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Morante-Palacios O. Interactive DNA Methylation Array Analysis with ShinyÉPICo. Methods Mol Biol 2023; 2624:7-18. [PMID: 36723806 DOI: 10.1007/978-1-0716-2962-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Arrays provide a cost-effective platform for the analysis of human DNA methylation. ShinyÉPICo is an interactive, web-based, and graphical tool that allows the user to analyze Illumina DNA methylation arrays (450 k and EPIC), from the user's own computer or from a server. This tool covers the analysis entirely, from the raw data input to the final list of differentially methylated positions or regions. Here, we describe the steps of the analysis, the different parameters available, and useful information to understand and select the best options in each step.
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Affiliation(s)
- Octavio Morante-Palacios
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain.,Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
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2
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Niccodemi G, Menta G, Turner J, D'Ambrosio C. Pace of aging, family environment and cognitive skills in children and adolescents. SSM Popul Health 2022; 20:101280. [DOI: 10.1016/j.ssmph.2022.101280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/16/2022] [Accepted: 10/29/2022] [Indexed: 11/08/2022] Open
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3
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Meisel RP, Asgari D, Schlamp F, Unckless RL. Induction and inhibition of Drosophila X chromosome gene expression are both impeded by the dosage compensation complex. G3 (BETHESDA, MD.) 2022; 12:6632659. [PMID: 35792851 PMCID: PMC9434221 DOI: 10.1093/g3journal/jkac165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/16/2022] [Indexed: 12/24/2022]
Abstract
Sex chromosomes frequently differ from the autosomes in the frequencies of genes with sexually dimorphic or tissue-specific expression. Multiple hypotheses have been put forth to explain the unique gene content of the X chromosome, including selection against male-beneficial X-linked alleles, expression limits imposed by the haploid dosage of the X in males, and interference by the dosage compensation complex on expression in males. Here, we investigate these hypotheses by examining differential gene expression in Drosophila melanogaster following several treatments that have widespread transcriptomic effects: bacterial infection, viral infection, and abiotic stress. We found that genes that are induced (upregulated) by these biotic and abiotic treatments are frequently under-represented on the X chromosome, but so are those that are repressed (downregulated) following treatment. We further show that whether a gene is bound by the dosage compensation complex in males can largely explain the paucity of both up- and downregulated genes on the X chromosome. Specifically, genes that are bound by the dosage compensation complex, or close to a dosage compensation complex high-affinity site, are unlikely to be up- or downregulated after treatment. This relationship, however, could partially be explained by a correlation between differential expression and breadth of expression across tissues. Nonetheless, our results suggest that dosage compensation complex binding, or the associated chromatin modifications, inhibit both up- and downregulation of X chromosome gene expression within specific contexts, including tissue-specific expression. We propose multiple possible mechanisms of action for the effect, including a role of Males absent on the first, a component of the dosage compensation complex, as a dampener of gene expression variance in both males and females. This effect could explain why the Drosophila X chromosome is depauperate in genes with tissue-specific or induced expression, while the mammalian X has an excess of genes with tissue-specific expression.
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Affiliation(s)
- Richard P Meisel
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5001, USA
| | - Danial Asgari
- Department of Biology and Biochemistry, University of Houston, 3455 Cullen Blvd, Houston, TX 77204-5001, USA
| | - Florencia Schlamp
- Department of Medicine, NYU Grossman School of Medicine, 435 E 30th St, New York, NY 10016, USA
| | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, 4055 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS 66045, USA
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4
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Fernandes N, Buchan JR. RNAs as Regulators of Cellular Matchmaking. Front Mol Biosci 2021; 8:634146. [PMID: 33898516 PMCID: PMC8062979 DOI: 10.3389/fmolb.2021.634146] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/22/2021] [Indexed: 12/30/2022] Open
Abstract
RNA molecules are increasingly being identified as facilitating or impeding the interaction of proteins and nucleic acids, serving as so-called scaffolds or decoys. Long non-coding RNAs have been commonly implicated in such roles, particularly in the regulation of nuclear processes including chromosome topology, regulation of chromatin state and gene transcription, and assembly of nuclear biomolecular condensates such as paraspeckles. Recently, an increased awareness of cytoplasmic RNA scaffolds and decoys has begun to emerge, including the identification of non-coding regions of mRNAs that can also function in a scaffold-like manner to regulate interactions of nascently translated proteins. Collectively, cytoplasmic RNA scaffolds and decoys are now implicated in processes such as mRNA translation, decay, protein localization, protein degradation and assembly of cytoplasmic biomolecular condensates such as P-bodies. Here, we review examples of RNA scaffolds and decoys in both the nucleus and cytoplasm, illustrating common themes, the suitability of RNA to such roles, and future challenges in identifying and better understanding RNA scaffolding and decoy functions.
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Affiliation(s)
| | - J. Ross Buchan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, United States
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5
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Chuang TD, Rehan A, Khorram O. Functional role of the long noncoding RNA X-inactive specific transcript in leiomyoma pathogenesis. Fertil Steril 2020; 115:238-247. [PMID: 33070965 DOI: 10.1016/j.fertnstert.2020.07.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 07/07/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To determine the expression and functional roles of a long noncoding RNA (lncRNA) X-inactive specific transcript (XIST) in leiomyoma. DESIGN Experimental study. SETTING Academic research laboratory. PATIENT(S) Women undergoing hysterectomy for leiomyoma. INTERVENTION(S) Overexpression and underexpression of XIST; blockade of specific protein 1 (SP1). MAIN OUTCOME MEASURE(S) Expression of XIST in leiomyoma and its effects on microRNA 29c (miR-29c), miR-200c, and their targets. RESULT(S) Leiomyoma expressed statistically significantly more XIST as compared with matched myometrium, independent of race/ethnicity and menstrual cycle phase. By use of a three-dimensional spheroid culture system, we found reduced XIST levels in leiomyoma smooth muscle cells (LSMC) after treatment with 17β-estradiol, progesterone, and their combination. The expression of XIST was down-regulated by treatment with the SP1-inhibitor mithramycin A and SP1 small interfering RNA. Knockdown of XIST resulted in inhibition of cell proliferation, up-regulation of miR-29c and miR-200c, and a concomitant inhibition of the target genes of these miRNAs, namely collagen type I (COL1A1), collagen type III (COL3A1), and fibronectin (FN1). By contrast, overexpression of XIST in myometrium smooth muscle cells repressed miR-29c and miR-200c, and induced COL1A1, COL3A1, and FN1 levels. By use of RNA immunoprecipitation analysis we confirmed XIST has sponge activity over miR-29c and miR-200c, which is more pronounced in leiomyoma as compared with myometrium. CONCLUSION(S) Our data demonstrate that increased expression of XIST in leiomyoma results in reduced expression of miR-29c and miR-200c with a consequent up-regulation of the genes targeted by these microRNAs including COL1A1, COL3A1, and FN1, which play key roles in extracellular matrix accumulation associated with fibroids.
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Affiliation(s)
- Tsai-Der Chuang
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, and Department of Obstetrics and Gynecology at Harbor-UCLA Medical Center, Torrance, California
| | - Anika Rehan
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, and Department of Obstetrics and Gynecology at Harbor-UCLA Medical Center, Torrance, California
| | - Omid Khorram
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, and Department of Obstetrics and Gynecology at Harbor-UCLA Medical Center, Torrance, California.
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6
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Chanda K, Mukhopadhyay D. LncRNA Xist, X-chromosome Instability and Alzheimer's Disease. Curr Alzheimer Res 2020; 17:499-507. [PMID: 32851944 DOI: 10.2174/1567205017666200807185624] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 05/08/2020] [Accepted: 05/20/2020] [Indexed: 02/07/2023]
Abstract
Neurodegenerative Diseases (NDD) are the major contributors to age-related causes of mental disability on a global scale. Most NDDs, like Alzheimer's Disease (AD), are complex in nature - implying that they are multi-parametric both in terms of heterogeneous clinical outcomes and underlying molecular paradigms. Emerging evidence from high throughput genomic, transcriptomic and small RNA sequencing experiments hint at the roles of long non-coding RNAs (lncRNAs) in AD. X-inactive Specific Transcript (XIST), a component of the Xic, the X-chromosome inactivation centre, is an RNA gene on the X chromosome of the placental mammals indispensable for the X inactivation process. An extensive literature survey shows that aberrations in Xist expression and in some cases, a disruption of the Xchromosome inactivation as a whole play a significant role in AD. Considering the enormous potential of Xist as an endogenous silencing molecule, the idea of using Xist as a non-conventional chromosome silencer to treat diseases harboring chromosomal alterations is also being implemented. Comprehensive knowledge about how Xist could play such a role in AD is still elusive. In this review, we have collated the available knowledge on the possible Xist involvement and deregulation from the perspective of molecular mechanisms governing NDDs with a primary focus on Alzheimer's disease. Possibilities of XIST mediated therapeutic intervention and linkages between XIC and preferential predisposition of females to AD have also been discussed.
