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Favilla BP, Meloni VA, Perez AB, Moretti-Ferreira D, de Souza DH, Bellucco FT, Melaragno MI. Spread of X-chromosome inactivation into autosomal regions in patients with unbalanced X-autosome translocations and its phenotypic effects. Am J Med Genet A 2021; 185:2295-2305. [PMID: 33913603 DOI: 10.1002/ajmg.a.62228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 12/21/2022]
Abstract
Patients with unbalanced X-autosome translocations are rare and usually present a skewed X-chromosome inactivation (XCI) pattern, with the derivative chromosome being preferentially inactivated, and with a possible spread of XCI into the autosomal regions attached to it, which can inactivate autosomal genes and affect the patients' phenotype. We describe three patients carrying different unbalanced X-autosome translocations, confirmed by G-banding karyotype and array techniques. We analyzed their XCI pattern and inactivation spread into autosomal regions, through HUMARA, ZDHHC15 gene assay and the novel 5-ethynyl-2'-deoxyuridine (EdU) incorporation assay, and identified an extremely skewed XCI pattern toward the derivative chromosomes for all the patients, and a variable pattern of late-replication on the autosomal regions of the derivative chromosomes. All patients showed phenotypical overlap with patients presenting deletions of the autosomal late-replicating regions, suggesting that the inactivation of autosomal segments may be responsible for their phenotype. Our data highlight the importance of the XCI spread into autosomal regions for establishing the clinical picture in patients carrying unbalanced X-autosome translocations, and the incorporation of EdU as a novel and precise tool to evaluate the inactivation status in such patients.
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Affiliation(s)
- Bianca Pereira Favilla
- Department of Morphology and Genetics, UNIFESP-Universidade Federal de São Paulo, São Paulo, Brazil
| | - Vera Ayres Meloni
- Department of Morphology and Genetics, UNIFESP-Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Beatriz Perez
- Department of Morphology and Genetics, UNIFESP-Universidade Federal de São Paulo, São Paulo, Brazil
| | - Danilo Moretti-Ferreira
- Department of Chemical and Biological Sciences, Biosciences Institute, UNESP-Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | - Deise Helena de Souza
- Department of Chemical and Biological Sciences, Biosciences Institute, UNESP-Universidade Estadual Paulista, Botucatu, São Paulo, Brazil
| | | | - Maria Isabel Melaragno
- Department of Morphology and Genetics, UNIFESP-Universidade Federal de São Paulo, São Paulo, Brazil
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2
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Hoel E, Levin M. Emergence of informative higher scales in biological systems: a computational toolkit for optimal prediction and control. Commun Integr Biol 2020; 13:108-118. [PMID: 33014263 PMCID: PMC7518458 DOI: 10.1080/19420889.2020.1802914] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023] Open
Abstract
The biological sciences span many spatial and temporal scales in attempts to understand the function and evolution of complex systems-level processes, such as embryogenesis. It is generally assumed that the most effective description of these processes is in terms of molecular interactions. However, recent developments in information theory and causal analysis now allow for the quantitative resolution of this question. In some cases, macro-scale models can minimize noise and increase the amount of information an experimenter or modeler has about "what does what." This result has numerous implications for evolution, pattern regulation, and biomedical strategies. Here, we provide an introduction to these quantitative techniques, and use them to show how informative macro-scales are common across biology. Our goal is to give biologists the tools to identify the maximally-informative scale at which to model, experiment on, predict, control, and understand complex biological systems.
