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Johnson ND, Cutler DJ, Conneely KN. Investigating the potential of single-cell DNA methylation data to detect allele-specific methylation and imprinting. Am J Hum Genet 2024; 111:654-667. [PMID: 38471507 PMCID: PMC11023823 DOI: 10.1016/j.ajhg.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Allele-specific methylation (ASM) is an epigenetic modification whereby one parental allele becomes methylated and the other unmethylated at a specific locus. ASM is most often driven by the presence of nearby heterozygous variants that influence methylation, but also occurs somatically in the context of genomic imprinting. In this study, we investigate ASM using publicly available single-cell reduced representation bisulfite sequencing (scRRBS) data on 608 B cells sampled from six healthy B cell samples and 1,230 cells from 11 chronic lymphocytic leukemia (CLL) samples. We developed a likelihood-based criterion to test whether a CpG exhibited ASM, based on the distributions of methylated and unmethylated reads both within and across cells. Applying our likelihood ratio test, 65,998 CpG sites exhibited ASM in healthy B cell samples according to a Bonferroni criterion (p < 8.4 × 10-9), and 32,862 CpG sites exhibited ASM in CLL samples (p < 8.5 × 10-9). We also called ASM at the sample level. To evaluate the accuracy of our method, we called heterozygous variants from the scRRBS data, which enabled variant-based calls of ASM within each cell. Comparing sample-level ASM calls to the variant-based measures of ASM, we observed a positive predictive value of 76%-100% across samples. We observed high concordance of ASM across samples and an overrepresentation of ASM in previously reported imprinted genes and genes with imprinting binding motifs. Our study demonstrates that single-cell bisulfite sequencing is a potentially powerful tool to investigate ASM, especially as studies expand to increase the number of samples and cells sequenced.
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Affiliation(s)
- Nicholas D Johnson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA; Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA; Population Biology, Ecology, and Evolution Program, Emory University, Atlanta, GA, USA.
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2
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Darneau D, Giabicani E, Netchine I, Pham A. Perinatal features of children with Silver-Russell syndrome due to 11p15 loss of methylation. Front Pediatr 2024; 12:1367433. [PMID: 38638586 PMCID: PMC11024461 DOI: 10.3389/fped.2024.1367433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 03/19/2024] [Indexed: 04/20/2024] Open
Abstract
Background A diagnosis of Silver-Russell syndrome (SRS), a rare imprinting disorder responsible for foetal growth restriction, is considered for patients presenting at least four criteria of the Netchine-Harbison clinical scoring system (NH-CSS). Certain items of the NH-CSS are not assessable until the age of 2 years. The objective was to determine perinatal characteristics of children with SRS to allow an early diagnosis. Methods We retrospectively compared the perinatal characteristics of children with SRS (n = 17) with those of newborns small for gestational age (SGA) due to placental insufficiency (PI) (n = 21). Results Children with SRS showed earlier and more severely altered foetal biometry than SGA newborns due to PI. Twenty-three percent of patients with SRS showed uterine artery Doppler anomalies. SRS children were significantly smaller at birth (birth length <-3 SDS in 77% of cases in the SRS group vs. 15% in the PI group, p = 0.0001). Conclusion The diagnosis of SRS must be evoked in the neonatal period for SGA newborns with a growth delay present from the second trimester of pregnancy, a birth length <-3 SDS and a relative macrocephaly. Doppler anomalies, classically used to orient the cause of SGA towards PI, did not rule out the diagnosis of SRS.
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Affiliation(s)
- Diane Darneau
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, APHP, Hôpital Armand Trousseau, Endocrinologie Moléculaire et Pathologies d’Empreinte, Paris, France
| | - Eloïse Giabicani
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, APHP, Hôpital Armand Trousseau, Endocrinologie Moléculaire et Pathologies d’Empreinte, Paris, France
| | - Irène Netchine
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, APHP, Hôpital Armand Trousseau, Endocrinologie Moléculaire et Pathologies d’Empreinte, Paris, France
| | - Aurélie Pham
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, APHP, Hôpital Armand Trousseau, Service de Néonatologie, Paris, France
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3
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Page L, Younge N, Freemark M. Hormonal Determinants of Growth and Weight Gain in the Human Fetus and Preterm Infant. Nutrients 2023; 15:4041. [PMID: 37764824 PMCID: PMC10537367 DOI: 10.3390/nu15184041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
The factors controlling linear growth and weight gain in the human fetus and newborn infant are poorly understood. We review here the changes in linear growth, weight gain, lean body mass, and fat mass during mid- and late gestation and the early postnatal period in the context of changes in the secretion and action of maternal, placental, fetal, and neonatal hormones, growth factors, and adipocytokines. We assess the effects of hormonal determinants on placental nutrient delivery and the impact of preterm delivery on hormone expression and postnatal growth and metabolic function. We then discuss the effects of various maternal disorders and nutritional and pharmacologic interventions on fetal and perinatal hormone and growth factor production, growth, and fat deposition and consider important unresolved questions in the field.
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Affiliation(s)
- Laura Page
- Division of Pediatric Endocrinology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Noelle Younge
- Neonatology, Duke University Medical Center, Durham, NC 27710, USA;
| | - Michael Freemark
- Division of Pediatric Endocrinology, Duke University Medical Center, Durham, NC 27710, USA;
- The Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
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Wang T, Li J, Yang L, Wu M, Ma Q. The Role of Long Non-coding RNAs in Human Imprinting Disorders: Prospective Therapeutic Targets. Front Cell Dev Biol 2021; 9:730014. [PMID: 34760887 PMCID: PMC8573313 DOI: 10.3389/fcell.2021.730014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022] Open
Abstract
Genomic imprinting is a term used for an intergenerational epigenetic inheritance and involves a subset of genes expressed in a parent-of-origin-dependent way. Imprinted genes are expressed preferentially from either the paternally or maternally inherited allele. Long non-coding RNAs play essential roles in regulating this allele-specific expression. In several well-studied imprinting clusters, long non-coding RNAs have been found to be essential in regulating temporal- and spatial-specific establishment and maintenance of imprinting patterns. Furthermore, recent insights into the epigenetic pathological mechanisms underlying human genomic imprinting disorders suggest that allele-specific expressed imprinted long non-coding RNAs serve as an upstream regulator of the expression of other protein-coding or non-coding imprinted genes in the same cluster. Aberrantly expressed long non-coding RNAs result in bi-allelic expression or silencing of neighboring imprinted genes. Here, we review the emerging roles of long non-coding RNAs in regulating the expression of imprinted genes, especially in human imprinting disorders, and discuss three strategies targeting the central long non-coding RNA UBE3A-ATS for the purpose of developing therapies for the imprinting disorders Prader-Willi syndrome and Angelman syndrome. In summary, a better understanding of long non-coding RNA-related mechanisms is key to the development of potential therapeutic targets for human imprinting disorders.
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Affiliation(s)
- Tingxuan Wang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jianjian Li
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liuyi Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Manyin Wu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qing Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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5
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Zhang Y, Xia Q, Lin J. LncRNA H19 Attenuates Apoptosis in MPTP-Induced Parkinson’s Disease Through Regulating miR-585-3p/PIK3R3. Neurochem Res 2020; 45:1700-10. [DOI: 10.1007/s11064-020-03035-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/09/2020] [Accepted: 04/15/2020] [Indexed: 12/21/2022]
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Masunaga Y, Inoue T, Yamoto K, Fujisawa Y, Sato Y, Kawashima-Sonoyama Y, Morisada N, Iijima K, Ohata Y, Namba N, Suzumura H, Kuribayashi R, Yamaguchi Y, Yoshihashi H, Fukami M, Saitsu H, Kagami M, Ogata T. IGF2 Mutations. J Clin Endocrinol Metab 2020; 105:5572642. [PMID: 31544945 DOI: 10.1210/clinem/dgz034] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE IGF2 is a paternally expressed growth-promoting gene. Here, we report five cases with IGF2 mutations and review IGF2 mutation-positive patients described in the literature. We also compare clinical features between patients with IGF2 mutations and those with H19/IGF2:IG-DMR epimutations. RESULTS We recruited five cases with IGF2 mutations: case 1 with a splice site mutation (c.-6-1G>C) leading to skipping of exon 2 and cases 2-5 with different missense mutations (p.(Cys70Tyr), p.(Cys71Arg), p.(Cys33Ser), and p.(Cys45Ser)) affecting cysteine residues involved in the S-S bindings. All the mutations resided on the paternally inherited allele, and the mutation of case 5 was present in a mosaic condition. Clinical assessment revealed Silver-Russell syndrome (SRS) phenotype with Netchine-Harbison scores of ≥5/6 in all the apparently nonmosaic 14 patients with IGF2 mutations (cases 1-4 described in this study and 10 patients reported in the literature). Furthermore, compared with H19/IGF2:IG-DMR epimutations, IGF2 mutations were associated with low frequency of hemihypoplasia, high frequency of feeding difficulty and/or reduced body mass index, and mild degree of relative macrocephaly, together with occasional development of severe limb malformations, high frequency of cardiovascular anomalies and developmental delay, and low serum IGF-II values. CONCLUSIONS This study indicates that IGF2 mutations constitute a rare but important cause of SRS. Furthermore, while both IGF2 mutations and H19/IGF2:IG-DMR epimutations lead to SRS, a certain degree of phenotypic difference is observed between the two groups, probably due to the different IGF2 expression pattern in target tissues.
