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Qiao J, Chen Y, Lu Y, Wang T, Li X, Qin W, Li A, Chen G. A Syndrome of Variable Allergy, Short Stature, and Fatty Liver. Front Genet 2022; 12:784135. [PMID: 35140738 PMCID: PMC8819686 DOI: 10.3389/fgene.2021.784135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/26/2021] [Indexed: 11/23/2022] Open
Abstract
SLC22A18 (solute carrier family 22 member 18) is an imprinted gene, but its role in growth and development is not clear. In the present study, we recorded the clinical information of six male patients of six unrelated families. Real-time quantitative PCR, Sanger sequencing, and DNA methylation sequencing were performed in these patients. The results suggested that the patients with the clinical characteristics of allergic allergy, short stature, and fatty liver had a lower expression of SLC22A18. One novel variant (chr11: 2899732 delA) with clinical significance was found in the core promoter region of the patients. Overall, this study found a syndrome associated with SLC22A18.
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Affiliation(s)
- Jing Qiao
- Department of Pediatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Jing Qiao,
| | - Yue Chen
- Department of Pediatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ying Lu
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Tiejun Wang
- Department of Pharmacy, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaoli Li
- Department of Pediatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Qin
- Department of Pediatrics, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Aifen Li
- Department of Pediatrics, Jian Hospital of Shanghai East Hospital, Jian, China
| | - Guangquan Chen
- Fetal Medicine Unit & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, Tongji University, Shanghai, China
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Edwards CA, Takahashi N, Corish JA, Ferguson-Smith AC. The origins of genomic imprinting in mammals. Reprod Fertil Dev 2020; 31:1203-1218. [PMID: 30615843 DOI: 10.1071/rd18176] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/01/2018] [Indexed: 12/13/2022] Open
Abstract
Genomic imprinting is a process that causes genes to be expressed according to their parental origin. Imprinting appears to have evolved gradually in two of the three mammalian subclasses, with no imprinted genes yet identified in prototheria and only six found to be imprinted in marsupials to date. By interrogating the genomes of eutherian suborders, we determine that imprinting evolved at the majority of eutherian specific genes before the eutherian radiation. Theories considering the evolution of imprinting often relate to resource allocation and recently consider maternal-offspring interactions more generally, which, in marsupials, places a greater emphasis on lactation. In eutherians, the imprint memory is retained at least in part by zinc finger protein 57 (ZFP57), a Kruppel associated box (KRAB) zinc finger protein that binds specifically to methylated imprinting control regions. Some imprints are less dependent on ZFP57invivo and it may be no coincidence that these are the imprints that are found in marsupials. Because marsupials lack ZFP57, this suggests another more ancestral protein evolved to regulate imprints in non-eutherian subclasses, and contributes to imprinting control in eutherians. Hence, understanding the mechanisms acting at imprinting control regions across mammals has the potential to provide valuable insights into our understanding of the origins and evolution of genomic imprinting.
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Affiliation(s)
- Carol A Edwards
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Nozomi Takahashi
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Jennifer A Corish
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Anne C Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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3
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Vincenz C, Lovett JL, Wu W, Shedden K, Strassmann BI. Loss of Imprinting in Human Placentas Is Widespread, Coordinated, and Predicts Birth Phenotypes. Mol Biol Evol 2020; 37:429-441. [PMID: 31639821 PMCID: PMC6993844 DOI: 10.1093/molbev/msz226] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Genomic imprinting leads to mono-allelic expression of genes based on parent of origin. Therian mammals and angiosperms evolved this mechanism in nutritive tissues, the placenta, and endosperm, where maternal and paternal genomes are in conflict with respect to resource allocation. We used RNA-seq to analyze allelic bias in the expression of 91 known imprinted genes in term human placentas from a prospective cohort study in Mali. A large fraction of the imprinted exons (39%) deviated from mono-allelic expression. Loss of imprinting (LOI) occurred in genes with either maternal or paternal expression bias, albeit more frequently in the former. We characterized LOI using binomial generalized linear mixed models. Variation in LOI was predominantly at the gene as opposed to the exon level, consistent with a single promoter driving the expression of most exons in a gene. Some genes were less prone to LOI than others, particularly lncRNA genes were rarely expressed from the repressed allele. Further, some individuals had more LOI than others and, within a person, the expression bias of maternally and paternally imprinted genes was correlated. We hypothesize that trans-acting maternal effect genes mediate correlated LOI and provide the mother with an additional lever to control fetal growth by extending her influence to LOI of the paternally imprinted genes. Limited evidence exists to support associations between LOI and offspring phenotypes. We show that birth length and placental weight were associated with allelic bias, making this the first comprehensive report of an association between LOI and a birth phenotype.
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Affiliation(s)
- Claudius Vincenz
- Research Center for Group Dynamics, Institute for Social Research, University of Michigan, Ann Arbor, MI
| | - Jennie L Lovett
- Department of Anthropology, University of Michigan, Ann Arbor, MI
| | - Weisheng Wu
- BRCF Bioinformatics Core, University of Michigan, Ann Arbor, MI
| | - Kerby Shedden
- Department of Statistics, University of Michigan, Ann Arbor, MI
| | - Beverly I Strassmann
- Research Center for Group Dynamics, Institute for Social Research, University of Michigan, Ann Arbor, MI
- Department of Anthropology, University of Michigan, Ann Arbor, MI
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4
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Knockdown of Orphan Transporter SLC22A18 Impairs Lipid Metabolism and Increases Invasiveness of HepG2 Cells. Pharm Res 2019; 36:39. [PMID: 30635741 DOI: 10.1007/s11095-018-2565-4] [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] [Received: 09/28/2018] [Accepted: 12/26/2018] [Indexed: 12/19/2022]
Abstract
PURPOSE The aim of this work is to investigate the roles of solute carrier family 22 member 18 (SLC22A18) in lipid metabolism and in establishing the tumor phenotype of HepG2 cells. METHODS SLC22A18-knockdown HepG2 cells were established by stable transfection with shRNA. Protein expression levels were measured by quantitative proteomics and Western blot analysis. Cell growth was examined by cell counting kit. Accumulation of triglyceride-rich lipid droplets was measured by Oil-Red O staining. Cell migration and invasion were examined by Transwell assays. RESULTS SLC22A18-knockdown HepG2 cells accumulated triglyceride-rich lipid droplets and showed decreased expression levels of lysosomal/autophagic proteins, suggesting that lipid degradation is suppressed. Growth of HepG2 cells was decreased by SLC22A18 knockdown, but was restored by free fatty acid supplementation. In addition, SLC22A18 knockdown decreased the expression of insulin-like growth factor-binding protein 1 (IGFBP-1) and increased the invasion ability of HepG2 cells. Exogenous IGFBP-1 blocked the increase of invasion activity induced by SLC22A18 knockdown. CONCLUSION Our results suggest that suppression of SLC22A18 decreased the supply of intracellular free fatty acids from triglyceride-rich lipid droplets by impairing the lysosomal/autophagy degradation pathway and reduced the invasive activity of HepG2 cells by decreasing IGFBP-1 expression.
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5
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Mai Q, Mai X, Huang X, Zhang D, Huang K, Zhou C. Imprinting Status in Two Human Parthenogenetic Embryonic Stem Cell Lines: Analysis of 63 Imprinted Gene Expression Levels in Undifferentiated and Early Differentiated Stages. Stem Cells Dev 2018; 27:430-439. [PMID: 29402175 DOI: 10.1089/scd.2017.0247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Human parthenogenetic embryonic stem cells (hPESCs) represent a source of histocompatible tissues for transplantation and carry two copies of the maternal genome, but lack the paternal genome. In this study, we selected 63 known human imprinted genes to investigate the imprinting status of hPESC. The expression level of these genes, including 27 maternally and 36 paternally imprinted were illustrated in hPESC and human embryonic stem cells (hESCs) derived from fertilized embryo lines. The expression activity changes of these genes were analyzed in undifferentiated and early differentiated hPESC lines. In addition, the methylation status of four differentially methylated regions (DMRs) of the imprinted genes was analyzed in undifferentiated and early differentiated hPESC and hESC lines. As a result, we found that all the maternally imprinted genes were expressed at similar levels in the undifferentiated hPESC lines and the hESC lines, except ZNF264 and ATP10A. Twenty-one analyzed paternal imprinted genes were expressed at the same level in two separated hPESC lines as well as compared with the hESC lines, whereas 15 other paternal imprinted genes were significantly downregulated or inactivated in hPESC lines as compared with the hESC line. During prolonged passage, the expression levels of the majority of imprinted genes remained stable in two hPESC lines. The four DMRs, including PEG3/ZIM2 (DMRs), SNURF/SNRPN DMRs, and KVDMR1 DMRs are highly methylated in the genes of two undifferentiated hPESCs and its embryonic bodies (EBs), whereas the genes of the undifferentiated hESCs and its EBs are half methylated. During the early differentiation stage, the imprinted genes showed the same expression trend and the expression levels of H19, IGF2, SLC22A2, SLC22A3/SLC22A18, and CPA4 were significantly upregulated in both hPESC lines. As conclusion, hPESCs show a substantial degree of epigenetic stability with respect to some imprinted genes.
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Affiliation(s)
- Qingyun Mai
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Xiuyun Mai
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China .,2 Reproductive Medical Center , Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xin Huang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Dan Zhang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Kejun Huang
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
| | - Canquan Zhou
- 1 Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-sen University , Guangzhou, China
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6
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Jung Y, Jun Y, Lee HY, Kim S, Jung Y, Keum J, Lee YS, Cho YB, Lee S, Kim J. Characterization of SLC22A18 as a tumor suppressor and novel biomarker in colorectal cancer. Oncotarget 2016. [PMID: 26196590 PMCID: PMC4694837 DOI: 10.18632/oncotarget.4681] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
SLC22A18, solute carrier family 22, member 18, has been proposed to function as a tumor suppressor based on its chromosomal location at 11p15.5, mutations and aberrant splicing in several types of cancer and down-regulation in glioblastoma. In this study, we sought to demonstrate the significance of SLC22A18 as a tumor suppressor in colorectal cancer (CRC) and provide mechanistic bases for its function. We first showed that the expression of SLC22A18 is significantly down-regulated in tumor tissues using matched normal-tumor samples from CRC patients. This finding was also supported by publically accessible data from The Cancer Genome Atlas (TCGA). Functionally, SLC22A18 inhibits colony formation and induces of G2/M arrest consistent with being a tumor suppressor. Interestingly, suppression of KRAS by RNA interference promotes SLC22A18 expression, and expression of SLC22A18 in turn inhibits KRASG12D-mediated anchorage independent growth of NIH3T3 cells indicating a mutual negative interaction. Finally, we evaluated diagnostic and prognostic values of SLC22A18 using clinical and gene expression data from TCGA which revealed a significantly worse long-term prognosis for patients with low level SLC22A18 expression. In sum, we established SLC22A18 as a tumor suppressor in colon epithelial cells and propose that SLC22A18 is potentially a marker of diagnostic and prognostic values.