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Affiliation(s)
- Erik Hoel
- Allen Discovery Center, Tufts University, Medford, MA, USA
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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3
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Santos-Rebouças CB, Boy R, Vianna EQ, Gonçalves AP, Piergiorge RM, Abdala BB, Dos Santos JM, Calassara V, Machado FB, Medina-Acosta E, Pimentel MMG. Skewed X-Chromosome Inactivation and Compensatory Upregulation of Escape Genes Precludes Major Clinical Symptoms in a Female With a Large Xq Deletion. Front Genet 2020; 11:101. [PMID: 32194616 PMCID: PMC7064548 DOI: 10.3389/fgene.2020.00101] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 01/29/2020] [Indexed: 11/13/2022] Open
Abstract
In mammalian females, X-chromosome inactivation (XCI) acts as a dosage compensation mechanism that equalizes X-linked genes expression between homo- and heterogametic sexes. However, approximately 12–23% of X-linked genes escape from XCI, being bi-allelic expressed. Herein, we report on genetic and functional data from an asymptomatic female of a Fragile X syndrome family, who harbors a large deletion on the X-chromosome. Array-CGH uncovered that the de novo, terminal, paternally originated 32 Mb deletion on Xq25-q28 spans 598 RefSeq genes, including escape and variable escape genes. Androgen receptor (AR) and retinitis pigmentosa 2 (RP2) methylation assays showed extreme skewed XCI ratios from both peripheral blood and buccal mucosa, silencing the abnormal X-chromosome. Surprisingly, transcriptome-wide analysis revealed that escape and variable escape genes spanning the deletion are mostly upregulated on the active X-chromosome, precluding major clinical/cognitive phenotypes in the female. Metaphase high count, hemizygosity concordance for microsatellite markers, and monoallelic expression of genes within the deletion suggest the absence of mosaicism in both blood and buccal mucosa. Taken together, our data suggest that an additional protective gene-by-gene mechanism occurs at the transcriptional level in the active X-chromosome to counterbalance detrimental phenotype effects of large Xq deletions.
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Affiliation(s)
- Cíntia B Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Boy
- Pedro Ernesto University Hospital, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Evelyn Q Vianna
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andressa P Gonçalves
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafael M Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bianca B Abdala
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jussara M Dos Santos
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Veluma Calassara
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Filipe B Machado
- Department of Biological Sciences, Minas Gerais State University, Ubá, Brazil
| | - Enrique Medina-Acosta
- Laboratory of Biotechnology, State University of Northern Rio de Janeiro Darcy Ribeiro, Rio de Janeiro, Brazil
| | - Márcia M G Pimentel
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
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Velychko S, Adachi K, Kim KP, Hou Y, MacCarthy CM, Wu G, Schöler HR. Excluding Oct4 from Yamanaka Cocktail Unleashes the Developmental Potential of iPSCs. Cell Stem Cell 2019; 25:737-753.e4. [PMID: 31708402 PMCID: PMC6900749 DOI: 10.1016/j.stem.2019.10.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/23/2019] [Accepted: 10/04/2019] [Indexed: 02/01/2023]
Abstract
Oct4 is widely considered the most important among the four Yamanaka reprogramming factors. Here, we show that the combination of Sox2, Klf4, and cMyc (SKM) suffices for reprogramming mouse somatic cells to induced pluripotent stem cells (iPSCs). Simultaneous induction of Sox2 and cMyc in fibroblasts triggers immediate retroviral silencing, which explains the discrepancy with previous studies that attempted but failed to generate iPSCs without Oct4 using retroviral vectors. SKM induction could partially activate the pluripotency network, even in Oct4-knockout fibroblasts. Importantly, reprogramming in the absence of exogenous Oct4 results in greatly improved developmental potential of iPSCs, determined by their ability to give rise to all-iPSC mice in the tetraploid complementation assay. Our data suggest that overexpression of Oct4 during reprogramming leads to off-target gene activation during reprogramming and epigenetic aberrations in resulting iPSCs and thereby bear major implications for further development and application of iPSC technology. SKM can induce pluripotency in somatic cells in the absence of exogenous Oct4 SM coexpression activates the retroviral silencing machinery in somatic cells Oct4 overexpression drives massive off-target gene activation during reprogramming OSKM, but not SKM, iPSCs show abnormal imprinting and differentiation patterns
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Affiliation(s)
- Sergiy Velychko
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Kenjiro Adachi
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Kee-Pyo Kim
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Yanlin Hou
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Caitlin M MacCarthy
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Guangming Wu
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, 6 Luoxuan Avenue, Haizhu District, 510320 Guangzhou, PRC.
| | - Hans R Schöler
- Department for Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany; Medical Faculty, University of Münster, Domagkstrasse 3, 48449 Münster, Germany.