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Affiliation(s)
- Yohei Masunaga
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takanobu Inoue
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kaori Yamoto
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yasuko Fujisawa
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yasuhiro Sato
- Department of Pediatrics, Teikyo University School of Medicine, Tokyo, Japan
| | - Yuki Kawashima-Sonoyama
- Division of Pediatrics and Perinatology, Faculty of Medicine Tottori University, Yonago, Japan
| | - Naoya Morisada
- Department of Clinical Genetics, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yasuhisa Ohata
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Noriyuki Namba
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Pediatrics, Osaka Hospital, Japan Community Healthcare Organization, Osaka, Japan
| | - Hiroshi Suzumura
- Department of Pediatrics, Dokkyo Medical University, Mibu, Japan
| | | | - Yu Yamaguchi
- Department of Genetics, Gunma Children's Medical Center, Shibukawa, Japan
| | - Hiroshi Yoshihashi
- Department of Clinical Genetics, Tokyo Metropolitan Children's Medical Center, Fuchu, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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7
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Giabicani E, Chantot-Bastaraud S, Bonnard A, Rachid M, Whalen S, Netchine I, Brioude F. Roles of Type 1 Insulin-Like Growth Factor (IGF) Receptor and IGF-II in Growth Regulation: Evidence From a Patient Carrying Both an 11p Paternal Duplication and 15q Deletion. Front Endocrinol (Lausanne) 2019; 10:263. [PMID: 31114545 PMCID: PMC6503735 DOI: 10.3389/fendo.2019.00263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/09/2019] [Indexed: 12/23/2022] Open
Abstract
We report an original association of complex genetic defects in a patient carrying both an 11p paternal duplication, resulting in the double expression of insulin-like growth factor 2 (IGF2), as reported in Beckwith-Wiedemann syndrome, and a 15q terminal deletion, including the type 1 IGF receptor gene (IGF1R), resulting in haploinsufficiency for this gene. The patient was born with measurements appropriate for her gestational age but experienced growth retardation in early childhood, allowing a better comprehension of the IGF system in the pathophysiology of growth. It is possible that IGF-II plays a key role in fetal growth, independently of IGF1R signaling, and that its role is less important in post-natal growth, leaving IGF-I and growth hormone as the main actors.
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Affiliation(s)
- Eloïse Giabicani
- Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, APHP, Hôpital Armand Trousseau, Explorations Fonctionnelles Endocriniennes, Paris, France
- *Correspondence: Eloïse Giabicani
| | - Sandra Chantot-Bastaraud
- Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, APHP, Hôpital Armand Trousseau, Explorations Fonctionnelles Endocriniennes, Paris, France
- APHP, Hôpital Armand Trousseau, Département de Génétique, UF de Génétique Chromosomique, Paris, France
| | - Adeline Bonnard
- APHP, Hôpital Armand Trousseau, Département de Génétique, UF de Génétique Chromosomique, Paris, France
| | - Myriam Rachid
- APHP, Hôpital Armand Trousseau, Département de Génétique, UF de Génétique Chromosomique, Paris, France
| | - Sandra Whalen
- AP-HP, Hôpital Armand Trousseau, Department of Medical Genetics and Centre de Référence Anomalies du Développement et Syndromes Malformatifs et Déficiences Intellectuelles de Causes rares, Paris, France
| | - Irène Netchine
- Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, APHP, Hôpital Armand Trousseau, Explorations Fonctionnelles Endocriniennes, Paris, France
| | - Frédéric Brioude
- Sorbonne Université, INSERM, Centre de Recherche Saint Antoine, APHP, Hôpital Armand Trousseau, Explorations Fonctionnelles Endocriniennes, Paris, France
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Abstract
The change of cellular glycosylation is one of the key events in malignant transformation and neoplastic progression, and tumor-related glycosylation alterations are promising targets in both tumor diagnosis and therapy. Both malignant transformation and neoplastic progression are the consequence of gene expression alterations and alterations in protein expression. Micro environmental factors such as extracellular matrix (ECM) also play an important role in their growth and metastasis. Tumor-associated glycans are important biomarker candidates for cancer diagnosis and prognosis, and analytical methods for their detection were developed recently. Glycoproteomics that use mass spectrometry for identification of cancer antigens and structural analysis of glycans play a key role in the investigation of changes of glycosylation during malignant transformation and tumor development and metastasis. Deep understanding of glycan remodeling in cancer and the role of glycosyltransferases that are involved in this process will require a detailed profiling of glycosylation patterns of tumor cells, and corresponding analytical methods for their detection were developed.
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Affiliation(s)
- Djuro Josic
- Department of Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA.,Department of Biotechnology, Centre for High-throughput technologies, University of Rijeka, Rijeka, Croatia.,University Juraj Dobrila, Pula, Croatia
| | - Tamara Martinovic
- Department of Biotechnology, Centre for High-throughput technologies, University of Rijeka, Rijeka, Croatia
| | - Kresimir Pavelic
- Department of Biotechnology, Centre for High-throughput technologies, University of Rijeka, Rijeka, Croatia.,University Juraj Dobrila, Pula, Croatia
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9
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Yamoto K, Saitsu H, Nakagawa N, Nakajima H, Hasegawa T, Fujisawa Y, Kagami M, Fukami M, Ogata T. De novo IGF2 mutation on the paternal allele in a patient with Silver-Russell syndrome and ectrodactyly. Hum Mutat 2017; 38:953-958. [PMID: 28489339 DOI: 10.1002/humu.23253] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 05/05/2017] [Accepted: 05/06/2017] [Indexed: 11/06/2022]
Abstract
Although paternally expressed IGF2 is known to play a critical role in placental and body growth, only a single mutation has been found in IGF2. We identified, through whole-exome sequencing, a de novo IGF2 indel mutation leading to frameshift (NM_000612.5:c.110_117delinsAGGTAA, p.(Leu37Glnfs*31)) in a patient with Silver-Russell syndrome, ectrodactyly, undermasculinized genitalia, developmental delay, and placental hypoplasia. Furthermore, we demonstrated that the mutation resided on the paternal allele by sequencing the long PCR product harboring the mutation- and methylation-sensitive SmaI and SalI sites before and after SmaI/SalI digestion. The results, together with the previous findings in four cases from a single family with a paternally inherited IGF2 nonsense mutation and those in patients with variable H19 differentially methylated region epimutations leading to compromised IGF2 expression, suggest that the whole phenotype of this patient is explainable by the IGF2 mutation, and that phenotypic severity is primarily determined by the IGF2 expression level in target tissues.
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Affiliation(s)
- Kaori Yamoto
- Departments of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Departments of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Norio Nakagawa
- Departments of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hisakazu Nakajima
- Departments of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tatsuji Hasegawa
- Departments of Perinatology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yasuko Fujisawa
- Departments of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Departments of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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Bar S, Schachter M, Eldar-Geva T, Benvenisty N. Large-Scale Analysis of Loss of Imprinting in Human Pluripotent Stem Cells. Cell Rep 2017; 19:957-968. [DOI: 10.1016/j.celrep.2017.04.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/01/2017] [Accepted: 04/06/2017] [Indexed: 12/30/2022] Open
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Dey A, Robitaille M, Remke M, Maier C, Malhotra A, Gregorieff A, Wrana JL, Taylor MD, Angers S, Kenney AM. YB-1 is elevated in medulloblastoma and drives proliferation in Sonic hedgehog-dependent cerebellar granule neuron progenitor cells and medulloblastoma cells. Oncogene 2016; 35:4256-68. [PMID: 26725322 DOI: 10.1038/onc.2015.491] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 10/26/2015] [Accepted: 11/27/2015] [Indexed: 12/29/2022]
Abstract
Postnatal proliferation of cerebellar granule neuron precursors (CGNPs), proposed cells of origin for the SHH-associated subgroup of medulloblastoma, is driven by Sonic hedgehog (Shh) and insulin-like growth factor (IGF) in the developing cerebellum. Shh induces the oncogene Yes-associated protein (YAP), which drives IGF2 expression in CGNPs and mouse Shh-associated medulloblastomas. To determine how IGF2 expression is regulated downstream of YAP, we carried out an unbiased screen for transcriptional regulators bound to IGF2 promoters. We report that Y-box binding protein-1 (YB-1), an onco-protein regulating transcription and translation, binds to IGF2 promoter P3. We observed that YB-1 is upregulated across human medulloblastoma subclasses as well as in other varieties of pediatric brain tumors. Utilizing the cerebellar progenitor model for the Shh subgroup of medulloblastoma in mice, we show for the first time that YB-1 is induced by Shh in CGNPs. Its expression is YAP-dependent and it is required for IGF2 expression in CGNPs. Finally, both gain-of function and loss-of-function experiments reveal that YB-1 activity is required for sustaining CGNP and medulloblastoma cell (MBC) proliferation. Collectively, our findings describe a novel role for YB-1 in driving proliferation in the developing cerebellum and MBCs and they identify the SHH:YAP:YB1:IGF2 axis as a powerful target for therapeutic intervention in medulloblastomas.