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Affiliation(s)
- Kaushik Chanda
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata 700 064, India
| | - Debashis Mukhopadhyay
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata 700 064, India
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7
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Flower CT, Chen L, Jung HJ, Raghuram V, Knepper MA, Yang CR. An integrative proteogenomics approach reveals peptides encoded by annotated lincRNA in the mouse kidney inner medulla. Physiol Genomics 2020; 52:485-491. [PMID: 32866085 DOI: 10.1152/physiolgenomics.00048.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are intracellular transcripts longer than 200 nucleotides and lack protein-coding information. A subclass of lncRNA known as long intergenic noncoding RNAs (lincRNAs) are transcribed from genomic regions that share no overlap with annotated protein-coding genes. Increasing evidence has shown that some annotated lincRNA transcripts do in fact contain open reading frames (ORFs) encoding functional short peptides in the cell. Few robust methods for lincRNA-encoded peptide identification have been reported, and the tissue-specific expression of these peptides has been largely unexplored. Here we propose an integrative workflow for lincRNA-encoded peptide discovery and test it on the mouse kidney inner medulla (IM). In brief, low molecular weight protein fractions were enriched from homogenate of IMs and trypsinized into shorter peptides, which were sequenced by high resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). To curate a hypothetical lincRNA-encoded peptide database for peptide-spectrum matching following LC-MS/MS, we performed RNA-Seq on IMs, computationally removed reads overlapping with annotated protein-coding genes, and remapped the remaining reads to a database of mouse noncoding transcripts to infer lincRNA expression. Expressed lincRNAs were searched for ORFs by an existing rule-based algorithm, and translated ORFs were used for peptide-spectrum matching. Peptides identified by LC-MS/MS were further evaluated by using several quality control criteria and bioinformatics methods. We discovered three novel lincRNA-encoded peptides, which are conserved in mouse, rat, and human. The workflow can be adapted for discovery of small protein-coding genes in any species or tissue where noncoding transcriptome information is available.
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Affiliation(s)
- Cameron T Flower
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Lihe Chen
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Hyun Jun Jung
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Viswanathan Raghuram
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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8
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DeOcesano-Pereira C, Machado RAC, Chudzinski-Tavassi AM, Sogayar MC. Emerging Roles and Potential Applications of Non-Coding RNAs in Glioblastoma. Int J Mol Sci 2020; 21:E2611. [PMID: 32283739 PMCID: PMC7178171 DOI: 10.3390/ijms21072611] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a diversity of RNA species, which do not have the potential to encode proteins. Non-coding RNAs include two classes of RNAs, namely: short regulatory ncRNAs and long non-coding RNAs (lncRNAs). The short regulatory RNAs, containing up to 200 nucleotides, include small RNAs, such as microRNAs (miRNA), short interfering RNAs (siRNAs), piwi-interacting RNAs (piRNAs), and small nucleolar RNAs (snoRNAs). The lncRNAs include long antisense RNAs and long intergenic RNAs (lincRNAs). Non-coding RNAs have been implicated as master regulators of several biological processes, their expression being strictly regulated under physiological conditions. In recent years, particularly in the last decade, substantial effort has been made to investigate the function of ncRNAs in several human diseases, including cancer. Glioblastoma is the most common and aggressive type of brain cancer in adults, with deregulated expression of small and long ncRNAs having been implicated in onset, progression, invasiveness, and recurrence of this tumor. The aim of this review is to guide the reader through important aspects of miRNA and lncRNA biology, focusing on the molecular mechanism associated with the progression of this highly malignant cancer type.
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Affiliation(s)
- Carlos DeOcesano-Pereira
- Center of Excellence in New Target Discovery (CENTD), Butantan Institute, 1500 Vital Brazil Avenue, São Paulo 05503-900 SP, Brazil; (C.D.-P.); (A.M.C.-T.)
| | - Raquel A. C. Machado
- Department of Life Science and Medicine, University of Luxembourg, Campus Belval, Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg;
| | - Ana Marisa Chudzinski-Tavassi
- Center of Excellence in New Target Discovery (CENTD), Butantan Institute, 1500 Vital Brazil Avenue, São Paulo 05503-900 SP, Brazil; (C.D.-P.); (A.M.C.-T.)
| | - Mari Cleide Sogayar
- Biochemistry Department, Chemistry Institute, University of São Paulo, São Paulo 05508-000, Brazil
- Cell and Molecular Therapy Center (NUCEL), School of Medicine, University of São Paulo, São Paulo 05360-130 SP, Brazil
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9
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A robust test for X-chromosome genetic association accounting for X-chromosome inactivation and imprinting. Genet Res (Camb) 2020; 102:e2. [PMID: 32234109 PMCID: PMC7132553 DOI: 10.1017/s0016672320000026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The X chromosome is known to play an important role in many sex-specific diseases. However, only a few single-nucleotide polymorphisms on the X chromosome have been found to be associated with diseases. Compared to the autosomes, conducting association tests on the X chromosome is more intractable due to the difference in the number of X chromosomes between females and males. On the other hand, X-chromosome inactivation takes place in female mammals, which is a phenomenon in which the expression of one copy of two X chromosomes in females is silenced in order to achieve the same gene expression level as that in males. In addition, imprinting effects may be related to certain diseases. Currently, there are some existing approaches taking X-chromosome inactivation into account when testing for associations on the X chromosome. However, none of them allows for imprinting effects. Therefore, in this paper, we propose a robust test, ZXCII, which accounts for both X-chromosome inactivation and imprinting effects without requiring specifying the genetic models in advance. Simulation studies are conducted in order to investigate the validity and performance of ZXCII under various scenarios of different parameter values. The simulation results show that ZXCII controls the type I error rate well when there is no association. Furthermore, with regards to power, ZXCII is robust in all of the situations considered and generally outperforms most of the existing methods in the presence of imprinting effects, especially under complete imprinting effects.
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10
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Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J 2020; 39:e103777. [PMID: 32090359 PMCID: PMC7073466 DOI: 10.15252/embj.2019103777] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.
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Affiliation(s)
- Ruth L Seal
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dawn O'Reilly
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra L Wolin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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11
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Chovanec M, Kalavska K, Mego M, Cheng L. Liquid biopsy in germ cell tumors: biology and clinical management. Expert Rev Mol Diagn 2019; 20:187-194. [PMID: 31652083 DOI: 10.1080/14737159.2019.1685383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction: Liquid biopsy is an increasingly studied approach for optimal and minimally invasive diagnostics of malignant tumors. The aim of this review is to provide evidence and discuss the utility of liquid biopsy in the management of germ cell tumors (GCTs).Areas covered: Herein, we summarize the evidence on liquid biopsy in GCTs including serum tumor markers, circulating tumor cells, microRNA and cell-free DNA. The search of literature was conducted from Pubmed/Medline, ASCO-meeting library searching for terms 'liquid biopsy', 'germ cell tumors', 'circulating tumor cells', 'microRNA', 'cell-free DNA'. Obtained original studies were included. Reference lists of review articles and key original articles were searched for additional original studies. We included articles published between1990 and 2019.Expert opinion: Liquid biopsy is a minimally invasive tool using body fluids for diagnostic purposes in cancer. The established value of serum tumor markers may be already considered a liquid biopsy technique in diagnosis of GCTs. Possible near-future refinements in diagnosis of GCTs are emerging. Further information on diagnosis, prognosis and resistance is added with recently described microRNAs, circulating tumor cells and cell-free DNA. While great promise is shown, further large-scale validation is needed to incorporate these novel liquid biopsies into clinical practice.
