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Gao F, Zhang J, Jiang P, Gong D, Wang JW, Xia Y, Østergaard MV, Wang J, Sangild PT. Marked methylation changes in intestinal genes during the perinatal period of preterm neonates. BMC Genomics 2014; 15:716. [PMID: 25163507 PMCID: PMC4153944 DOI: 10.1186/1471-2164-15-716] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/15/2014] [Indexed: 11/10/2022] Open
Abstract
Background The serious feeding- and microbiota-associated intestinal disease, necrotizing enterocolitis (NEC), occurs mainly in infants born prematurely (5-10% of all newborns) and most frequently after formula-feeding. We hypothesized that changes in gene methylation is involved in the prenatal maturation of the intestine and its response to the first days of formula feeding, potentially leading to NEC in preterm pigs used as models for preterm infants. Results Reduced Representation Bisulfite Sequencing (RRBS) was used to assess if changes in intestinal DNA methylation are associated with formula-induced NEC outbreak and advancing age from 10 days before birth to 4 days after birth. Selected key genes with differentially methylated gene regions (DMRs) between groups were further validated by HiSeq-based bisulfite sequencing PCR and RT-qPCR to assess methylation and expression levels. Consistent with the maturation of many intestinal functions in the perinatal period, methylation level of most genes decreased with advancing pre- and postnatal age. The highest number of DMRs was identified between the newborn and 4 d-old preterm pigs. There were few intestinal DMR differences between unaffected pigs and pigs with initial evidence of NEC. In the 4 d-old formula-fed preterm pigs, four genes associated with intestinal metabolism (CYP2W1, GPR146, TOP1MT, CEND1) showed significant hyper-methylation in their promoter CGIs, and thus, down-regulated transcription. Methylation-driven down-regulation of such genes may predispose the immature intestine to later metabolic dysfunctions and severe NEC lesions. Conclusions Pre- and postnatal changes in intestinal DNA methylation may contribute to high NEC sensitivity in preterm neonates. Optimizing gene methylation changes via environmental stimuli (e.g. diet, nutrition, gut microbiota), may help to make immature newborn infants more resistant to gut dysfunctions, both short and long term. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-716) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Jun Wang
- Department of Science & Technology, BGI-Shenzhen, Shenzhen, China.
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Abstract
In mammals, the process of X-chromosome inactivation ensures equivalent levels of X-linked gene expression between males and females through the silencing of one of the two X chromosomes in female cells. The process is established early in development and is initiated by a unique locus, which produces a long noncoding RNA, Xist. The Xist transcript triggers gene silencing in cis by coating the future inactive X chromosome. It also induces a cascade of chromatin changes, including posttranslational histone modifications and DNA methylation, and leads to the stable repression of all X-linked genes throughout development and adult life. We review here recent progress in our understanding of the molecular mechanisms involved in the initiation of Xist expression, the propagation of the Xist RNA along the chromosome, and the cis-elements and trans-acting factors involved in the maintenance of the repressed state. We also describe the diverse strategies used by nonplacental mammals for X-chromosome dosage compensation and highlight the common features and differences between eutherians and metatherians, in particular regarding the involvement of long noncoding RNAs.
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Affiliation(s)
- Anne-Valerie Gendrel
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, 75248 Paris, France;
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53
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Dearden L, Balthasar N. Sexual dimorphism in offspring glucose-sensitive hypothalamic gene expression and physiological responses to maternal high-fat diet feeding. Endocrinology 2014; 155:2144-54. [PMID: 24684305 PMCID: PMC4183922 DOI: 10.1210/en.2014-1131] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A wealth of animal and human studies demonstrate that early life environment significantly influences adult metabolic balance, however the etiology for offspring metabolic misprogramming remains incompletely understood. Here, we determine the effect of maternal diet per se on offspring sex-specific outcomes in metabolic health and hypothalamic transcriptome regulation in mice. Furthermore, to define developmental periods of maternal diet misprogramming aspects of offspring metabolic balance, we investigated offspring physiological and transcriptomic consequences of maternal high-fat/high-sugar diet feeding during pregnancy and/or lactation. We demonstrate that female offspring of high-fat/high-sugar diet-fed dams are particularly vulnerable to metabolic perturbation with body weight increases due to postnatal processes, whereas in utero effects of the diet ultimately lead to glucose homeostasis dysregulation. Furthermore, glucose- and maternal-diet sensitive gene expression modulation in the paraventricular hypothalamus is strikingly sexually dimorphic. In summary, we uncover female-specific, maternal diet-mediated in utero misprogramming of offspring glucose homeostasis and a striking sexual dimorphism in glucose- and maternal diet-sensitive paraventricular hypothalamus gene expression adjustment. Notably, female offspring metabolic vulnerability to maternal high-fat/high-sugar diet propagates a vicious cycle of obesity and type 2 diabetes in subsequent generations.
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Affiliation(s)
- Laura Dearden
- School of Physiology and Pharmacology, University of Bristol, Bristol BS8 1TD, United Kingdom
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54
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Tai PWL, Zaidi SK, Wu H, Grandy RA, Montecino MM, van Wijnen AJ, Lian JB, Stein GS, Stein JL. The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease. J Cell Physiol 2014; 229:711-27. [PMID: 24242872 PMCID: PMC3996806 DOI: 10.1002/jcp.24508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 11/11/2013] [Indexed: 12/31/2022]
Abstract
Compaction of the eukaryotic genome into the confined space of the cell nucleus must occur faithfully throughout each cell cycle to retain gene expression fidelity. For decades, experimental limitations to study the structural organization of the interphase nucleus restricted our understanding of its contributions towards gene regulation and disease. However, within the past few years, our capability to visualize chromosomes in vivo with sophisticated fluorescence microscopy, and to characterize chromosomal regulatory environments via massively parallel sequencing methodologies have drastically changed how we currently understand epigenetic gene control within the context of three-dimensional nuclear structure. The rapid rate at which information on nuclear structure is unfolding brings challenges to compare and contrast recent observations with historic findings. In this review, we discuss experimental breakthroughs that have influenced how we understand and explore the dynamic structure and function of the nucleus, and how we can incorporate historical perspectives with insights acquired from the ever-evolving advances in molecular biology and pathology.
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Affiliation(s)
- Phillip W. L. Tai
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Sayyed K. Zaidi
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Hai Wu
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Rodrigo A. Grandy
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Martin M. Montecino
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | - Jane B. Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Gary S. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Janet L. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
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55
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Bhan A, Mandal SS. Long noncoding RNAs: emerging stars in gene regulation, epigenetics and human disease. ChemMedChem 2014; 9:1932-56. [PMID: 24677606 DOI: 10.1002/cmdc.201300534] [Citation(s) in RCA: 199] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Indexed: 12/19/2022]
Abstract
Noncoding RNAs (ncRNAs) are classes of transcripts that are encoded by the genome and transcribed but never get translated into proteins. Though not translated into proteins, ncRNAs play pivotal roles in a variety of cellular functions. Here, we review the functions of long noncoding RNAs (lncRNAs) and their implications in various human diseases. Increasing numbers of studies demonstrate that lncRNAs play critical roles in regulation of protein-coding genes, maintenance of genomic integrity, dosage compensation, genomic imprinting, mRNA processing, cell differentiation, and development. Misregulation of lncRNAs is associated with a variety of human diseases, including cancer, immune and neurological disorders. Different classes of lncRNAs, their functions, mechanisms of action, and associations with different human diseases are summarized in detail, highlighting their as yet untapped potential in therapy.
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Affiliation(s)
- Arunoday Bhan
- Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019 (USA)
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Niklas KJ, Kutschera U. Amphimixis and the individual in evolving populations: does Weismann's Doctrine apply to all, most or a few organisms? Naturwissenschaften 2014; 101:357-72. [PMID: 24633620 DOI: 10.1007/s00114-014-1164-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 02/19/2014] [Accepted: 02/21/2014] [Indexed: 11/24/2022]
Abstract
The German biologist August Weismann (1834-1914) proposed that amphimixis (sexual reproduction) creates variability for natural selection to act upon, and hence he became one of the founders of the Neo-Darwinian theory of biological evolution. He is perhaps best known for what is called "Weismann's Doctrine" or "Weismann's Barrier" (i.e. the irreversible separation of somatic and germ cell functionalities early during ontogeny in multicellular organisms). This concept provided an unassailable argument against "soft inheritance" sensu Lamarck and informed subsequent theorists that the only "individual" in the context of evolution is the mature, reproductive organism. Herein, we review representative model organisms whose embryology conforms to Weismann's Doctrine (e.g. flies and mammals) and those that do not (e.g. freshwater hydroids and plants) based on this survey and the Five Kingdoms of Life scheme; we point out that most species (notably bacteria, fungi, protists and plants) are "non-Weismannian" in ways that make a canonical definition of the "individual" problematic if not impossible. We also review critical life history functional traits that allow us to create a matrix of all theoretically conceivable life cycles (for eukaryotic algae, embryophytes, fungi and animals), which permits us to establish where this scheme Weismann's Doctrine holds true and where it does not. In addition, we argue that bacteria, the dominant organisms of the biosphere, exist in super-cellular biofilms but rarely as single (planktonic) microbes. Our analysis attempts to show that competition among genomic variants in cell lineages played a critical part in the evolution of multicellularity and life cycle diversity. This feature was largely ignored during the formulation of the synthetic theory of biological evolution and its subsequent elaborations.