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Affiliation(s)
- Yeonjoo Jung
- Ewha Research Center for Systems Biology, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Yukyung Jun
- Ewha Research Center for Systems Biology, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Hee-Young Lee
- Ewha Research Center for Systems Biology, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Suyeon Kim
- Ewha Research Center for Systems Biology, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Yeonhwa Jung
- Ewha Research Center for Systems Biology, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Juhee Keum
- Ewha Research Center for Systems Biology, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Yeo Song Lee
- Samsung Biomedical Research Institute, Seoul, Korea
| | - Yong Beom Cho
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sanghyuk Lee
- Ewha Research Center for Systems Biology, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
| | - Jaesang Kim
- Ewha Research Center for Systems Biology, Seoul, Korea.,Department of Life Science, Ewha Womans University, Seoul, Korea
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7
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Perez JD, Rubinstein ND, Fernandez DE, Santoro SW, Needleman LA, Ho-Shing O, Choi JJ, Zirlinger M, Chen SK, Liu JS, Dulac C. Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain. eLife 2015; 4:e07860. [PMID: 26140685 PMCID: PMC4512258 DOI: 10.7554/elife.07860] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/02/2015] [Indexed: 12/14/2022] Open
Abstract
The maternal and paternal genomes play different roles in mammalian brains as a result of genomic imprinting, an epigenetic regulation leading to differential expression of the parental alleles of some genes. Here we investigate genomic imprinting in the cerebellum using a newly developed Bayesian statistical model that provides unprecedented transcript-level resolution. We uncover 160 imprinted transcripts, including 41 novel and independently validated imprinted genes. Strikingly, many genes exhibit parentally biased--rather than monoallelic--expression, with different magnitudes according to age, organ, and brain region. Developmental changes in parental bias and overall gene expression are strongly correlated, suggesting combined roles in regulating gene dosage. Finally, brain-specific deletion of the paternal, but not maternal, allele of the paternally-biased Bcl-x, (Bcl2l1) results in loss of specific neuron types, supporting the functional significance of parental biases. These findings reveal the remarkable complexity of genomic imprinting, with important implications for understanding the normal and diseased brain.
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Affiliation(s)
- Julio D Perez
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Nimrod D Rubinstein
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | | | - Stephen W Santoro
- Neuroscience Program, Department of Zoology and Physiology, University of Wyoming, Laramie, United States
| | - Leigh A Needleman
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Olivia Ho-Shing
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - John J Choi
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | | | | | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, United States
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
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8
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Cheong CY, Chng K, Ng S, Chew SB, Chan L, Ferguson-Smith AC. Germline and somatic imprinting in the nonhuman primate highlights species differences in oocyte methylation. Genome Res 2015; 25:611-23. [PMID: 25862382 PMCID: PMC4417110 DOI: 10.1101/gr.183301.114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 03/04/2015] [Indexed: 12/22/2022]
Abstract
Genomic imprinting is an epigenetic mechanism resulting in parental allele-specific gene expression. Defects in normal imprinting are found in cancer, assisted reproductive technologies, and several human syndromes. In mouse models, germline-derived DNA methylation is shown to regulate imprinting. Though imprinting is largely conserved between mammals, species- and tissue-specific domains of imprinted expression exist. Using the cynomolgus macaque (Macaca fascicularis) to assess primate-specific imprinting, we present a comprehensive view of tissue-specific imprinted expression and DNA methylation at established imprinted gene clusters. For example, like mouse and unlike human, macaque IGF2R is consistently imprinted, and the PLAGL1, INPP5F transcript variant 2, and PEG3 imprinting control regions are not methylated in the macaque germline but acquire this post-fertilization. Methylome data from human early embryos appear to support this finding. These suggest fundamental differences in imprinting control mechanisms between primate species and rodents at some imprinted domains, with implications for our understanding of the epigenetic programming process in humans and its influence on disease.
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Affiliation(s)
- Clara Y Cheong
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Keefe Chng
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Shilen Ng
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Siew Boom Chew
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Louiza Chan
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609
| | - Anne C Ferguson-Smith
- Growth, Development and Metabolism Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A-STAR), Singapore 117609; Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
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9
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Varmuza S, Miri K. What does genetics tell us about imprinting and the placenta connection? Cell Mol Life Sci 2015; 72:51-72. [PMID: 25194419 PMCID: PMC11114082 DOI: 10.1007/s00018-014-1714-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 01/07/2023]
Abstract
Genomic imprinting is an epigenetic gene silencing phenomenon that is specific to eutherians in the vertebrate lineage. The acquisition of both placentation and genomic imprinting has spurred interest in the possible evolutionary link for many years. In this review we examine the genetic evidence and find that while many imprinted domains are anchored by genes required for proper placenta development in a parent of origin fashion, an equal number of imprinted genes have no apparent function that depends on imprinting. Examination of recent data from studies of molecular and genetic mechanisms points to a maternal control of the selection and maintenance of imprint marks, reinforcing the importance of the oocyte in the healthy development of the placenta and fetus.
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Affiliation(s)
- Susannah Varmuza
- Department of Cell and Systems Biology, University of Toronto, 611-25 Harbord Street, Toronto, M5S 3G5, Canada,
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10
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Matthews BF, Beard H, Brewer E, Kabir S, MacDonald MH, Youssef RM. Arabidopsis genes, AtNPR1, AtTGA2 and AtPR-5, confer partial resistance to soybean cyst nematode (Heterodera glycines) when overexpressed in transgenic soybean roots. BMC PLANT BIOLOGY 2014; 14:96. [PMID: 24739302 PMCID: PMC4021311 DOI: 10.1186/1471-2229-14-96] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 03/28/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Extensive studies using the model system Arabidopsis thaliana to elucidate plant defense signaling and pathway networks indicate that salicylic acid (SA) is the key hormone triggering the plant defense response against biotrophic and hemi-biotrophic pathogens, while jasmonic acid (JA) and derivatives are critical to the defense response against necrotrophic pathogens. Several reports demonstrate that SA limits nematode reproduction. RESULTS Here we translate knowledge gained from studies using Arabidopsis to soybean. The ability of thirty-one Arabidopsis genes encoding important components of SA and JA synthesis and signaling in conferring resistance to soybean cyst nematode (SCN: Heterodera glycines) are investigated. We demonstrate that overexpression of three of thirty-one Arabidoposis genes in transgenic soybean roots of composite plants decreased the number of cysts formed by SCN to less than 50% of those found on control roots, namely AtNPR1(33%), AtTGA2 (38%), and AtPR-5 (38%). Three additional Arabidopsis genes decreased the number of SCN cysts by 40% or more: AtACBP3 (53% of the control value), AtACD2 (55%), and AtCM-3 (57%). Other genes having less or no effect included AtEDS5 (77%), AtNDR1 (82%), AtEDS1 (107%), and AtPR-1 (80%), as compared to control. Overexpression of AtDND1 greatly increased susceptibility as indicated by a large increase in the number of SCN cysts (175% of control). CONCLUSIONS Knowledge of the pathogen defense system gained from studies of the model system, Arabidopsis, can be directly translated to soybean through direct overexpression of Arabidopsis genes. When the genes, AtNPR1, AtGA2, and AtPR-5, encoding specific components involved in SA regulation, synthesis, and signaling, are overexpressed in soybean roots, resistance to SCN is enhanced. This demonstrates functional compatibility of some Arabidopsis genes with soybean and identifies genes that may be used to engineer resistance to nematodes.
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Affiliation(s)
- Benjamin F Matthews
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Hunter Beard
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Eric Brewer
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Sara Kabir
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Margaret H MacDonald
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Reham M Youssef
- United States Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
- Fayoum University, Fayoum, Egypt
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11
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A novel link between Slc22a18 and fat accumulation revealed by a mutation in the spontaneously hypertensive rat. Biochem Biophys Res Commun 2013; 440:521-6. [DOI: 10.1016/j.bbrc.2013.09.096] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 09/18/2013] [Indexed: 11/17/2022]
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12
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Tunster SJ, Jensen AB, John RM. Imprinted genes in mouse placental development and the regulation of fetal energy stores. Reproduction 2013; 145:R117-37. [PMID: 23445556 DOI: 10.1530/rep-12-0511] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Imprinted genes, which are preferentially expressed from one or other parental chromosome as a consequence of epigenetic events in the germline, are known to functionally converge on biological processes that enable in utero development in mammals. Over 100 imprinted genes have been identified in the mouse, the majority of which are both expressed and imprinted in the placenta. The purpose of this review is to provide a summary of the current knowledge regarding imprinted gene function in the mouse placenta. Few imprinted genes have been assessed with respect to their dosage-related action in the placenta. Nonetheless, current data indicate that imprinted genes converge on two key functions of the placenta, nutrient transport and placental signalling. Murine studies may provide a greater understanding of certain human pathologies, including low birth weight and the programming of metabolic diseases in the adult, and complications of pregnancy, such as pre-eclampsia and gestational diabetes, resulting from fetuses carrying abnormal imprints.