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Affiliation(s)
- Michal Chovanec
- 2nd Department of Oncology, Faculty of Medicine, Comenius University and National Cancer Institute, Bratislava, Slovakia.,Division of Hematology Oncology, Indiana University Simon Cancer Center, Indianapolis, IN, USA
| | - Katarina Kalavska
- Translational Research Unit at 2nd Department of Oncology, Faculty of Medicine, Comenius University and National Cancer Institute, Bratislava, Slovakia
| | - Michal Mego
- 2nd Department of Oncology, Faculty of Medicine, Comenius University and National Cancer Institute, Bratislava, Slovakia.,Translational Research Unit at 2nd Department of Oncology, Faculty of Medicine, Comenius University and National Cancer Institute, Bratislava, Slovakia
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine0, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
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12
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Maldonado MBC, de Rezende Neto NB, Nagamatsu ST, Carazzolle MF, Hoff JL, Whitacre LK, Schnabel RD, Behura SK, McKay SD, Taylor JF, Lopes FL. Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation. PLoS One 2019; 14:e0222329. [PMID: 31513639 PMCID: PMC6742455 DOI: 10.1371/journal.pone.0222329] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/27/2019] [Indexed: 12/13/2022] Open
Abstract
Methylation patterns established and maintained at CpG sites may be altered by single nucleotide polymorphisms (SNPs) within these sites and may affect the regulation of nearby genes. Our aims were to: 1) identify and generate a database of SNPs potentially subject to epigenetic control by DNA methylation via their involvement in creating, removing or displacing CpG sites (meSNPs), and; 2) investigate the association of these meSNPs with CpG islands (CGIs), and with methylation profiles of DNA extracted from tissues from cattle with divergent feed efficiencies detected using MIRA-Seq. Using the variant annotation for 56,969,697 SNPs identified in Run5 of the 1000 Bull Genomes Project and the UMD3.1.1 bovine reference genome sequence assembly, we identified and classified 12,836,763 meSNPs according to the nature of variation created at CpGs. The majority of the meSNPs were located in intergenic regions (68%) or introns (26.3%). We found an enrichment (p<0.01) of meSNPs located in CGIs relative to the genome as a whole, and also in differentially methylated sequences in tissues from animals divergent for feed efficiency. Seven meSNPs, located in differentially methylated regions, were fixed for methylation site creating (MSC) or destroying (MSD) alleles in the differentially methylated genomic sequences of animals differing in feed efficiency. These meSNPs may be mechanistically responsible for creating or deleting methylation targets responsible for the differential expression of genes underlying differences in feed efficiency. Our methyl SNP database (dbmeSNP) is useful for identifying potentially functional "epigenetic polymorphisms" underlying variation in bovine phenotypes.
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Affiliation(s)
| | | | - Sheila T Nagamatsu
- Genomics and Expression Laboratory, University of Campinas, Campinas, São Paulo, Brazil.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, Brazil
| | - Marcelo F Carazzolle
- Genomics and Expression Laboratory, University of Campinas, Campinas, São Paulo, Brazil.,National Center for High Performance Computing (CENAPAD-SP), University of Campinas, Campinas, São Paulo, Brazil
| | - Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Lynsey K Whitacre
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America.,Informatics Institute, University of Missouri, Columbia, Missouri, United States of America
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Stephanie D McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, Vermont, United States of America
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Flavia L Lopes
- São Paulo State University (Unesp), School of Veterinary Medicine, Araçatuba, São Paulo, Brazil
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13
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Anguita-Ruiz A, Plaza-Diaz J, Ruiz-Ojeda FJ, Rupérez AI, Leis R, Bueno G, Gil-Campos M, Vázquez-Cobela R, Cañete R, Moreno LA, Gil Á, Aguilera CM. X chromosome genetic data in a Spanish children cohort, dataset description and analysis pipeline. Sci Data 2019; 6:130. [PMID: 31332195 PMCID: PMC6646348 DOI: 10.1038/s41597-019-0109-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/24/2019] [Indexed: 01/01/2023] Open
Abstract
X chromosome genetic variation has been proposed as a potential source of missing heritability for many complex diseases, including obesity. Currently, there is a lack of public available genetic datasets incorporating X chromosome genotype data. Although several X chromosome-specific statistics have been developed, there is also a lack of readily available implementations for routine analysis. Here, we aimed: (1) to make public and describe a dataset incorporating phenotype and X chromosome genotype data from a cohort of 915 normal-weight, overweight and obese children, and (2) to deeply describe a whole implementation of the special X chromosome analytic process in genetics. Datasets and pipelines like this are crucial to get familiar with the steps in which X chromosome requires special attention and may raise awareness of the importance of this genomic region. Design Type(s) | disease analysis objective • factorial design • genetic structural variation analysis objective • genotyping design | Measurement Type(s) | genotyping assay | Technology Type(s) | genotyping | Factor Type(s) | sex • experimental condition | Sample Characteristic(s) | Homo sapiens • blood |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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Affiliation(s)
- Augusto Anguita-Ruiz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, 18011, Spain. .,Institute of Nutrition and Food Technology "José Mataix", Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n, Granada, 18016, Spain. .,Biosanitary Research Institute of Granada (IBS.GRANADA), University Clinical Hospital San Cecilio, Av. de la Investigación, s/n, Granada, 18016, Spain. .,CIBEROBN, (Physiopathology of Obesity and Nutrition CB12/03/30038), Institute of Health Carlos III (ISCIII), Madrid, 28029, Spain.
| | - Julio Plaza-Diaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, 18011, Spain.,Institute of Nutrition and Food Technology "José Mataix", Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n, Granada, 18016, Spain.,Biosanitary Research Institute of Granada (IBS.GRANADA), University Clinical Hospital San Cecilio, Av. de la Investigación, s/n, Granada, 18016, Spain
| | - Francisco Javier Ruiz-Ojeda
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, 18011, Spain.,Biosanitary Research Institute of Granada (IBS.GRANADA), University Clinical Hospital San Cecilio, Av. de la Investigación, s/n, Granada, 18016, Spain.,RG Adipocytes and metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Center Munich, Munich, Germany
| | - Azahara I Rupérez
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, 18011, Spain.,Growth, Exercise, Nutrition and Development (GENUD) Research Group, Universidad de Zaragoza, Zaragoza, Spain.,Instituto Agroalimentario de Aragón (IA2) and Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain
| | - Rosaura Leis
- CIBEROBN, (Physiopathology of Obesity and Nutrition CB12/03/30038), Institute of Health Carlos III (ISCIII), Madrid, 28029, Spain.,Unit of Investigation in Nutrition, Growth and Human Development of Galicia, Pediatric Department (USC). Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University Clinical Hospital, Santiago de Compostela, Spain
| | - Gloria Bueno
- CIBEROBN, (Physiopathology of Obesity and Nutrition CB12/03/30038), Institute of Health Carlos III (ISCIII), Madrid, 28029, Spain.,Growth, Exercise, Nutrition and Development (GENUD) Research Group, Universidad de Zaragoza, Zaragoza, Spain.,Instituto Agroalimentario de Aragón (IA2) and Instituto de Investigación Sanitaria de Aragón (IIS Aragón), Zaragoza, Spain
| | - Mercedes Gil-Campos
- CIBEROBN, (Physiopathology of Obesity and Nutrition CB12/03/30038), Institute of Health Carlos III (ISCIII), Madrid, 28029, Spain.,Department of Pediatric Endocrinology, Reina Sofia University Clinical Hospital, Institute Maimónides of Biomedicine Investigation of Córdoba (IMIBIC), University of Córdoba, Avda. Menéndez Pidal s/n, 14004, Córdoba, Spain
| | - Rocío Vázquez-Cobela
- CIBEROBN, (Physiopathology of Obesity and Nutrition CB12/03/30038), Institute of Health Carlos III (ISCIII), Madrid, 28029, Spain.,Unit of Investigation in Nutrition, Growth and Human Development of Galicia, Pediatric Department (USC). Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), University Clinical Hospital, Santiago de Compostela, Spain
| | - Ramón Cañete
- CIBEROBN, (Physiopathology of Obesity and Nutrition CB12/03/30038), Institute of Health Carlos III (ISCIII), Madrid, 28029, Spain.,Department of Pediatric Endocrinology, Reina Sofia University Clinical Hospital, Institute Maimónides of Biomedicine Investigation of Córdoba (IMIBIC), University of Córdoba, Avda. Menéndez Pidal s/n, 14004, Córdoba, Spain
| | - Luis A Moreno
- Growth, Exercise, Nutrition and Development (GENUD) Research Group, Universidad de Zaragoza, Zaragoza, Spain
| | - Ángel Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, 18011, Spain.,Institute of Nutrition and Food Technology "José Mataix", Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n, Granada, 18016, Spain.,Biosanitary Research Institute of Granada (IBS.GRANADA), University Clinical Hospital San Cecilio, Av. de la Investigación, s/n, Granada, 18016, Spain.,CIBEROBN, (Physiopathology of Obesity and Nutrition CB12/03/30038), Institute of Health Carlos III (ISCIII), Madrid, 28029, Spain
| | - Concepción María Aguilera