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Ye X, Kohtz A, Pollonini G, Riccio A, Alberini CM. Insulin Like Growth Factor 2 Expression in the Rat Brain Both in Basal Condition and following Learning Predominantly Derives from the Maternal Allele. PLoS One 2015; 10:e0141078. [PMID: 26495851 PMCID: PMC4619677 DOI: 10.1371/journal.pone.0141078] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 10/04/2015] [Indexed: 11/19/2022] Open
Abstract
Insulin like growth factor 2 (Igf2) is known as a maternally imprinted gene involved in growth and development. Recently, Igf2 was found to also be regulated and required in the adult rat hippocampus for long-term memory formation, raising the question of its allelic regulation in adult brain regions following experience and in cognitive processes. We show that, in adult rats, Igf2 is abundantly expressed in brain regions involved in cognitive functions, like hippocampus and prefrontal cortex, compared to the peripheral tissues. In contrast to its maternal imprinting in peripheral tissues, Igf2 is mainly expressed from the maternal allele in these brain regions. The training-dependent increase in Igf2 expression derives proportionally from both parental alleles, and, hence, is mostly maternal. Thus, Igf2 parental expression in the adult rat brain does not follow the imprinting rules found in peripheral tissues, suggesting differential expression regulation and functions of imprinted genes in the brain.
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Affiliation(s)
- Xiaojing Ye
- Center for Neural Science, New York University, New York, NY, 10003, United States of America
| | - Amy Kohtz
- Center for Neural Science, New York University, New York, NY, 10003, United States of America
- Graduate Program in Psychology, University at Albany–SUNY, Albany, NY, 12222, United States of America
| | - Gabriella Pollonini
- Center for Neural Science, New York University, New York, NY, 10003, United States of America
| | - Andrea Riccio
- DiSTABiF, Second University of Naples, Caserta 81100, Italy
- Institute of Genetics and Biophysics A. Buzzati-Traverso, CNR, Naples, 80131, Italy
| | - Cristina M. Alberini
- Center for Neural Science, New York University, New York, NY, 10003, United States of America
- * E-mail:
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13
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Fanganiello RD, Ishiy FAA, Kobayashi GS, Alvizi L, Sunaga DY, Passos-Bueno MR. Increased In Vitro Osteopotential in SHED Associated with Higher IGF2 Expression When Compared with hASCs. Stem Cell Rev Rep 2015; 11:635-44. [DOI: 10.1007/s12015-015-9592-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Li H, Hui X, Li P, Xu A, Li S, Jin S, Wu D. Expression and efficient purification of tag-cleaved active recombinant human insulin-like growth factor-II from Escherichia coli. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0562-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Abstract
OBJECTIVES Silver-Russell syndrome (SRS) is an imprinted disorder characterised by intrauterine growth retardation, relative macrocephaly, failure to thrive, typical facial phenotype and frequent body asymmetry. Feeding difficulties are frequently noted, but no study described evolution of gastrointestinal signs during infancy and their management in SRS. The aim of this study was to describe these abnormalities in a large cohort of children with SRS. DESIGN We included 75 patients (median age 24.3 months (5.1-135.2)) in the study. We retrospectively analysed nutritional status before growth hormone therapy, the frequency of gastrointestinal signs, such as gastroesophageal reflux (GER), vomiting, constipation and feeding difficulties, and nutritional management. RESULTS Maternal uniparental disomy for chromosome 7 was found in 10 patients and 11p15 hypomethylation in 65 patients. Malnutrition (defined as a weight/expected weight for height ratio <80%) was detected in 70% of the children. Gastrointestinal signs were found in 77%, including severe vomiting before the age of 1 year in 50% of cases, persistent vomiting from the age of 1 year in 29% of cases and constipation in 20% of cases. Severe GER was diagnosed in 55% of children by 24 h oesophageal pH-metry. Feeding difficulties were described in 65% of cases, with indications for dietary enrichment in 49%. Enteral nutrition by gastrostomy was indicated in 22% of cases. CONCLUSIONS Digestive signs (GER, constipation) and malnutrition are frequent in children with SRS. The systematic exploration and management of these signs are crucial to improve the nutritional status of these children before initiating growth hormone therapy.
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Affiliation(s)
- Céline Marsaud
- Nutrition et Gastroentérologie Pédiatrique, AP-HP, Hôpital Armand-Trousseau, Paris, France
| | - Sylvie Rossignol
- AP-HP, Hôpital Armand-Trousseau, Explorations Fonctionnelles Endocriniennes, INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Université Pierre et Marie Curie-Paris 6, Institut National de la Sante´́et de la Recherche Médicale U 515, Paris, France
| | - Patrick Tounian
- Nutrition et Gastroentérologie Pédiatrique, AP-HP, Hôpital Armand-Trousseau, Paris, France Institut de Cardiométabolisme et Nutrition (ICAN), INSERM UMRS U872 (Eq7) Nutriomique, Université Pierre et Marie Curie-Paris 6, Centre de Recherche des Cordeliers, Paris, France
| | - Irène Netchine
- AP-HP, Hôpital Armand-Trousseau, Explorations Fonctionnelles Endocriniennes, INSERM, UMR_S 938, CDR Saint-Antoine, Paris, France Université Pierre et Marie Curie-Paris 6, Institut National de la Sante´́et de la Recherche Médicale U 515, Paris, France
| | - Béatrice Dubern
- Nutrition et Gastroentérologie Pédiatrique, AP-HP, Hôpital Armand-Trousseau, Paris, France Institut de Cardiométabolisme et Nutrition (ICAN), INSERM UMRS U872 (Eq7) Nutriomique, Université Pierre et Marie Curie-Paris 6, Centre de Recherche des Cordeliers, Paris, France
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16
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Abstract
Neural stem cells (NSCs) are found in two regions in the adult brain: the subgranular zone (SGZ) in the hippocampal dentate gyrus and the subventricular zone (SVZ) adjacent to the lateral ventricles. Similarly to other somatic stem cells, adult NSCs are found within specialized niches that are organized to facilitate NSC self-renewal. Alterations in stem-cell homeostasis can contribute to the consequences of neurodegenerative diseases, healthy ageing and tissue repair after damage. Insulin and the insulin-like growth factors (IGFs) function in stem-cell homeostasis across species. Studies in the mammalian central nervous system support essential roles for IGF and/or insulin signalling in NSC self-renewal, neurogenesis, cognition and sensory function through distinct ligand-receptor interactions. IGF-II is of particular interest as a result of its production by the choroid plexus and presence in cerebrospinal fluid (CSF). CSF regulates and supports the development, division and migration of cells in the adult brain and is required for NSC maintenance. In this Review, we discuss emerging data on the functions of IGF-II and IGF and/or insulin receptor signalling in the context of NSC regulation in the SVZ and SGZ. We also propose a model for IGF-II in which the choroid plexus is a major component of the NSC niche.
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Affiliation(s)
- Amber N Ziegler
- Department of Neurology &Neuroscience, New Jersey Medical School, Rutgers Biomedical &Health Sciences, Cancer Centre, 205 South Orange Avenue, Newark, NJ 07101, USA
| | - Steven W Levison
- Department of Neurology &Neuroscience, New Jersey Medical School, Rutgers Biomedical &Health Sciences, Cancer Centre, 205 South Orange Avenue, Newark, NJ 07101, USA
| | - Teresa L Wood
- Department of Neurology &Neuroscience, New Jersey Medical School, Rutgers Biomedical &Health Sciences, Cancer Centre, 205 South Orange Avenue, Newark, NJ 07101, USA
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17
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Harper KM, Tunc-Ozcan E, Graf EN, Herzing LBK, Redei EE. Intergenerational and parent of origin effects of maternal calorie restriction on Igf2 expression in the adult rat hippocampus. Psychoneuroendocrinology 2014; 45:187-91. [PMID: 24845189 PMCID: PMC4076822 DOI: 10.1016/j.psyneuen.2014.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 03/31/2014] [Accepted: 04/01/2014] [Indexed: 11/18/2022]
Abstract
Insulin-like growth factor 2 (Igf2) regulates development, memory and adult neurogenesis in the hippocampus. Calorie restriction (CR) is known to modulate non-neuronal Igf2 expression intergenerationally, but its effect has not been evaluated on brain Igf2. Here, Sprague-Dawley (S) dams underwent moderate CR between gestational days 8-21. To identify parent of origin expression pattern of the imprinted Igf2 gene, their offspring (SS F1) were mated with naïve male or female Brown Norway (B) rats to obtain the second generation (BS and SB F2) progeny. CR did not affect adult hippocampal Igf2 transcript levels in SS F1 males or their BS F2 progeny, but increased it in SS F1 females and their SB F2 offspring. The preferentially maternal Igf2 expression in the SB F2 control male hippocampus relaxed to biallelic with CR, with no effect of grandmaternal diet in any other groups. Thus, allele-specific and total expression of hippocampal Igf2 is affected by maternal, grandmaternal CR in a strain and sex-specific manner.
