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Newman T, Ishihara T, Shaw G, Renfree MB. The structure of the TH/INS locus and the parental allele expressed are not conserved between mammals. Heredity (Edinb) 2024; 133:21-32. [PMID: 38834866 PMCID: PMC11222543 DOI: 10.1038/s41437-024-00689-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 06/06/2024] Open
Abstract
Parent-of-origin-specific expression of imprinted genes is critical for successful mammalian growth and development. Insulin, coded by the INS gene, is an important growth factor expressed from the paternal allele in the yolk sac placenta of therian mammals. The tyrosine hydroxylase gene TH encodes an enzyme involved in dopamine synthesis. TH and INS are closely associated in most vertebrates, but the mouse orthologues, Th and Ins2, are separated by repeated DNA. In mice, Th is expressed from the maternal allele, but the parental origin of expression is not known for any other mammal so it is unclear whether the maternal expression observed in the mouse represents an evolutionary divergence or an ancestral condition. We compared the length of the DNA segment between TH and INS across species and show that separation of these genes occurred in the rodent lineage with an accumulation of repeated DNA. We found that the region containing TH and INS in the tammar wallaby produces at least five distinct RNA transcripts: TH, TH-INS1, TH-INS2, lncINS and INS. Using allele-specific expression analysis, we show that the TH/INS locus is expressed from the paternal allele in pre- and postnatal tammar wallaby tissues. Determining the imprinting pattern of TH/INS in other mammals might clarify if paternal expression is the ancestral condition which has been flipped to maternal expression in rodents by the accumulation of repeat sequences.
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Affiliation(s)
- Trent Newman
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Teruhito Ishihara
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
- Epigenetics Programme, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Geoff Shaw
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, VIC, Australia.
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2
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Bogutz AB, Oh-McGinnis R, Jacob KJ, Ho-Lau R, Gu T, Gertsenstein M, Nagy A, Lefebvre L. Transcription factor ASCL2 is required for development of the glycogen trophoblast cell lineage. PLoS Genet 2018; 14:e1007587. [PMID: 30096149 PMCID: PMC6105033 DOI: 10.1371/journal.pgen.1007587] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/22/2018] [Accepted: 07/24/2018] [Indexed: 12/22/2022] Open
Abstract
The basic helix-loop-helix (bHLH) transcription factor ASCL2 plays essential roles in diploid multipotent trophoblast progenitors, intestinal stem cells, follicular T-helper cells, as well as during epidermal development and myogenesis. During early development, Ascl2 expression is regulated by genomic imprinting and only the maternally inherited allele is transcriptionally active in trophoblast. The paternal allele-specific silencing of Ascl2 requires expression of the long non-coding RNA Kcnq1ot1 in cis and the deposition of repressive histone marks. Here we show that Del7AI, a 280-kb deletion allele neighboring Ascl2, interferes with this process in cis and leads to a partial loss of silencing at Ascl2. Genetic rescue experiments show that the low level of Ascl2 expression from the paternal Del7AI allele can rescue the embryonic lethality associated with maternally inherited Ascl2 mutations, in a level-dependent manner. Despite their ability to support development to term, the rescued placentae have a pronounced phenotype characterized by severe hypoplasia of the junctional zone, expansion of the parietal trophoblast giant cell layer, and complete absence of invasive glycogen trophoblast cells. Transcriptome analysis of ectoplacental cones at E7.5 and differentiation assays of Ascl2 mutant trophoblast stem cells show that ASCL2 is required for the emergence or early maintenance of glycogen trophoblast cells during development. Our work identifies a new cis-acting mutation interfering with Kcnq1ot1 silencing function and establishes a novel critical developmental role for the transcription factor ASCL2. By controlling precise networks of target genes, transcription factors play important roles in cell fate determination during development. The Ascl2 gene codes for a transcription factor essential for the maintenance of progenitor cell populations able to differentiate into specialized cell types in the intestine and in the extra-embryonic trophoblast lineage. The trophoblast is an essential component of the placenta, an organ required for development of the embryo in placental mammals. Ascl2 belongs to a group of unusual genes, called imprinted genes, which are expressed from only a single parental copy. Ascl2 is only expressed from the maternally inherited copy in the trophoblast, the paternal copy being kept silent. Here, we describe an engineered deletion neighboring Ascl2 that interferes with the complete silencing of the paternal copy of the gene. We show that the low amount of ASCL2 produced from this deletion can rescue the embryonic lethality associated with non-functional maternal copies of Ascl2. Although the rescued embryos can often survive to term, their placenta is highly disorganized and lacks members of a specific cell lineage, the trophoblast glycogen cells. By analyzing the transcriptional profile of mutant trophoblast progenitors in vivo and of differentiated trophoblast stem cells, we show that ASCL2 plays a very early role in the formation of this cell lineage.