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, 18011, Spain.,Institute of Nutrition and Food Technology "José Mataix", Center of Biomedical Research, University of Granada, Avda. del Conocimiento s/n, Granada, 18016, Spain.,Biosanitary Research Institute of Granada (IBS.GRANADA), University Clinical Hospital San Cecilio, Av. de la Investigación, s/n, Granada, 18016, Spain.,CIBEROBN, (Physiopathology of Obesity and Nutrition CB12/03/30038), Institute of Health Carlos III (ISCIII), Madrid, 28029, Spain
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14
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Andrés-Benito P, Gelpi E, Povedano M, Ausín K, Fernández-Irigoyen J, Santamaría E, Ferrer I. Combined Transcriptomics and Proteomics in Frontal Cortex Area 8 in Frontotemporal Lobar Degeneration Linked to C9ORF72 Expansion. J Alzheimers Dis 2019; 68:1287-1307. [DOI: 10.3233/jad-181123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Pol Andrés-Benito
- Neuropathology, Pathologic Anatomy Service, Bellvitge University Hospital - Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain
- Biomedical Network Research Center on Neurodegenerative Diseases (CIBERNED), Institute of Health Carlos III, Hospitalet de Llobregat, Spain
| | - Ellen Gelpi
- Neurological Tissue Bank of the Biobanc-Hospital Clínic-Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Mónica Povedano
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, Hospitalet de Llobregat, Spain
| | - Karina Ausín
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain
- Clinical Neuroproteomics group and Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Department of Health, Public University of Navarra, Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain
- Clinical Neuroproteomics group and Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Department of Health, Public University of Navarra, Pamplona, Spain
| | - Enrique Santamaría
- IDISNA, Navarra Institute for Health Research, Pamplona, Spain
- Clinical Neuroproteomics group and Proteored-ISCIII, Proteomics Unit, Navarrabiomed, Department of Health, Public University of Navarra, Pamplona, Spain
| | - Isidro Ferrer
- Neuropathology, Pathologic Anatomy Service, Bellvitge University Hospital - Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Spain
- Biomedical Network Research Center on Neurodegenerative Diseases (CIBERNED), Institute of Health Carlos III, Hospitalet de Llobregat, Spain
- Department of Pathology and Experimental Therapeutics, University of Barcelona, Hospitalet de Llobregat, Spain
- Institute of Neurosciences, University of Barcelona, Barcelona, Spain
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15
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Li F, Li H, Zhang L, Li W, Deng J, An M, Wu S, Lu X, Ma R, Wang Y, Guo B, Lu J, Zhou Y. X chromosome-linked long noncoding RNA lnc-XLEC1 regulates c-Myc-dependent cell growth by collaborating with MBP-1 in endometrial cancer. Int J Cancer 2019; 145:927-940. [PMID: 30698832 DOI: 10.1002/ijc.32166] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 12/12/2018] [Accepted: 12/20/2018] [Indexed: 01/05/2023]
Abstract
LncRNAs (long noncoding RNAs) are noncoding transcripts that are more than 200 nt long and have been described as the largest subclass in the noncoding transcriptome in humans. Although studies of lncRNAs in cancer have been continuing for a long time, no much has been known about X chromosome-linked lncRNAs. Here, by using RNA-seq we report the identification of a new X chromosome-linked lncRNA (lnc-XLEC1) that is aberrantly downregulated during the development of endometrial carcinoma (EC). The overexpression of lnc-XLEC1 reduces the migration and proliferation of EC cells. Flow cytometry analysis indicated that lnc-XLEC1 overexpression resulted in a substantial accumulation of EC cells in the G1 phase. In addition, lnc-XLEC1 had inhibitive effects that may result from its collaboration with MBP-1 during the suppression of the c-Myc expression and the negative regulating of the Cdk/Rb/E2F pathway. The anti-tumor effects of lnc-XLEC1 on EC progression suggest that lnc-XLEC1 has some potential value in anti-carcinoma therapies and deserves further investigation. Our study reported for the first time that the lnc-XLEC1 might be related to the incidence and prognosis of EC. Moreover, we discovered that this process might be related to somatic X dosage compensation and skewed X chromosome inactivation (SXCI).
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Affiliation(s)
- Fang Li
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Hua Li
- Department of Obstetrics and Gynecology, Third Hospital, Peking University, Beijing, China
| | - Liyuan Zhang
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Wei Li
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Jieqiong Deng
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Mingxing An
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Siqi Wu
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Xiaoxiao Lu
- Department of English study, Faculty of Languages and Literatures, Ludwig Maximilian University (LMU), Munich, Germany
| | - Rui Ma
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Yirong Wang
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Binbin Guo
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Jiachun Lu
- Department of Epidemiology, The State Key Lab of Respiratory Disease, The First Affiliated Hospital, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Yifeng Zhou
- Department of Genetics, Medical College of Soochow University, Suzhou, China
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16
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Xu SQ, Zhang Y, Wang P, Liu W, Wu XB, Zhou JY. A statistical measure for the skewness of X chromosome inactivation based on family trios. BMC Genet 2018; 19:109. [PMID: 30518319 PMCID: PMC6282303 DOI: 10.1186/s12863-018-0694-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/08/2018] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND X chromosome inactivation (XCI) is an important gene regulation mechanism in females to equalize the expression levels of X chromosome between two sexes. Generally, one of two X chromosomes in females is randomly chosen to be inactivated. Nonrandom XCI (XCI skewing) is also observed in females, which has been reported to play an important role in many X-linked diseases. However, there is no statistical measure available for the degree of the XCI skewing based on family data in population genetics. RESULTS In this article, we propose a statistical approach to measure the degree of the XCI skewing based on family trios, which is represented by a ratio of two genotypic relative risks in females. The point estimate of the ratio is obtained from the maximum likelihood estimates of two genotypic relative risks. When parental genotypes are missing in some family trios, the expectation-conditional-maximization algorithm is adopted to obtain the corresponding maximum likelihood estimates. Further, the confidence interval of the ratio is derived based on the likelihood ratio test. Simulation results show that the likelihood-based confidence interval has an accurate coverage probability under the situations considered. Also, we apply our proposed method to the rheumatoid arthritis data from USA for its practical use, and find out that a locus, rs2238907, may undergo the XCI skewing against the at-risk allele. But this needs to be further confirmed by molecular genetics. CONCLUSIONS The proposed statistical measure for the skewness of XCI is applicable to complete family trio data or family trio data with some paternal genotypes missing. The likelihood-based confidence interval has an accurate coverage probability under the situations considered. Therefore, our proposed statistical measure is generally recommended in practice for discovering the potential loci which undergo the XCI skewing.
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Affiliation(s)
- Si-Qi Xu
- State Key Laboratory of Organ Failure Research, Ministry of Education and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yu Zhang
- State Key Laboratory of Organ Failure Research, Ministry of Education and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
| | - Peng Wang
- State Key Laboratory of Organ Failure Research, Ministry of Education and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
| | - Wei Liu
- State Key Laboratory of Organ Failure Research, Ministry of Education and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xian-Bo Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, China.
| | - Ji-Yuan Zhou
- State Key Laboratory of Organ Failure Research, Ministry of Education and Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou, China.
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17
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Ocklenburg S, Anderson C, Gerding WM, Fraenz C, Schlüter C, Friedrich P, Raane M, Mädler B, Schlaffke L, Arning L, Epplen JT, Güntürkün O, Beste C, Genç E. Myelin Water Fraction Imaging Reveals Hemispheric Asymmetries in Human White Matter That Are Associated with Genetic Variation in PLP1. Mol Neurobiol 2018; 56:3999-4012. [PMID: 30242727 DOI: 10.1007/s12035-018-1351-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/13/2018] [Indexed: 12/18/2022]
Abstract
Myelination of axons in the central nervous system is critical for human cognition and behavior. The predominant protein in myelin is proteolipid protein-making PLP1, the gene that encodes for proteolipid protein, one of the primary candidate genes for white matter structure in the human brain. Here, we investigated the relation of genetic variation within PLP1 and white matter microstructure as assessed with myelin water fraction imaging, a neuroimaging technique that has the advantage over conventional diffusion tensor imaging in that it allows for a more direct assessment of myelin content. We observed significant asymmetries in myelin water fraction that were strongest and rightward in the parietal lobe. Importantly, these parietal myelin water fraction asymmetries were associated with genetic variation in PLP1. These findings support the assumption that genetic variation in PLP1 affects white matter myelination in the healthy human brain.