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5
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Duan JE, Jiang ZC, Alqahtani F, Mandoiu I, Dong H, Zheng X, Marjani SL, Chen J, Tian XC. Methylome Dynamics of Bovine Gametes and in vivo Early Embryos. Front Genet 2019; 10:512. [PMID: 31191619 PMCID: PMC6546829 DOI: 10.3389/fgene.2019.00512] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/10/2019] [Indexed: 01/12/2023] Open
Abstract
DNA methylation undergoes drastic fluctuation during early mammalian embryogenesis. The dynamics of global DNA methylation in bovine embryos, however, have mostly been studied by immunostaining. We adopted the whole genome bisulfite sequencing (WGBS) method to characterize stage-specific genome-wide DNA methylation in bovine sperm, immature oocytes, oocytes matured in vivo and in vitro, as well as in vivo developed single embryos at the 2-, 4-, 8-, and 16-cell stages. We found that the major wave of genome-wide DNA demethylation was complete by the 8-cell stage when de novo methylation became prominent. Sperm and oocytes were differentially methylated in numerous regions (DMRs), which were primarily intergenic, suggesting that these non-coding regions may play important roles in gamete specification. DMRs were also identified between in vivo and in vitro matured oocytes, suggesting environmental effects on epigenetic modifications. In addition, virtually no (less than 1.5%) DNA methylation was found in mitochondrial DNA. Finally, by using RNA-seq data generated from embryos at the same developmental stages, we revealed a weak inverse correlation between gene expression and promoter methylation. This comprehensive analysis provides insight into the critical features of the bovine embryo methylome, and serves as an important reference for embryos produced in vitro, such as by in vitro fertilization and cloning. Lastly, these data can also provide a model for the epigenetic dynamics in human early embryos.
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Affiliation(s)
- Jingyue Ellie Duan
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
| | - Zongliang Carl Jiang
- School of Animal Science, AgCenter, Louisiana State University, Baton Rouge, LA, United States
| | - Fahad Alqahtani
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, United States
| | - Ion Mandoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, United States
| | - Hong Dong
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Xinbao Zheng
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Sadie L Marjani
- Department of Biology, Central Connecticut State University, New Britain, CT, United States
| | - Jingbo Chen
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Ürümqi, China
| | - Xiuchun Cindy Tian
- Department of Animal Science, University of Connecticut, Storrs, CT, United States
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Placental imprinted gene expression mediates the effects of maternal psychosocial stress during pregnancy on fetal growth. J Dev Orig Health Dis 2019; 10:196-205. [PMID: 30968809 DOI: 10.1017/s2040174418000545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Imprinted genes uniquely drive and support fetoplacental growth by controlling the allocation of maternal resources to the fetus and affecting the newborn's growth. We previously showed that alterations of the placental imprinted gene expression are associated with suboptimal perinatal growth and respond to environmental stimuli including socio-economic determinants. At the same time, maternal psychosocial stress during pregnancy (MPSP) has been shown to affect fetal growth. Here, we set out to test the hypothesis that placental imprinted gene expression mediates the effects of MPSP on fetal growth in a well-characterized birth cohort, the Stress in Pregnancy (SIP) Study. We observed that mothers experiencing high MPSP deliver infants with lower birthweight (P=0.047). Among the 109 imprinted genes tested, we detected panels of placental imprinted gene expression of 23 imprinted genes associated with MPSP and 26 with birthweight. Among these genes, five imprinted genes (CPXM2, glucosidase alpha acid (GAA), GPR1, SH3 and multiple ankyrin repeat domains 2 (SHANK2) and THSD7A) were common to the two panels. In multivariate analyses, controlling for maternal age and education and gestational age at birth and infant gender, two genes, GAA and SHANK2, each showed a 22% mediation of MPSP on fetal growth. These data provide new insights into the role that imprinted genes play in translating the maternal stress message into a fetoplacental growth pattern.