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Affiliation(s)
- Karl J Niklas
- Department of Plant Biology, Cornell University, Ithaca, NY, 14893, USA,
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57
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Huang X, Zuo J. Emerging roles of miR-210 and other non-coding RNAs in the hypoxic response. Acta Biochim Biophys Sin (Shanghai) 2014; 46:220-32. [PMID: 24395300 DOI: 10.1093/abbs/gmt141] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Hypoxia is a key component of the tumor microenvironment and represents a well-documented source of therapeutic failure in clinical oncology. Recent work has provided support for the idea that non-coding RNAs, and in particular, microRNAs, may play important roles in the adaptive response to low oxygen in tumors. Specifically, all published studies agree that the induction of microRNA-210 (miR-210) is a consistent feature of the hypoxic response in both normal and malignant cells. miR-210 is a robust target of hypoxia-inducible factors, and its overexpression has been detected in a variety of diseases with a hypoxic component, including most solid tumors. High levels of miR-210 have been linked to an in vivo hypoxic signature and to adverse prognosis in breast and pancreatic cancer patients. A wide variety of miR-210 targets have been identified, pointing to roles in mitochondrial metabolism, angiogenesis, DNA damage response, apoptosis, and cell survival. Such targets are suspected to affect the development of tumors in multiple ways; therefore, an increased knowledge about miR-210's functions may lead to novel diagnostic and therapeutic approaches in cancer.
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Affiliation(s)
- Xin Huang
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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58
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Lee SH, Lee EB, Shin ES, Lee JE, Cho SH, Min KU, Park HW. The Interaction Between Allelic Variants of CD86 and CD40LG: A Common Risk Factor of Allergic Asthma and Rheumatoid Arthritis. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2014; 6:137-41. [PMID: 24587950 PMCID: PMC3936042 DOI: 10.4168/aair.2014.6.2.137] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 04/15/2013] [Accepted: 05/03/2013] [Indexed: 11/20/2022]
Abstract
PURPOSE Allergic asthma (AA) and rheumatoid arthritis (RA) are immune tolerance-related diseases, and immune tolerance is known to be influenced by costimulatory molecules. In this study, we sought to identify common genetic susceptibility in AA and RA. METHODS Two hundred cases of AA, 184 cases of RA, and 182 healthy controls were recruited at the Seoul National University Hospital, Seoul, Korea. Eight single nucleotide polymorphisms (SNPs) in five genes coding costimulatory molecules, namely, -318C>T, +49A>G, and 6230G>A in CTLA4, IVS3+17T>C in CD28, -3479T>G and I179V in CD86, -1C>T in CD40, and -3458A>G in CD40LG were scored, and genetic interactions were evaluated by multifactor dimensionality reduction (MDR) analysis. RESULTS MDR analysis revealed a significant gene-gene interaction between -3479T>G CD86 and -3458A>G CD40LG for AA. Subjects with the T/T genotype of -3479T>G CD86 and the A/A genotype of -3458A>G CD40LG were found to be significantly more likely to develop AA than those with the T/T genotype of -3479T>G CD86 and A/- genotype of -3458A>G CD40LG (adjusted OR, 6.09; 95% CI, 2.89-12.98; logistic regression analysis controlled by age). Similarly those subjects showed a significant risk of developing RA (adjusted OR, 39.35; 95% CI, 15.01-107.00, logistic regression analysis controlled by age). CONCLUSIONS Our findings suggest that a genetic interaction between CD86 and CD40LG favors the development of both AA and RA.
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Affiliation(s)
- So-Hee Lee
- Institute of Allergy and Clinical Immunology, Seoul National University College of Medicine, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Eun-Bong Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | | | | | - Sang-Heon Cho
- Institute of Allergy and Clinical Immunology, Seoul National University College of Medicine, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kyung-Up Min
- Institute of Allergy and Clinical Immunology, Seoul National University College of Medicine, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Heung-Woo Park
- Institute of Allergy and Clinical Immunology, Seoul National University College of Medicine, Seoul, Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
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59
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Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 2014; 505:635-40. [PMID: 24463510 DOI: 10.1038/nature12943] [Citation(s) in RCA: 730] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 12/05/2013] [Indexed: 01/06/2023]
Abstract
Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.
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Affiliation(s)
- Anamaria Necsulea
- 1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland [3] Laboratory of Developmental Genomics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland (A.N.); Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA, and Broad Institute, Cambridge, Massachusetts 02142, USA (M.S.)
| | - Magali Soumillon
- 1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland [3] Laboratory of Developmental Genomics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland (A.N.); Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA, and Broad Institute, Cambridge, Massachusetts 02142, USA (M.S.)
| | - Maria Warnefors
- 1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Angélica Liechti
- 1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tasman Daish
- The Robinson Institute, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ulrich Zeller
- Department of Systematic Zoology, Faculty of Agriculture and Horticulture, Humboldt University Berlin, 10099 Berlin, Germany
| | - Julie C Baker
- Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA
| | - Frank Grützner
- The Robinson Institute, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Henrik Kaessmann
- 1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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60
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Jang HJ, Seo HW, Lee BR, Yoo M, Womack JE, Han JY. Gene expression and DNA methylation status of chicken primordial germ cells. Mol Biotechnol 2013; 54:177-86. [PMID: 22678927 DOI: 10.1007/s12033-012-9560-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
DNA methylation reprogramming of primordial germ cells (PGCs) in mammals establishes monoallelic expression of imprinting genes, maintains retrotransposons in an inactive state, inactivates one of the two X chromosomes, and suppresses gene expression. However, the roles of DNA methylation in chickens PGCs are unknown. In this study, we found a 1.5-fold or greater difference in the expression of 261 transcripts when comparing PGCs and chicken embryonic fibroblasts (CEFs) using an Affymetrix GeneChip Chicken Genome Array. In addition, we analyzed the methylation patterns of the regions ~5-kb upstream of 261 sorted genes, 51 of which were imprinting homologous loci and 49 of which were X-linked homologous loci in chicken using the MeDIP Array by Roche NimbleGen. Seven hypomethylated and five hypermethylated regions within the 5-kb upstream regions of 261 genes were found in PGCs when compared with CEFs. These differentially methylated regions were restrictively matched to differentially expressed genes in PGCs. We also detected 203 differentially methylated regions within imprinting and X-linked homologous regions between male PGCs and female PGCs. These differentially methylated regions may be directly or indirectly associated with gene expression during early embryonic development, and the epigenetic difference could be evolutionally conserved between mammals and birds.
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Affiliation(s)
- Hyun-Jun Jang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
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61
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Hong C, Clement NL, Clement S, Hammoud SS, Carrell DT, Cairns BR, Snell Q, Clement MJ, Johnson WE. Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data. BMC Bioinformatics 2013; 14:337. [PMID: 24261665 PMCID: PMC3924334 DOI: 10.1186/1471-2105-14-337] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation has been linked to many important biological phenomena. Researchers have recently begun to sequence bisulfite treated DNA to determine its pattern of methylation. However, sequencing reads from bisulfite-converted DNA can vary significantly from the reference genome because of incomplete bisulfite conversion, genome variation, sequencing errors, and poor quality bases. Therefore, it is often difficult to align reads to the correct locations in the reference genome. Furthermore, bisulfite sequencing experiments have the additional complexity of having to estimate the DNA methylation levels within the sample. RESULTS Here, we present a highly accurate probabilistic algorithm, which is an extension of the Genomic Next-generation Universal MAPper to accommodate bisulfite sequencing data (GNUMAP-bs), that addresses the computational problems associated with aligning bisulfite sequencing data to a reference genome. GNUMAP-bs integrates uncertainty from read and mapping qualities to help resolve the difference between poor quality bases and the ambiguity inherent in bisulfite conversion. We tested GNUMAP-bs and other commonly-used bisulfite alignment methods using both simulated and real bisulfite reads and found that GNUMAP-bs and other dynamic programming methods were more accurate than the more heuristic methods. CONCLUSIONS The GNUMAP-bs aligner is a highly accurate alignment approach for processing the data from bisulfite sequencing experiments. The GNUMAP-bs algorithm is freely available for download at: http://dna.cs.byu.edu/gnumap. The software runs on multiple threads and multiple processors to increase the alignment speed.