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Affiliation(s)
- Sebastian Ocklenburg
- Institute of Cognitive Neuroscience, Biopsychology, Department of Psychology, Ruhr University Bochum, Bochum, Germany.
| | - Catrona Anderson
- Institute of Cognitive Neuroscience, Biopsychology, Department of Psychology, Ruhr University Bochum, Bochum, Germany.,Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Wanda M Gerding
- Department of Human Genetics, Ruhr University Bochum, Bochum, Germany
| | - Christoph Fraenz
- Institute of Cognitive Neuroscience, Biopsychology, Department of Psychology, Ruhr University Bochum, Bochum, Germany
| | - Caroline Schlüter
- Institute of Cognitive Neuroscience, Biopsychology, Department of Psychology, Ruhr University Bochum, Bochum, Germany
| | - Patrick Friedrich
- Institute of Cognitive Neuroscience, Biopsychology, Department of Psychology, Ruhr University Bochum, Bochum, Germany
| | - Maximilian Raane
- Faculty of Health, ZBAF, University of Witten/Herdecke, Witten, Germany
| | | | - Lara Schlaffke
- Department of Neurology, BG-University Hospital Bergmannsheil, Ruhr University Bochum, Bochum, Germany
| | - Larissa Arning
- Department of Human Genetics, Ruhr University Bochum, Bochum, Germany
| | - Jörg T Epplen
- Department of Human Genetics, Ruhr University Bochum, Bochum, Germany.,Faculty of Health, ZBAF, University of Witten/Herdecke, Witten, Germany
| | - Onur Güntürkün
- Institute of Cognitive Neuroscience, Biopsychology, Department of Psychology, Ruhr University Bochum, Bochum, Germany
| | - Christian Beste
- Cognitive Neurophysiology, Department of Child and Adolescent Psychiatry, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Erhan Genç
- Institute of Cognitive Neuroscience, Biopsychology, Department of Psychology, Ruhr University Bochum, Bochum, Germany
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18
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Ostrom QT, Kinnersley B, Wrensch MR, Eckel-Passow JE, Armstrong G, Rice T, Chen Y, Wiencke JK, McCoy LS, Hansen HM, Amos CI, Bernstein JL, Claus EB, Il'yasova D, Johansen C, Lachance DH, Lai RK, Merrell RT, Olson SH, Sadetzki S, Schildkraut JM, Shete S, Rubin JB, Lathia JD, Berens ME, Andersson U, Rajaraman P, Chanock SJ, Linet MS, Wang Z, Yeager M, Houlston RS, Jenkins RB, Melin B, Bondy ML, Barnholtz-Sloan JS. Sex-specific glioma genome-wide association study identifies new risk locus at 3p21.31 in females, and finds sex-differences in risk at 8q24.21. Sci Rep 2018; 8:7352. [PMID: 29743610 PMCID: PMC5943590 DOI: 10.1038/s41598-018-24580-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/06/2018] [Indexed: 01/07/2023] Open
Abstract
Incidence of glioma is approximately 50% higher in males. Previous analyses have examined exposures related to sex hormones in women as potential protective factors for these tumors, with inconsistent results. Previous glioma genome-wide association studies (GWAS) have not stratified by sex. Potential sex-specific genetic effects were assessed in autosomal SNPs and sex chromosome variants for all glioma, GBM and non-GBM patients using data from four previous glioma GWAS. Datasets were analyzed using sex-stratified logistic regression models and combined using meta-analysis. There were 4,831 male cases, 5,216 male controls, 3,206 female cases and 5,470 female controls. A significant association was detected at rs11979158 (7p11.2) in males only. Association at rs55705857 (8q24.21) was stronger in females than in males. A large region on 3p21.31 was identified with significant association in females only. The identified differences in effect of risk variants do not fully explain the observed incidence difference in glioma by sex.
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Affiliation(s)
- Quinn T Ostrom
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- Department of Population and Quantitative Heath Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Margaret R Wrensch
- Department of Neurological Surgery and Institute of Human Genetics, School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Jeanette E Eckel-Passow
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Georgina Armstrong
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Terri Rice
- Department of Neurological Surgery and Institute of Human Genetics, School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Yanwen Chen
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - John K Wiencke
- Department of Neurological Surgery and Institute of Human Genetics, School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Lucie S McCoy
- Department of Neurological Surgery and Institute of Human Genetics, School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Helen M Hansen
- Department of Neurological Surgery and Institute of Human Genetics, School of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jonine L Bernstein
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Elizabeth B Claus
- School of Public Health, Yale University, New Haven, Connecticut, United States of America
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Dora Il'yasova
- Department of Epidemiology and Biostatistics, School of Public Health, Georgia State University, Atlanta, Georgia, United States of America
- Cancer Control and Prevention Program, Department of Community and Family Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Christoffer Johansen
- Oncology clinic, Finsen Center, Rigshospitalet, Copenhagen, Denmark
- Survivorship Research Unit, The Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Daniel H Lachance
- Department of Neurology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Rose K Lai
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Ryan T Merrell
- Department of Neurology, NorthShore University HealthSystem, Evanston, Illinois, United States of America
| | - Sara H Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Siegal Sadetzki
- Cancer and Radiation Epidemiology Unit, Gertner Institute, Chaim Sheba Medical Center, Tel Hashomer, Israel
- Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Joellen M Schildkraut
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Sanjay Shete
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Neuroscience, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Justin D Lathia
- Department of Stem Cell Biology and Regenerative Medicine, Cleveland Clinic Foundation, Cleveland, Ohio, United States of America
| | - Michael E Berens
- Cancer and Cell Biology Division, The Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Ulrika Andersson
- Department of Radiation Sciences, Faculty of Medicine, Umeå University, Umeå, Sweden
| | - Preetha Rajaraman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc, Gaithersburg, Maryland, United States of America
| | - Martha S Linet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc, Gaithersburg, Maryland, United States of America
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Core Genotyping Facility, National Cancer Institute, SAIC-Frederick, Inc, Gaithersburg, Maryland, United States of America
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey, United Kingdom
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic Comprehensive Cancer Center, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Beatrice Melin
- Department of Radiation Sciences, Faculty of Medicine, Umeå University, Umeå, Sweden
| | - Melissa L Bondy
- Department of Medicine, Section of Epidemiology and Population Sciences, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America.
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19
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A powerful parent-of-origin effects test for qualitative traits on X chromosome in general pedigrees. BMC Bioinformatics 2018; 19:8. [PMID: 29304743 PMCID: PMC5756386 DOI: 10.1186/s12859-017-2001-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/18/2017] [Indexed: 11/10/2022] Open
Abstract
Background Genomic imprinting is one of the well-known epigenetic factors causing the association between traits and genes, and has generally been examined by detecting parent-of-origin effects of alleles. A lot of methods have been proposed to test for parent-of-origin effects on autosomes based on nuclear families and general pedigrees. Although these parent-of-origin effects tests on autosomes have been available for more than 15 years, there has been no statistical test developed to test for parent-of-origin effects on X chromosome, until the parental-asymmetry test on X chromosome (XPAT) and its extensions were recently proposed. However, these methods on X chromosome are only applicable to nuclear families and thus are not suitable for general pedigrees. Results In this article, we propose the pedigree parental-asymmetry test on X chromosome (XPPAT) statistic to test for parent-of-origin effects in the presence of association, which can accommodate general pedigrees. When there are missing genotypes in some pedigrees, we further develop the Monte Carlo pedigree parental-asymmetry test on X chromosome (XMCPPAT) to test for parent-of-origin effects, by inferring the missing genotypes given the observed genotypes based on a Monte Carlo estimation. An extensive simulation study has been carried out to investigate the type I error rates and the powers of the proposed tests. Our simulation results show that the proposed methods control the size well under the null hypothesis of no parent-of-origin effects. Moreover, XMCPPAT substantially outperforms the existing tests and has a much higher power than XPPAT which only uses complete nuclear families (with both parents) from pedigrees. We also apply the proposed methods to analyze rheumatoid arthritis data for their practical use. Conclusions The proposed XPPAT and XMCPPAT test statistics are valid and powerful in detecting parent-of-origin effects on X chromosome for qualitative traits based on general pedigrees and thus are recommended. Electronic supplementary material The online version of this article (10.1186/s12859-017-2001-5) contains supplementary material, which is available to authorized users.