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Affiliation(s)
- S J Tunster
- Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff, Wales CF10 3AX, UK
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13
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Wan ES, Qiu W, Baccarelli A, Carey VJ, Bacherman H, Rennard SI, Agustí A, Anderson WH, Lomas DA, DeMeo DL. Systemic steroid exposure is associated with differential methylation in chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2012; 186:1248-55. [PMID: 23065012 PMCID: PMC3622442 DOI: 10.1164/rccm.201207-1280oc] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 09/27/2012] [Indexed: 02/06/2023] Open
Abstract
RATIONALE Systemic glucocorticoids are used therapeutically to treat a variety of medical conditions. Epigenetic processes such as DNA methylation may reflect exposure to glucocorticoids and may be involved in mediating the responses and side effects associated with these medications. OBJECTIVES To test the hypothesis that differences in DNA methylation are associated with current systemic steroid use. METHODS We obtained DNA methylation data at 27,578 CpG sites in 14,475 genes throughout the genome in two large, independent cohorts: the International COPD Genetics Network (n(discovery) = 1,085) and the Boston Early Onset COPD study (n(replication) = 369). Sites were tested for association with current systemic steroid use using generalized linear mixed models. MEASUREMENTS AND MAIN RESULTS A total of 511 sites demonstrated significant differential methylation by systemic corticosteroid use in all three of our primary models. Pyrosequencing validation confirmed robust differential methylation at CpG sites annotated to genes such as SLC22A18, LRP3, HIPK3, SCNN1A, FXYD1, IRF7, AZU1, SIT1, GPR97, ABHD16B, and RABGEF1. Functional annotation clustering demonstrated significant enrichment in intrinsic membrane components, hemostasis and coagulation, cellular ion homeostasis, leukocyte and lymphocyte activation and chemotaxis, protein transport, and responses to nutrients. CONCLUSIONS Our analyses suggest that systemic steroid use is associated with site-specific differential methylation throughout the genome. Differentially methylated CpG sites were found in biologically plausible and previously unsuspected pathways; these genes and pathways may be relevant in the development of novel targeted therapies.
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Affiliation(s)
- Emily S Wan
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA.
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14
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Simonis M, Atanur SS, Linsen S, Guryev V, Ruzius FP, Game L, Lansu N, de Bruijn E, van Heesch S, Jones SJM, Pravenec M, Aitman TJ, Cuppen E. Genetic basis of transcriptome differences between the founder strains of the rat HXB/BXH recombinant inbred panel. Genome Biol 2012; 13:r31. [PMID: 22541052 PMCID: PMC3446305 DOI: 10.1186/gb-2012-13-4-r31] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/13/2012] [Accepted: 04/27/2012] [Indexed: 12/30/2022] Open
Abstract
Background With the advent of next generation sequencing it has become possible to detect genomic variation on a large scale. However, predicting which genomic variants are damaging to gene function remains a challenge, as knowledge of the effects of genomic variation on gene expression is still limited. Recombinant inbred panels are powerful tools to study the cis and trans effects of genetic variation on molecular phenotypes such as gene expression. Results We generated a comprehensive inventory of genomic differences between the two founder strains of the rat HXB/BXH recombinant inbred panel: SHR/OlaIpcv and BN-Lx/Cub. We identified 3.2 million single nucleotide variants, 425,924 small insertions and deletions, 907 copy number changes and 1,094 large structural genetic variants. RNA-sequencing analyses on liver tissue of the two strains identified 532 differentially expressed genes and 40 alterations in transcript structure. We identified both coding and non-coding variants that correlate with differential expression and alternative splicing. Furthermore, structural variants, in particular gene duplications, show a strong correlation with transcriptome alterations. Conclusions We show that the panel is a good model for assessing the genetic basis of phenotypic heterogeneity and for providing insights into possible underlying molecular mechanisms. Our results reveal a high diversity and complexity underlying quantitative and qualitative transcriptional differences.
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Affiliation(s)
- Marieke Simonis
- Genome Biology Group, Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Golding MC, Magri LS, Zhang L, Lalone SA, Higgins MJ, Mann MRW. Depletion of Kcnq1ot1 non-coding RNA does not affect imprinting maintenance in stem cells. Development 2011; 138:3667-78. [PMID: 21775415 PMCID: PMC3152924 DOI: 10.1242/dev.057778] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2011] [Indexed: 01/18/2023]
Abstract
To understand the complex regulation of genomic imprinting it is important to determine how early embryos establish imprinted gene expression across large chromosomal domains. Long non-coding RNAs (ncRNAs) have been associated with the regulation of imprinting domains, yet their function remains undefined. Here, we investigated the mouse Kcnq1ot1 ncRNA and its role in imprinted gene regulation during preimplantation development by utilizing mouse embryonic and extra-embryonic stem cell models. Our findings demonstrate that the Kcnq1ot1 ncRNA extends 471 kb from the transcription start site. This is significant as it raises the possibility that transcription through downstream genes might play a role in their silencing, including Th, which we demonstrate possesses maternal-specific expression during early development. To distinguish between a functional role for the transcript and properties inherent to transcription of long ncRNAs, we employed RNA interference-based technology to deplete Kcnq1ot1 transcripts. We hypothesized that post-transcriptional depletion of Kcnq1ot1 ncRNA would lead to activation of normally maternal-specific protein-coding genes on the paternal chromosome. Post-transcriptional short hairpin RNA-mediated depletion in embryonic stem, trophoblast stem and extra-embryonic endoderm stem cells had no observable effect on the imprinted expression of genes within the domain, or on Kcnq1ot1 imprinting center DNA methylation, although a significant decrease in Kcnq1ot1 RNA signal volume in the nucleus was observed. These data support the argument that it is the act of transcription that plays a role in imprint maintenance during early development rather than a post-transcriptional role for the RNA itself.
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Affiliation(s)
- Michael C. Golding
- Departments of Obstetrics and Gynecology and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON N6A 5W9, Canada
- Children's Health Research Institute, London, ON N6C 2V5, Canada
- Lawson Health Research Institute, London, ON N6C 2V5, Canada
| | - Lauren S. Magri
- Departments of Obstetrics and Gynecology and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON N6A 5W9, Canada
- Children's Health Research Institute, London, ON N6C 2V5, Canada
- Lawson Health Research Institute, London, ON N6C 2V5, Canada
| | - Liyue Zhang
- Children's Health Research Institute, London, ON N6C 2V5, Canada
- Lawson Health Research Institute, London, ON N6C 2V5, Canada
| | - Sarah A. Lalone
- Departments of Obstetrics and Gynecology and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON N6A 5W9, Canada
- Children's Health Research Institute, London, ON N6C 2V5, Canada
- Lawson Health Research Institute, London, ON N6C 2V5, Canada
| | - Michael J. Higgins
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
| | - Mellissa R. W. Mann
- Departments of Obstetrics and Gynecology and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, ON N6A 5W9, Canada
- Children's Health Research Institute, London, ON N6C 2V5, Canada
- Lawson Health Research Institute, London, ON N6C 2V5, Canada
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Abstract
Many questions about the regulation, functional specialization, computational prediction, and evolution of genomic imprinting would be better addressed by having an exhaustive genome-wide catalog of genes that display parent-of-origin differential expression. As a first-pass scan for novel imprinted genes, we performed mRNA-seq experiments on embryonic day 17.5 (E17.5) mouse placenta cDNA samples from reciprocal cross F1 progeny of AKR and PWD mouse strains and quantified the allele-specific expression and the degree of parent-of-origin allelic imbalance. We confirmed the imprinting status of 23 known imprinted genes in the placenta and found that 12 genes reported previously to be imprinted in other tissues are also imprinted in mouse placenta. Through a well-replicated design using an orthogonal allelic-expression technology, we verified 5 novel imprinted genes that were not previously known to be imprinted in mouse (Pde10, Phf17, Phactr2, Zfp64, and Htra3). Our data suggest that most of the strongly imprinted genes have already been identified, at least in the placenta, and that evidence supports perhaps 100 additional weakly imprinted genes. Despite previous appearance that the placenta tends to display an excess of maternally expressed imprinted genes, with the addition of our validated set of placenta-imprinted genes, this maternal bias has disappeared.
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17
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Chromosome-wide analysis of parental allele-specific chromatin and DNA methylation. Mol Cell Biol 2011; 31:1757-70. [PMID: 21321082 DOI: 10.1128/mcb.00961-10] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To reveal the extent of domain-wide epigenetic features at imprinted gene clusters, we performed a high-resolution allele-specific chromatin analysis of over 100 megabases along the maternally or paternally duplicated distal chromosome 7 (Chr7) and Chr15 in mouse embryo fibroblasts (MEFs). We found that reciprocal allele-specific features are limited to imprinted genes and their differentially methylated regions (DMRs), whereas broad local enrichment of H3K27me3 (BLOC) is a domain-wide feature at imprinted clusters. We uncovered novel allele-specific features of BLOCs. A maternally biased BLOC was found along the H19-Igf2 domain. A paternal allele-specific gap was found along Kcnq1ot1, interrupting a biallelic BLOC in the Kcnq1-Cdkn1c domain. We report novel allele-specific chromatin marks at the Peg13 and Slc38a4 DMRs, Cdkn1c upstream region, and Inpp5f_v2 DMR and paternal allele-specific CTCF binding at the Peg13 DMR. Additionally, we derived an imprinted gene predictor algorithm based on our allele-specific chromatin mapping data. The binary predictor H3K9ac and CTCF or H3K4me3 in one allele and H3K9me3 in the reciprocal allele, using a sliding-window approach, recognized with precision the parental allele specificity of known imprinted genes, H19, Igf2, Igf2as, Cdkn1c, Kcnq1ot1, and Inpp5f_v2 on Chr7 and Peg13 and Slc38a4 on Chr15. Chromatin features, therefore, can unequivocally identify genes with imprinted expression.
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18
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Mai X, Mai Q, Li T, Zhou C. Dynamic expression patterns of imprinted genes in human embryonic stem cells following prolonged passaging and differentiation. J Assist Reprod Genet 2010; 28:315-23. [PMID: 21161363 DOI: 10.1007/s10815-010-9524-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 12/01/2010] [Indexed: 11/26/2022] Open
Abstract
PURPOSE To evaluate the overall expression patterns of imprinted genes in human embryonic stem cells following long term culture and differentiation. MATERIALS AND METHODS Expression levels of 65 imprinted genes determined by PCR array were analyzed in one human embryonic stem cell line (cHES1) following prolonged passaging and differentiation. RESULTS Transcripts of 63 imprinted genes were detected in cHES1 cells. Expression levels of all but 5 imprinted genes did not correlate with passage numbers or differ in cells after passage 50 compared with those before passage 50. SLC22A2, SLC22A3, CPA, H19, COPG2IT1 and IGF2 expression were significantly increased in embryoid bodies compared with undifferentiated cells. CONCLUSIONS The global expression profiles of imprinted genes are generally stable in human embryonic stem cells after prolonged passaging and differentiation.