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Affiliation(s)
- Changjin Hong
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Nathan L Clement
- Department of Computer Science, University of Texas, Austin, TX, USA
| | - Spencer Clement
- Department of Computer Science, Brigham Young University, Provo, UT, USA
| | - Saher Sue Hammoud
- IVF and Andrology Laboratories, Departments of Surgery, Obstetrics and Gynecology, and Physiology, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Douglas T Carrell
- IVF and Andrology Laboratories, Departments of Surgery, Obstetrics and Gynecology, and Physiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bradley R Cairns
- Department of Oncological Sciences, Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Quinn Snell
- Department of Computer Science, Brigham Young University, Provo, UT, USA
| | - Mark J Clement
- Department of Computer Science, Brigham Young University, Provo, UT, USA
| | - William Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
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Lu Q, Ren S, Lu M, Zhang Y, Zhu D, Zhang X, Li T. Computational prediction of associations between long non-coding RNAs and proteins. BMC Genomics 2013; 14:651. [PMID: 24063787 PMCID: PMC3827931 DOI: 10.1186/1471-2164-14-651] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 09/17/2013] [Indexed: 12/18/2022] Open
Abstract
Background Though most of the transcripts are long non-coding RNAs (lncRNAs), little is known about their functions. lncRNAs usually function through interactions with proteins, which implies the importance of identifying the binding proteins of lncRNAs in understanding the molecular mechanisms underlying the functions of lncRNAs. Only a few approaches are available for predicting interactions between lncRNAs and proteins. In this study, we introduce a new method lncPro. Results By encoding RNA and protein sequences into numeric vectors, we used matrix multiplication to score each RNA–protein pair. This score can be used to measure the interactions between an RNA–protein pair. This method effectively discriminates interacting and non-interacting RNA–protein pairs and predicts RNA–protein interactions within a given complex. Applying this method on all human proteins, we found that the long non-coding RNAs we collected tend to interact with nuclear proteins and RNA-binding proteins. Conclusions Compared with the existing approaches, our method shortens the time for training matrix and obtains optimal results based on the model being used. The ability of predicting the associations between lncRNAs and proteins has also been enhanced. Our method provides an idea on how to integrate different information into the prediction process.
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Affiliation(s)
- Qiongshi Lu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.
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Crystal structures of isoorotate decarboxylases reveal a novel catalytic mechanism of 5-carboxyl-uracil decarboxylation and shed light on the search for DNA decarboxylase. Cell Res 2013; 23:1296-309. [PMID: 23917530 DOI: 10.1038/cr.2013.107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/15/2013] [Accepted: 07/17/2013] [Indexed: 12/18/2022] Open
Abstract
DNA methylation and demethylation regulate many crucial biological processes in mammals and are linked to many diseases. Active DNA demethylation is believed to be catalyzed by TET proteins and a putative DNA decarboxylase that may share some similarities in sequence, structure and catalytic mechanism with isoorotate decarboxylase (IDCase) that catalyzes decarboxylation of 5caU to U in fungi. We report here the structures of wild-type and mutant IDCases from Cordyceps militaris and Metarhizium anisopliae in apo form or in complexes with 5caU, U, and an inhibitor 5-nitro-uracil. IDCases adopt a typical (β/α)8 barrel fold of the amidohydrolase superfamily and function as dimers. A Zn(2+) is bound at the active site and coordinated by four strictly conserved residues, one Asp and three His. The substrate is recognized by several strictly conserved residues. The functional roles of the key residues at the active site are validated by mutagenesis and biochemical studies. Based on the structural and biochemical data, we present for the first time a novel catalytic mechanism of decarboxylation for IDCases, which might also apply to other members of the amidohydrolase superfamily. In addition, our biochemical data show that IDCases can catalyze decarboxylation of 5caC to C albeit with weak activity, which is the first in vitro evidence for direct decarboxylation of 5caC to C by an enzyme. These findings are valuable in the identification of potential DNA decarboxylase in mammals.
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Ragunath P, Abhinand P. Systems biological approach to investigate the lack of familial link between Down's Syndrome & Neural Tube Disorders. Bioinformation 2013; 9:610-6. [PMID: 23904737 PMCID: PMC3725001 DOI: 10.6026/97320630009610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/06/2013] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED Systems Biology involves the study of the interactions of biological systems and ultimately their functions. Down's syndrome (DS) is one of the most common genetic disorders which are caused by complete, or occasionally partial, triplication of chromosome 21, characterized by cognitive and language dysfunction coupled with sensory and neuromotor deficits. Neural Tube Disorders (NTDs) are a group of congenital malformations of the central nervous system and neighboring structures related to defective neural tube closure during the first trimester of pregnancy usually occurring between days 18-29 of gestation. Several studies in the past have provided considerable evidence that abnormal folate and methyl metabolism are associated with onset of DS & NTDs. There is a possible common etiological pathway for both NTDs and Down's syndrome. But, various research studies over the years have indicated very little evidence for familial link between the two disorders. Our research aimed at the gene expression profiling of microarray datasets pertaining to the two disorders to identify genes whose expression levels are significantly altered in these conditions. The genes which were 1.5 fold unregulated and having a p-value <0.05 were filtered out and gene interaction network were constructed for both NTDs and DS. The top ranked dense clique for both the disorders were recognized and over representation analysis was carried out for each of the constituent genes. The comprehensive manual analysis of these genes yields a hypothetical understanding of the lack of familial link between DS and NTDs. There were no genes involved with folic acid present in the dense cliques. Only - CBL, EGFR genes were commonly present, which makes the allelic variants of these genes - good candidates for future studies regarding the familial link between DS and NTDs. ABBREVIATIONS NTD - Neural Tube Disorders, DS - Down's Syndrome, MTHFR - Methylenetetrahydrofolate reductase, MTRR- 5 - methyltetrahydrofolate-homocysteine methyltransferase reductase.
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Affiliation(s)
- Pk Ragunath
- Department of Bioinformatics, Sri Ramachandra University, Porur, Chennai - 600 116, India
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GWAS of DNA Methylation Variation Within Imprinting Control Regions Suggests Parent-of-Origin Association. Twin Res Hum Genet 2013; 16:767-81. [DOI: 10.1017/thg.2013.30] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Imprinting control regions (ICRs) play a fundamental role in establishing and maintaining the non-random monoallelic expression of certain genes, via common regulatory elements such as non-coding RNAs and differentially methylated regions (DMRs) of DNA. We recently surveyed DNA methylation levels within four ICRs (H19-ICR, IGF2-DMR, KvDMR, and NESPAS-ICR) in whole-blood genomic DNA from 128 monozygotic (MZ) and 128 dizygotic (DZ) human twin pairs. Our analyses revealed high individual variation and intra-domain covariation in methylation levels across CpGs and emphasized the interaction between epigenetic variation and the underlying genetic sequence in a parent-of-origin fashion. Here, we extend our analysis to conduct two genome-wide screenings of single nucleotide polymorphisms (SNPs) underlying either intra-domain covariation or parent-of-origin-dependent association with methylation status at individual CpG sites located within ICRs. Although genome-wide significance was not surpassed due to sample size limitations, the most significantly associated SNPs found through multiple-trait genome-wide association (MQFAM) included the previously described rs10732516, which is located in the vicinity of the H19-ICR. Similarly, we identified an association between rs965808 and methylation status within the NESPAS-ICR. This SNP is positioned within an intronic region of the overlapping genes GNAS and GNAS-AS1, which are imprinted genes regulated by the NESPAS-ICR. Sixteen other SNPs located in regions apart from the analyzed regions displayed suggestive association with intra-domain methylation. Additionally, we identified 13 SNPs displaying parent-of-origin association with individual methylation sites through family-based association testing. In this exploratory study, we show the value and feasibility of using alternative GWAS approaches in the study of the interaction between epigenetic state and genetic sequence within imprinting regulatory domains. Despite the relatively small sample size, we identified a number of SNPs displaying suggestive association either in a domain-wide or in a parent-of-origin fashion. Nevertheless, these associations will require future experimental validation or replication in larger and independent samples.