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Affiliation(s)
- Kathryn M Harper
- The Asher Center, Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Elif Tunc-Ozcan
- The Asher Center, Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Evan N Graf
- The Asher Center, Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Laura B K Herzing
- Lurie's Children Research Center, Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States
| | - Eva E Redei
- The Asher Center, Department of Psychiatry and Behavioral Sciences, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, United States.
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Stringer JM, Pask AJ, Shaw G, Renfree MB. Post-natal imprinting: evidence from marsupials. Heredity (Edinb) 2014; 113:145-55. [PMID: 24595366 DOI: 10.1038/hdy.2014.10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 12/19/2013] [Accepted: 01/09/2014] [Indexed: 12/31/2022] Open
Abstract
Genomic imprinting has been identified in therian (eutherian and marsupial) mammals but not in prototherian (monotreme) mammals. Imprinting has an important role in optimising pre-natal nutrition and growth, and most imprinted genes are expressed and imprinted in the placenta and developing fetus. In marsupials, however, the placental attachment is short-lived, and most growth and development occurs post-natally, supported by a changing milk composition tailor-made for each stage of development. Therefore there is a much greater demand on marsupial females during post-natal lactation than during pre-natal placentation, so there may be greater selection for genomic imprinting in the mammary gland than in the short-lived placenta. Recent studies in the tammar wallaby confirm the presence of genomic imprinting in nutrient-regulatory genes in the adult mammary gland. This suggests that imprinting may influence infant post-natal growth via the mammary gland as it does pre-natally via the placenta. Similarly, an increasing number of imprinted genes have been implicated in regulating feeding and nurturing behaviour in both the adult and the developing neonate/offspring in mice. Together these studies provide evidence that genomic imprinting is critical for regulating growth and subsequently the survival of offspring not only pre-natally but also post-natally.
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Autuoro JM, Pirnie SP, Carmichael GG. Long noncoding RNAs in imprinting and X chromosome inactivation. Biomolecules 2014; 4:76-100. [PMID: 24970206 PMCID: PMC4030979 DOI: 10.3390/biom4010076] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 12/18/2013] [Accepted: 12/27/2013] [Indexed: 12/11/2022] Open
Abstract
The field of long noncoding RNA (lncRNA) research has been rapidly advancing in recent years. Technological advancements and deep-sequencing of the transcriptome have facilitated the identification of numerous new lncRNAs, many with unusual properties, however, the function of most of these molecules is still largely unknown. Some evidence suggests that several of these lncRNAs may regulate their own transcription in cis, and that of nearby genes, by recruiting remodeling factors to local chromatin. Notably, lncRNAs are known to exist at many imprinted gene clusters. Genomic imprinting is a complex and highly regulated process resulting in the monoallelic silencing of certain genes, based on the parent-of-origin of the allele. It is thought that lncRNAs may regulate many imprinted loci, however, the mechanism by which they exert such influence is poorly understood. This review will discuss what is known about the lncRNAs of major imprinted loci, and the roles they play in the regulation of imprinting.
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Affiliation(s)
- Joseph M Autuoro
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA.
| | - Stephan P Pirnie
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA.
| | - Gordon G Carmichael
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030, USA.
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20
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Wu L, Wang L, Shangguan S, Chang S, Wang Z, Lu X, Zhang Q, Wang J, Zhao H, Wang F, Guo J, Niu B, Guo J, Zhang T. Altered methylation of IGF2 DMR0 is associated with neural tube defects. Mol Cell Biochem 2013; 380:33-42. [DOI: 10.1007/s11010-013-1655-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 04/13/2013] [Indexed: 12/26/2022]
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21
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Fuke T, Mizuno S, Nagai T, Hasegawa T, Horikawa R, Miyoshi Y, Muroya K, Kondoh T, Numakura C, Sato S, Nakabayashi K, Tayama C, Hata K, Sano S, Matsubara K, Kagami M, Yamazawa K, Ogata T. Molecular and clinical studies in 138 Japanese patients with Silver-Russell syndrome. PLoS One 2013; 8:e60105. [PMID: 23533668 PMCID: PMC3606247 DOI: 10.1371/journal.pone.0060105] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 02/21/2013] [Indexed: 12/22/2022] Open
Abstract
Background Recent studies have revealed relative frequency and characteristic phenotype of two major causative factors for Silver-Russell syndrome (SRS), i.e. epimutation of the H19-differentially methylated region (DMR) and uniparental maternal disomy 7 (upd(7)mat), as well as multilocus methylation abnormalities and positive correlation between methylation index and body and placental sizes in H19-DMR epimutation. Furthermore, rare genomic alterations have been found in a few of patients with idiopathic SRS. Here, we performed molecular and clinical findings in 138 Japanese SRS patients, and examined these matters. Methodology/Principal Findings We identified H19-DMR epimutation in cases 1–43 (group 1), upd(7)mat in cases 44–52 (group 2), and neither H19-DMR epimutation nor upd(7)mat in cases 53–138 (group 3). Multilocus analysis revealed hyper- or hypomethylated DMRs in 2.4% of examined DMRs in group 1; in particular, an extremely hypomethylated ARHI-DMR was identified in case 13. Oligonucleotide array comparative genomic hybridization identified a ∼3.86 Mb deletion at chromosome 17q24 in case 73. Epigenotype-phenotype analysis revealed that group 1 had more reduced birth length and weight, more preserved birth occipitofrontal circumference (OFC), more frequent body asymmetry and brachydactyly, and less frequent speech delay than group 2. The degree of placental hypoplasia was similar between the two groups. In group 1, the methylation index for the H19-DMR was positively correlated with birth length and weight, present height and weight, and placental weight, but with neither birth nor present OFC. Conclusions/Significance The results are grossly consistent with the previously reported data, although the frequency of epimutations is lower in the Japanese SRS patients than in the Western European SRS patients. Furthermore, the results provide useful information regarding placental hypoplasia in SRS, clinical phenotypes of the hypomethylated ARHI-DMR, and underlying causative factors for idiopathic SRS.
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Affiliation(s)
- Tomoko Fuke
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Aichi, Japan
| | - Toshiro Nagai
- Department of Pediatrics, Dokkyo Medical University Koshigaya Hospital, Saitama, Japan
| | - Tomonobu Hasegawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Reiko Horikawa
- Division of Endocrinology and Metabolism, National Center for Child Health and Development, Tokyo, Japan
| | - Yoko Miyoshi
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Koji Muroya
- Department of Endocrinology and Metabolism, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Tatsuro Kondoh
- Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Isahaya, Japan
| | - Chikahiko Numakura
- Department of Pediatrics, Yamagata University School of Medicine, Yamagata, Japan
| | - Seiji Sato
- Department of Pediatrics, Saitama Municipal Hospital, Saitama, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Shinichiro Sano
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuki Yamazawa
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tsutomu Ogata
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
- * E-mail:
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Kaur P, Liu F, Tan JR, Lim KY, Sepramaniam S, Karolina DS, Armugam A, Jeyaseelan K. Non-Coding RNAs as Potential Neuroprotectants against Ischemic Brain Injury. Brain Sci 2013; 3:360-95. [PMID: 24961318 PMCID: PMC4061830 DOI: 10.3390/brainsci3010360] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/19/2013] [Accepted: 03/06/2013] [Indexed: 01/24/2023] Open
Abstract
Over the past decade, scientific discoveries have highlighted new roles for a unique class of non-coding RNAs. Transcribed from the genome, these non-coding RNAs have been implicated in determining the biological complexity seen in mammals by acting as transcriptional and translational regulators. Non-coding RNAs, which can be sub-classified into long non-coding RNAs, microRNAs, PIWI-interacting RNAs and several others, are widely expressed in the nervous system with roles in neurogenesis, development and maintenance of the neuronal phenotype. Perturbations of these non-coding transcripts have been observed in ischemic preconditioning as well as ischemic brain injury with characterization of the mechanisms by which they confer toxicity. Their dysregulation may also confer pathogenic conditions in neurovascular diseases. A better understanding of their expression patterns and functions has uncovered the potential use of these riboregulators as neuroprotectants to antagonize the detrimental molecular events taking place upon ischemic-reperfusion injury. In this review, we discuss the various roles of non-coding RNAs in brain development and their mechanisms of gene regulation in relation to ischemic brain injury. We will also address the future directions and open questions for identifying promising non-coding RNAs that could eventually serve as potential neuroprotectants against ischemic brain injury.