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Affiliation(s)
- Xiuyun Mai
- Reproductive Medical Center, The First Affiliated Hospital of Sun Yat-Sen University, 58 Zhongshan 2nd Avenue, Yuexiu, 510080, Guangzhou, China
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19
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He H, Xu C, Zhao Z, Qin X, Xu H, Zhang H. Low expression of SLC22A18 predicts poor survival outcome in patients with breast cancer after surgery. Cancer Epidemiol 2010; 35:279-85. [PMID: 21144813 DOI: 10.1016/j.canep.2010.09.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 09/09/2010] [Accepted: 09/14/2010] [Indexed: 10/18/2022]
Abstract
PURPOSE The aims of this study were to evaluate the relationship between SLC22A18 expression and clinicopathologic features while investigate the prognostic value of SLC22A18 expression in breast cancer after surgery. SPECIMENS AND METHODS: Immunohistochemistry was used to examine SLC22A18 protein expression in the breast tumors. Prognostic value of SLC22A18 protein and other clinicopathologic factors were evaluated. The Kaplan-Meier method and the Cox proportional hazards model were used to predict factors with a significant independent prognostic value. Digital image analysis was employed to quantify immunostaining. RESULTS SLC22A18 expression was correlated with tumor size, lymph node metastasis, clinical stage, and extensive lyphovascular invasion. The results of Kaplan-Meier analysis indicated that SLC22A18 expression was associated with relapse-free survival (RFS) of breast cancer. The survival of higher expression SLC22A18 group had longer cum survival compared to the group with low expression. The difference was significant (p=0.003, log-rank test). Cox's regression analysis showed that tumor size, lymph nodes metastasis, nuclear stage, extensive lymphovascular invasion, and SLC22A18 expression might be used as prognostic factor for RFS. Nuclear stage and SLC22A18 expression were the most meaningful histopathologic parameter in predicting tumor recurrence. Compared with the group of higher SLC22A18 expression, the lower expression group was more likely to relapse. The HR is 2.624 (p=0.035). CONCLUSION Low expression of SLC22A18 was associated with tumor progression, recurrence and poor survival after breast surgery. Testing expression of SLC22A18 will be helpful for predicting prognosis in breast cancer.
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Affiliation(s)
- Hongyu He
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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20
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Kato Y, Zembutsu H, Takata R, Miya F, Tsunoda T, Obara W, Fujioka T, Nakamura Y. Predicting response of bladder cancers to gemcitabine and carboplatin neoadjuvant chemotherapy through genome-wide gene expression profiling. Exp Ther Med 2010; 2:47-56. [PMID: 22977468 DOI: 10.3892/etm.2010.166] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 11/04/2010] [Indexed: 11/05/2022] Open
Abstract
Neoadjuvant chemotherapy with gemcitabine and carboplatin (GC) for invasive bladder cancer increases the chance of a radical response for a subset of patients, while other patients suffer from severe adverse drug reactions without any benefit. To establish a method for predicting the response to chemotherapy with GC, the expression profiles of biopsy samples from 37 advanced bladder cancers were analyzed using a microarray consisting of 38,500 genes or ESTs. Upon analysis of 9 'responder' and 9 'non-responder' tumors, 12 'predictive' genes were found to be significantly differentially expressed between the 'responder' and 'non-responder' groups, and a numerical prediction scoring system that clearly separated the responder group from the non-responder group was established. This system accurately predicted the drug responses of 18 of 19 additional test cases that were reserved from the original 37 cases. Moreover, a quantitative PCR-based prediction system was developed that may be feasible for routine clinical use, and the sensitivity of invasive bladder cancer to neoadjuvant chemotherapy with GC was able to be predicted by the expression patterns in this set of genes. Nearly 50% of patients treated with GC or methotrexate, vinblastine, doxorubicin and cisplatin (M-VAC) therapy have been reported to achieve complete or partial response to either of these therapies. When we applied this prediction system as well as the system for M-VAC, we expected that approximately 80% of the patients would achieve significant tumor shrinking (>60%) by selection of either the GC or M-VAC regimens. Our results suggest that the two prediction scoring systems lead to achievement of 'personalized therapy' for the treatment of invasive bladder cancer and should improve the quality of life for patients with this disease.
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Affiliation(s)
- Yoichiro Kato
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo 108-8639
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Stefancsik R, Randall JD, Mao C, Sarkar S. Structure and sequence of the human fast skeletal troponin T (TNNT3) gene: insight into the evolution of the gene and the origin of the developmentally regulated isoforms. Comp Funct Genomics 2010; 4:609-25. [PMID: 18629027 PMCID: PMC2447309 DOI: 10.1002/cfg.343] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2003] [Revised: 09/24/2003] [Accepted: 10/06/2003] [Indexed: 11/21/2022] Open
Abstract
We describe the cloning, sequencing and structure of the human fast skeletal troponin T (TNNT3) gene located on chromosome 11p15.5. The single-copy gene encodes 19
exons and 18 introns. Eleven of these exons, 1–3, 9–15 and 18, are constitutively
spliced, whereas exons 4–8 are alternatively spliced. The gene contains an additional
subset of developmentally regulated and alternatively spliced exons, including a foetal
exon located between exon 8 and 9 and exon 16 or α (adult) and 17 or β (foetal and
neonatal). Exon phasing suggests that the majority of the alternatively spliced exons
located at the 5′ end of the gene may have evolved as a result of exon shuffling, because
they are of the same phase class. In contrast, the 3′ exons encoding an evolutionarily
conserved heptad repeat domain, shared by both TnT and troponin I (TnI), may be
remnants of an ancient ancestral gene. The sequence of the 5′ flanking region shows
that the putative promoter contains motifs including binding sites for MyoD, MEF-2
and several transcription factors which may play a role in transcriptional regulation
and tissue-specific expression of TnT. The coding region of TNNT3 exhibits strong
similarity to the corresponding rat sequence. However, unlike the rat TnT gene,
TNNT3 possesses two repeat regions of CCA and TC. The exclusive presence of
these repetitive elements in the human gene indicates divergence in the evolutionary
dynamics of mammalian TnT genes. Homologous muscle-specific splicing enhancer
motifs are present in the introns upstream and downstream of the foetal exon, and
may play a role in the developmental pattern of alternative splicing of the gene. The
genomic correlates of TNNT3 are relevant to our understanding of the evolution and
regulation of expression of the gene, as well as the structure and function of the protein
isoforms. The nucleotide sequence of TNNT3 has been submitted to EMBL/GenBank
under Accession No. AF026276.
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Affiliation(s)
- Raymund Stefancsik
- Department of Anatomy and Cellular Biology, Tufts University, Health Science Campus, 136 Harrison Avenue, Boston, MA 02111, USA
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22
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Rescue of placental phenotype in a mechanistic model of Beckwith-Wiedemann syndrome. BMC DEVELOPMENTAL BIOLOGY 2010; 10:50. [PMID: 20459838 PMCID: PMC2881899 DOI: 10.1186/1471-213x-10-50] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 05/11/2010] [Indexed: 12/21/2022]
Abstract
Background Several imprinted genes have been implicated in the process of placentation. The distal region of mouse chromosome 7 (Chr 7) contains at least ten imprinted genes, several of which are expressed from the maternal homologue in the placenta. The corresponding paternal alleles of these genes are silenced in cis by an incompletely understood mechanism involving the formation of a repressive nuclear compartment mediated by the long non-coding RNA Kcnq1ot1 initiated from imprinting centre 2 (IC2). However, it is unknown whether some maternally expressed genes are silenced on the paternal homologue via a Kcnq1ot1-independent mechanism. We have previously reported that maternal inheritance of a large truncation of Chr7 encompassing the entire IC2-regulated domain (DelTel7 allele) leads to embryonic lethality at mid-gestation accompanied by severe placental abnormalities. Kcnq1ot1 expression can be abolished on the paternal chromosome by deleting IC2 (IC2KO allele). When the IC2KO mutation is paternally inherited, epigenetic silencing is lost in the region and the DelTel7 lethality is rescued in compound heterozygotes, leading to viable DelTel7/IC2KO mice. Results Considering the important functions of several IC2-regulated genes in placentation, we set out to determine whether these DelTel7/IC2KO rescued conceptuses develop normal placentae. We report no abnormalities with respect to the architecture and vasculature of the DelTel7/IC2KO rescued placentae. Imprinted expression of several of the IC2-regulated genes critical to placentation is also faithfully recapitulated in DelTel7/IC2KO placentae. Conclusion Taken together, our results demonstrate that all the distal chromosome 7 imprinted genes implicated in placental function are silenced by IC2 and Kcnq1ot1 on the paternal allele. Furthermore, our results demonstrate that the methylated maternal IC2 is not required for the regulation of nearby genes. The results show the potential for fully rescuing trans placental abnormalities that are caused by imprinting defects.
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23
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Genomic imprinting mechanisms in embryonic and extraembryonic mouse tissues. Heredity (Edinb) 2010; 105:45-56. [PMID: 20234385 DOI: 10.1038/hdy.2010.23] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Imprinted genes in mice and humans mainly occur in clusters that are associated with differential DNA methylation of an imprint control element (ICE) and at least one nonprotein-coding RNA (ncRNA). Imprinted gene silencing is achieved by parental-specific insulator activity of the unmethylated ICE mediated by CTCF (CCCTC-binding factor) binding, or by ncRNA expression from a promoter in the unmethylated ICE. In many imprinted clusters, some genes, particularly those located furthest away from the ICE, show imprinted expression only in extraembryonic tissues. Recent research indicates that genes showing imprinted expression only in extraembryonic tissues may be regulated by different epigenetic mechanisms compared with genes showing imprinted expression in extraembryonic tissues and in embryonic/adult tissues. The study of extraembryonic imprinted expression, thus, has the potential to illuminate novel epigenetic strategies, but is complicated by the need to collect tissue from early stages of mouse development, when extraembryonic tissues may be contaminated by maternal cells or be present in limited amounts. Research in this area would be advanced by the development of an in vitro model system in which genetic experiments could be conducted in less time and at a lower cost than with mouse models. Here, we summarize what is known about the mechanisms regulating imprinted expression in mouse extraembryonic tissues and explore the possibilities for developing an in vitro model.