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Chu X, Shen M, Xie F, Miao XJ, Shou WH, Liu L, Yang PP, Bai YN, Zhang KY, Yang L, Hua Q, Liu WD, Dong Y, Wang HF, Shi JX, Wang Y, Song HD, Chen SJ, Chen Z, Huang W. An X chromosome-wide association analysis identifies variants in GPR174 as a risk factor for Graves' disease. J Med Genet 2013; 50:479-85. [PMID: 23667180 PMCID: PMC3686253 DOI: 10.1136/jmedgenet-2013-101595] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Background Graves’ disease is a female preponderant autoimmune illness and the contribution of the X chromosome to its risk has long been appreciated. However, no X-linked susceptibility loci have been indentified from recent genome-wide association studies (GWAS). Methods We re-examined the X chromosome data from our recent GWAS for Graves’ disease by including males that were previously excluded from the X chromosome analyses. The data were analysed using logistic regression analysis including sex as a covariate, and an additive method assuming X chromosome inactivation, implemented in snpMatrix. Results A cluster of single nucleotide polymorphism (SNPs) at Xq21.1 was found showing association with genome-wide significance, among which rs3827440 was a non-synonymous SNP of GPR174 (Plogistic regression=
9.52×10−8; PsnpMatrix=4.60×10−9; OR=1.76, 95% CI 1.45 to 2.13). The association was reproduced in an independent sample collection set including 4564 Graves’ disease cases and 3968 sex matched controls (combined Plogistic regression=5.53×10−21; combined PsnpMatrix=4.26×10−22; OR=1.69, 95% CI 1.53 to 1.86). Notably, GPR174 was widely expressed in immune related tissues and rs3827440 genotypes were associated with distinct mRNA levels (p=0.002). GPR174 did not show sex biased gene expression in our expression analysis. Resequencing study suggested the contribution of some rare variants in the GPR174 gene region to disease risk with a collapsing p value of 1.16×10−3. Conclusions The finding of an X-linked risk locus for Graves’ disease expands our understanding of the role of the X chromosome in disease susceptibility.
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Affiliation(s)
- Xun Chu
- Department of Genetics, Chinese National Human Genome Center, Bldg. 1, 250 BiBo Road, Shanghai 201203, China
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Aberrant expression of long noncoding RNAs in cervical intraepithelial neoplasia. Int J Gynecol Cancer 2013; 22:1557-63. [PMID: 23095774 DOI: 10.1097/igc.0b013e318272f2c9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE Long noncoding RNAs (lncRNAs) are a unique class of messenger RNA-like transcripts of at least 200 nucleotides in length with no significant protein-coding capacity. Aberrant lncRNA expression is emerging as a major component of the cancer transcriptome. Here, we sought to determine if differential lncRNA expression is a feature of the human cervical intraepithelial neoplasia (CIN) transcriptome. METHODS Sequence data were derived from 16 long serial analyses of gene expression (L-SAGE) libraries constructed from cervical specimens representing mild (CIN1), moderate (CIN2), and severe (CIN3) histopathologic grades of CIN. A novel lncRNA discovery pipeline was developed to query the expression of lncRNAs within the SAGE data sets. RESULTS A total of 2,230,370 sequence tags were delineated from the 16 SAGE libraries, representing the expression of 367,482 unique tags at varying abundance. Using a novel stepwise filtering strategy, we analyzed the cervical SAGE libraries and identified the expression profiles of 1056 lncRNAs in the human cervix. We present the first lncRNA expression profile derived from nonneoplastic cervical tissue and establish that changes in lncRNA expression do occur in cervical intraepithelial lesions. Our analysis also shows statistically significant aberrant expression of lncRNAs in the 3 CIN grades, suggesting that these unique noncoding RNA transcripts may contribute to the development and progression of precursor lesions. CONCLUSIONS Through the analysis of L-SAGE libraries constructed from cervical specimens, we provide the first lncRNA expression profile of the cervix and demonstrate aberrant expression in early-stage neoplasia.
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Pinter SF, Sadreyev RI, Yildirim E, Jeon Y, Ohsumi TK, Borowsky M, Lee JT. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations. Genome Res 2012; 22:1864-76. [PMID: 22948768 PMCID: PMC3460182 DOI: 10.1101/gr.133751.111] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
X chromosome inactivation (XCI) achieves dosage balance in mammals by repressing one of two X chromosomes in females. During XCI, the long noncoding Xist RNA and Polycomb proteins spread along the inactive X (Xi) to initiate chromosome-wide silencing. Although inactivation is known to commence at the X-inactivation center (Xic), how it propagates remains unknown. Here, we examine allele-specific binding of Polycomb repressive complex 2 (PRC2) and chromatin composition during XCI and generate a chromosome-wide profile of Xi and Xa (active X) at nucleosome-resolution. Initially, Polycomb proteins are localized to ∼150 strong sites along the X and concentrated predominantly within bivalent domains coinciding with CpG islands (“canonical sites”). As XCI proceeds, ∼4000 noncanonical sites are recruited, most of which are intergenic, nonbivalent, and lack CpG islands. Polycomb sites are depleted of LINE repeats but enriched for SINEs and simple repeats. Noncanonical sites cluster around the ∼150 strong sites, and their H3K27me3 levels reflect a graded concentration originating from strong sites. This suggests that PRC2 and H3K27 methylation spread along a gradient unique to XCI. We propose that XCI is governed by a hierarchy of defined Polycomb stations that spread H3K27 methylation in cis.
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Affiliation(s)
- Stefan F Pinter
- Howard Hughes Medical Institute, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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Yang L, Li Y, Hong H, Chang CW, Guo LW, Lyn-Cook B, Shi L, Ning B. Sex Differences in the Expression of Drug-Metabolizing and Transporter Genes in Human Liver. ACTA ACUST UNITED AC 2012; 3:1000119. [PMID: 29177108 PMCID: PMC5699760 DOI: 10.4172/2157-7609.1000119] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human sex differences in the gene expression of drug metabolizing enzymes and transporters (DMETs) introduce differences in drug absorption, distribution, metabolism and excretion, possibly affecting drug efficacy and adverse reactions. However, existing studies aimed at identifying dimorphic expression differences of DMET genes are limited by sample size and the number of genes profiled. Focusing on a list of 374 DMET genes, we analyzed a previously published gene expression data set consisting of human male (n=234) and female (n=193) liver samples, and identified 77 genes showing differential expression due to sex. To delineate the biological functionalities and regulatory mechanisms for the differentially expressed DMET genes, we conducted a co-expression network analysis. Moreover, clinical implications of sex differences in the expression of human hepatic DMETs are discussed. This study may contribute to the realization of personalized medicine by better understanding the inter-individual differences between males and females in drug/xenobiotic responses and human disease susceptibilities.
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Affiliation(s)
- Lun Yang
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Yan Li
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Huixiao Hong
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Ching-Wei Chang
- Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Li-Wu Guo
- Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Beverly Lyn-Cook
- Office of Associate Director of Regulatory Activities, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Leming Shi
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
| | - Baitang Ning
- Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
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Dunlop MG, Dobbins SE, Farrington SM, Jones AM, Palles C, Whiffin N, Tenesa A, Spain S, Broderick P, Ooi LY, Domingo E, Smillie C, Henrion M, Frampton M, Martin L, Grimes G, Gorman M, Semple C, Ma Y, Barclay E, Prendergast J, Cazier JB, Olver B, Carvajal-Carmona LG, Ballereau S, Lloyd A, Vijayakrishnan J, Zgaga L, Rudan I, Theodoratou E, Starr JM, Deary I, Kirac I, Kovačević D, Aaltonen LA, Renkonen-Sinisalo L, Mecklin JP, Matsuda K, Nakamura Y, Okada Y, Gallinger S, Duggan DJ, Conti D, Newcomb P, Hopper J, Jenkins MA, Schumacher F, Casey G, Easton D, Shah M, Pharoah P, Lindblom A, Liu T, Smith CG, West H, Cheadle JP, Midgley R, Kerr DJ, Campbell H, Tomlinson IP, Houlston RS. Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. Nat Genet 2012; 44:770-6. [PMID: 22634755 PMCID: PMC4747430 DOI: 10.1038/ng.2293] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 04/30/2012] [Indexed: 12/12/2022]
Abstract
We performed a meta-analysis of five genome-wide association studies to identify common variants influencing colorectal cancer (CRC) risk comprising 8,682 cases and 9,649 controls. Replication analysis was performed in case-control sets totaling 21,096 cases and 19,555 controls. We identified three new CRC risk loci at 6p21 (rs1321311, near CDKN1A; P = 1.14 × 10(-10)), 11q13.4 (rs3824999, intronic to POLD3; P = 3.65 × 10(-10)) and Xp22.2 (rs5934683, near SHROOM2; P = 7.30 × 10(-10)) This brings the number of independent loci associated with CRC risk to 20 and provides further insight into the genetic architecture of inherited susceptibility to CRC.