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20
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Xu J, Peng X, Chen Y, Zhang Y, Ma Q, Liang L, Carter AC, Lu X, Wu CI. Free-living human cells reconfigure their chromosomes in the evolution back to uni-cellularity. eLife 2017; 6. [PMID: 29251591 PMCID: PMC5734875 DOI: 10.7554/elife.28070] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/28/2017] [Indexed: 01/06/2023] Open
Abstract
Cells of multi-cellular organisms evolve toward uni-cellularity in the form of cancer and, if humans intervene, continue to evolve in cell culture. During this process, gene dosage relationships may evolve in novel ways to cope with the new environment and may regress back to the ancestral uni-cellular state. In this context, the evolution of sex chromosomes vis-a-vis autosomes is of particular interest. Here, we report the chromosomal evolution in ~ 600 cancer cell lines. Many of them jettisoned either Y or the inactive X; thus, free-living male and female cells converge by becoming ‘de-sexualized’. Surprisingly, the active X often doubled, accompanied by the addition of one haploid complement of autosomes, leading to an X:A ratio of 2:3 from the extant ratio of 1:2. Theoretical modeling of the frequency distribution of X:A karyotypes suggests that the 2:3 ratio confers a higher fitness and may reflect aspects of sex chromosome evolution. Multicellular life relies on a group of cells working together for a common interest. To study these cells, researchers take them out of the organism and grow them in the laboratory. Instead of growing as part of organs and tissues, the cells normally have a free-living lifestyle. Because multicellular life evolved from single-celled organisms, laboratory-grown cells can be considered as life forms that are evolving backward from a multicellular to a single-celled existence. Normally, the cells that make up most of the tissues in the human body have 22 pairs of chromosomes known as autosomes and a pair of sex chromosomes. The cells of women have two X sex chromosomes, one of which is inactive, while those of men have one X and one Y chromosome. However, free-living single cells do not need to distinguish between male and female cells. Xu, Peng, Chen et al. have now studied the chromosomes of cancer cells taken from over 600 people and grown in the laboratory. As the cells evolved in response to their free-living lifestyle, they became ‘de-sexualized’; male cells lost their Y chromosome, while female cells abandoned their inactive X chromosome. The cells then evolved toward a new state in which they possessed two active X chromosomes and three sets of autosomes. This new configuration suggests that the current X chromosome to autosome ratio may not be optimal for fitness and hence sheds some light on how mammalian sex chromosomes evolved. It is currently thought that as cancerous tumors grow, their cells evolve to favor their own interests over the common interests of the rest of the organism. In this way, they develop characteristics more like those of single cells. Further research is therefore needed to investigate whether changes occur to the chromosomes of cancer cells growing within the body, and whether this gives them an advantage over normal cells.
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Affiliation(s)
- Jin Xu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinxin Peng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yuxin Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Yuezheng Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Qin Ma
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liang Liang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, United States
| | - Xuemei Lu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Chung-I Wu
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.,Department of Ecology and Evolution, University of Chicago, Chicago, United States
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21
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Wang J, Talluri R, Shete S. Selection of X-chromosome Inactivation Model. Cancer Inform 2017; 16:1176935117747272. [PMID: 29308008 PMCID: PMC5751921 DOI: 10.1177/1176935117747272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/18/2017] [Indexed: 11/15/2022] Open
Abstract
To address the complexity of the X-chromosome inactivation (XCI) process, we previously developed a unified approach for the association test for X-chromosomal single-nucleotide polymorphisms (SNPs) and the disease of interest, accounting for different biological possibilities of XCI: random, skewed, and escaping XCI. In the original study, we focused on the SNP-disease association test but did not provide knowledge regarding the underlying XCI models. One can use the highest likelihood ratio (LLR) to select XCI models (max-LLR approach). However, that approach does not formally compare the LLRs corresponding to different XCI models to assess whether the models are distinguishable. Therefore, we propose an LLR comparison procedure (comp-LLR approach), inspired by the Cox test, to formally compare the LLRs of different XCI models to select the most likely XCI model that describes the underlying XCI process. We conduct simulation studies to investigate the max-LLR and comp-LLR approaches. The simulation results show that compared with the max-LLR, the comp-LLR approach has higher probability of identifying the correct underlying XCI model for the scenarios when the underlying XCI process is random XCI, escaping XCI, or skewed XCI to the deleterious allele. We applied both approaches to a head and neck cancer genetic study to investigate the underlying XCI processes for the X-chromosomal genetic variants.
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Affiliation(s)
- Jian Wang
- Department of Biostatistics–Unit 1411, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajesh Talluri
- Department of Data Science, The University of Mississippi Medical Center, Jackson, MS, USA
| | - Sanjay Shete
- Department of Biostatistics–Unit 1411, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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22
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Sharma D, Koshy G, Gupta S, Sharma B, Grover S. Deciphering the Role of the Barr Body in Malignancy: An insight into head and neck cancer. Sultan Qaboos Univ Med J 2017; 17:e389-e397. [PMID: 29372079 PMCID: PMC5766293 DOI: 10.18295/squmj.2017.17.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 08/03/2017] [Accepted: 08/24/2017] [Indexed: 01/20/2023] Open
Abstract
X chromosome inactivation is the epitome of epigenetic regulation and long non-coding ribonucleic acid function. The differentiation status of cells has been ascribed to X chromosome activity, with two active X chromosomes generally only observed in undifferentiated or poorly differentiated cells. Recently, several studies have indicated that the reactivation of an inactive X chromosome or X chromosome multiplication correlates with the development of malignancy; however, this concept is still controversial. This review sought to shed light on the role of the X chromosome in cancer development. In particular, there is a need for further exploration of the expression patterns of X-linked genes in cancer cells, especially those in head and neck squamous cell carcinoma (HNSCC), in order to identify different prognostic subpopulations with distinct clinical implications. This article proposes a functional relationship between the loss of the Barr body and the disproportional expression of X-linked genes in HNSCC development.
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Affiliation(s)
- Deepti Sharma
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - George Koshy
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - Shruti Gupta
- Department of Oral Anatomy, Postgraduate Institute of Dental Sciences, Rohtak, Haryana, India
| | - Bhushan Sharma
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - Sonal Grover
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
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23
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Xie C, Chen X, Liu Y, Wu Z, Ping P. Multicenter study of genetic abnormalities associated with severe oligospermia and non-obstructive azoospermia. J Int Med Res 2017; 46:107-114. [PMID: 28730893 PMCID: PMC6011285 DOI: 10.1177/0300060517718771] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Objective Chong Xie, Xiangfeng Chen, and Yulin Liu contributed equally to this work. Genetic defects are identified in nearly 20% of infertile males. Determining the frequency and types of major genetic abnormalities in severe male infertility helps inform appropriate genetic counseling before assisted reproductive techniques.
Methods Cytogenetic results of 912 patients with non-obstructive azoospermia (NOA) and severe oligozoospermia (SOS) in Eastern China were reviewed in this multicenter study from January 2011 to December 2015. Controls were 215 normozoospermic men with offspring. Results Among all patients, 22.6% (206/912) had genetic abnormalities, including 27.3% (146/534) of NOA patients and 15.9% (60/378) of SOS patients. Chromosomal abnormalities (all autosomal) were detected in only 1.9% (4 /215) of controls. In NOA patients, sex chromosomal abnormalities were identified in 25.8% (138/534), of which 8% (43/534) had a 47,XXY karyotype or its mosaic; higher than the SOS group prevalence (1.1%; 4/378). The incidence of Y chromosome microdeletions was lower in the SOS group (13.2%; 50/378) than in the NOA group (17.8%; 95/534). Conclusions The high prevalence of genetic abnormalities in our study indicates the importance of routine genetic testing in severe male infertility diagnosis. This may help determine the choice of assisted reproductive technique and allow specific pre-implantation genetic testing to minimize the risk of transmitting genetic defects.
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Affiliation(s)
- Chong Xie
- 1 Assisted Reproductive Center, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangfeng Chen
- 2 Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Human Sperm Bank, Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
| | - Yulin Liu
- 3 Shanghai Ji Ai Genetic and IVF Institute, Shanghai, China
| | - Zhengmu Wu
- 1 Assisted Reproductive Center, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Ping
- 1 Assisted Reproductive Center, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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24
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Bravo-Alegria J, McCullough LD, Liu F. Sex differences in stroke across the lifespan: The role of T lymphocytes. Neurochem Int 2017; 107:127-137. [PMID: 28131898 PMCID: PMC5461203 DOI: 10.1016/j.neuint.2017.01.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 01/13/2017] [Accepted: 01/20/2017] [Indexed: 12/22/2022]
Abstract
Stroke is a sexually dimorphic disease. Ischemic sensitivity changes throughout the lifespan and outcomes depend largely on variables like age, sex, hormonal status, inflammation, and other existing risk factors. Immune responses after stroke play a central role in how these factors interact. Although the post-stroke immune response has been extensively studied, the contribution of lymphocytes to stroke is still not well understood. T cells participate in both innate and adaptive immune responses at both acute and chronic stages of stroke. T cell responses also change at different ages and are modulated by hormones and sex chromosome complement. T cells have also been implicated in the development of hypertension, one of the most important risk factors for vascular disease. In this review, we highlight recent literature on the lymphocytic responses to stroke in the context of age and sex, with a focus on T cell response and the interaction with important stroke risk factors.