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Affiliation(s)
- Aaron B. Bogutz
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
| | - Rosemary Oh-McGinnis
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
| | - Karen J. Jacob
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
| | - Rita Ho-Lau
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ting Gu
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
| | - Marina Gertsenstein
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Louis Lefebvre
- Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia, Vancouver, BC, Canada
- * E-mail:
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Sachani SS, Landschoot LS, Zhang L, White CR, MacDonald WA, Golding MC, Mann MRW. Nucleoporin 107, 62 and 153 mediate Kcnq1ot1 imprinted domain regulation in extraembryonic endoderm stem cells. Nat Commun 2018; 9:2795. [PMID: 30022050 PMCID: PMC6052020 DOI: 10.1038/s41467-018-05208-2] [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: 09/28/2016] [Accepted: 06/21/2018] [Indexed: 12/19/2022] Open
Abstract
Genomic imprinting is a phenomenon that restricts transcription to predominantly one parental allele. How this transcriptional duality is regulated is poorly understood. Here we perform an RNA interference screen for epigenetic factors involved in paternal allelic silencing at the Kcnq1ot1 imprinted domain in mouse extraembryonic endoderm stem cells. Multiple factors are identified, including nucleoporin 107 (NUP107). To determine NUP107's role and specificity in Kcnq1ot1 imprinted domain regulation, we deplete Nup107, as well as Nup62, Nup98/96 and Nup153. Nup107, Nup62 and Nup153, but not Nup98/96 depletion, reduce Kcnq1ot1 noncoding RNA volume, displace the Kcnq1ot1 domain from the nuclear periphery, reactivate a subset of normally silent paternal alleles in the domain, alter histone modifications with concomitant changes in KMT2A, EZH2 and EHMT2 occupancy, as well as reduce cohesin interactions at the Kcnq1ot1 imprinting control region. Our results establish an important role for specific nucleoporins in mediating Kcnq1ot1 imprinted domain regulation.
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Affiliation(s)
- Saqib S Sachani
- Departments of Obstetrics & Gynaecology, and Biochemistry, Western University, Schulich School of Medicine and Dentistry, London, ON, N6A 5W9, Canada
- Children's Health Research Institute, London, ON, N6C 2V5, Canada
- Departments of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Magee-Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Lauren S Landschoot
- Departments of Obstetrics & Gynaecology, and Biochemistry, Western University, Schulich School of Medicine and Dentistry, London, ON, N6A 5W9, Canada
- Children's Health Research Institute, London, ON, N6C 2V5, Canada
| | - Liyue Zhang
- Departments of Obstetrics & Gynaecology, and Biochemistry, Western University, Schulich School of Medicine and Dentistry, London, ON, N6A 5W9, Canada
- Children's Health Research Institute, London, ON, N6C 2V5, Canada
| | - Carlee R White
- Departments of Obstetrics & Gynaecology, and Biochemistry, Western University, Schulich School of Medicine and Dentistry, London, ON, N6A 5W9, Canada
- Children's Health Research Institute, London, ON, N6C 2V5, Canada
| | - William A MacDonald
- Departments of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- Magee-Womens Research Institute, Pittsburgh, PA, 15213, USA
| | - Michael C Golding
- Department of Veterinary Physiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Mellissa R W Mann
- Departments of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- Magee-Womens Research Institute, Pittsburgh, PA, 15213, USA.