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Affiliation(s)
- Prameet Kaur
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Fujia Liu
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Jun Rong Tan
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Kai Ying Lim
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Sugunavathi Sepramaniam
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Dwi Setyowati Karolina
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Arunmozhiarasi Armugam
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Kandiah Jeyaseelan
- Department of Biochemistry and Neuroscience Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
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Khan QES, Sehic A, Skalleberg N, Landin MA, Khuu C, Risnes S, Osmundsen H. Expression of delta-like 1 homologue and insulin-like growth factor 2 through epigenetic regulation of the genes during development of mouse molar. Eur J Oral Sci 2013; 120:292-302. [PMID: 22813219 DOI: 10.1111/j.1600-0722.2012.00976.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Delta-like 1 homolog (Dlk1) and insulin-like growth factor 2 (Igf2) are two of six well-studied mouse imprinted gene clusters that are paternally expressed. Their expression is also linked to their maternally expressed non-coding RNAs, encoded by Gene trap locus 2 (Gtl2) and Imprinted maternally expressed transcript (H19), co-located as imprinted gene clusters. Using deoxyoligonucleotide microarrays and real-time RT-PCR analysis we showed Dlk1 and Gtl2 to exhibit a time-course of expression during tooth development that was similar to that of Igf2 and H19. Western blot analysis of proteins encoded by Dlk1 and Igf2 suggested that the levels of these proteins reflected those of the corresponding mRNAs. Immunohistochemical studies of DLK1 in murine molars detected the protein in both epithelial and mesenchymal regions, in developing cusp mesenchyme, and in newly synthesized enamel and dentin tubules. IGF2 protein was detected primarily at prenatal stages, suggesting that it may be active before birth. Analysis of methylation of cytosine-phosphate-guanine (CpG) islands in both Dlk1 and Igf2 suggested the presence of an increasing fraction of hypermethylated bases with increasing time of development. The increased levels of hypermethylation coincided both with the diminished levels of expression of Dlk1 and Igf2 and with decreased levels of DLK1 and IGF2 proteins in the tooth germ, suggesting that their expression is regulated via methylation of CpG islands present in these genes.
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Barbaux S, Gascoin-Lachambre G, Buffat C, Monnier P, Mondon F, Tonanny MB, Pinard A, Auer J, Bessières B, Barlier A, Jacques S, Simeoni U, Dandolo L, Letourneur F, Jammes H, Vaiman D. A genome-wide approach reveals novel imprinted genes expressed in the human placenta. Epigenetics 2012; 7:1079-90. [PMID: 22894909 PMCID: PMC3466192 DOI: 10.4161/epi.21495] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Genomic imprinting characterizes genes with a monoallelic expression, which is dependent on the parental origin of each allele. Approximately 150 imprinted genes are known to date, in humans and mice but, though computational searches have tried to extract intrinsic characteristics of these genes to identify new ones, the existing list is probably far from being comprehensive. We used a high-throughput strategy by diverting the classical use of genotyping microarrays to compare the genotypes of mRNA/cDNA vs. genomic DNA to identify new genes presenting monoallelic expression, starting from human placental material. After filtering of data, we obtained a list of 1,082 putative candidate monoallelic SNPs located in more than one hundred candidate genes. Among these, we found known imprinted genes, such as IPW, GRB10, INPP5F and ZNF597, which contribute to validate the approach. We also explored some likely candidates of our list and identified seven new imprinted genes, including ZFAT, ZFAT-AS1, GLIS3, NTM, MAGI2, ZC3H12Cand LIN28B, four of which encode zinc finger transcription factors. They are, however, not imprinted in the mouse placenta, except for Magi2. We analyzed in more details the ZFAT gene, which is paternally expressed in the placenta (as ZFAT-AS1, a non-coding antisense RNA) but biallelic in other tissues. The ZFAT protein is expressed in endothelial cells, as well as in syncytiotrophoblasts. The expression of this gene is, moreover, downregulated in placentas from complicated pregnancies. With this work we increase by about 10% the number of known imprinted genes in humans.
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Alfimova MV, Lezheiko TV, Gritsenko IK, Golimbet VE. Association of the insulin-like growth factor II (IGF2) gene with human cognitive functions. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412080029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Stringer JM, Suzuki S, Pask AJ, Shaw G, Renfree MB. Promoter-specific expression and imprint status of marsupial IGF2. PLoS One 2012; 7:e41690. [PMID: 22848567 DOI: 10.1371/journal.pone.0041690] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 06/25/2012] [Indexed: 11/19/2022] Open
Abstract
In mice and humans, IGF2 has multiple promoters to maintain its complex tissue- and developmental stage-specific imprinting and expression. IGF2 is also imprinted in marsupials, but little is known about its promoter region. In this study, three IGF2 transcripts were isolated from placental and liver samples of the tammar wallaby, Macropus eugenii. Each transcript contained a unique 5' untranslated region, orthologous to the non-coding exons derived from promoters P1–P3 in the human and mouse IGF2 locus. The expression of tammar IGF2 was predominantly from the P2 promoter, similar to humans. Expression of IGF2 was higher in pouch young than in the adult and imprinting was highly tissue and developmental-stage specific. Interestingly, while IGF2 was expressed throughout the placenta, imprinting seemed to be restricted to the vascular, trilaminar region. In addition, IGF2 was monoallelically expressed in the adult mammary gland while in the liver it switched from monoalleleic expression in the pouch young to biallelic in the adult. These data suggest a complex mode of IGF2 regulation in marsupials as seen in eutherian mammals. The conservation of the IGF2 promoters suggests they originated before the divergence of marsupials and eutherians, and have been selectively maintained for at least 160 million years.
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Abstract
Central and peripheral insulin-like peptides (ILPs), which include insulin, insulin-like growth factor 1 (IGF1) and IGF2, exert many effects in the brain. Through their actions on brain growth and differentiation, ILPs contribute to building circuitries that subserve metabolic and behavioural adaptation to internal and external cues of energy availability. In the adult brain each ILP has distinct effects, but together their actions ultimately regulate energy homeostasis - they affect nutrient sensing and regulate neuronal plasticity to modulate adaptive behaviours involved in food seeking, including high-level cognitive operations such as spatial memory. In essence, the multifaceted activity of ILPs in the brain may be viewed as a system organization involved in the control of energy allocation.
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Affiliation(s)
- Ana M Fernandez
- Cajal Institute, CSIC and Ciberned, Avenida Doctor Arce, 37, Madrid 28002, Spain
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Frost JM, Monk D, Stojilkovic-Mikic T, Woodfine K, Chitty LS, Murrell A, Stanier P, Moore GE. Evaluation of allelic expression of imprinted genes in adult human blood. PLoS One 2010; 5:e13556. [PMID: 21042416 DOI: 10.1371/journal.pone.0013556] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 09/17/2010] [Indexed: 01/08/2023] Open
Abstract
Background Imprinted genes are expressed from only one allele in a parent-of-origin dependent manner. Loss of imprinted (LOI) expression can result in a variety of human disorders and is frequently reported in cancer. Biallelic expression of imprinted genes in adult blood has been suggested as a useful biomarker and is currently being investigated in colorectal cancer. In general, the expression profiles of imprinted genes are well characterised during human and mouse fetal development, but not in human adults. Methodology/Principal Findings We investigated quantitative expression of 36 imprinted genes in adult human peripheral blood leukocytes obtained from healthy individuals. Allelic expression was also investigated in B and T lymphocytes and myeloid cells. We found that 21 genes were essentially undetectable in adult blood. Only six genes were demonstrably monoallelic, and most importantly, we found that nine genes were either biallelic or showed variable expression in different individuals. Separated leukocyte populations showed the same expression patterns as whole blood. Differential methylation at each of the imprinting control loci analysed was maintained, including regions that contained biallelically expressed genes. This suggests in some cases methylation has become uncoupled from its role in regulating gene expression. Conclusions/Significance We conclude that only a limited set of imprinted genes, including IGF2 and SNRPN, may be useful for LOI cancer biomarker studies. In addition, blood is not a good tissue to use for the discovery of new imprinted genes. Finally, lymphocyte DNA methylation status in the adult may not always be a reliable indicator of monoallelic gene expression.