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Bressan FF, De Bem THC, Perecin F, Lopes FL, Ambrosio CE, Meirelles FV, Miglino MA. Unearthing the roles of imprinted genes in the placenta. Placenta 2009; 30:823-34. [PMID: 19679348 DOI: 10.1016/j.placenta.2009.07.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Accepted: 07/22/2009] [Indexed: 11/17/2022]
Abstract
Mammalian fetal survival and growth are dependent on a well-established and functional placenta. Although transient, the placenta is the first organ to be formed during pregnancy and is responsible for important functions during development, such as the control of metabolism and fetal nutrition, gas and metabolite exchange, and endocrine control. Epigenetic marks and gene expression patterns in early development play an essential role in embryo and fetal development. Specifically, the epigenetic phenomenon known as genomic imprinting, represented by the non-equivalence of the paternal and maternal genome, may be one of the most important regulatory pathways involved in the development and function of the placenta in eutherian mammals. A lack of pattern or an imprecise pattern of genomic imprinting can lead to either embryonic losses or a disruption in fetal and placental development. Genetically modified animals present a powerful approach for revealing the interplay between gene expression and placental function in vivo and allow a single gene disruption to be analyzed, particularly focusing on its role in placenta function. In this paper, we review the recent transgenic strategies that have been successfully created in order to provide a better understanding of the epigenetic patterns of the placenta, with a special focus on imprinted genes. We summarize a number of phenotypes derived from the genetic manipulation of imprinted genes and other epigenetic modulators in an attempt to demonstrate that gene-targeting studies have contributed considerably to the knowledge of placentation and conceptus development.
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Affiliation(s)
- F F Bressan
- Department of Basic Sciences, Faculty of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
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25
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Miri K, Varmuza S. Chapter 5 Imprinting and Extraembryonic Tissues—Mom Takes Control. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 276:215-62. [DOI: 10.1016/s1937-6448(09)76005-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ali AM, Bajaj V, Gopinath KS, Kumar A. Characterization of the human SLC22A18 gene promoter and its regulation by the transcription factor Sp1. Gene 2008; 429:37-43. [PMID: 18996451 DOI: 10.1016/j.gene.2008.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Revised: 10/10/2008] [Accepted: 10/11/2008] [Indexed: 11/19/2022]
Abstract
SLC22A18, a poly-specific organic cation transporter, is paternally imprinted in humans and mice. It shows loss-of-heterozygosity in childhood and adult tumors, and gain-of-imprinting in hepatocarcinomas and breast cancers. Despite the importance of this gene, its transcriptional regulation has not been studied, and the promoter has not yet been characterized. We therefore set out to identify the potential cis-regulatory elements including the promoter of this gene. The luciferase reporter assay in human cells indicated that a region from -120 bp to +78 bp is required for the core promoter activity. No consensus TATA or CAAT boxes were found in this region, but two Sp1 binding sites were conserved in human, chimpanzee, mouse and rat. Mutational analysis of the two Sp1 sites suggested their requirement for the promoter activity. Chromatin-immunoprecipitation showed binding of Sp1 to the promoter region in vivo. Overexpression of Sp1 in Drosophila Sp1-null SL2 cells suggested that Sp1 is the transactivator of the promoter. The human core promoter was functional in mouse 3T3 and monkey COS7 cells. We found a CpG island which spanned the core promoter and exon 1. COBRA technique did not reveal promoter methylation in 10 normal oral tissues, 14 oral tumors, and two human cell lines HuH7 and A549. This study provides the first insight into the mechanism that controls expression of this imprinted tumor suppressor gene. A COBRA-based assay has been developed to look for promoter methylation in different cancers. The present data will help to understand the regulation of this gene and its role in tumorigenesis.
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Affiliation(s)
- Abdullah Mahmood Ali
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore 560012, India
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27
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Wong CL, Lee KH, Lo KM, Chan OC, Goggins W, O WS, Chow PH. Ablation of paternal accessory sex glands imparts physical and behavioural abnormalities to the progeny: an in vivo study in the golden hamster. Theriogenology 2007; 68:654-62. [PMID: 17597198 DOI: 10.1016/j.theriogenology.2007.04.062] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Accepted: 04/19/2007] [Indexed: 11/21/2022]
Abstract
The functional significance of male accessory sex glands (ASG) remains unclear. This study explored their importance in reproduction. In previous investigations, embryos sired by males with ASG either totally or partially removed had a shift in the cell cycle and delayed cleavage during preimplantation development, higher incidence of apoptosis, early oviductal-uterine transit, higher proportion of embryo degeneration, lower implantation rate, and ultimately reduced fertility and fecundity. Some pups were born alive; but would they be normal? We hypothesized that the first generation offspring (F1) could also bear undesirable traits. To test our hypothesis, we raised and studied these F1 pups from birth to 8 weeks. We monitored physical growth and assessed behaviour such as nest patch odor preference, acoustic startle response (ASR) and exploratory activity. We detected deviations from the norm in physical growth, a premature cessation of nest patch odor preferences, accelerated acoustic startle habituation and more frequent rearing when exposed to a novel environment. In terms of structure, we found one incidence of diphallus with duplicated urethra. We concluded that sperm lacking contact with ASG secretions gave rise to progeny with abnormal traits.
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Affiliation(s)
- C L Wong
- Department of Anatomy, the Chinese University of Hong Kong, Hong Kong
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28
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Adewumi O, Aflatoonian B, Ahrlund-Richter L, Amit M, Andrews PW, Beighton G, Bello PA, Benvenisty N, Berry LS, Bevan S, Blum B, Brooking J, Chen KG, Choo ABH, Churchill GA, Corbel M, Damjanov I, Draper JS, Dvorak P, Emanuelsson K, Fleck RA, Ford A, Gertow K, Gertsenstein M, Gokhale PJ, Hamilton RS, Hampl A, Healy LE, Hovatta O, Hyllner J, Imreh MP, Itskovitz-Eldor J, Jackson J, Johnson JL, Jones M, Kee K, King BL, Knowles BB, Lako M, Lebrin F, Mallon BS, Manning D, Mayshar Y, McKay RDG, Michalska AE, Mikkola M, Mileikovsky M, Minger SL, Moore HD, Mummery CL, Nagy A, Nakatsuji N, O'Brien CM, Oh SKW, Olsson C, Otonkoski T, Park KY, Passier R, Patel H, Patel M, Pedersen R, Pera MF, Piekarczyk MS, Pera RAR, Reubinoff BE, Robins AJ, Rossant J, Rugg-Gunn P, Schulz TC, Semb H, Sherrer ES, Siemen H, Stacey GN, Stojkovic M, Suemori H, Szatkiewicz J, Turetsky T, Tuuri T, van den Brink S, Vintersten K, Vuoristo S, Ward D, Weaver TA, Young LA, Zhang W. Characterization of human embryonic stem cell lines by the International Stem Cell Initiative. Nat Biotechnol 2007; 25:803-16. [PMID: 17572666 DOI: 10.1038/nbt1318] [Citation(s) in RCA: 765] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Accepted: 05/31/2007] [Indexed: 11/09/2022]
Abstract
The International Stem Cell Initiative characterized 59 human embryonic stem cell lines from 17 laboratories worldwide. Despite diverse genotypes and different techniques used for derivation and maintenance, all lines exhibited similar expression patterns for several markers of human embryonic stem cells. They expressed the glycolipid antigens SSEA3 and SSEA4, the keratan sulfate antigens TRA-1-60, TRA-1-81, GCTM2 and GCT343, and the protein antigens CD9, Thy1 (also known as CD90), tissue-nonspecific alkaline phosphatase and class 1 HLA, as well as the strongly developmentally regulated genes NANOG, POU5F1 (formerly known as OCT4), TDGF1, DNMT3B, GABRB3 and GDF3. Nevertheless, the lines were not identical: differences in expression of several lineage markers were evident, and several imprinted genes showed generally similar allele-specific expression patterns, but some gene-dependent variation was observed. Also, some female lines expressed readily detectable levels of XIST whereas others did not. No significant contamination of the lines with mycoplasma, bacteria or cytopathic viruses was detected.
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Cdkn1c (p57Kip2) is the major regulator of embryonic growth within its imprinted domain on mouse distal chromosome 7. BMC DEVELOPMENTAL BIOLOGY 2007; 7:53. [PMID: 17517131 PMCID: PMC1891291 DOI: 10.1186/1471-213x-7-53] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Accepted: 05/21/2007] [Indexed: 11/17/2022]
Abstract
Background Cdkn1c encodes an embryonic cyclin-dependant kinase inhibitor that acts to negatively regulate cell proliferation and, in some tissues, to actively direct differentiation. This gene, which is an imprinted gene expressed only from the maternal allele, lies within a complex region on mouse distal chromosome 7, called the IC2 domain, which contains several other imprinted genes. Studies on mouse embryos suggest a key role for genomic imprinting in regulating embryonic growth and this has led to the proposal that imprinting evolved as a consequence of the mismatched contribution of parental resources in mammals. Results In this study, we characterised the phenotype of mice carrying different copy number integrations of a bacterial artificial chromosome spanning Cdkn1c. Excess Cdkn1c resulted in embryonic growth retardation that was dosage-dependent and also responsive to the genetic background. Two-fold expression of Cdkn1c in a subset of tissues caused a 10–30% reduction in embryonic weight, embryonic lethality and was associated with a reduction in the expression of the potent, non-imprinted embryonic growth factor, Igf1. Conversely, loss of expression of Cdkn1c resulted in embryos that were 11% heavier with a two-fold increase in Igf1. Conclusion We have shown that embryonic growth in mice is exquisitely sensitive to the precise dosage of Cdkn1c. Cdkn1c is a maternally expressed gene and our findings support the prediction of the parental conflict hypothesis that that the paternal genome silences genes that have an inhibitory role in embryonic growth. Within the IC2 imprinted domain, Cdkn1c encodes the major regulator of embryonic growth and we propose that Cdkn1c was the focal point of the selective pressure for imprinting of this domain.