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Affiliation(s)
- Javiera Bravo-Alegria
- Department of Neurology, Univeristy of Texas Health Science Center at Houston, Houston, TX, 77030, United States
| | - Louise D McCullough
- Department of Neurology, Univeristy of Texas Health Science Center at Houston, Houston, TX, 77030, United States
| | - Fudong Liu
- Department of Neurology, Univeristy of Texas Health Science Center at Houston, Houston, TX, 77030, United States.
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25
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Barad DH, Darmon S, Weghofer A, Latham GJ, Wang Q, Kushnir VA, Albertini DF, Gleicher N. Association of skewed X-chromosome inactivation with FMR1 CGG repeat length and anti-Mullerian hormone levels: a cohort study. Reprod Biol Endocrinol 2017; 15:34. [PMID: 28454580 PMCID: PMC5410032 DOI: 10.1186/s12958-017-0250-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/19/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Premutation range CGGn repeats of the FMR1 gene denote risk toward primary ovarian insufficiency (POI), also called premature ovarian failure (POF). This prospective cohort study was undertaken to determine if X-chromosome inactivation skew (sXCI) is associated with variations in FMR1 CGG repeat length and, if so, is also associated with age adjusted antimüllerian hormone (AMH) levels as an indicator of functional ovarian reserve (FOR). METHODS DNA samples of 58 women were analyzed for methylation status and confirmation of CGGn repeat length. Based on previously described FMR1 genotypes, there were 18 women with norm FMR1 (both alleles in range of CGG n=26-34), and 40 women who had at least one allele at CGGn<26 or CGG>34 ( not-norm FMR1). As part of a routine evaluation of ovarian reserve, patients at our fertility center have their serum AMH assessed at first visit. Regression models were used to test the association of ovarian reserve, as indicated by serum AMH, with sXCI. RESULTS sXCI was significantly lower among infertility patients with norm FMR1 (6.5 ± 11.1, median and IQR) compared to those with not-norm FMR1 (12.0 ± 14.6, P = 0.005), though among young oocyte donors the opposite effect was observed. Women age >30 to 38 years old demonstrated greater ovarian reserve in the presence of lower sXCI as evidenced by significantly higher AMH levels (GLM sXCI_10%, f = 11.27; P = 0.004). CONCLUSIONS Together these findings suggest that FMR1 CGG repeat length may have a role in determining X-chromosome inactivation which could represent a possible mechanism for previously observed association of low age adjusted ovarian reserve with FMR1 variations in repeat length. Further, larger, investigations will be required to test this hypothesis.
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Affiliation(s)
- David H. Barad
- 0000 0004 0585 2042grid.417602.6The Center for Human Reproduction (CHR), New York, NY USA
- The Foundation for Reproductive Medicine, New York, NY USA
| | - Sarah Darmon
- 0000 0004 0585 2042grid.417602.6The Center for Human Reproduction (CHR), New York, NY USA
| | - Andrea Weghofer
- 0000 0004 0585 2042grid.417602.6The Center for Human Reproduction (CHR), New York, NY USA
- 0000 0001 2286 1424grid.10420.37Department of Obstetrics and Gynecology, Vienna University School of Medicine, Vienna, Austria
| | | | - Qi Wang
- 0000 0004 0585 2042grid.417602.6The Center for Human Reproduction (CHR), New York, NY USA
| | - Vitaly A. Kushnir
- 0000 0004 0585 2042grid.417602.6The Center for Human Reproduction (CHR), New York, NY USA
- 0000 0001 2185 3318grid.241167.7Department of Obstetrics and Gynecology, Wake Forest University, Winston Salem, NC USA
| | - David F. Albertini
- 0000 0004 0585 2042grid.417602.6The Center for Human Reproduction (CHR), New York, NY USA
- 0000 0001 2177 6375grid.412016.0Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas, USA
| | - Norbert Gleicher
- 0000 0004 0585 2042grid.417602.6The Center for Human Reproduction (CHR), New York, NY USA
- The Foundation for Reproductive Medicine, New York, NY USA
- 0000 0001 2166 1519grid.134907.8Stem Cell and Molecular Embryology Laboratory, The Rockefeller University, New York, NY USA
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26
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Ramsay L, Marchetto MC, Caron M, Chen SH, Busche S, Kwan T, Pastinen T, Gage FH, Bourque G. Conserved expression of transposon-derived non-coding transcripts in primate stem cells. BMC Genomics 2017; 18:214. [PMID: 28245871 PMCID: PMC5331655 DOI: 10.1186/s12864-017-3568-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/07/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND A significant portion of expressed non-coding RNAs in human cells is derived from transposable elements (TEs). Moreover, it has been shown that various long non-coding RNAs (lncRNAs), which come from the human endogenous retrovirus subfamily H (HERVH), are not only expressed but required for pluripotency in human embryonic stem cells (hESCs). RESULTS To identify additional TE-derived functional non-coding transcripts, we generated RNA-seq data from induced pluripotent stem cells (iPSCs) of four primate species (human, chimpanzee, gorilla, and rhesus) and searched for transcripts whose expression was conserved. We observed that about 30% of TE instances expressed in human iPSCs had orthologous TE instances that were also expressed in chimpanzee and gorilla. Notably, our analysis revealed a number of repeat families with highly conserved expression profiles including HERVH but also MER53, which is known to be the source of a placental-specific family of microRNAs (miRNAs). We also identified a number of repeat families from all classes of TEs, including MLT1-type and Tigger families, that contributed a significant amount of sequence to primate lncRNAs whose expression was conserved. CONCLUSIONS Together, these results describe TE families and TE-derived lncRNAs whose conserved expression patterns can be used to identify what are likely functional TE-derived non-coding transcripts in primate iPSCs.
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Affiliation(s)
- LeeAnn Ramsay
- Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada
| | - Maria C Marchetto
- Lab of Genetics, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Maxime Caron
- Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada
| | - Shu-Huang Chen
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada
| | - Stephan Busche
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada
| | - Fred H Gage
- Lab of Genetics, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada.
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada.
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27
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Abstract
Long non-coding RNAs (lncRNAs) are over 200 nucleotides in length and are transcribed from the mammalian genome in a tissue-specific and developmentally regulated pattern. There is growing recognition that lncRNAs are novel biomarkers and/or key regulators of toxicological responses in humans and animal models. Lacking protein-coding capacity, the numerous types of lncRNAs possess a myriad of transcriptional regulatory functions that include cis and trans gene expression, transcription factor activity, chromatin remodeling, imprinting, and enhancer up-regulation. LncRNAs also influence mRNA processing, post-transcriptional regulation, and protein trafficking. Dysregulation of lncRNAs has been implicated in various human health outcomes such as various cancers, Alzheimer's disease, cardiovascular disease, autoimmune diseases, as well as intermediary metabolism such as glucose, lipid, and bile acid homeostasis. Interestingly, emerging evidence in the literature over the past five years has shown that lncRNA regulation is impacted by exposures to various chemicals such as polycyclic aromatic hydrocarbons, benzene, cadmium, chlorpyrifos-methyl, bisphenol A, phthalates, phenols, and bile acids. Recent technological advancements, including next-generation sequencing technologies and novel computational algorithms, have enabled the profiling and functional characterizations of lncRNAs on a genomic scale. In this review, we summarize the biogenesis and general biological functions of lncRNAs, highlight the important roles of lncRNAs in human diseases and especially during the toxicological responses to various xenobiotics, evaluate current methods for identifying aberrant lncRNA expression and molecular target interactions, and discuss the potential to implement these tools to address fundamental questions in toxicology.