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30
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Lee SH, Appleby V, Jeyapalan JN, Palmer RD, Nicholson JC, Sottile V, Gao E, Coleman N, Scotting PJ. Variable methylation of the imprinted gene, SNRPN, supports a relationship between intracranial germ cell tumours and neural stem cells. J Neurooncol 2010; 101:419-28. [DOI: 10.1007/s11060-010-0275-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 06/16/2010] [Indexed: 12/14/2022]
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Kernohan KD, Jiang Y, Tremblay DC, Bonvissuto AC, Eubanks JH, Mann MRW, Bérubé NG. ATRX partners with cohesin and MeCP2 and contributes to developmental silencing of imprinted genes in the brain. Dev Cell 2010; 18:191-202. [PMID: 20159591 DOI: 10.1016/j.devcel.2009.12.017] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Revised: 10/12/2009] [Accepted: 12/17/2009] [Indexed: 11/27/2022]
Abstract
Human developmental disorders caused by chromatin dysfunction often display overlapping clinical manifestations, such as cognitive deficits, but the underlying molecular links are poorly defined. Here, we show that ATRX, MeCP2, and cohesin, chromatin regulators implicated in ATR-X, RTT, and CdLS syndromes, respectively, interact in the brain and colocalize at the H19 imprinting control region (ICR) with preferential binding on the maternal allele. Importantly, we show that ATRX loss of function alters enrichment of cohesin, CTCF, and histone modifications at the H19 ICR, without affecting DNA methylation on the paternal allele. ATRX also affects cohesin, CTCF, and MeCP2 occupancy within the Gtl2/Dlk1 imprinted domain. Finally, we show that loss of ATRX interferes with the postnatal silencing of the maternal H19 gene along with a larger network of imprinted genes. We propose that ATRX, cohesin, and MeCP2 cooperate to silence a subset of imprinted genes in the postnatal mouse brain.
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Affiliation(s)
- Kristin D Kernohan
- Department of Paediatrics, 800 Commissioners Road East, London, ON N6C 2V5, Canada
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Souren NY, Paulussen AD, Steyls A, Loos RJ, Brandao RD, Gielen M, Smeets HJ, Beunen G, Fagard R, Derom C, Vlietinck R, Geraedts JP, Zeegers MP. Parent-of-origin specific linkage and association of the IGF2 gene region with birth weight and adult metabolic risk factors. Int J Obes (Lond) 2009; 33:962-70. [PMID: 19546867 DOI: 10.1038/ijo.2009.126] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVE The maternally imprinted insulin-like growth factor 2 (IGF2) gene is an important fetal growth factor and is also suggested to have postnatal metabolic effects. In this study, we examined whether common polymorphisms in IGF2 (6815_6819delAGGGC, 1156T>C and 820G>A (ApaI)) and a microsatellite marker in the close vicinity of IGF2 were linked to or associated with birth weight and adult metabolic risk factors. DESIGN AND PARTICIPANTS Polymorphisms were genotyped in 199 monozygotic complete twin pairs, 109 dizygotic complete twin pairs, 15 single twins, 231 mothers and 228 fathers recruited from the East Flanders Prospective Twin Survey. Conventional and parent-of-origin specific linkage and association analyses were carried out with birth weight, adult body height and parameters quantifying obesity, insulin sensitivity and dyslipidaemia measured at adult age (mean age 25 years). RESULTS In the parent-of-origin specific association analysis, in which only the paternally inherited allele was incorporated, the 1156T>C SNP (single nucleotide polymorphism) showed significant association with IGF-binding protein 1 (IGFBP1) levels (T and C (mean (95% CI)): 13.2 (12.1-14.3) and 16.2 (14.6-18.0) ng ml(-1), P=0.002). No linkage was observed in either the conventional or in the parent-of-origin specific linkage analysis. CONCLUSION This study suggests that paternally inherited alleles of a common polymorphism in the IGF2 gene affect IGFBP1 levels.
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Ouko LA, Shantikumar K, Knezovich J, Haycock P, Schnugh DJ, Ramsay M. Effect of alcohol consumption on CpG methylation in the differentially methylated regions of H19 and IG-DMR in male gametes: implications for fetal alcohol spectrum disorders. Alcohol Clin Exp Res 2009; 33:1615-27. [PMID: 19519716 DOI: 10.1111/j.1530-0277.2009.00993.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Exposure to alcohol in utero is the main attributable cause of fetal alcohol spectrum disorders (FASD) which in its most severe form is characterized by irreversible behavioral and cognitive disability. Paternal preconception drinking is not considered to be a significant risk factor, even though animal studies have demonstrated that chronic paternal alcohol consumption has a detrimental effect on the physical and mental development of offspring even in the absence of in utero alcohol exposure. It has been documented that alcohol can reduce the levels and activity of DNA methyltransferases resulting in DNA hypomethylation and that reduced methyltransferase activity can cause activation of normally silenced genes. The aim of this study was to establish a link between alcohol use in men and hypomethylation of paternally imprinted loci in sperm DNA in genomic regions critical for embryonic development, thus providing a mechanism for paternal effects in the aetiology of FASD. METHODS Sperm DNA from male volunteers was bisulfite treated and the methylation patterns of 2 differentially methylated regions (DMRs), H19 and IG-DMR, analyzed following sequencing of individual clones. The methylation patterns were correlated with the alcohol consumption levels of the volunteer males. RESULTS There was a pattern of increased demethylation with alcohol consumption at the 2 imprinted loci with a significant difference observed at the IG-DMR between the nondrinking and heavy alcohol consuming groups. Greater inter-individual variation in average methylation was observed at the H19 DMR and individual clones were more extensively demethylated than those of the IG-DMR. CpG site #4 in the IG-DMR was preferentially demethylated among all individuals and along with the H19 DMR CpG site #7 located within the CTCF binding site 6 showed significant demethylation in the alcohol consuming groups compared with the control group. CONCLUSION This study demonstrates a correlation between chronic alcohol use and demethylation of normally hypermethylated imprinted regions in sperm DNA. We hypothesize that, should these epigenetic changes in imprinted genes be transmitted through fertilization, they would alter the critical gene expression dosages required for normal prenatal development resulting in offspring with features of FASD.
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Affiliation(s)
- Lillian A Ouko
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
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Yamazawa K, Kagami M, Nagai T, Kondoh T, Onigata K, Maeyama K, Hasegawa T, Hasegawa Y, Yamazaki T, Mizuno S, Miyoshi Y, Miyagawa S, Horikawa R, Matsuoka K, Ogata T. Molecular and clinical findings and their correlations in Silver-Russell syndrome: implications for a positive role of IGF2 in growth determination and differential imprinting regulation of the IGF2–H19 domain in bodies and placentas. J Mol Med (Berl) 2008; 86:1171-81. [DOI: 10.1007/s00109-008-0377-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 05/08/2008] [Accepted: 05/30/2008] [Indexed: 01/15/2023]
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Grbesa I, Marinkovic M, Ivkic M, Kruslin B, Novak-Kujundzic R, Pegan B, Bogdanovic O, Bedekovic V, Gall-Troselj K. Loss of imprinting of IGF2 and H19, loss of heterozygosity of IGF2R and CTCF, and Helicobacter pylori infection in laryngeal squamous cell carcinoma. J Mol Med (Berl) 2008; 86:1057-66. [DOI: 10.1007/s00109-008-0369-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2006] [Revised: 05/07/2008] [Accepted: 05/09/2008] [Indexed: 01/13/2023]
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Sutherland G, Mellick G, Newman J, Double KL, Stevens J, Lee L, Rowe D, Silburn P, Halliday GM. Haplotype analysis of the IGF2-INS-TH gene cluster in Parkinson's disease. Am J Med Genet B Neuropsychiatr Genet 2008; 147B:495-9. [PMID: 18085551 DOI: 10.1002/ajmg.b.30633] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Idiopathic Parkinson's disease is a common movement disorder characterized by a loss of dopaminergic neurons in the substantia nigra. Its pathogenesis is postulated to involve complex interactions between genetic susceptibility and environmental exposures. The IGF2-INS-TH gene cluster on the telomeric end of human chromosome 11 is a gene rich region expressing several proteins important for dopamine neuron homeostasis. We used a haplotyping approach to determine whether common genetic variation in the IGF2-INS-TH cluster influences the risk of idiopathic Parkinson's disease in a Caucasian case-control group recruited from Brisbane, Australia. Three tagging polymorphisms, the SNPs, rs680 and rs689 and the microsatellite, HUMTH01, were genotyped in 215 cases and 215 age- and gender-matched controls. Eight common haplotypes accounted for 91% of the genetic variation in our control group and one haplotype, IGF2-INS-TH*6, was significantly under-represented among the cases with idiopathic Parkinson's disease (OR = 0.42, 95% CI = 0.25-0.72, P-value = 0.001). Analysis of the individual polymorphisms showed that the IGF2-rs680 alternate 'A' allele accounted for the majority of the protective effect. Our findings suggest that common genetic variants in the IGF2-INS-TH cluster modify susceptibility to idiopathic Parkinson's disease.