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Cutfield WS, Hofman PL, Mitchell M, Morison IM. Could epigenetics play a role in the developmental origins of health and disease? Pediatr Res 2007; 61:68R-75R. [PMID: 17413843 DOI: 10.1203/pdr.0b013e318045764c] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Following Barker's observations of an association between birth size and later adult diseases, considerable efforts have been made to define the characteristics of low birth weight groups in childhood. In this review, the phenotypic and biochemical characteristics during childhood of three low birth weight groups are summarized: children born following inviter fertilization (IVF), small for gestational age (SGA), or very premature. Each of these groups is likely to have been exposed to an adverse environment at different developmental stages. The triggers and mechanisms leading to programmed changes in growth, development, and metabolism of these groups of children have yet to be identified. Epigenetics has been proposed as a potential mechanism for these programmed changes through environmentally induced changes in gene expression. Data from animal models in which environmental, particularly nutritional, manipulation leads to changes in DNA methylation are presented. The relevance of these animal studies to IVF, SGA, and very premature children are discussed as are potential candidate genes that may have undergone epigenetic modification to alter growth and metabolism.
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Affiliation(s)
- Wayne S Cutfield
- Liggins Institute, National Research Centre for Growth and Development, University of Auckland, Department of Pediatrics, New Zealand.
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Abstract
Imprinted genes are monoallelically expressed in a parent-of-origin-specific manner, but for many genes reported to be imprinted, the occurrence of preferential expression--where both alleles are expressed but one is expressed more strongly than the other in a parent-of-origin-specific way--has been reported. This preferential expression found in genes described as imprinted has not been thoroughly addressed in genomic imprinting studies. To study this phenomenon, 50 genes, reported to be imprinted in the mouse, were chosen for investigation. Preferential expression was observed for 21 of 27 maternally expressed genes. However, only 5 of 23 paternally expressed genes showed preferential expression. Recently, it has been reported that a remarkable proportion of non-imprinted genes show differential allelic expression. If there is overlap between non-imprinted genes that are differentially expressed and imprinted genes that are preferentially expressed, we need to set new definitions of imprinted genes that, in turn, would probably lead to reassessments of the total number of imprinted genes in mammalian species.
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Affiliation(s)
- Hasan Khatib
- Department of Dairy Science, 1675 Observatory Drive, University of Wisconsin, Madison, WI 53706, USA
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Smith FM, Garfield AS, Ward A. Regulation of growth and metabolism by imprinted genes. Cytogenet Genome Res 2006; 113:279-91. [PMID: 16575191 DOI: 10.1159/000090843] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2005] [Accepted: 07/21/2005] [Indexed: 01/05/2023] Open
Abstract
A small sub-set of mammalian genes are subject to regulation by genomic imprinting such that only one parental allele is active in at least some sites of expression. Imprinted genes have diverse functions, notably including the regulation of growth. Much attention has been devoted to the insulin-like growth factor signalling pathway that has a major influence on fetal size and contains two components encoded by the oppositely imprinted genes, Igf2 (a growth promoting factor expressed from the paternal allele) and Igf2r (a growth inhibitory factor expressed from the maternal allele). These genes fit the parent-offspring conflict hypothesis for the evolution of genomic imprinting. Accumulated evidence indicates that at least one other fetal growth pathway exists that has also fallen under the influence of imprinting. It is clear that not all components of growth regulatory pathways are encoded by imprinted genes and instead it may be that within a pathway the influence of a single gene by each of the parental genomes may be sufficient for parent-offspring conflict to be enacted. A number of imprinted genes have been found to influence energy homeostasis and some, including Igf2 and Grb10, may coordinate growth with glucose-regulated metabolism. Since perturbation of fetal growth can be correlated with metabolic disorders in adulthood these imprinted genes are considered as candidates for involvement in this phenomenon of fetal programming.
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Affiliation(s)
- F M Smith
- Centre for Regenerative Medicine and Developmental Biology Programme, Department of Biology and Biochemistry, University of Bath, Bath, UK
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Yamada HY, Gorbsky GJ. Tumor suppressor candidate TSSC5 is regulated by UbcH6 and a novel ubiquitin ligase RING105. Oncogene 2006; 25:1330-9. [PMID: 16314844 PMCID: PMC2713668 DOI: 10.1038/sj.onc.1209167] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The region of human chromosome 11p15.5 is linked with Beckwith-Wiedemann syndrome that is associated with susceptibility to Wilms' tumor, rhabdomyosarcoma and hepatoblastoma. TSSC5 (tumor-suppressing subchromosomal transferable fragment cDNA; also known as ORCTL2/IMPT1/BWR1A/SLC22A1L) is located in the region. The expression of TSSC5 and other genes in the region is regulated through paternal imprinting. Mutations and/or reduced expression of TSSC5 have been found in certain tumors. TSSC5 encodes an efflux transporter-like protein with 10 transmembrane domains, whose regulation may affect drug sensitivity, cellular metabolism and growth. Here, we present evidences indicating that RING105, a novel conserved RING-finger protein with a PA (protease-associated) domain and a PEST sequence, is a ubiquitin ligase for TSSC5 that can function in concert with the ubiquitin-conjugating enzyme UbcH6. The polyubiquitin target site on TSSC5 was mapped to a region in the 6th hydrophilic loop. Ectopic expression of RING105 in HeLa cells caused an accumulation of cells during G1 that was not observed with the expression of a form of RING105 in which a residue within the RING finger was mutated to inactivate its ligase activity. UbcH6-RING105 may define a novel ubiquitin-proteasome pathway that targets TSSC5 in mammalian cells.
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Affiliation(s)
- H Y Yamada
- Oklahoma Medical Research Foundation (OMRF), Molecular, Cell and Developmental Biology Research Program, Oklahoma City, OK 73104, USA.
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Tycko B. Imprinted genes in placental growth and obstetric disorders. Cytogenet Genome Res 2006; 113:271-8. [PMID: 16575190 DOI: 10.1159/000090842] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2005] [Accepted: 08/27/2005] [Indexed: 01/12/2023] Open
Abstract
Genomic imprinting has a special role in placental biology. Imprinted genes are often strongly expressed in the placenta, and the allelic expression bias due to imprinting is sometimes stronger in this extraembryonic organ than in the embryo and adult. Mutations, epimutations, and uniparental disomies affecting imprinted loci cause placental stunting or overgrowth in mice and humans, and placental neoplasms (complete hydatidiform moles) are androgenetic. Whether imprinted genes might also play a role in the more common medical conditions that affect the placenta, including preeclampsia and intrauterine growth restriction (IUGR), is an important question that is now receiving some attention. Here we review this area and describe recent data indicating altered expression of imprinted genes in the placental response to maternal vascular underperfusion associated with IUGR.
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Affiliation(s)
- B Tycko
- Institute for Cancer Genetics, Department of Pathology, Columbia University, New York, NY 10032, USA.
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35
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Wagschal A, Feil R. Genomic imprinting in the placenta. Cytogenet Genome Res 2006; 113:90-8. [PMID: 16575167 DOI: 10.1159/000090819] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2005] [Accepted: 07/21/2005] [Indexed: 12/22/2022] Open
Abstract
Genomic imprinting is an epigenetic mechanism that is important for the development and function of the extra-embryonic tissues in the mouse. Remarkably all the autosomal genes which were found to be imprinted in the trophoblast (placenta) only are active on the maternal and repressed on the paternal allele. It was shown for several of these genes that their paternal silencing is not dependent on DNA methylation, at least not in its somatic maintenance. Rather, recent studies in the mouse suggest that placenta-specific imprinting involves repressive histone modifications and non-coding RNAs. This mechanism of autosomal imprinting is similar to imprinted X chromosome inactivation in the placenta. Although the underlying reasons remain to be explored, this suggests that imprinting in the placenta and imprinted X inactivation are evolutionarily related.
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Affiliation(s)
- A Wagschal
- Institute of Molecular Genetics, CNRS and University of Montpellier II, Montpellier, France
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Nishimura M, Naito S. Tissue-specific mRNA expression profiles of human ATP-binding cassette and solute carrier transporter superfamilies. Drug Metab Pharmacokinet 2006; 20:452-77. [PMID: 16415531 DOI: 10.2133/dmpk.20.452] [Citation(s) in RCA: 286] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pairs of forward and reverse primers and TaqMan probes specific to each of 46 human ATP-binding cassette (ABC) transporters and 108 human solute carrier (SLC) transporters were prepared. The mRNA expression level of each target transporter was analyzed in total RNA from single and pooled specimens of various human tissues (adrenal gland, bone marrow, brain, colon, heart, kidney, liver, lung, pancreas, peripheral leukocytes, placenta, prostate, salivary gland, skeletal muscle, small intestine, spinal cord, spleen, stomach, testis, thymus, thyroid gland, trachea, and uterus) by real-time reverse transcription PCR using an ABI PRISM 7700 sequence detector system. In contrast to previous methods for analyzing the mRNA expression of single ABC and SLC genes such as Northern blotting, our method allowed us to perform sensitive, semiautomatic, rapid, and complete analysis of ABC and SLC transporters in total RNA samples. Our newly determined expression profiles were then used to study the gene expression in 23 different human tissues, and tissues with high transcriptional activity for human ABC and SLC transporters were identified. These results are expected to be valuable for establishing drug transport-mediated screening systems for new chemical entities in new drug development and for research concerning the clinical diagnosis of disease.
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Affiliation(s)
- Masuhiro Nishimura
- Division of Pharmacology, Drug Safety and Metabolism, Otsuka Pharmaceutical Factory, Inc., Tokushima, Japan.