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Affiliation(s)
- Malcolm G Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Sara E Dobbins
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Susan Mary Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Angela M Jones
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Nicola Whiffin
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Albert Tenesa
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Sarah Spain
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Peter Broderick
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Li-Yin Ooi
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Enric Domingo
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Claire Smillie
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Marc Henrion
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Matthew Frampton
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Lynn Martin
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Graeme Grimes
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Maggie Gorman
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Colin Semple
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Yussanne Ma
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | - Ella Barclay
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - James Prendergast
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | | | - Bianca Olver
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | | | - Stephane Ballereau
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
| | - Amy Lloyd
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
| | | | - Lina Zgaga
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
- Public Health Sciences, Teviot Place, University of Edinburgh, UK
| | - Igor Rudan
- Public Health Sciences, Teviot Place, University of Edinburgh, UK
| | | | | | - John M Starr
- University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8, 9AG
| | - Ian Deary
- University of Edinburgh Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, EH8, 9AG
| | - Iva Kirac
- Department of Surgical Oncology, University Hospital for Tumors, University Hospital Center ‘Sestre milosrdnice’, Zagreb, Croatia
| | - Dujo Kovačević
- Department of Surgery, University Hospital Center ‘Sestre milosrdnice’, Zagreb, Croatia
| | - Lauri A Aaltonen
- Department of Medical Genetics, Genome-Scale Biology Research Program, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | | | - Jukka-Pekka Mecklin
- Jyväskylä Central Hospital, University of Eastern Finland, Jyväskylä, Finland
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Nakamura
- Laboratory of Molecular Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yukinori Okada
- Laboratory for Statistical Analysis, Center for Genomic Medicine, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - David J Duggan
- Translational Genomics Research Institute (TGen), Phoenix, AZ 85004, USA
| | - David Conti
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, CA 90089, USA
| | - Polly Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - John Hopper
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Australia
| | - Mark A. Jenkins
- Centre for Molecular, Environmental, Genetic, and Analytic Epidemiology, The University of Melbourne, Australia
| | - Fredrick Schumacher
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, CA 90089, USA
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, CA 90089, USA
| | - Douglas Easton
- Departments of Oncology and Public Health and Primary Care, University of Cambridge, CB1 RN, UK
| | - Mitul Shah
- Departments of Oncology and Public Health and Primary Care, University of Cambridge, CB1 RN, UK
| | - Paul Pharoah
- Departments of Oncology and Public Health and Primary Care, University of Cambridge, CB1 RN, UK
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, S17176 Stockholm
| | - Tao Liu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, S17176 Stockholm
| | | | - Christopher G Smith
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Hannah West
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Jeremy P. Cheadle
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | | | - Rachel Midgley
- Department of Oncology, Oxford University, Radcliffe Infirmary, Old Road Campus Research Building, Headington, Oxford, OX3 7DQ, UK
| | - David J Kerr
- Department of Oncology, Oxford University, Radcliffe Infirmary, Old Road Campus Research Building, Headington, Oxford, OX3 7DQ, UK
| | - Harry Campbell
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit, Edinburgh, EH4 2XU, UK
- Public Health Sciences, Teviot Place, University of Edinburgh, UK
| | - Ian P Tomlinson
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
- Oxford NIHR Comprehensive Biomedical Research Centre
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, Sutton, UK
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Bao Y, Zheng J, Han C, Jin J, Han H, Liu Y, Lau YL, Tu W, Cao X. Tyrosine kinase Btk is required for NK cell activation. J Biol Chem 2012; 287:23769-78. [PMID: 22589540 DOI: 10.1074/jbc.m112.372425] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Bruton tyrosine kinase (Btk) is not only critical for B cell development and differentiation but is also involved in the regulation of Toll-like receptor-triggered innate response of macrophages. However, whether Btk is involved in the regulation of natural killer (NK) cell innate function remains unknown. Here, we show that Btk expression is up-regulated during maturation and activation of mouse NK cells. Murine Btk(-/-) NK cells have decreased innate immune responses to the TLR3 ligand, with reduced expressions of IFN-γ, perforin, and granzyme-B and decreased cytotoxic activity. Furthermore, Btk is found to promote TLR3-triggered NK cell activation mainly by activating the NF-κB pathway. Poly(I:C)-induced NK cell-mediated acute hepatitis was observed to be attenuated in Btk(-/-) mice or the mice with in vivo administration of the Btk inhibitor. Correspondingly, liver damage was aggravated in Btk(-/-) mice after the adoptive transfer of Btk(+/+) NK cells, further indicating that Btk-mediated NK cell activation contributes to TLR3-triggered acute liver injury. Importantly, reduced TLR3-triggered activation of human NK cells was observed in Btk-deficient patients with X-linked agammaglobulinemia, as evidenced by the reduced IFN-γ, CD69, and CD107a expression and cytotoxic activity. These results indicate that Btk is required for activation of NK cells, thus providing insight into the physiological significance of Btk in the regulation of immune cell functions and innate inflammatory response.
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Affiliation(s)
- Yan Bao
- Translational Medicine Center, Changzheng Hospital, Shanghai 200433, China.
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Bermejo-Alvarez P, Ramos-Ibeas P, Gutierrez-Adan A. Solving the "X" in embryos and stem cells. Stem Cells Dev 2012; 21:1215-24. [PMID: 22309156 DOI: 10.1089/scd.2011.0685] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
X-chromosome inactivation (XCI) is a complex epigenetic process that ensures that most X-linked genes are expressed equally for both sexes. Female eutherian mammals inactivate randomly the maternal or paternal inherited X-chromosome early in embryogenesis, whereas the extra-embryonic tissues experience an imprinting XCI that results in the inactivation of the paternal X-chromosome in mice. Although the phenomenon was initially described 40 years ago, many aspects remain obscure. In the last 2 years, some trademark publications have shed new light on the ongoing debate regarding the timing and mechanism of imprinted or random XCI. It has been observed that XCI is not accomplished at the blastocyst stage in bovines, rabbits, and humans, contrasting with the situation reported in mice, the standard model. All the species present 2 active X-chromosomes (Xa) in the early epiblast of the blastocyst, the cellular source for embryonic stem cells (ESCs). In this perspective, it would make sense to expect an absence of XCI in undifferentiated ESCs, but human ESCs are highly heterogeneous for this parameter and the presence of 2 Xa has been proposed as a true hallmark of ground-state pluripotency and a quality marker for female ESCs. Similarly, XCI reversal in female induced pluripotent stem cells is a key reprogramming event on the path to achieve the naïve pluripotency, and key pluripotency regulators can interact directly or indirectly with Xist. Finally, the presence of 2 Xa may lead to a sex-specific transcriptional regulation resulting in sexual dimorphism in reprogramming and differentiation.
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Lee JT. Gracefully ageing at 50, X-chromosome inactivation becomes a paradigm for RNA and chromatin control. Nat Rev Mol Cell Biol 2011; 12:815-26. [DOI: 10.1038/nrm3231] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Ladwein KI, Jung M. Oxidized Cytosine Metabolites Offer a Fresh Perspective for Active DNA Demethylation. Angew Chem Int Ed Engl 2011; 50:12143-5. [DOI: 10.1002/anie.201106690] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Indexed: 01/13/2023]
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Ladwein KI, Jung M. Oxidierte Cytosin-Derivate - der Schlüssel zur aktiven DNA-Demethylierung? Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106690] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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76
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Wang RT, Ahn S, Park CC, Khan AH, Lange K, Smith DJ. Effects of genome-wide copy number variation on expression in mammalian cells. BMC Genomics 2011; 12:562. [PMID: 22085887 PMCID: PMC3287593 DOI: 10.1186/1471-2164-12-562] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 11/16/2011] [Indexed: 11/17/2022] Open
Abstract
Background There is only a limited understanding of the relation between copy number and expression for mammalian genes. We fine mapped cis and trans regulatory loci due to copy number change for essentially all genes using a human-hamster radiation hybrid (RH) panel. These loci are called copy number expression quantitative trait loci (ceQTLs). Results Unexpected findings from a previous study of a mouse-hamster RH panel were replicated. These findings included decreased expression as a result of increased copy number for 30% of genes and an attenuated relationship between expression and copy number on the X chromosome suggesting an Xist independent form of dosage compensation. In a separate glioblastoma dataset, we found conservation of genes in which dosage was negatively correlated with gene expression. These genes were enriched in signaling and receptor activities. The observation of attenuated X-linked gene expression in response to increased gene number was also replicated in the glioblastoma dataset. Of 523 gene deserts of size > 600 kb in the human RH panel, 325 contained trans ceQTLs with -log10 P > 4.1. Recently discovered genes, ultra conserved regions, noncoding RNAs and microRNAs explained only a small fraction of the results, suggesting a substantial portion of gene deserts harbor as yet unidentified functional elements. Conclusion Radiation hybrids are a useful tool for high resolution mapping of cis and trans loci capable of affecting gene expression due to copy number change. Analysis of two independent radiation hybrid panels show agreement in their findings and may serve as a discovery source for novel regulatory loci in noncoding regions of the genome.