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Nomura Y, John RM, Janssen AB, Davey C, Finik J, Buthmann J, Glover V, Lambertini L. Neurodevelopmental consequences in offspring of mothers with preeclampsia during pregnancy: underlying biological mechanism via imprinting genes. Arch Gynecol Obstet 2017; 295:1319-1329. [PMID: 28382413 PMCID: PMC6058691 DOI: 10.1007/s00404-017-4347-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 03/07/2017] [Indexed: 11/29/2022]
Abstract
PURPOSE Preeclampsia is known to be a leading cause of mortality and morbidity among mothers and their infants. Approximately 3-8% of all pregnancies in the US are complicated by preeclampsia and another 5-7% by hypertensive symptoms. However, less is known about its long-term influence on infant neurobehavioral development. The current review attempts to demonstrate new evidence for imprinting gene dysregulation caused by hypertension, which may explain the link between maternal preeclampsia and neurocognitive dysregulation in offspring. METHOD Pub Med and Web of Science databases were searched using the terms "preeclampsia," "gestational hypertension," "imprinting genes," "imprinting dysregulation," and "epigenetic modification," in order to review the evidence demonstrating associations between preeclampsia and suboptimal child neurodevelopment, and suggest dysregulation of placental genomic imprinting as a potential underlying mechanism. RESULTS The high mortality and morbidity among mothers and fetuses due to preeclampsia is well known, but there is little research on the long-term biological consequences of preeclampsia and resulting hypoxia on the fetal/child neurodevelopment. In the past decade, accumulating evidence from studies that transcend disciplinary boundaries have begun to show that imprinted genes expressed in the placenta might hold clues for a link between preeclampsia and impaired cognitive neurodevelopment. A sudden onset of maternal hypertension detected by the placenta may result in misguided biological programming of the fetus via changes in the epigenome, resulting in suboptimal infant development. CONCLUSION Furthering our understanding of the molecular and cellular mechanisms through which neurodevelopmental trajectories of the fetus/infant are affected by preeclampsia and hypertension will represent an important first step toward preventing adverse neurodevelopment in infants.
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Affiliation(s)
- Yoko Nomura
- Department of Psychology, Queens College, the City University of New York, 65-30 Kissena Blvd, Flushing, NY, 11367, USA.
- Graduate Center, the City University of New York, Flushing, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA.
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, USA.
| | - Rosalind M John
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | | | - Charles Davey
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jackie Finik
- Department of Psychology, Queens College, the City University of New York, 65-30 Kissena Blvd, Flushing, NY, 11367, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Jessica Buthmann
- Department of Psychology, Queens College, the City University of New York, 65-30 Kissena Blvd, Flushing, NY, 11367, USA
- Graduate Center, the City University of New York, Flushing, USA
| | | | - Luca Lambertini
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Obstetrics, Gynecology and Reproductive Science, Icahn School of Medicine at Mount Sinai, New York, USA
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8
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Xu GF, Liao Y, Li JY, Liu YF, Huang Y, Wu YQ, Liu J, Lv PP, Zhang RJ, Zhang D. Ovarian stimulation perturbs methylation status of placental imprinting genes and reduces blood pressure in the second generation offspring. Eur J Obstet Gynecol Reprod Biol 2017; 211:140-145. [PMID: 28259006 DOI: 10.1016/j.ejogrb.2017.02.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/03/2017] [Accepted: 02/17/2017] [Indexed: 10/20/2022]
Abstract
OBJECTIVE(S) Assisted reproductive technology (ART) is associated with DNA methylation dysfunction of offspring. However, it is unclear whether ovarian stimulation (OS) is responsible for DNA methylation dysfunction of offspring STUDY DESIGN: We built the first-generation (F1) and second-generation (F2) offspring mice model of ovarian stimulation. Bodyweight of F1 and F2 were measured. Expression levels of several imprinted genes (Impact, H19, Igf2, Plagl1, Mest, and Snrpn) in F1 placenta were tested. Methylation status of Plagl1 and H19 promoters was examined with bisulfite sequencing. Glucose tolerance, blood pressure, and heart rate were evaluated in F2 mice. RESULTS The OS F1 showed elevated bodyweights in the 2nd, 3rd and 4th weeks, but the difference disappeared in the 5th week. Plagl1 was down-regulated in OS F1. Promoters of Plagl1 and H19 were also hypermethylated in OS F1. F2 of OS mice had the similar bodyweight and glucose tolerance compared with the control F2. However, F2 of OS ♂F1+OS♀ F1 showed the decreased systolic pressure, diastolic pressure, and heart rate. CONCLUSIONS Ovarian stimulation perturbs expression levels and methylation status of imprinted genes in offspring. The effect of ovarian stimulation may be passed to F2.