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Abstract
Fetal programming occurs when the normal pattern of fetal development is disrupted by an abnormal stimulus or 'insult' applied at a critical point in in utero development. This then leads to an effect, for example diabetes or hypertension, which manifests itself in adult life. As the placenta is the regulator of nutrient composition and supply from mother to fetus and the source of hormonal signals that affect maternal and fetal metabolism, appropriate development of the placenta is crucial to normal fetal development. Placental function evolves in a carefully orchestrated developmental cascade throughout gestation. Disruption of this cascade can lead to abnormal development of the placental vasculature or of the trophoblast. Timing of a developmental 'insult' will be critical in consequent placental function and hence programming of the fetus. The 'insults' that alter placental development include hypoxia and abnormal maternal nutrient status, to which the placenta may adapt by alterations in transporter expression and activity to maintain fetal growth or by epigenetic regulation of placental gene expression. Hypoxia is physiological for organogenesis and placental tissue normally exists in a relatively hypoxic environment, but intrauterine growth restriction (IUGR) and pre-eclampsia are associated with a greater degree of trophoblast hypoxia. The metabolic activity of placental mitochondria leads to oxidative stress even in normal pregnancy which is exacerbated further in IUGR, diabetic and pre-eclamptic pregnancies and may also give nitrative stress known to lead to covalent modification and hence altered activity of proteins. Hypoxia, oxidative and nitrative stress all alter placenta development and may be a general underlying mechanism that links altered placental function to fetal programming.
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Affiliation(s)
- Leslie Myatt
- Department of Obstetrics and Gynecology, University of Cincinnati, College of Medicine, PO Box 670526, Cincinnati, OH 45267, USA.
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Li T, Vu TH, Ulaner GA, Littman E, Ling JQ, Chen HL, Hu JF, Behr B, Giudice L, Hoffman AR. IVF results in de novo DNA methylation and histone methylation at an Igf2-H19 imprinting epigenetic switch. ACTA ACUST UNITED AC 2005; 11:631-40. [PMID: 16219628 DOI: 10.1093/molehr/gah230] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recent studies suggest that IVF and assisted reproduction technologies (ART) may result in abnormal genomic imprinting, leading to an increased frequency of Angelman syndrome (AS) and Beckwith-Weidemann syndrome (BWS) in IVF children. To learn how ART might alter the epigenome, we examined morulas and blastocysts derived from C57BL/6J X M. spretus F1 mice conceived in vivo and in vitro and determined the allelic expression of four imprinted genes: Igf2, H19, Cdkn1c and Slc221L. IVF-derived mouse embryos that were cultured in human tubal fluid (HTF) (Quinn's advantage) media displayed a high frequency of aberrant H19 imprinting, whereas in vivo and IVF embryos showed normal maternal expression of Cdkn1c and normal biallelic expression of Igf2 and Slc221L. Embryonic stem (ES) cells derived from IVF blastocysts also showed abnormal Igf2/H19 imprinting. Allele-specific bisulphite PCR reveals abnormal DNA methylation at a CCCTC-binding factor (CTCF) site in the imprinting control region (ICR), as the normally unmethylated maternal allele acquired a paternal methylation pattern. Chromatin immunoprecipitation (ChIP) assays indicate an increase of lysine 4 methylation (dimethyl Lys4-H3) on the paternal chromatin and a gain in lysine 9 methylation (trimethyl Lys9-H3) on the maternal chromatin at the same CTCF-binding site. Our results indicate that de novo DNA methylation on the maternal allele and allele-specific acquisition of histone methylation lead to aberrant Igf2/H19 imprinting in IVF-derived ES cells. We suggest that ART, which includes IVF and various culture media, might cause imprinting errors that involve both aberrant DNA methylation and histone methylation at an epigenetic switch of the Igf2-H19 gene region.
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Affiliation(s)
- Tao Li
- Medical Service, VA Palo Alto Health Care System, CA 94304, USA
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39
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Weksberg R, Shuman C, Smith AC. Beckwith-Wiedemann syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2005; 137C:12-23. [PMID: 16010676 DOI: 10.1002/ajmg.c.30058] [Citation(s) in RCA: 253] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Beckwith-Wiedemann syndrome (BWS) is a clinically heterogeneous overgrowth syndrome associated with an increased risk for embryonal tumor development. BWS provides an ideal model system to study epigenetic mechanisms. This condition is caused by a variety of genetic or epigenetic alterations within two domains of imprinted growth regulatory genes on human chromosome 11p15. Molecular studies of BWS have provided important data with respect to epigenotype/genotype-phenotype correlations; for example, alterations of Domain 1 are associated with the highest risk for tumor development, specifically Wilms' tumor. Further, the elucidation of the molecular basis for monozygotic twinning in BWS defined a critical period for imprint maintenance during pre-implantation embryonic development. In the future, such molecular studies in BWS will permit enhanced medical management and targeted genetic counseling.
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40
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Salas M, John R, Saxena A, Barton S, Frank D, Fitzpatrick G, Higgins MJ, Tycko B. Placental growth retardation due to loss of imprinting of Phlda2. Mech Dev 2005; 121:1199-210. [PMID: 15327781 DOI: 10.1016/j.mod.2004.05.017] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Revised: 05/28/2004] [Accepted: 05/28/2004] [Indexed: 01/10/2023]
Abstract
The maternally expressed/paternally silenced genes Phlda2 (a.k.a. Ipl/Tssc3), Slc22a1l, Cdkn1c, Kcnq1, and Ascl2 are clustered in an imprinted domain on mouse chromosome 7. Paternal deletion of a cis-acting differentially methylated DNA element, Kvdmr1, causes coordinate loss of imprinting and over-expression of all of these genes and the resulting conceptuses show intrauterine growth restriction (IUGR). To test the specific contribution of Phlda2 to IUGR in the Kvdmr1-knockout, we crossed Kvdmr1(+/-) males with Phlda2(+/-) females. Conceptuses with the (Phlda2(+/+); Kvdmr1(+/-)) genotype showed fetal and placental growth retardation. Restoration of Phlda2 dosage to normal, as occurred in the conceptuses with the (Phlda2(-/+); Kvdmr1(+/-)) genotype, had a marginally positive effect on fetal weights and no effect on post-natal weights, but significantly rescued the placental weights. As we previously reported, loss of Phlda2 expression in the wild-type background (Phlda2(-/+); Kvdmr1(+/+) genotype) caused placentomegaly. Thus Phlda2 acts as a true rheostat for placental growth, with overgrowth after gene deletion and growth retardation after loss of imprinting. Consistent with this conclusion, we observed significant placental stunting in BAC-transgenic mice that over-expressed Phlda2 and one flanking gene, Slc22a1l, but did not over-express Cdkn1c.
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Affiliation(s)
- Martha Salas
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY 10032, USA
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41
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Abstract
Imprinted genes are expressed monoallelically depending on their parental origin. High expression of the majority of imprinted genes tested to date has been demonstrated in extraembryonic tissues; placenta and yolk sac. Several mouse models where specific imprinted genes have been disrupted demonstrate that fetal and placental growth may be regulated by imprinted genes, in which paternally expressed genes enhance, and maternally expressed genes restrain, growth. We review the current information on, and suggest possible functional roles for, imprinted genes in placental development.
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Affiliation(s)
- P M Coan
- Department of Anatomy, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
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Hirota T, Ieiri I, Takane H, Maegawa S, Hosokawa M, Kobayashi K, Chiba K, Nanba E, Oshimura M, Sato T, Higuchi S, Otsubo K. Allelic expression imbalance of the human CYP3A4 gene and individual phenotypic status. Hum Mol Genet 2004; 13:2959-69. [PMID: 15459178 DOI: 10.1093/hmg/ddh313] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The human cytochrome P450 3A4 (CYP3A4) plays a dominant role in the metabolism of numerous clinically useful drugs. Alterations in the activity or expression of this enzyme may account for a major part of the variation in drug responsiveness and toxicity. However, it is generally accepted that most of the known single nucleotide polymorphisms in the coding and 5'-flanking regions are not the main determinants for the large inter-individual variability of CYP3A4 expression and activity. We show that the allelic variation is critically involved in determining the individual total hepatic CYP3A4 mRNA level and metabolic capability. There exists a definite correlation between the total CYP3A4 mRNA level and allelic expression ratio, the relative transcript level ratio derived from the two alleles. Individuals with a low expression ratio, exhibiting a large difference of transcript level between the two alleles, revealed extremely low levels of total hepatic CYP3A4 mRNA, and thus low metabolic capability as assessed by testosterone 6beta-hydroxylation. These results present a new insight into the individualized CYP3A4-dependent pharmacotherapy and the importance of expression imbalance to human phenotypic diversity.
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Affiliation(s)
- Takeshi Hirota
- Clinical Pharmacokinetics, Division of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
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Thomae TL, Glover E, Bradfield CA. A maternal Ahr null genotype sensitizes embryos to chemical teratogenesis. J Biol Chem 2004; 279:30189-94. [PMID: 15145931 DOI: 10.1074/jbc.m403690200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The aryl hydrocarbon receptor (encoded by the Ahr locus) is a ligand-activated transcription factor that mediates the toxicology and teratology of 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin). In an effort to understand the role of the maternal compartment in dioxin teratology, we designed a breeding strategy that allowed us to compare the teratogenic response in embryos from Ahr(-/-) (null) and Ahr(+/+) (wild-type) dams. Using this strategy, we demonstrate that embryos from the Ahr(-/-) dams are 5-fold more sensitive to dioxin-induced cleft palate and hydronephrosis as compared with embryos from an Ahr(+/+) dam. Moreover, this increased teratogenic sensitivity extends beyond dioxin, because embryos from Ahr(-/-) dams exhibited a 9-fold increase in their sensitivity to the fetotoxic effects of the glucocorticoid, dexamethasone. In searching for an explanation for this increased sensitivity, we found that more dioxin and dexamethasone reached the embryos from Ahr(-/-) dams as compared with embryos from Ahr(+/+) dams. We propose that increased deposition of teratogens/fetotoxicants to the embryonic compartment is the result of porto-systemic shunting and/or blocked P4501A induction in Ahr(-/-) dams. In addition to demonstrating the importance of maternal AHR in teratogenesis, these data may have implications that reach beyond the mechanism of action of dioxin. In this regard, the Ahr(-/-) mouse may provide a system that allows pharmacological agents and toxicants to be more easily studied in a model where first pass clearance is a significant obstacle.