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Van de Pette M, Abbas A, Feytout A, McNamara G, Bruno L, To WK, Dimond A, Sardini A, Webster Z, McGinty J, Paul EJ, Ungless MA, French PMW, Withers DJ, Uren A, Ferguson-Smith AC, Merkenschlager M, John RM, Fisher AG. Visualizing Changes in Cdkn1c Expression Links Early-Life Adversity to Imprint Mis-regulation in Adults. Cell Rep 2017; 18:1090-1099. [PMID: 28147266 PMCID: PMC5300902 DOI: 10.1016/j.celrep.2017.01.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 12/22/2016] [Accepted: 01/07/2017] [Indexed: 12/13/2022] Open
Abstract
Imprinted genes are regulated according to parental origin and can influence embryonic growth and metabolism and confer disease susceptibility. Here, we designed sensitive allele-specific reporters to non-invasively monitor imprinted Cdkn1c expression in mice and showed that expression was modulated by environmental factors encountered in utero. Acute exposure to chromatin-modifying drugs resulted in de-repression of paternally inherited (silent) Cdkn1c alleles in embryos that was temporary and resolved after birth. In contrast, deprivation of maternal dietary protein in utero provoked permanent de-repression of imprinted Cdkn1c expression that was sustained into adulthood and occurred through a folate-dependent mechanism of DNA methylation loss. Given the function of imprinted genes in regulating behavior and metabolic processes in adults, these results establish imprinting deregulation as a credible mechanism linking early-life adversity to later-life outcomes. Furthermore, Cdkn1c-luciferase mice offer non-invasive tools to identify factors that disrupt epigenetic processes and strategies to limit their long-term impact. Allele-specific expression of imprinted Cdkn1c imaged in vivo using bioluminescence Chromatin-modifying drugs applied in utero transiently de-repress Cdkn1c imprinting In utero exposure to low-protein diet permanently disrupts the Cdkn1c imprint Folate supplements during gestation protect against loss of Cdkn1c imprinting
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Affiliation(s)
- Mathew Van de Pette
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Allifia Abbas
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Amelie Feytout
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Gráinne McNamara
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Ludovica Bruno
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Wilson K To
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Andrew Dimond
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Alessandro Sardini
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Zoe Webster
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - James McGinty
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London SW7 2AZ, UK
| | - Eleanor J Paul
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Mark A Ungless
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Blackett Laboratory, Imperial College London, London SW7 2AZ, UK
| | - Dominic J Withers
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Anthony Uren
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Matthias Merkenschlager
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Rosalind M John
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Amanda G Fisher
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
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5
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Long non-coding RNAs: Mechanism of action and functional utility. Noncoding RNA Res 2016; 1:43-50. [PMID: 30159410 PMCID: PMC6096411 DOI: 10.1016/j.ncrna.2016.11.002] [Citation(s) in RCA: 181] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 12/22/2022] Open
Abstract
Recent RNA sequencing studies have revealed that most of the human genome is transcribed, but very little of the total transcriptomes has the ability to encode proteins. Long non-coding RNAs (lncRNAs) are non-coding transcripts longer than 200 nucleotides. Members of the non-coding genome include microRNA (miRNA), small regulatory RNAs and other short RNAs. Most of long non-coding RNA (lncRNAs) are poorly annotated. Recent recognition about lncRNAs highlights their effects in many biological and pathological processes. LncRNAs are dysfunctional in a variety of human diseases varying from cancerous to non-cancerous diseases. Characterization of these lncRNA genes and their modes of action may allow their use for diagnosis, monitoring of progression and targeted therapies in various diseases. In this review, we summarize the functional perspectives as well as the mechanism of action of lncRNAs.
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6
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Massah S, Beischlag TV, Prefontaine GG. Epigenetic events regulating monoallelic gene expression. Crit Rev Biochem Mol Biol 2015; 50:337-58. [PMID: 26155735 DOI: 10.3109/10409238.2015.1064350] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In mammals, generally it is assumed that the genes inherited from each parent are expressed to similar levels. However, it is now apparent that in non-sex chromosomes, 6-10% of genes are selected for monoallelic expression. Monoallelic expression or allelic exclusion is established either in an imprinted (parent-of-origin) or a stochastic manner. The stochastic model explains random selection while the imprinted model describes parent-of-origin specific selection of alleles for expression. Allelic exclusion occurs during X chromosome inactivation, parent-of-origin expression of imprinted genes and stochastic monoallelic expression of cell surface molecules, clustered protocadherin (PCDH) genes. Mis-regulation or loss of allelic exclusion contributes to developmental diseases. Epigenetic mechanisms are fundamental players that determine this type of expression despite a homogenous genetic background. DNA methylation and histone modifications are two mediators of the epigenetic phenomena. The majority of DNA methylation is found on cytosines of the CpG dinucleotide in mammals. Several covalent modifications of histones change the electrostatic forces between DNA and histones modifying gene expression. Long-range chromatin interactions organize chromatin into transcriptionally permissive and prohibitive regions leading to simultaneous regulation of gene expression and repression. Non-coding RNAs (ncRNAs) are also players in regulating gene expression. Together, these epigenetic mechanisms fine-tune gene expression levels essential for normal development and survival. In this review, first we discuss what is known about monoallelic gene expression. Then, we focus on the molecular mechanisms that regulate expression of three monoallelically expressed gene classes: the X-linked genes, selected imprinted genes and PCDH genes.