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Affiliation(s)
- Gu-Feng Xu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Yun Liao
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jing-Yi Li
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Yi-Feng Liu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Yun Huang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Yi-Qing Wu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Juan Liu
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Ping-Ping Lv
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Run-Jv Zhang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Dan Zhang
- Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China; Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China.
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Disteche CM. Dosage compensation of the sex chromosomes and autosomes. Semin Cell Dev Biol 2016; 56:9-18. [PMID: 27112542 DOI: 10.1016/j.semcdb.2016.04.013] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 12/16/2022]
Abstract
Males are XY and females are XX in most mammalian species. Other species such as birds have a different sex chromosome make-up: ZZ in males and ZW in females. In both types of organisms one of the sex chromosomes, Y or W, has degenerated due to lack of recombination with its respective homolog X or Z. Since autosomes are present in two copies in diploid organisms the heterogametic sex has become a natural "aneuploid" with haploinsufficiency for X- or Z-linked genes. Specific mechanisms have evolved to restore a balance between critical gene products throughout the genome and between males and females. Some of these mechanisms were co-opted from and/or added to compensatory processes that alleviate autosomal aneuploidy. Surprisingly, several modes of dosage compensation have evolved. In this review we will consider the evidence for dosage compensation and the molecular mechanisms implicated.
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Affiliation(s)
- Christine M Disteche
- Department of Pathology, School of Medicine, University of Washington, 1959 NE Pacific St. Seattle, WA 98115, USA; Department of Medicine, School of Medicine, University of Washington, 1959 NE Pacific St. Seattle, WA 98115, USA.
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Abstract
PURPOSE OF REVIEW Genomic imprinting is an epigenetically-driven phenomenon that responds to environmental stimuli to determine the fetal growth trajectory. This review aims at describing the transgenerational meaning of genomic imprinting while supporting the study of genomic imprinting in placenta for the determination of an important biomarker of chronic and developmental disorders in children as driven by the environment. RECENT FINDINGS Recent work has shown that genomic imprinting reaches beyond the basic significance of an epigenetic mark regulating gene expression. Genomic imprinting has been theorized as the main determinant of epigenetic inheritance. Concomitantly, new studies in the field of molecular epidemiology became available that tie the fetal growth trajectory to genomic imprinting in response to environmental stimuli, making of genomic imprinting the driving force of the fetal growth. When carried out in placenta, the effector of the intrauterine environment as conveyed by the maternal exposure to the general life environment, the study of genomic imprinting may reveal critical information on alterations of the fetal growth trajectory. SUMMARY The study of genomic imprinting profiles in placentas from birth cohorts of individuals exposed to different environmental stimuli can provide a new, much needed, tool for the elaboration of effective public health intervention plans for child health.