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Affiliation(s)
- Tami L Thomae
- McArdle Laboratory for Cancer Research, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA
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Albrecht S, Hartmann W, Houshdaran F, Koch A, Gärtner B, Prawitt D, Zabel BU, Russo P, Von Schweinitz D, Pietsch T. Allelic loss but absence of mutations in the polyspecific transporter geneBWR1Aon 11p15.5 in hepatoblastoma. Int J Cancer 2004; 111:627-32. [PMID: 15239143 DOI: 10.1002/ijc.20280] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chromosomal region 11p15.5 shows frequent maternal allelic loss in embryonal tumors, including rhabdomyosarcoma (RMS), Wilms' tumor (WT) and hepatoblastoma (HB), consistent with the presence of at least one tumor suppressor gene in this region, which should be paternally imprinted, i.e., expressed from the maternal allele only. The BWR1A gene encodes a polyspecific transmembrane transporter and is located on 11p15.5. It is highly expressed in liver, paternally imprinted and was found to be mutated in an RMS cell line, making it a plausible tumor suppressor gene for HB. We therefore screened 62 HBs, 3 HB cell lines and 1 pediatric hepatocellular carcinoma for BWR1A mutations using single-strand conformation polymorphism analysis. Allelic loss on 11p15.5 was assessed by PCR-based microsatellite analysis in 56 of the cases for which constitutional DNA was available. BWR1A mRNA expression was determined in 14 HBs by differential RT-PCR of matched cDNA samples from tumor and normal liver. Western blot analysis was performed on 4 tumors and matching normal liver tissue. Except for sequence polymorphisms (in exons 2, 3 and 10 as well as in introns 6 and 7), no mutations were found. Thirteen HBs (23%) had allelic loss on 11p15.5; this included BWR1A in 12 but it was telomeric to BWR1A in 1. Expression of BWR1A mRNA was reduced in 11 out of 14 cases by 19-92%, independent from allelic loss of 11p15.5. By Western blot analysis, all 4 tumors and matching liver samples displayed a 48-51 kd band corresponding to BWR1A. These results make it unlikely that BWR1A is the target of the allelic deletions in HB. However, similar to the putative 11p15.5 tumor suppressor H19, BWR1A appears to be reduced in expression. Reduced expression in the absence of mutations may contribute to HB development; however, to understand the significance of this finding will require further studies on the function of BWR1A, specifically its role in liver development.
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Affiliation(s)
- Steffen Albrecht
- Department of Pathology, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, Canada
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45
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Affiliation(s)
- Andrew P Feinberg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
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Wang Y, Joh K, Masuko S, Yatsuki H, Soejima H, Nabetani A, Beechey CV, Okinami S, Mukai T. The mouse Murr1 gene is imprinted in the adult brain, presumably due to transcriptional interference by the antisense-oriented U2af1-rs1 gene. Mol Cell Biol 2004; 24:270-9. [PMID: 14673161 PMCID: PMC303337 DOI: 10.1128/mcb.24.1.270-279.2004] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The mouse Murr1 gene contains an imprinted gene, U2af1-rs1, in its first intron. U2af1-rs1 shows paternal allele-specific expression and is transcribed in the direction opposite to that of the Murr1 gene. In contrast to a previous report of biallelic expression of Murr1 in neonatal mice, we have found that the maternal allele is expressed predominantly in the adult brain and also preferentially in other adult tissues. This maternal-predominant expression is not observed in embryonic and neonatal brains. In situ hybridization experiments that used the adult brain indicated that Murr1 gene was maternally expressed in neuronal cells in all regions of the brain. We analyzed the developmental change in the expression levels of both Murr1 and U2af1-rs1 in the brain and liver, and we propose that the maternal-predominant expression of Murr1 results from transcriptional interference of the gene by U2af1-rs1 through the Murr1 promoter region.
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Affiliation(s)
- Youdong Wang
- Department of Biomolecular Sciences, Saga Medical School, Saga 849-8501, Japan
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47
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Tzortzaki EG, Yang M, Glass D, Deng L, Evan AP, Bledsoe SB, Stambrook PJ, Sahota A, Tischfield JA. Impaired expression of an organic cation transporter, IMPT1, in a knockout mouse model for kidney stone disease. UROLOGICAL RESEARCH 2003; 31:257-61. [PMID: 12856169 DOI: 10.1007/s00240-003-0318-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2002] [Accepted: 03/20/2003] [Indexed: 10/26/2022]
Abstract
The imprinted multimembrane-spanning polyspecific transporter-like gene 1 ( IMPT1) encodes a predicted protein with organic cation transport capabilities. As a first step in understanding the function of IMPT1, we identified the renal structures expressing this gene in knockout mice with adenine phosphoribosyltransferase (APRT) deficiency and 2,8-dihydroxyadenine (DHA) nephrolithiasis. IMPT1 mRNA was not detected using a standard in situ hybridization (ISH) protocol, but we observed intense staining in cortico-medullary tubules and glomeruli in wild-type mice using an improved reverse transcription-polymerase chain reaction (RT-PCR) ISH procedure. IMPT1 mRNA expression was significantly decreased in the cortical region in kidney sections from APRT-deficient male mice. APRT-deficient female mice are less severely affected by DHA-induced kidney stone disease, and we observed only a modest reduction in IMPT1 expression in kidneys from these mice. IMPT1 expression in APRT heterozygous mice was comparable to that in wild-type mice, suggesting imprinting of one of the parental alleles. These findings suggest that decreased IMPT1 mRNA expression may contribute to the impaired renal function in APRT-deficient male mice, and that RT-PCR ISH is a valuable tool for localizing the site of expression of transcripts that are not detectable using standard ISH procedures.
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Affiliation(s)
- Eleni G Tzortzaki
- Department of Genetics, Rutgers University, 604 Allison Road, NJ 08854-8082, Piscataway, USA
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48
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Abstract
Genomic imprinting is traditionally defined as an epigenetic process leading to parental origin-dependent monoallelic expression of some genes. The current paradigm considers this unusual expression mode as the biological raison d être of imprinting. The present chapter proposes a critical review of our ideas about genomic imprinting in light of more recent investigatory progress. Many observations are difficult to explain on the basis of the current paradigm. Studies of allelic expression of many imprinted genes and other characteristics of chromatin domains containing clustered imprinted genes, such as replication and chromatin structure, revealed an unexpectedly complex situation that challenged the role of genomic imprinting as a mechanism of transcriptional regulation. The emerging picture is that parental imprinting is a feature of large chromatin domains with their own domain-wide characteristics. The primary biological function of imprinting may reside in the differential chromatin structure of the parental chromosomal regions and not in the monoallelic expression of some of the genes contained within them.
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Affiliation(s)
- Andras Paldi
- Institut Jacques Monod, CNRS, Ecole Pratique des Hautes Etudes, 75005 Paris, France
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Reik W, Constância M, Fowden A, Anderson N, Dean W, Ferguson-Smith A, Tycko B, Sibley C. Regulation of supply and demand for maternal nutrients in mammals by imprinted genes. J Physiol 2003; 547:35-44. [PMID: 12562908 PMCID: PMC2342627 DOI: 10.1113/jphysiol.2002.033274] [Citation(s) in RCA: 281] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2002] [Accepted: 01/15/2003] [Indexed: 01/10/2023] Open
Abstract
The placenta has evolved in eutherian mammals primarily to provide nutrients for the developing fetus. The genetic control of the regulation of supply and demand for maternal nutrients is not understood. In this review we argue that imprinted genes have central roles in controlling both the fetal demand for, and the placental supply of, maternal nutrients. Recent studies on Igf2 (insulin-like growth factor 2) knockout mouse models provide experimental support for this hypothesis. These show effects on placental transport capacity consistent with a role of IGF-II in modulating both the placental supply and fetal demand for nutrients. Imprinting of genes with such functions may have coevolved with the placenta and new evidence suggests that transporter proteins, as well as the regulators themselves, may also be imprinted. These data and hypotheses are important, as deregulation of supply and demand affects fetal growth and has long term consequences for health in mammals both in the neonatal period and, as a result of fetal programming, in adulthood.
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Affiliation(s)
- Wolf Reik
- Laboratory of Developmental Genetics and Imprinting, Developmental Genetics Programme, The Babraham Institute, Cambridge CB2 4AT, UK.
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Yatsuki H, Joh K, Higashimoto K, Soejima H, Arai Y, Wang Y, Hatada I, Obata Y, Morisaki H, Zhang Z, Nakagawachi T, Satoh Y, Mukai T. Domain regulation of imprinting cluster in Kip2/Lit1 subdomain on mouse chromosome 7F4/F5: large-scale DNA methylation analysis reveals that DMR-Lit1 is a putative imprinting control region. Genome Res 2002; 12:1860-70. [PMID: 12466290 PMCID: PMC187562 DOI: 10.1101/gr.110702] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mouse chromosome 7F4/F5, where the imprinting domain is located, is syntenic to human 11p15.5, the locus for Beckwith-Wiedemann syndrome. The domain is thought to consist of the two subdomains Kip2 (p57(kip2))/Lit1 and Igf2/H19. Because DNA methylation is believed to be a key factor in genomic imprinting, we performed large-scale DNA methylation analysis to identify the cis-element crucial for the regulation of the Kip2/Lit1 subdomain. Ten CpG islands (CGIs) were found, and these were located at the promoter sites, upstream of genes, and within intergenic regions. Bisulphite sequencing revealed that CGIs 4, 5, 8, and 10 were differentially methylated regions (DMRs). CGIs 4, 5, and 10 were methylated paternally in somatic tissues but not in germ cells. CGI8 was methylated in oocyte and maternally in somatic tissues during development. Parental-specific DNase I hypersensitive sites (HSSs) were found near CGI8. These data indicate that CGI8, called DMR-Lit1, is not only the region for gametic methylation but might also be the imprinting control region (ICR) of the subdomain.
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Affiliation(s)
- Hitomi Yatsuki
- Department of Biochemistry, Saga Medical School, Saga, Saga 849-8501, Japan
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