmental process that uses epigenetic mechanisms to induce monoallelic and parental-specific expression of particular autosomal genes. A crucial epigenetic event consists of DNA methylation of CpG-islands, which become differentially methylated regions (DMRs) on the maternal and paternal alleles during oogenesis or spermatogenesis (germline DMRs). By contrast, somatic DMRs are acquired after fertilization. While there are several studies referring to methylation acquisition within germline DMRs in the mouse and human, a comparable methylation analysis of orthologous sequences is still lacking in sheep. To identify germline DMRs, this study analysed the methylation status of the available CpG-islands of five ovine imprinted genes (H19, IGF2R, DLK1, DIO3 and BEGAIN) in mature spermatozoa and in female gametes at different stages of their follicle growth, including in vitro matured oocytes. The 5'-end CpG-island of H19 showed a full methylation in spermatozoa and an absent methylation in growing and fully grown oocytes. The intron 2 CpG-island of IGF2R was unmethylated in male gametes, while it showed a high level of methylation in early stages of oogenesis. The promoter CpG-islands of DLK1 and DIO3 were found to be unmethylated both in spermatozoa and oocytes. Finally, the exon 9 CpG-island of BEGAIN was hypermethylated in mature male gametes, while it showed an almost complete methylation only in late stages of oocyte development. Our findings suggest that DNA methylation establishment during early stages of sheep oogenesis and subsequent in vitro maturation is gene-specific and that, of the five genes investigated, only the CpG-islands of H19 and IGF2R might represent ovine germline DMRs.
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Affiliation(s)
- A Colosimo
- Department of Comparative Biomedical Sciences, Faculty of Veterinary Medicine, Teramo University, Piazza Aldo Moro 45, 64100 Teramo, Italy.
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Hagan JP, O'Neill BL, Stewart CL, Kozlov SV, Croce CM. At least ten genes define the imprinted Dlk1-Dio3 cluster on mouse chromosome 12qF1. PLoS One 2009; 4:e4352. [PMID: 19194500 PMCID: PMC2632752 DOI: 10.1371/journal.pone.0004352] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 12/09/2008] [Indexed: 11/25/2022] Open
Abstract
Background Genomic imprinting is an exception to Mendelian genetics in that imprinted genes are expressed monoallelically, dependent on parental origin. In mammals, imprinted genes are critical in numerous developmental and physiological processes. Aberrant imprinted gene expression is implicated in several diseases including Prader-Willi/Angelman syndromes and cancer. Methodology/Principal Findings To identify novel imprinted genes, transcription profiling was performed on two uniparentally derived cell lines, androgenetic and parthenogenetic primary mouse embryonic fibroblasts. A maternally expressed transcript termed Imprinted RNA near Meg3/Gtl2 (Irm) was identified and its expression studied by Northern blotting and whole mounts in situ hybridization. The imprinted region that contains Irm has a parent of origin effect in three mammalian species, including the sheep callipyge locus. In mice and humans, both maternal and paternal uniparental disomies (UPD) cause embryonic growth and musculoskeletal abnormalities, indicating that both alleles likely express essential genes. To catalog all imprinted genes in this chromosomal region, twenty-five mouse mRNAs in a 1.96Mb span were investigated for allele specific expression. Conclusions/Significance Ten imprinted genes were elucidated. The imprinting of three paternally expressed protein coding genes (Dlk1, Peg11, and Dio3) was confirmed. Seven noncoding RNAs (Meg3/Gtl2, Anti-Peg11, Meg8, Irm/“Rian”, AK050713, AK053394, and Meg9/Mirg) are characterized by exclusive maternal expression. Intriguingly, the majority of these noncoding RNA genes contain microRNAs and/or snoRNAs within their introns, as do their human orthologs. Of the 52 identified microRNAs that map to this region, six are predicted to regulate negatively Dlk1, suggesting an additional mechanism for interactions between allelic gene products. Since several previous studies relied heavily on in silico analysis and RT-PCR, our findings from Northerns and cDNA cloning clarify the genomic organization of this region. Our results expand the number of maternally expressed noncoding RNAs whose loss may be responsible for the phenotypes associated with mouse pUPD12 and human pUPD14 syndromes.