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Padmanabhan N, Jia D, Geary-Joo C, Wu X, Ferguson-Smith AC, Fung E, Bieda MC, Snyder FF, Gravel RA, Cross JC, Watson ED. Mutation in folate metabolism causes epigenetic instability and transgenerational effects on development. Cell 2013; 155:81-93. [PMID: 24074862 PMCID: PMC3844871 DOI: 10.1016/j.cell.2013.09.002] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 06/01/2013] [Accepted: 08/28/2013] [Indexed: 11/25/2022]
Abstract
The importance of maternal folate consumption for normal development is well established, yet the molecular mechanism linking folate metabolism to development remains poorly understood. The enzyme methionine synthase reductase (Mtrr) is necessary for utilization of methyl groups from the folate cycle. We found that a hypomorphic mutation of the mouse Mtrr gene results in intrauterine growth restriction, developmental delay, and congenital malformations, including neural tube, heart, and placental defects. Importantly, these defects were dependent upon the Mtrr genotypes of the maternal grandparents. Furthermore, we observed widespread epigenetic instability associated with altered gene expression in the placentas of wild-type grandprogeny of Mtrr-deficient maternal grandparents. Embryo transfer experiments revealed that Mtrr deficiency in mice lead to two distinct, separable phenotypes: adverse effects on their wild-type daughters' uterine environment, leading to growth defects in wild-type grandprogeny, and the appearance of congenital malformations independent of maternal environment that persist for five generations, likely through transgenerational epigenetic inheritance.
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Affiliation(s)
- Nisha Padmanabhan
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
| | - Dongxin Jia
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada
| | - Colleen Geary-Joo
- Transgenic Services, Clara Christie Centre for Mouse Genomics, University of Calgary, Calgary, T2N 4N1, Canada
| | - Xuchu Wu
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada
| | - Anne C. Ferguson-Smith
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Ernest Fung
- Department of Medical Genetics, University of Calgary, Calgary, T2N 4N1, Canada
| | - Mark C. Bieda
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada
- Alberta Children’s Hospital Research Institute for Child & Maternal Health, University of Calgary, Calgary, T2N 4N1, Canada
| | - Floyd F. Snyder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada
- Department of Medical Genetics, University of Calgary, Calgary, T2N 4N1, Canada
- Alberta Children’s Hospital Research Institute for Child & Maternal Health, University of Calgary, Calgary, T2N 4N1, Canada
| | - Roy A. Gravel
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada
- Department of Medical Genetics, University of Calgary, Calgary, T2N 4N1, Canada
- Alberta Children’s Hospital Research Institute for Child & Maternal Health, University of Calgary, Calgary, T2N 4N1, Canada
| | - James C. Cross
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada
- Department of Medical Genetics, University of Calgary, Calgary, T2N 4N1, Canada
- Alberta Children’s Hospital Research Institute for Child & Maternal Health, University of Calgary, Calgary, T2N 4N1, Canada
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, T2N 4N1, Canada
| | - Erica D. Watson
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3EG, UK
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, T2N 4N1, Canada
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Type 2 diabetes: the genetic conflict hypothesis. Med Hypotheses 2013; 80:436-40. [PMID: 23374424 DOI: 10.1016/j.mehy.2012.12.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 12/05/2012] [Accepted: 12/29/2012] [Indexed: 11/24/2022]
Abstract
We propose that conflict between paternally and maternally derived genes in the fetus explains three apparently unrelated observations in epidemiological studies of type 2 diabetes mellitus (DM2): (i) low birth weight is a risk factor for the development of DM2, (ii) there is a high prevalence of low birth weight among babies of fathers who develop DM2, and (iii) an exceptionally high prevalence of DM2 exists in modern day Arabs. Genetic conflict is caused by a particular relationship between the parents, their genes and their offspring: (i) mothers are sometimes polyandrous i.e. have children with more than one man, (ii) mothers provide more biological resources to the fetus than fathers, and (iii) the genes that regulate fetal growth come from both parents and both sets of genes determine the use of resources which are only those of the mother. There is a tendency for maternally derived genes (that promote fetal growth) to be suppressed, in order to spare use of mother's resources, while the same paternally derived genes tend to be expressed (to enhance use of the mother's resources). These same genes are pleiotropic: they affect not only fetal growth (birth weight) but also insulin resistance and hence the development of DM2. Polyandry increases differences in the expression between two parental alleles in the fetus i.e. increases genetic conflict and results in the production of bigger babies whereas monandry has the opposite effect. Consequently, parent-of-origin-biased expression of pleiotropic developmental genes could explain why smaller babies are more common when the fathers have DM2. Similarly less genetic conflict in Arabs (resulting from the tradition of strict monandry, the practice of levirate, and preference for a paternal cousin as spouse) could explain, at least in part, their exceptionally high prevalence of DM2. This hypothesis links human mate selection with the risk of developing DM2.