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Affiliation(s)
- Richard T Wang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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77
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Gibb EA, Enfield KSS, Stewart GL, Lonergan KM, Chari R, Ng RT, Zhang L, MacAulay CE, Rosin MP, Lam WL. Long non-coding RNAs are expressed in oral mucosa and altered in oral premalignant lesions. Oral Oncol 2011; 47:1055-61. [PMID: 21835683 DOI: 10.1016/j.oraloncology.2011.07.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 06/17/2011] [Accepted: 07/09/2011] [Indexed: 01/01/2023]
Abstract
Oral epithelial dysplasias are believed to progress through a series of histopathological stages; from mild to severe dysplasia, to carcinoma in situ, and finally to invasive OSCC. Underlying this change in histopathological grade are gross chromosome alterations and changes in gene expression of both protein-coding genes and non-coding RNAs. Recent papers have described associations of aberrant expression of microRNAs, one class of non-coding RNAs, with oral cancer. However, expression profiling of long non-coding RNAs (lncRNAs) has not been reported. Long non-coding RNAs are a novel class of mRNA-like transcripts with no protein coding capacity, but with a variety of functions including roles in epigenetics and gene regulation. In recent reports, the aberrant expression of lncRNAs has been associated with human cancers, suggesting a critical role in tumorigenesis. Here, we present the first long non-coding RNA expression map for the human oral mucosa. We describe the expression of 325 long non-coding RNAs, suggesting lncRNA expression contributes significantly to the oral transcriptome. Intriguingly, ∼60% of the detected lncRNAs show aberrant expression in oral premalignant lesions. A number of these lncRNAs have been previously associated with other human cancers.
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Affiliation(s)
- Ewan A Gibb
- British Columbia Cancer Agency Research Centre, Vancouver, Canada V5Z 1L3.
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78
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Koroma AP, Jones R, Michalak P. Snapshot of DNA methylation changes associated with hybridization in Xenopus. Physiol Genomics 2011; 43:1276-80. [PMID: 21914783 DOI: 10.1152/physiolgenomics.00110.2011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Hybridization often results in dramatic genome reconfigurations including epigenetic changes that control gene expression. Here we survey methylation patterns of interspecific Xenopus F1 hybrids relative to parental species X. laevis and X. muelleri, using methyl-sensitive amplification polymorphisms (MSAPs). Out of a total of 546 MSAP markers, 364 were effective in elucidating the difference in methylation patterns between the hybrids and the parental species. Principal coordinate analysis of methylated fragments revealed four distinct clusters with the two parental species separate from hybrid males and females. On average, hybrids were characterized by a higher proportion (70.6%) of methylated fragments compared with the parental species (64.5%), and this difference was consistent with previously observed disruptions of hybrid transcriptomes. The proportion of methylated fragments did not correlate with variation in genome size, as measured with flow cytometry. The levels of methylation in sterile hybrid males (73.8%) were higher than in fertile hybrid females (68.6%), but this difference was not statistically significant. A total of 76 methylated fragments (20.9%) were hybrid-unique, presumably originating from methylation alterations in hybrid genomes.
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79
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Cytosine methylation regulates oviposition in the pathogenic blood fluke Schistosoma mansoni. Nat Commun 2011; 2:424. [PMID: 21829186 PMCID: PMC3265374 DOI: 10.1038/ncomms1433] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2010] [Accepted: 07/13/2011] [Indexed: 12/31/2022] Open
Abstract
Similar to other metazoan pathogens, Schistosoma mansoni undergoes transcriptional and developmental regulation during its complex lifecycle and host interactions. DNA methylation as a mechanism to control these processes has, to date, been discounted in this parasite. Here we show the first evidence for cytosine methylation in the S. mansoni genome. Transcriptional coregulation of novel DNA methyltransferase (SmDnmt2) and methyl-CpG-binding domain proteins mirrors the detection of cytosine methylation abundance and implicates the presence of a functional DNA methylation machinery. Genome losses in cytosine methylation upon SmDnmt2 silencing and the identification of a hypermethylated, repetitive intron within a predicted forkhead gene confirm this assertion. Importantly, disruption of egg production and egg maturation by 5-azacytidine establishes an essential role for 5-methylcytosine in this parasite. These findings provide the first functional confirmation for this epigenetic modification in any worm species and link the cytosine methylation machinery to platyhelminth oviposition processes. The chronic disease schistosomiasis is caused by the blood fluke Schistosoma mansoni. By studying DNA modifications throughout the lifecycle of the pathogen, the authors identify DNA methylation as a factor in egg development and suggest that the epigenetic machinery responsible may be a therapeutic target.
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80
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Hickey PF, Bahlo M. X chromosome association testing in genome wide association studies. Genet Epidemiol 2011; 35:664-70. [PMID: 21818774 DOI: 10.1002/gepi.20616] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 06/14/2011] [Accepted: 06/15/2011] [Indexed: 11/05/2022]
Abstract
Genome wide association studies (GWAS) have revealed many fascinating insights into complex diseases even from simple, single-marker statistical tests. Most of these tests are designed for testing of associations between a phenotype and an autosomal genotype and are therefore not applicable to X chromosome data. Testing for association on the X chromosome raises unique challenges that have motivated the development of X-specific statistical tests in the literature. However, to date there has been no study of these methods under a wide range of realistic study designs, allele frequencies and disease models to assess the size and power of each test. To address this, we have performed an extensive simulation study to investigate the effects of the sex ratios in the case and control cohorts, as well as the allele frequencies, on the size and power of eight test statistics under three different disease models that each account for X-inactivation. We show that existing, but under-used, methods that make use of both male and female data are uniformly more powerful than popular methods that make use of only female data. In particular, we show that Clayton's one degree of freedom statistic [Clayton, 2008] is robust and powerful across a wide range of realistic simulation parameters. Our results provide guidance on selecting the most appropriate test statistic to analyse X chromosome data from GWAS and show that much power can be gained by a more careful analysis of X chromosome GWAS data.
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Affiliation(s)
- Peter F Hickey
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
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81
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Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation. Nat Rev Genet 2011; 12:542-53. [PMID: 21765457 DOI: 10.1038/nrg3035] [Citation(s) in RCA: 263] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In female mammals, one of the two X chromosomes is silenced for dosage compensation between the sexes. X-chromosome inactivation is initiated in early embryogenesis by the Xist RNA that localizes to the inactive X chromosome. During development, the inactive X chromosome is further modified, a specialized form of facultative heterochromatin is formed and gene repression becomes stable and independent of Xist in somatic cells. The recent identification of several factors involved in this process has provided insights into the mechanism of Xist localization and gene silencing. The emerging picture is complex and suggests that chromosome-wide silencing can be partitioned into several steps, the molecular components of which are starting to be defined.
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82
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Day JJ, Sweatt JD. Cognitive neuroepigenetics: a role for epigenetic mechanisms in learning and memory. Neurobiol Learn Mem 2011; 96:2-12. [PMID: 21195202 PMCID: PMC3111867 DOI: 10.1016/j.nlm.2010.12.008] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 12/13/2010] [Accepted: 12/20/2010] [Indexed: 01/09/2023]
Abstract
Although long-lasting behavioral memories have long been thought to require equally persistent molecular changes, little is known about the biochemical underpinnings of memory storage and maintenance. Increasing evidence now suggests that long-term behavioral change may be associated with epigenetic regulation of transcription in the central nervous system. In this review, we present evidence that changes in DNA methylation contribute to memory formation and maintenance, consider how DNA methylation affects readout of memory-related genes, and discuss how these changes may be important in the large-scale context of memory circuits. Finally, we discuss potential challenges involved in examining epigenetic changes in the brain and highlight how epigenetic mechanisms may be relevant for other cognitive processes.
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Affiliation(s)
- Jeremy J Day
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, University of Alabama at Birmingham, United States
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83
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Hochberg Z, Feil R, Constancia M, Fraga M, Junien C, Carel JC, Boileau P, Le Bouc Y, Deal CL, Lillycrop K, Scharfmann R, Sheppard A, Skinner M, Szyf M, Waterland RA, Waxman DJ, Whitelaw E, Ong K, Albertsson-Wikland K. Child health, developmental plasticity, and epigenetic programming. Endocr Rev 2011; 32:159-224. [PMID: 20971919 PMCID: PMC3365792 DOI: 10.1210/er.2009-0039] [Citation(s) in RCA: 401] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Accepted: 08/27/2010] [Indexed: 11/19/2022]
Abstract
Plasticity in developmental programming has evolved in order to provide the best chances of survival and reproductive success to the organism under changing environments. Environmental conditions that are experienced in early life can profoundly influence human biology and long-term health. Developmental origins of health and disease and life-history transitions are purported to use placental, nutritional, and endocrine cues for setting long-term biological, mental, and behavioral strategies in response to local ecological and/or social conditions. The window of developmental plasticity extends from preconception to early childhood and involves epigenetic responses to environmental changes, which exert their effects during life-history phase transitions. These epigenetic responses influence development, cell- and tissue-specific gene expression, and sexual dimorphism, and, in exceptional cases, could be transmitted transgenerationally. Translational epigenetic research in child health is a reiterative process that ranges from research in the basic sciences, preclinical research, and pediatric clinical research. Identifying the epigenetic consequences of fetal programming creates potential applications in clinical practice: the development of epigenetic biomarkers for early diagnosis of disease, the ability to identify susceptible individuals at risk for adult diseases, and the development of novel preventive and curative measures that are based on diet and/or novel epigenetic drugs.
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Affiliation(s)
- Z Hochberg
- Rambam Medical Center, Rappaport Faculty of Medicine and Research Institute, Technion–Israel Institute of Technology, Haifa, Israel.