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Affiliation(s)
- Greg Sutherland
- School of Biomolecular and Biomedical Sciences, Eskitis Institute, Griffith University, Brisbane, Australia
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Abstract
Imprinted genes expressed in the brain are numerous and it has become clear that they play an important role in nervous system development and function. The significant influence of genomic imprinting during development sets the stage for structural and physiological variations affecting psychological function and behaviour, as well as other physiological systems mediating health and well-being. However, our understanding of the role of imprinted genes in behaviour lags far behind our understanding of their roles in perinatal growth and development. Knowledge of genomic imprinting remains limited among behavioral scientists and clinicians and research regarding the influence of imprinted genes on normal cognitive processes and the most common forms of neuropathology has been limited to date. In this chapter, we will explore how knowledge of genomic imprinting can be used to inform our study of normal human cognitive and behavioral processes as well as their disruption. Behavioural analyses of rare imprinted disorders, such as Prader-Willi and Angelman syndromes, provide insight regarding the phenotypic impact of imprinted genes in the brain, and can be used to guide the study of normal behaviour as well as more common but etiologically complex disorders such as ADHD and autism. Furthermore, hypotheses regarding the evolutionary development of imprinted genes can be used to derive predictions about their role in normal behavioural variation, such as that observed in food-related and social interactions.
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Abstract
The inheritance pattern of a number of major genetic disorders suggests the possible involvement of genes that are expressed from one allele and silent on the other, but such genes are difficult to detect. Since DNA methylation in regulatory regions is often a mark of gene silencing, we modified existing microarray-based assays to detect both methylated and unmethylated DNA sequences in the same sample, a variation we term the MAUD assay. We probed a 65 Mb region of mouse Chr 7 for gene-associated sequences that show two distinct DNA methylation patterns in the mouse CNS. Selected genes were then tested for allele-specific expression in clonal neural stem cell lines derived from reciprocal F(1) (C57BL/6xJF1) hybrid mice. In addition, using a separate approach, we directly analyzed allele-specific expression of a group of genes interspersed within clusters of OlfR genes, since the latter are subject to allelic exclusion. Altogether, of the 500 known genes in the chromosomal region surveyed, five show monoallelic expression, four identified by the MAUD assay (Agc1, p (pink-eyed dilution), P4ha3 and Thrsp), and one by its proximity to OlfR genes (Trim12). Thrsp (thyroid hormone responsive SPOT14 homolog) is expressed in hippocampus, but the human protein homolog, S14, has also been implicated in aggressive breast cancer. Monoallelic expression of the five genes is not coordinated at a chromosome-wide level, but rather regulated at individual loci. Taken together, our results suggest that at least 1% of previously untested genes are subject to allelic exclusion, and demonstrate a dual approach to expedite their identification.
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Affiliation(s)
- Jinhui Wang
- Division of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
- Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
| | - Zuzana Valo
- Division of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
- Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
| | - David Smith
- Division of Information Sciences, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
| | - Judith Singer-Sam
- Division of Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
- Beckman Research Institute, City of Hope National Medical Center, Duarte, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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Kovacheva VP, Mellott TJ, Davison JM, Wagner N, Lopez-Coviella I, Schnitzler AC, Blusztajn JK. Gestational choline deficiency causes global and Igf2 gene DNA hypermethylation by up-regulation of Dnmt1 expression. J Biol Chem 2007; 282:31777-88. [PMID: 17724018 DOI: 10.1074/jbc.m705539200] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During gestation there is a high demand for the essential nutrient choline. Adult rats supplemented with choline during embryonic days (E) 11-17 have improved memory performance and do not exhibit age-related memory decline, whereas prenatally choline-deficient animals have memory deficits. Choline, via betaine, provides methyl groups for the production of S-adenosylmethionine, a substrate of DNA methyltransferases (DNMTs). We describe an apparently adaptive epigenomic response to varied gestational choline supply in rat fetal liver and brain. S-Adenosylmethionine levels increased in both organs of E17 fetuses whose mothers consumed a choline-supplemented diet. Surprisingly, global DNA methylation increased in choline-deficient animals, and this was accompanied by overexpression of Dnmt1 mRNA. Previous studies showed that the prenatal choline supply affects the expression of multiple genes, including insulin-like growth factor 2 (Igf2), whose expression is regulated in a DNA methylation-dependent manner. The differentially methylated region 2 of Igf2 was hypermethylated in the liver of E17 choline-deficient fetuses, and this as well as Igf2 mRNA levels correlated with the expression of Dnmt1 and with hypomethylation of a regulatory CpG within the Dnmt1 locus. Moreover, mRNA expression of brain and liver Dnmt3a and methyl CpG-binding domain 2 (Mbd2) protein as well as cerebral Dnmt3l was inversely correlated to the intake of choline. Thus, choline deficiency modulates fetal DNA methylation machinery in a complex fashion that includes hypomethylation of the regulatory CpGs within the Dnmt1 gene, leading to its overexpression and the resultant increased global and gene-specific (e.g. Igf2) DNA methylation. These epigenomic responses to gestational choline supply may initiate the long term developmental changes observed in rats exposed to varied choline intake in utero.
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Affiliation(s)
- Vesela P Kovacheva
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA
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Abstract
Insulin-like growth factor 2 (IGF2) is an imprinted gene expressed in most tissues affecting lean muscle content in mice, pigs and cattle. We previously identified the bovine IGF2 c.-292C>T SNP in the non-translated exon 2. Using this SNP, we demonstrated biallelic expression of IGF2 after birth. Seven alternatively spliced mRNA transcripts of IGF2 were expressed among 15 tissues. An IGF2 pseudogene (psiIGF2) was identified with sequence identical to at least IGF2 exons 2 and 3 without the intervening intron. The biallelic expression of this c.-292C>T SNP was associated with an increase in rib eye area (REA) in two populations of cattle, with the C.-292C allele associated with a 10% increase. A significant association with per cent fat was found in one of the populations.
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Affiliation(s)
- J J Goodall
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
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Abstract
We describe a new hypothesis for the development of autism, that it is driven by imbalances in brain development involving enhanced effects of paternally expressed imprinted genes, deficits of effects from maternally expressed genes, or both. This hypothesis is supported by: (1) the strong genomic-imprinting component to the genetic and developmental mechanisms of autism, Angelman syndrome, Rett syndrome and Turner syndrome; (2) the core behavioural features of autism, such as self-focused behaviour, altered social interactions and language, and enhanced spatial and mechanistic cognition and abilities, and (3) the degree to which relevant brain functions and structures are altered in autism and related disorders. The imprinted brain theory of autism has important implications for understanding the genetic, epigenetic, neurological and cognitive bases of autism, as ultimately due to imbalances in the outcomes of intragenomic conflict between effects of maternally vs. paternally expressed genes.
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Affiliation(s)
- C Badcock
- Department of Sociology, London School of Economics, London, UK
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Grbesa I, Ivkic M, Pegan B, Gall-Troselj K. Loss of imprinting and promoter usage of the IGF2 in laryngeal squamous cell carcinoma. Cancer Lett 2006; 238:224-9. [PMID: 16111804 DOI: 10.1016/j.canlet.2005.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Revised: 07/07/2005] [Accepted: 07/08/2005] [Indexed: 10/25/2022]
Abstract
The gene for insulin-like growth factor two, IGF2 is maternally imprinted. Fifteen heterozygous samples were analyzed for the IGF2 imprinting status and promoter usage. IGF2 LOI was detected in four non-tumorous tissues and in six laryngeal squamous cell carcinoma (LSCC) tumors. There was no clear pattern of specific promoter activity in LSCC tumors and the adjacent normal tissues. P1 promoter usage was active in eight LSCCs, among them four with LOI. As it was activated in four tumors with maintenance of imprinting (MOI) and four non-tumors, we concluded that P1 promoter is not exclusively connected with IGF2 LOI in LSCC.
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Affiliation(s)
- Ivana Grbesa
- Laboratory of Molecular Pathology, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka cesta 54, 10002 Zagreb, Croatia.
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Affiliation(s)
- Gregory J Popken
- Division Pediatric Endocrinology, Department of Pediatrics, University of North Carolina at Chapel Hill, NC 27599-7039, USA
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Sumi H, Naito E, Dewa K, Fukuda M, Xu HD, Yamanouchi H. Applicability of the parentally imprinted allele (PIA) typing of a VNTR upstream the H19 gene to forensic samples of different tissues. Leg Med (Tokyo) 2005; 7:179-82. [PMID: 15847827 DOI: 10.1016/j.legalmed.2004.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Revised: 10/20/2004] [Accepted: 10/29/2004] [Indexed: 11/19/2022]
Abstract
The parentally imprinted allele (PIA) typing that we have recently developed determines parental alleles at a VNTR locus in the differentially methylated region upstream of the human H19 gene. The usefulness of this typing was demonstrated by its application to blood samples in paternity cases. However, its applicability to other tissue DNA remains to be tested. DNA samples from fifteen different postmortem tissues such as cerebrum, skeletal muscle and skin were examined, all of which were obtained from three autopsy cases 2-11h after death. DNA was digested with a methylation-sensitive HhaI enzyme and diluted solutions of the digests were subjected to the first PCR amplification, providing amplification of only the paternal H19 methylated allele. Subsequent VNTR typing was carried out for the amplified products to determine which allele was of paternal origin. No tissue-dependent difference was observed and all the samples examined, though degraded, were successfully used for determining the paternal allele. These results substantiate the usefulness of PIA typing in forensic examinations. Its application to two identity cases, a burned male body and a male body with adipocere formation, was also shown.