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Affiliation(s)
- John P. Hagan
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Medical Center, Columbus, Ohio, United States of America
- * E-mail:
| | - Brittany L. O'Neill
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Medical Center, Columbus, Ohio, United States of America
| | - Colin L. Stewart
- Cancer and Developmental Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Serguei V. Kozlov
- Center for Advanced Preclinical Research and Mouse Cancer Genetics Program, SAIC-Frederick, Inc., National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Carlo M. Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Medical Center, Columbus, Ohio, United States of America
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Wan LB, Bartolomei MS. Regulation of imprinting in clusters: noncoding RNAs versus insulators. ADVANCES IN GENETICS 2008; 61:207-23. [PMID: 18282507 DOI: 10.1016/s0065-2660(07)00007-7] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genomic imprinting is an epigenetic mechanism of transcriptional regulation through which expression of a subset of mammalian genes is restricted to one parental allele. An intriguing characteristic of imprinted genes is that they often cluster in megabase-sized chromosomal domains, indicating that domain-specific mechanisms regulate imprinting. Detailed study of the known imprinted domains has revealed a number of common characteristics. First, all clusters have an imprinting control region (ICR) that is typically 1-5 kb in size and differentially methylated, and that regulates imprinting across the entire domain. Second, the clusters have at least one noncoding RNA (ncRNA) that is usually expressed from the maternal allele and multiple paternally expressed protein-coding genes. Finally, the clusters are likely regulated by one of two mechanisms, transcription of a long ncRNA that silences expression of protein-coding genes bidirectionally in cis and blocking of shared enhancer elements by CCCTC binding factor (CTCF) binding insulators. More recent experiments may even suggest that both mechanisms operate at some clusters. In this chapter, we will describe what is known about imprinting at five well-studied imprinted loci and highlight some of the critical experiments that are required before a full understanding of imprinting mechanisms is achieved.
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Affiliation(s)
- Le-Ben Wan
- Department of Cell and Developmental Biology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA
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Takeda H, Caiment F, Smit M, Hiard S, Tordoir X, Cockett N, Georges M, Charlier C. The callipyge mutation enhances bidirectional long-range DLK1-GTL2 intergenic transcription in cis. Proc Natl Acad Sci U S A 2006; 103:8119-24. [PMID: 16690740 PMCID: PMC1472439 DOI: 10.1073/pnas.0602844103] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The callipyge mutation (CLPG) is an A to G transition that affects a muscle-specific long-range control element located in the middle of the 90-kb DLK1-GTL2 intergenic (IG) region. It causes ectopic expression of a 327-kb cluster of imprinted genes in skeletal muscle, resulting in the callipyge muscular hypertrophy and its non-Mendelian inheritance pattern known as polar overdominance. We herein demonstrate that the CLPG mutation alters the muscular epigenotype of the DLK1-GTL2 IG region in cis, including hypomethylation, acquisition of novel DNase-I hypersentivite sites, and, most strikingly, strongly enhanced bidirectional, long-range IG transcription. The callipyge phenotype thus emerges as a unique model to study the functional significance of IG transcription, which recently has proven to be a widespread, yet elusive, feature of the mammalian genome.
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Affiliation(s)
- Haruko Takeda
- *Unit of Animal Genetics, Faculty of Veterinary Medicine and Centre of Biomedical Integrative Genoproteomics (CBIG), University of Liège (B43), 20 Boulevard de Colonster, 4000-Liège, Belgium
| | - Florian Caiment
- *Unit of Animal Genetics, Faculty of Veterinary Medicine and Centre of Biomedical Integrative Genoproteomics (CBIG), University of Liège (B43), 20 Boulevard de Colonster, 4000-Liège, Belgium
| | - Maria Smit
- Animal, Dairy, and Veterinary Sciences, College of Agriculture, Utah State University, Logan, UT 84322-4700; and
| | - Samuel Hiard
- Research Unit in Systems and Modelling, Department of Electrical Engineering and Computer Science and CBIG, Faculty of Applied Sciences, University of Liège (B29), 4000-Liège, Belgium
| | - Xavier Tordoir
- *Unit of Animal Genetics, Faculty of Veterinary Medicine and Centre of Biomedical Integrative Genoproteomics (CBIG), University of Liège (B43), 20 Boulevard de Colonster, 4000-Liège, Belgium
| | - Noelle Cockett
- Animal, Dairy, and Veterinary Sciences, College of Agriculture, Utah State University, Logan, UT 84322-4700; and
| | - Michel Georges
- *Unit of Animal Genetics, Faculty of Veterinary Medicine and Centre of Biomedical Integrative Genoproteomics (CBIG), University of Liège (B43), 20 Boulevard de Colonster, 4000-Liège, Belgium
- To whom correspondence should be addressed. E-mail:
| | - Carole Charlier
- *Unit of Animal Genetics, Faculty of Veterinary Medicine and Centre of Biomedical Integrative Genoproteomics (CBIG), University of Liège (B43), 20 Boulevard de Colonster, 4000-Liège, Belgium
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