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Lambertini L, Marsit CJ, Sharma P, Maccani M, Ma Y, Hu J, Chen J. Imprinted gene expression in fetal growth and development. Placenta 2012; 33:480-6. [PMID: 22465419 DOI: 10.1016/j.placenta.2012.03.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 02/29/2012] [Accepted: 03/01/2012] [Indexed: 01/01/2023]
Abstract
Experimental studies showed that genomic imprinting is fundamental in fetoplacental development by timely regulating the expression of the imprinted genes to overlook a set of events determining placenta implantation, growth and embryogenesis. We examined the expression profile of 22 imprinted genes which have been linked to pregnancy abnormalities that may ultimately influence childhood development. The study was conducted in a subset of 106 placenta samples, overrepresented with small and large for gestational age cases, from the Rhode Island Child Health Study. We investigated associations between imprinted gene expression and three fetal development parameters: newborn head circumference, birth weight, and size for gestational age. Results from our investigation show that the maternally imprinted/paternally expressed gene ZNF331 inversely associates with each parameter to drive smaller fetal size, while paternally imprinted/maternally expressed gene SLC22A18 directly associates with the newborn head circumference promoting growth. Multidimensional Scaling analysis revealed two clusters within the 22 imprinted genes which are independently associated with fetoplacental development. Our data suggest that cluster 1 genes work by assuring cell growth and tissue development, while cluster 2 genes act by coordinating these processes. Results from this epidemiologic study offer solid support for the key role of imprinting in fetoplacental development.
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Affiliation(s)
- L Lambertini
- Department of Preventive Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA.
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Lambertini L, Lee TL, Chan WY, Lee MJ, Diplas A, Wetmur J, Chen J. Differential methylation of imprinted genes in growth-restricted placentas. Reprod Sci 2011; 18:1111-7. [PMID: 21693779 DOI: 10.1177/1933719111404611] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A complex network of epigenetic factors participates in regulating the monoallelic expression of a small subset of genes (~1%) in the human genome. This phenomenon goes under the definition of genomic imprinting, a parent-of-origin effect that, when altered during early embryogenesis, may influence fetal development into adulthood. Pertubations in genomic imprinting have been associated with placental and fetal growth restrictions. We analyzed the differential DNA methylation of all known imprinted genes on 10 appropriate-for-gestational-age, clinically normal, placentas and 7 severe intrauterine growth-restricted placentas. Samples were pooled according to the diagnosis and analyzed by methylated DNA immunoprecipitation (MeDIP) on a tiling microarray platform. The distribution of the differentially methylated regions (DMRs) identified in growth-restricted placentas showed a slight tendency toward hypermethylation. Imprinted genes not expressed in placenta showed a unique DMR profile with the fewest hyper- and hypomethylated DMRs. Promoter and CpG island DMRs were sporadic and randomly distributed. The vast majority of DMR identified (~99%) were mapped in introns, showing no common sequence features. Also, by using the more advanced array data mining softwares, no significant patterns emerged. In contrast, differential methylation showed a highly significant correlation with gene length. Overall these data suggest that differential methylation changes in growth-restricted placentas occur throughout the genomic regions, encompassing genes actively expressed in the placenta. These findings warrant caution in interpreting the significance of genes carrying clustered DMRs because the distribution of DMRs in a gene may be attributed as a function of its length rather than as a specific biological role.
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Affiliation(s)
- Luca Lambertini
- Department of Preventive Medicine, Mount Sinai School of Medicine, New York, NY 10029, USA.
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