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Affiliation(s)
- Hirokazu Sumi
- Division of Legal Medicine, Institute of Medicine and Dentistry, Niigata University Academic Assembly, 1-757 Asahimachidori, Niigata 951-8510, Japan
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Dindot SV, Kent KC, Evers B, Loskutoff N, Womack J, Piedrahita JA. Conservation of genomic imprinting at the XIST, IGF2, and GTL2 loci in the bovine. Mamm Genome 2004; 15:966-74. [PMID: 15599555 DOI: 10.1007/s00335-004-2407-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2004] [Accepted: 08/20/2004] [Indexed: 10/24/2022]
Abstract
Genomic imprinting is theorized to exist in all placental mammals and some marsupials; however, extensive comparative analysis of animals aside from humans and mice remains incomplete. Here we report conservation of genomic imprinting in the bovine at the X chromosome inactivation-specific transcript (XIST), insulin-like growth factor 2 (IGF2), and gene trap locus 2 (GTL2) loci. Coding single nucleotide polymorphisms (SNPs) between Bos gaurus and Bos taurus were detected at the XIST, IGF2, and GTL2 loci, which have previously been identified as imprinted in either humans, mice, or sheep. Expression patterns of parental alleles in F1 hybrids indicated preferential paternal expression at the XIST locus solely in the chorion of females, whereas analysis of the IGF2 and GTL2 loci indicated preferential paternal and maternal expression of alleles, respectively, in both fetal and placental tissues. Comparative sequence analysis of the XIST locus and adjacent regions suggests that repression of the maternal allele in the bovine is controlled by a different mechanism than in mice, further reinforcing the importance of comparative analysis of imprinting.
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Affiliation(s)
- Scott V Dindot
- Department of Veterinary Anatomy and Public Health, College of Veterinary Medicine, Texas A&M University, College Station, Texas 77843, USA
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Rakyan VK, Hildmann T, Novik KL, Lewin J, Tost J, Cox AV, Andrews TD, Howe KL, Otto T, Olek A, Fischer J, Gut IG, Berlin K, Beck S. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol 2004; 2:e405. [PMID: 15550986 PMCID: PMC529316 DOI: 10.1371/journal.pbio.0020405] [Citation(s) in RCA: 276] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2004] [Accepted: 09/23/2004] [Indexed: 11/25/2022] Open
Abstract
The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine–guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated), tissue specificity, inter-individual variation, and correlation with independent gene expression data. DNA is frequently modified by methylation, which can affect its function. The Human Epigenome Project aims to identify, catalog, and interpret DNA methylation throughout the genome
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Affiliation(s)
- Vardhman K Rakyan
- 1The Wellcome Trust Sanger Institute, HinxtonCambridgeUnited Kingdom
| | | | - Karen L Novik
- 1The Wellcome Trust Sanger Institute, HinxtonCambridgeUnited Kingdom
| | | | - Jörg Tost
- 3Centre National de GénotypageEvry CedexFrance
| | - Antony V Cox
- 1The Wellcome Trust Sanger Institute, HinxtonCambridgeUnited Kingdom
| | - T. Dan Andrews
- 1The Wellcome Trust Sanger Institute, HinxtonCambridgeUnited Kingdom
| | - Kevin L Howe
- 1The Wellcome Trust Sanger Institute, HinxtonCambridgeUnited Kingdom
| | | | | | | | - Ivo G Gut
- 3Centre National de GénotypageEvry CedexFrance
| | | | - Stephan Beck
- 1The Wellcome Trust Sanger Institute, HinxtonCambridgeUnited Kingdom
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Rakyan VK, Hildmann T, Novik KL, Lewin J, Tost J, Cox AV, Andrews TD, Howe KL, Otto T, Olek A. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol. 2004;2:e405. [PMID: 15550986 DOI: 10.1101/gr.077479.108] [Citation(s) in RCA: 314] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The Human Epigenome Project aims to identify, catalogue, and interpret genome-wide DNA methylation phenomena. Occurring naturally on cytosine bases at cytosine-guanine dinucleotides, DNA methylation is intimately involved in diverse biological processes and the aetiology of many diseases. Differentially methylated cytosines give rise to distinct profiles, thought to be specific for gene activity, tissue type, and disease state. The identification of such methylation variable positions will significantly improve our understanding of genome biology and our ability to diagnose disease. Here, we report the results of the pilot study for the Human Epigenome Project entailing the methylation analysis of the human major histocompatibility complex. This study involved the development of an integrated pipeline for high-throughput methylation analysis using bisulphite DNA sequencing, discovery of methylation variable positions, epigenotyping by matrix-assisted laser desorption/ionisation mass spectrometry, and development of an integrated public database available at http://www.epigenome.org. Our analysis of DNA methylation levels within the major histocompatibility complex, including regulatory exonic and intronic regions associated with 90 genes in multiple tissues and individuals, reveals a bimodal distribution of methylation profiles (i.e., the vast majority of the analysed regions were either hypo- or hypermethylated), tissue specificity, inter-individual variation, and correlation with independent gene expression data.
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Buettner VL, Longmate JA, Barish ME, Mann JR, Singer-Sam J. Analysis of imprinting in mice with uniparental duplication of proximal chromosomes 7 and 15 by use of a custom oligonucleotide microarray. Mamm Genome 2004; 15:199-209. [PMID: 15014969 DOI: 10.1007/s00335-003-2322-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Accepted: 10/15/2003] [Indexed: 12/23/2022]
Abstract
We have developed an imprinting assay combining the use of mice carrying maternal or paternal duplication of chromosomal regions of interest with custom oligonucleotide microarrays. As a model system, we analyzed RNA from CNS tissue of neonatal mice carrying the reciprocal translocation T(7;15)9H and uniparental duplication of proximal Chr 7 and 15. The duplicated region includes the locus on proximal Chr 7 corresponding to the human Prader-Willi/Angelman Syndrome. The microarray contained 322 oligonucleotides, including probes to detect major genes involved in neural excitability and synaptic transmission, as well as known imprinted genes mapping to proximal Chr 7: Ndn, Snrpn, Mkrn3, Magel2, Peg3, and Ube3a. Imprinting of these genes in neonatal cortex and cerebellum was first confirmed by quantitative RT-PCR. Their inclusion on the microarray thus provided positive controls for evaluating the effect of background on the sensitivity of the assay, and for establishing the minimum level of expression required to detect imprinting. Our analysis extended previous work by revealing bi-allelic expression in CNS tissue of those queried genes mapping to proximal Chr 7 or 15, including the Gabrb3 gene, for which there have been conflicting reports. Microarray analysis also revealed no effect of the maternal or paternal disomy on expression levels of the unlinked genes detected, including those potentially implicated in the Prader-Willi or Angelman Syndrome. In addition, quantitative RT-PCR revealed a gene dosage effect in both cerebellum and cortex for all of the known imprinted genes assayed, except for Ube3a in cerebellum.
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Affiliation(s)
- Victoria L Buettner
- Division of Biology, Beckman Research Institute, City of Hope, CA 91010, USA
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Yang Y, Hu JF, Ulaner GA, Li T, Yao X, Vu TH, Hoffman AR. Epigenetic regulation of Igf2/H19 imprinting at CTCF insulator binding sites. J Cell Biochem 2004; 90:1038-55. [PMID: 14624463 DOI: 10.1002/jcb.10684] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The mouse insulin-like growth factor II (Igf2) and H19 genes are located adjacent to each other on chromosome 7q11-13 and are reciprocally imprinted. It is believed that the allelic expression of these two genes is regulated by the binding of CTCF insulators to four parent-specific DNA methylation sites in an imprinting control center (ICR) located between these two genes. Although monoallelically expressed in peripheral tissues, Igf2 is biallelically transcribed in the CNS. In this study, we examined the allelic DNA methylation and CTCF binding in the Igf2/H19 imprinting center in CNS, hypothesizing that the aberrant CTCF binding as one of the mechanisms leads to biallelic expression of Igf2 in CNS. Using hybrid F1 mice (M. spretus males x C57BL/6 females), we showed that in CNS, CTCF binding sites in the ICR were methylated exclusively on the paternal allele, and CTCF bound only to the unmethylated maternal allele, showing no differences from the imprinted peripheral tissues. Among three other epigenetic modifications examined, histone H3 lysine 9 methylation correlated well with Igf2 allelic expression in CNS. These results suggest that CTCF binding to the ICR alone is not sufficient to insulate the Igf2 maternal promoter and to regulate the allelic expression of the gene in the CNS, thus challenging the aberrant CTCF binding as a common mechanism for lack of Igf2 imprinting in CNS. Further studies should be focused on the identification of factors that are involved in histone methylation and CTCF-associated factors that may be needed to coordinate Igf2 imprinting.
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Affiliation(s)
- Youwen Yang
- Medical Service, VA Palo Alto Health Care System, and Division of Endocrinology, Department of Medicine, Stanford University, Palo Alto, California 94304, USA
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