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Affiliation(s)
- Shabnam Massah
- a The Faculty of Health Sciences , Simon Fraser University , Burnaby , BC , Canada
| | - Timothy V Beischlag
- a The Faculty of Health Sciences , Simon Fraser University , Burnaby , BC , Canada
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7
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MacDonald WA, Sachani SS, White CR, Mann MRW. A role for chromatin topology in imprinted domain regulation. Biochem Cell Biol 2015. [PMID: 26222733 DOI: 10.1139/bcb-2015-0032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.
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Affiliation(s)
- William A MacDonald
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Saqib S Sachani
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Carlee R White
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Mellissa R W Mann
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
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8
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Cao J. The functional role of long non-coding RNAs and epigenetics. Biol Proced Online 2014; 16:11. [PMID: 25276098 PMCID: PMC4177375 DOI: 10.1186/1480-9222-16-11] [Citation(s) in RCA: 249] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/06/2014] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, involving in diverse cellular processes. The regulation of gene expression by lncRNAs at the epigenetic level, transcriptional and post-transcriptional level have been well known and widely studied. Recent recognition that lncRNAs make effects in many biological and pathological processes such as stem cell pluripotency, neurogenesis, oncogenesis and etc. This review will focus on the functional roles of lncRNAs in epigenetics and related research progress will be summarized.
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Affiliation(s)
- Jinneng Cao
- Department of respiratory medicine, Fuyong People's Hospital, Baoan District, Shenzhen 518103, Guangdong, People's Republic of China
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9
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Xu Z, Lefevre GM, Felsenfeld G. Chromatin structure, epigenetic mechanisms and long-range interactions in the human insulin locus. Diabetes Obes Metab 2012; 14 Suppl 3:1-11. [PMID: 22928559 PMCID: PMC6398329 DOI: 10.1111/j.1463-1326.2012.01645.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Regulation of gene expression in eukaryotes is largely dependent on variations in chromatin structure. More recently, it has become clear that this may involve not only local chromatin organization but also distant regulatory elements that participate in large-scale chromatin architecture within the nucleus. We describe recent methods that make possible the detection of such structures and apply them to analysis of the human insulin (INS) locus in pancreatic islets. We show that the INS gene is part of an extended 'open' chromatin domain that includes adjacent genes as well. We also find that in islets, the INS promoter is in physical contact with distant sites on the same human chromosome and notably, with the SYT8 gene, located nearly 300 kb away. The strength of the contact between INS and SYT8 is increased by glucose, and this results in stimulation of SYT8 expression. Inhibition of INS transcription decreases SYT8 expression. Furthermore, downregulation of SYT8 results in decreased secretion of insulin. Our results thus establish the existence of a regulatory network between the INS gene and other distant genes through long-range physical interactions, and suggest that such networks may have general importance for insulin biology and diabetes.
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Affiliation(s)
- Z Xu
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Lefebvre L. The placental imprintome and imprinted gene function in the trophoblast glycogen cell lineage. Reprod Biomed Online 2012; 25:44-57. [PMID: 22560119 DOI: 10.1016/j.rbmo.2012.03.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/08/2012] [Accepted: 03/14/2012] [Indexed: 10/28/2022]
Abstract
Imprinted genes represent a unique class of autosomal genes expressed from only one of the parental alleles during development. The choice of the expressed allele is not random but rather is determined by the parental origin of the allele. Consequently, the mouse genome contains more than 100 genes expressed preferentially or exclusively from the maternally or the paternally inherited allele. Current research efforts are focused on understanding the molecular mechanism of this epigenetic phenomenon as well as the biological functions of the genes under its regulation. Both theoretical considerations and experimental results support a role for genomic imprinting in the regulation of embryonic growth and placental biology. In this review, recent efforts to establish the complete set of genes showing imprinted expression in the mouse placenta are first discussed. Then, the evidence suggesting that imprinted genes might be implicated in the emergence, maintenance and function of trophoblast glycogen cells is presented. Although the origin and functions of this trophoblast cell lineage are currently unknown, the analysis of mutations in imprinted genes in the mouse are providing new insights into these issues. The implications of this work for placental pathologies in human are also discussed.
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Affiliation(s)
- Louis Lefebvre
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, University of British Columbia, Vancouver, Canada.