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84
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Agrawal P, Dey P. Barr body in fine needle aspiration cytology of ovarian malignancies. Diagn Cytopathol 2011; 40:964-6. [PMID: 21416650 DOI: 10.1002/dc.21688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Accepted: 02/09/2011] [Indexed: 11/11/2022]
Abstract
The Barr body is the inactive X chromosome in a female somatic cell. It is readily identified as plano-convex structure of 2-3 micron in diameter on the periphery of the nuclear membrane. The aim of this study is to evaluate the significance of Barr body count in malignant ovarian tumors on fine needle aspiration cytology (FNAC) smears. In this retrospective study, Barr body was counted in FNAC smears of 20 successive malignant ovarian lesions and expressed as percentage. Mean (±SD) Barr body score was 2.4 ± 2.58. Minimum Barr body count was 1 and maximum was 9. The gross reduction of Barr body in ovarian neoplasms is an interesting cytomorphologic finding.
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Affiliation(s)
- Pallavi Agrawal
- Department of Cytology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
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85
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Loley C, Ziegler A, König IR. Association tests for X-chromosomal markers--a comparison of different test statistics. Hum Hered 2011; 71:23-36. [PMID: 21325864 DOI: 10.1159/000323768] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 12/21/2010] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Genome-wide association studies have successfully elucidated the genetic background of complex diseases, but X chromosomal data have usually not been analyzed. A reason for this is that there is no consensus approach for the analysis taking into account the specific features of X chromosomal data. This contribution evaluates test statistics proposed for X chromosomal markers regarding type I error frequencies and power. METHODS We performed extensive simulation studies covering a wide range of different settings. Besides characteristics of the general population, we investigated sex-balanced or unbalanced sampling procedures as well as sex-specific effect sizes, allele frequencies and prevalence. Finally, we applied the test statistics to an association data set on Crohn's disease. RESULTS Simulation results imply that in addition to standard quality control, sex-specific allele frequencies should be checked to control for type I errors. Furthermore, we observed distinct differences in power between test statistics which are determined by sampling design and sex specificity of effect sizes. Analysis of the Crohn's disease data detects two previously unknown genetic regions on the X chromosome. CONCLUSION Although no test is uniformly most powerful under all settings, recommendations are offered as to which test performs best under certain conditions.
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Affiliation(s)
- Christina Loley
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Lübeck, Deutschland
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86
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Abstract
The development of next-generation sequencing technologies has enabled the transcriptome to be measured and characterized at a level which was previously unattainable. Shot gun sequencing of RNAs, or RNA-Seq as it is known, is providing the means to simultaneously survey locus activity, transcript-specific expression, sequence content of transcripts and transcriptome discovery. This article discusses the current state of RNA-Seq, its potential for redefining transcriptomics and some of the challenges associated with this revolutionary technology.
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Affiliation(s)
- Karin S Kassahn
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, Brisbane, Australia
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87
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Zackay A, Steinhoff C. MethVisual - visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing. BMC Res Notes 2010; 3:337. [PMID: 21159174 PMCID: PMC3012040 DOI: 10.1186/1756-0500-3-337] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 12/15/2010] [Indexed: 11/23/2022] Open
Abstract
Background Exploration of DNA methylation and its impact on various regulatory mechanisms has become a very active field of research. Simultaneously there is an arising need for tools to process and analyse the data together with statistical investigation and visualisation. Findings MethVisual is a new application that enables exploratory analysis and intuitive visualization of DNA methylation data as is typically generated by bisulfite sequencing. The package allows the import of DNA methylation sequences, aligns them and performs quality control comparison. It comprises basic analysis steps as lollipop visualization, co-occurrence display of methylation of neighbouring and distant CpG sites, summary statistics on methylation status, clustering and correspondence analysis. The package has been developed for methylation data but can be also used for other data types for which binary coding can be inferred. The application of the package, as well as a comparison to existing DNA methylation analysis tools and its workflow based on two datasets is presented in this paper. Conclusions The R package MethVisual offers various analysis procedures for data that can be binarized, in particular for bisulfite sequenced methylation data. R/Bioconductor has become one of the most important environments for statistical analysis of various types of biological and medical data. Therefore, any data analysis within R that allows the integration of various data types as provided from different technological platforms is convenient. It is the first and so far the only specific package for DNA methylation analysis, in particular for bisulfite sequenced data available in R/Bioconductor enviroment. The package is available for free at http://methvisual.molgen.mpg.de/ and from the Bioconductor Consortium http://www.bioconductor.org.
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Affiliation(s)
- Arie Zackay
- Department of Computational Biology, Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany.
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88
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Arnold AP. Promoting the understanding of sex differences to enhance equity and excellence in biomedical science. Biol Sex Differ 2010; 1:1. [PMID: 21208467 PMCID: PMC3010102 DOI: 10.1186/2042-6410-1-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 11/04/2010] [Indexed: 01/10/2023] Open
Affiliation(s)
- Arthur P Arnold
- Department of Integrative Biology and Physiology, University of California, Los Angeles.
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89
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Reinius B, Shi C, Hengshuo L, Sandhu KS, Radomska KJ, Rosen GD, Lu L, Kullander K, Williams RW, Jazin E. Female-biased expression of long non-coding RNAs in domains that escape X-inactivation in mouse. BMC Genomics 2010; 11:614. [PMID: 21047393 PMCID: PMC3091755 DOI: 10.1186/1471-2164-11-614] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 11/03/2010] [Indexed: 02/01/2023] Open
Abstract
Background Sexual dimorphism in brain gene expression has been recognized in several animal species. However, the relevant regulatory mechanisms remain poorly understood. To investigate whether sex-biased gene expression in mammalian brain is globally regulated or locally regulated in diverse brain structures, and to study the genomic organisation of brain-expressed sex-biased genes, we performed a large scale gene expression analysis of distinct brain regions in adult male and female mice. Results This study revealed spatial specificity in sex-biased transcription in the mouse brain, and identified 173 sex-biased genes in the striatum; 19 in the neocortex; 12 in the hippocampus and 31 in the eye. Genes located on sex chromosomes were consistently over-represented in all brain regions. Analysis on a subset of genes with sex-bias in more than one tissue revealed Y-encoded male-biased transcripts and X-encoded female-biased transcripts known to escape X-inactivation. In addition, we identified novel coding and non-coding X-linked genes with female-biased expression in multiple tissues. Interestingly, the chromosomal positions of all of the female-biased non-coding genes are in close proximity to protein-coding genes that escape X-inactivation. This defines X-chromosome domains each of which contains a coding and a non-coding female-biased gene. Lack of repressive chromatin marks in non-coding transcribed loci supports the possibility that they escape X-inactivation. Moreover, RNA-DNA combined FISH experiments confirmed the biallelic expression of one such novel domain. Conclusion This study demonstrated that the amount of genes with sex-biased expression varies between individual brain regions in mouse. The sex-biased genes identified are localized on many chromosomes. At the same time, sexually dimorphic gene expression that is common to several parts of the brain is mostly restricted to the sex chromosomes. Moreover, the study uncovered multiple female-biased non-coding genes that are non-randomly co-localized on the X-chromosome with protein-coding genes that escape X-inactivation. This raises the possibility that expression of long non-coding RNAs may play a role in modulating gene expression in domains that escape X-inactivation in mouse.
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Affiliation(s)
- Björn Reinius
- Department of Evolution and Development, EBC, Uppsala University, Sweden.
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90
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Cotton S, Wedekind C. Male mutation bias and possible long-term effects of human activities. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2010; 24:1190-1197. [PMID: 20507353 DOI: 10.1111/j.1523-1739.2010.01524.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The ability of a population to adapt to changing environments depends critically on the amount and kind of genetic variability it possesses. Mutations are an important source of new genetic variability and may lead to new adaptations, especially if the population size is large. Mutation rates are extremely variable between and within species, and males usually have higher mutation rates as a result of elevated rates of male germ cell division. This male bias affects the overall mutation rate. We examined the factors that influence male mutation bias, and focused on the effects of classical life-history parameters, such as the average age at reproduction and elevated rates of sperm production in response to sexual selection and sperm competition. We argue that human-induced changes in age at reproduction or in sexual selection will affect male mutation biases and hence overall mutation rates. Depending on the effective population size, these changes are likely to influence the long-term persistence of a population.
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Affiliation(s)
- Samuel Cotton
- Research Department of Genetics, Evolution & Environment, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, United Kingdom.
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91
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Wong CCY, Caspi A, Williams B, Craig IW, Houts R, Ambler A, Moffitt TE, Mill J. A longitudinal study of epigenetic variation in twins. Epigenetics 2010; 5:516-26. [PMID: 20505345 DOI: 10.4161/epi.5.6.12226] [Citation(s) in RCA: 210] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is a key epigenetic mechanism involved in the developmental regulation of gene expression. Alterations in DNA methylation are established contributors to inter-individual phenotypic variation and have been associated with disease susceptibility. The degree to which changes in loci-specific DNA methylation are under the influence of heritable and environmental factors is largely unknown. In this study, we quantitatively measured DNA methylation across the promoter regions of the dopamine receptor 4 gene (DRD4), the serotonin transporter gene (SLC6A4/SERT) and the X-linked monoamine oxidase A gene (MAOA) using DNA sampled at both ages 5 and 10 years in 46 MZ twin-pairs and 45 DZ twin-pairs (total n=182). Our data suggest that DNA methylation differences are apparent already in early childhood, even between genetically identical individuals, and that individual differences in methylation are not stable over time. Our longitudinal-developmental study suggests that environmental influences are important factors accounting for interindividual DNA methylation differences, and that these influences differ across the genome. The observation of dynamic changes in DNA methylation over time highlights the importance of longitudinal research designs for epigenetic research.
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Affiliation(s)
- Chloe Chung Yi Wong
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, UK.
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92
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Taxilaga-Zetina O, Pliego-Pastrana P, Carbajal-Tinoco MD. Three-dimensional structures of RNA obtained by means of knowledge-based interaction potentials. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:041914. [PMID: 20481760 DOI: 10.1103/physreve.81.041914] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 03/24/2010] [Indexed: 05/29/2023]
Abstract
We derive a set of effective potentials describing the interaction between pairs of nucleotides that belong to an RNA molecule. Such interaction potentials are then used as the main constituents of a simplified simulation model, which is tested in the description of small secondary structure motifs. Our simulated RNA hairpins are consistent with the experimental structures obtained by NMR.
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Affiliation(s)
- Oscar Taxilaga-Zetina
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del IPN, Apartado Postal 14-740, 07000 México, Distrito Federal, Mexico
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93
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Wistuba J. Animal models for Klinefelter's syndrome and their relevance for the clinic. Mol Hum Reprod 2010; 16:375-85. [DOI: 10.1093/molehr/gaq024] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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94
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Kvikstad EM, Makova KD. The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Res 2010; 20:600-13. [PMID: 20219940 DOI: 10.1101/gr.099044.109] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the sex chromosomes. Here, using a multiple regression framework, we investigate primate Alu and L1 densities shaped by regional genome features and location on a particular chromosome type. As a result of our analysis, first, we build statistical models explaining up to 79% and 44% of variation in Alu and L1 element density, respectively. Second, we analyze sex chromosome versus autosome TE densities corrected for regional genomic effects. We discover that sex-chromosome bias in Alu and L1 distributions not only persists after accounting for these effects, but even presents differences in patterns, confirming preferential Alu integration in the male germline, yet likely integration of L1s in both male and female germlines or in early embryogenesis. Additionally, our models reveal that local base composition (measured by GC content and density of L1 target sites) and natural selection (inferred via density of most conserved elements) are significant to predicting densities of L1s. Interestingly, measurements of local double-stranded breaks (a 13-mer associated with genome instability) strongly correlate with densities of Alu elements; little evidence was found for the role of recombination-driven deletion in driving TE distributions over evolutionary time. Thus, Alu and L1 densities have been influenced by the combination of distinct local genome landscapes and the unique evolutionary dynamics of sex chromosomes.
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Affiliation(s)
- Erika M Kvikstad
- Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA.
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95
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Lelièvre JM, Le Bourhis D, Breton A, Hayes H, Servely JL, Vignon X. Heat-induced and spontaneous expression of Hsp70.1Luciferase transgene copies localized on Xp22 in female bovine cells. BMC Res Notes 2010; 3:17. [PMID: 20180997 PMCID: PMC2832894 DOI: 10.1186/1756-0500-3-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 01/22/2010] [Indexed: 12/03/2022] Open
Abstract
Background Expression of several copies of the heat-inducible Hsp70.1Luciferase (LUC) transgene inserted at a single X chromosome locus of a bull (Bos taurus) was assessed in females after X-chromosome inactivation (XCI). Furthermore, impact of the chromosomal environment on the spontaneous expression of these transgene copies before XCI was studied during early development in embryos obtained after in vitro fertilization (IVF), when the locus was carried by the X chromosome inherited from the bull, and after somatic cell nuclear transfer (SCNT) cloning, when the locus could be carried by the inactive Xi or the active Xa chromosome in a female donor cell, or by the (active) X in a male donor cell. Findings Transgene copies were mapped to bovine Xp22. In XXLUC female fibroblasts, i.e. after random XCI, the proportions of late-replicating inactive and early-replicating active XLUC chromosomes were not biased and the proportion of cells displaying an increase in the level of immunostained luciferase protein after heat-shock induction was similar to that in male fibroblasts. Spontaneous transgene expression occurred at the 8-16-cell stage both in transgenic (female) embryos obtained after IVF and in male and female embryos obtained after SCNT. Conclusions The XLUC chromosome is normally inactivated but at least part of the inactivated X-linked Hsp70.1Luciferase transgene copies remains heat-inducible after random XCI in somatic cells. Before XCI, the profile of the transgenes' spontaneous expression is independent of the epigenetic origin of the XLUC chromosome since it is similar in IVF female, SCNT male and SCNT female embryos.
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Affiliation(s)
- Jean-Marc Lelièvre
- INRA, UMR 1198 Biologie du Développement et Reproduction, F-78350 Jouy en Josas, France.
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96
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97
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98
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Abstract
Although the literature concerning statistical testing for genotype-phenotype association in family-based and population-based studies is very extensive, until recently the sex chromosomes have received little attention. Here it is shown that the X chromosome in particular presents special problems with respect to efficient analysis of mixed-sex population studies, and as a result of X inactivation. This paper reviews recent developments in approaching these problems.
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Affiliation(s)
- David G Clayton
- Wellcome Trust/Juvenile Diabetes Research Foundation Diabetes and Inflammation Laboratory, Cambridge University, Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Addenbrooke's Hospital, Cambridge CB2 0XY, UK
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Dinger ME, Amaral PP, Mercer TR, Mattick JS. Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:407-23. [PMID: 19770204 DOI: 10.1093/bfgp/elp038] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genome-wide analyses of the eukaryotic transcriptome have revealed that the majority of the genome is transcribed, producing large numbers of non-protein-coding RNAs (ncRNAs). This surprising observation challenges many assumptions about the genetic programming of higher organisms and how information is stored and organized within the genome. Moreover, the rapid advances in genomics have given little opportunity for biologists to integrate these emerging findings into their intellectual and experimental frameworks. This problem has been compounded by the perception that genome-wide studies often generate more questions than answers, which in turn has led to confusion and controversy. In this article, we address common questions associated with the phenomenon of pervasive transcription and consider the indices that can be used to evaluate the function (or lack thereof) of the resulting ncRNAs. We suggest that many lines of evidence, including expression profiles, conservation signatures, chromatin modification patterns and examination of increasing numbers of individual cases, argue in favour of the widespread functionality of non-coding transcription. We also discuss how informatic and experimental approaches used to analyse protein-coding genes may not be applicable to ncRNAs and how the general perception that protein-coding genes form the main informational output of the genome has resulted in much of the misunderstanding surrounding pervasive transcription and its potential significance. Finally, we present the conceptual implications of the majority of the eukaryotic genome being functional and describe how appreciating this perspective will provide considerable opportunity to further understand the molecular basis of development and complex diseases.
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Affiliation(s)
- Marcel E Dinger
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
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Cantrell MA, Carstens BC, Wichman HA. X chromosome inactivation and Xist evolution in a rodent lacking LINE-1 activity. PLoS One 2009; 4:e6252. [PMID: 19603076 PMCID: PMC2705805 DOI: 10.1371/journal.pone.0006252] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 05/28/2009] [Indexed: 02/05/2023] Open
Abstract
Dosage compensation in eutherian mammals occurs by inactivation of one X chromosome in females. Silencing of that X chromosome is initiated by Xist, a large non-coding RNA, whose coating of the chromosome extends in cis from the X inactivation center. LINE-1 (L1) retrotransposons have been implicated as possible players for propagation of the Xist signal, but it has remained unclear whether they are essential components. We previously identified a group of South American rodents in which L1 retrotransposition ceased over 8 million years ago and have now determined that at least one species of these rodents, Oryzomys palustris, still retains X inactivation. We have also isolated and analyzed the majority of the Xist RNA from O. palustris and a sister species retaining L1 activity, Sigmodon hispidus, to determine if evolution in these sequences has left signatures that might suggest a critical role for L1 elements in Xist function. Comparison of rates of Xist evolution in the two species fails to support L1 involvement, although other explanations are possible. Similarly, comparison of known repeats and potential RNA secondary structures reveals no major differences with the exception of a new repeat in O. palustris that has potential to form new secondary structures.
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Affiliation(s)
- Michael A. Cantrell
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Bryan C. Carstens
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Holly A. Wichman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
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