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11
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Zuo X, Sheng J, Lau HT, McDonald CM, Andrade M, Cullen DE, Bell FT, Iacovino M, Kyba M, Xu G, Li X. Zinc finger protein ZFP57 requires its co-factor to recruit DNA methyltransferases and maintains DNA methylation imprint in embryonic stem cells via its transcriptional repression domain. J Biol Chem 2011; 287:2107-18. [PMID: 22144682 DOI: 10.1074/jbc.m111.322644] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Previously, we discovered that ZFP57 is a maternal-zygotic effect gene, and it maintains DNA methylation genomic imprint at multiple imprinted regions in mouse embryos. Despite these findings, it remains elusive how DNA methyltransferases are targeted to the imprinting control regions to initiate and maintain DNA methylation imprint. To gain insights into these essential processes in genomic imprinting, we examined how ZFP57 maintains genomic DNA methylation imprint in mouse embryonic stem (ES) cells. Here we demonstrate that the loss of ZFP57 in mouse ES cells led to a complete loss of genomic DNA methylation imprint at multiple imprinted regions, similar to its role in mouse embryos. However, reintroduction of ZFP57 into Zfp57-null ES cells did not result in reacquisition of DNA methylation imprint, suggesting that the memory for genomic imprinting had been lost or altered in Zfp57-null ES cells in culture. Interestingly, ZFP57 and DNA methyltransferases could form complexes in the presence of KAP1/TRIM28/TIF1β when co-expressed in COS cells. We also found that the wild-type exogenous ZFP57 but not the mutant ZFP57 lacking the KRAB box that interacts with its co-factor KAP1/TRIM28/TIF1β could substitute for the endogenous ZFP57 in maintaining the DNA methylation imprint in ES cells. These results suggest that ZFP57 may recruit DNA methyltransferases to its target regions to maintain DNA methylation imprint, and this interaction is likely facilitated by KAP1/TRIM28/TIF1β.
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Affiliation(s)
- Xiaopan Zuo
- Black Family Stem Cell Institute, Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York 10029, USA
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Golding MC, Magri LS, Zhang L, Lalone SA, Higgins MJ, Mann MRW. Depletion of Kcnq1ot1 non-coding RNA does not affect imprinting maintenance in stem cells. Development 2011; 138:3667-78. [PMID: 21775415 PMCID: PMC3152924 DOI: 10.1242/dev.057778] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2011] [Indexed: 01/18/2023]
Abstract
To understand the complex regulation of genomic imprinting it is important to determine how early embryos establish imprinted gene expression across large chromosomal domains. Long non-coding RNAs (ncRNAs) have been associated with the regulation of imprinting domains, yet their function remains undefined. Here, we investigated the mouse Kcnq1ot1 ncRNA and its role in imprinted gene regulation during preimplantation development by utilizing mouse embryonic and extra-embryonic stem cell models. Our findings demonstrate that the Kcnq1ot1 ncRNA extends 471 kb from the transcription start site. This is significant as it raises the possibility that transcription through downstream genes might play a role in their silencing, including Th, which we demonstrate possesses maternal-specific expression during early development. To distinguish between a functional role for the transcript and properties inherent to transcription of long ncRNAs, we employed RNA interference-based technology to deplete Kcnq1ot1 transcripts. We hypothesized that post-transcriptional depletion of Kcnq1ot1 ncRNA would lead to activation of normally maternal-specific protein-coding genes on the paternal chromosome. Post-transcriptional short hairpin RNA-mediated depletion in embryonic stem, trophoblast stem and extra-embryonic endoderm stem cells had no observable effect on the imprinted expression of genes within the domain, or on Kcnq1ot1 imprinting center DNA methylation, although a significant decrease in Kcnq1ot1 RNA signal volume in the nucleus was observed. These data support the argument that it is the act of transcription that plays a role in imprint maintenance during early development rather than a post-transcriptional role for the RNA itself.
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Affiliation(s)
- Michael C. Golding
- Departments of Obstetrics and Gynecology and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON N6A 5W9, Canada
- Children's Health Research Institute, London, ON N6C 2V5, Canada
- Lawson Health Research Institute, London, ON N6C 2V5, Canada
| | - Lauren S. Magri
- Departments of Obstetrics and Gynecology and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON N6A 5W9, Canada
- Children's Health Research Institute, London, ON N6C 2V5, Canada
- Lawson Health Research Institute, London, ON N6C 2V5, Canada
| | - Liyue Zhang
- Children's Health Research Institute, London, ON N6C 2V5, Canada
- Lawson Health Research Institute, London, ON N6C 2V5, Canada
| | - Sarah A. Lalone
- Departments of Obstetrics and Gynecology and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON N6A 5W9, Canada
- Children's Health Research Institute, London, ON N6C 2V5, Canada
- Lawson Health Research Institute, London, ON N6C 2V5, Canada
| | - Michael J. Higgins
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Mellissa R. W. Mann
- Departments of Obstetrics and Gynecology and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON N6A 5W9, Canada
- Children's Health Research Institute, London, ON N6C 2V5, Canada
- Lawson Health Research Institute, London, ON N6C 2V5, Canada
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