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Affiliation(s)
- Joseph L Dempsey
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
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28
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The Bleeding Assessment Tool and laboratory data in the characterisation of a female with inherited haemophilia A. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2016; 16:114-117. [PMID: 27893350 DOI: 10.2450/2016.0132-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/22/2016] [Indexed: 11/21/2022]
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29
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van den Berge M, Sijen T. A male and female RNA marker to infer sex in forensic analysis. Forensic Sci Int Genet 2016; 26:70-76. [PMID: 27816848 DOI: 10.1016/j.fsigen.2016.10.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/17/2016] [Accepted: 10/24/2016] [Indexed: 01/18/2023]
Abstract
In forensics, DNA profiling is used for the identification of the donor of a trace, while messenger RNA (mRNA) profiling can be applied to identify the cellular origin such as body fluids or organ tissues. The presence of male cell material can be readily assessed by the incorporation of Y-chromosomal markers in quantitation or STR profiling systems. However, no forensic marker exists to positively identify female cell material; merely the presence of female DNA is deduced from the absence of a Y peak, or unbalanced X-Y signals at the Amelogenin locus or unbalanced response of the total and Y-specific quantifier. The presence of two X-chromosomes in female cells invokes dosage compensation, which is achieved through inactivation of one of the X-chromosomes in females. Since this process involves specific RNA molecules, identification of female cellular material may be possible through RNA profiling. Additionally, male material may be identified through RNAs expressed from the Y-chromosome. RNAs preferentially expressed in either sex were assessed for their potential to act as sex markers in forensic RNA assays. To confirm sex-specificity, body fluids and organ tissues of multiple donors of either sex were tested. Additionally, sensitivity of the markers and the suitability of positively identifying male-female mixtures were assessed and degraded samples were used to assess performance of the markers in forensic settings. The addition of sex-specific markers is of added informative value in any RNA profiling system and both markers were incorporated into existing RNA assays that either target body fluids or organs. These are the first forensic assays that enable positive identification of female cellular material.
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Affiliation(s)
- M van den Berge
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands, The Netherlands.
| | - T Sijen
- Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands, The Netherlands.
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30
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Loley C, Alver M, Assimes TL, Bjonnes A, Goel A, Gustafsson S, Hernesniemi J, Hopewell JC, Kanoni S, Kleber ME, Lau KW, Lu Y, Lyytikäinen LP, Nelson CP, Nikpay M, Qu L, Salfati E, Scholz M, Tukiainen T, Willenborg C, Won HH, Zeng L, Zhang W, Anand SS, Beutner F, Bottinger EP, Clarke R, Dedoussis G, Do R, Esko T, Eskola M, Farrall M, Gauguier D, Giedraitis V, Granger CB, Hall AS, Hamsten A, Hazen SL, Huang J, Kähönen M, Kyriakou T, Laaksonen R, Lind L, Lindgren C, Magnusson PKE, Marouli E, Mihailov E, Morris AP, Nikus K, Pedersen N, Rallidis L, Salomaa V, Shah SH, Stewart AFR, Thompson JR, Zalloua PA, Chambers JC, Collins R, Ingelsson E, Iribarren C, Karhunen PJ, Kooner JS, Lehtimäki T, Loos RJF, März W, McPherson R, Metspalu A, Reilly MP, Ripatti S, Sanghera DK, Thiery J, Watkins H, Deloukas P, Kathiresan S, Samani NJ, Schunkert H, Erdmann J, König IR. No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis. Sci Rep 2016; 6:35278. [PMID: 27731410 PMCID: PMC5059659 DOI: 10.1038/srep35278] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/26/2016] [Indexed: 11/09/2022] Open
Abstract
In recent years, genome-wide association studies have identified 58 independent risk loci for coronary artery disease (CAD) on the autosome. However, due to the sex-specific data structure of the X chromosome, it has been excluded from most of these analyses. While females have 2 copies of chromosome X, males have only one. Also, one of the female X chromosomes may be inactivated. Therefore, special test statistics and quality control procedures are required. Thus, little is known about the role of X-chromosomal variants in CAD. To fill this gap, we conducted a comprehensive X-chromosome-wide meta-analysis including more than 43,000 CAD cases and 58,000 controls from 35 international study cohorts. For quality control, sex-specific filters were used to adequately take the special structure of X-chromosomal data into account. For single study analyses, several logistic regression models were calculated allowing for inactivation of one female X-chromosome, adjusting for sex and investigating interactions between sex and genetic variants. Then, meta-analyses including all 35 studies were conducted using random effects models. None of the investigated models revealed genome-wide significant associations for any variant. Although we analyzed the largest-to-date sample, currently available methods were not able to detect any associations of X-chromosomal variants with CAD.
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Affiliation(s)
- Christina Loley
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg-Lübeck-Kiel, Lübeck, Germany
| | - Maris Alver
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Institute of Molecular and Cell Biology, Tartu, Estonia
| | - Themistocles L Assimes
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine Stanford, Standford, California, USA
| | - Andrew Bjonnes
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Anuj Goel
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Stefan Gustafsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jussi Hernesniemi
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland.,Department of Cardiology, Heart Hospital and University of Tampere School of Medicine, Tampere, Finland
| | - Jemma C Hopewell
- CTSU, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Stavroula Kanoni
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - King Wai Lau
- CTSU, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland.,Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK.,NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Majid Nikpay
- Ruddy Canadian Cardiovascular Genetics Centre University of Ottawa Heart Institute, Ottawa, Canada
| | - Liming Qu
- Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elias Salfati
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine Stanford, Standford, California, USA
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology/Medical Faculty/University of Leipzig, Leipzig, Germany.,LIFE Research Center of Civilization Diseases, Leipzig, Germany
| | - Taru Tukiainen
- Analytic and Translation Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Christina Willenborg
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg-Lübeck-Kiel, Lübeck, Germany.,Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany and University Heart Center Luebeck, Campus Lübeck, Lübeck, Germany
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Korea
| | - Lingyao Zeng
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, München, Germany
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.,Department of Cardiology, Ealing Hospital National Health Service (NHS) Trust, Middlesex, UK
| | - Sonia S Anand
- Population Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Frank Beutner
- LIFE Research Center of Civilization Diseases, Leipzig, Germany.,Heart Center Leipzig, Cardiology, University of Leipzig, Leipzig, Germany
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Robert Clarke
- CTSU, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Ron Do
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA.,The Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, New York, USA.,The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA.,The Zena and Michael A. Weiner Cardiovascular Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Markku Eskola
- Department of Cardiology, Heart Hospital and University of Tampere School of Medicine, Tampere, Finland
| | - Martin Farrall
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Geriatrics, Uppsala Universit, Uppsala, Sweden
| | | | - Alistair S Hall
- Leeds Institute of Genetics, Health and Therapeutics, University of Leeds, UK
| | - Anders Hamsten
- Cardiovascular Genetics and Genomics Group, Atherosclerosis Research Unit, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | | | - Jie Huang
- Boston VA Research Institute, Inc., Boston, Massachusetts, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland.,Department of Clinical Physiology, University of Tampere School of Medicine, Tampere, Finland
| | - Theodosios Kyriakou
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Reijo Laaksonen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland.,Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland.,Zora Biosciences, Espoo, Finland
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Cecilia Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Eirini Marouli
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | | | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Kjell Nikus
- Department of Cardiology, Heart Hospital and University of Tampere School of Medicine, Tampere, Finland
| | - Nancy Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Loukianos Rallidis
- Second Department of Cardiology, University General Hospital Attikon, Athens, Greece
| | - Veikko Salomaa
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | - Svati H Shah
- Duke University School of Medicine, Durham, North Carolina, USA
| | - Alexandre F R Stewart
- Ruddy Canadian Cardiovascular Genetics Centre University of Ottawa Heart Institute, Ottawa, Canada
| | - John R Thompson
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Pierre A Zalloua
- Lebanese American University, School of Medicine, Beirut, Lebanon.,Harvard School of Public Health, Boston, Massachusetts, USA
| | - John C Chambers
- Department of Cardiology, Ealing Hospital National Health Service (NHS) Trust, Middlesex, UK.,Population Health Research Institute, McMaster University, Hamilton, Ontario, Canada.,Imperial College Healthcare NHS Trust, London, UK
| | - Rory Collins
- CTSU, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Erik Ingelsson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Carlos Iribarren
- Kaiser Permanente, Division of Research, Oakland, California, USA
| | - Pekka J Karhunen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland.,Department of Forensic Medicine, University of Tampere School of Medicine, Tampere, Finland
| | - Jaspal S Kooner
- Population Health Research Institute, McMaster University, Hamilton, Ontario, Canada.,Imperial College Healthcare NHS Trust, London, UK.,Cardiovascular Science, National Heart and Lung Institute, Imperial College London, London, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland.,Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere, Finland
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Synlab Academy, Synlab Services GmbH, Mannheim, Germany.,Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Ruth McPherson
- Ruddy Canadian Cardiovascular Genetics Centre University of Ottawa Heart Institute, Ottawa, Canada
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia.,Institute of Molecular and Cell Biology, Tartu, Estonia
| | - Muredach P Reilly
- Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Samuli Ripatti
- Kaiser Permanente, Division of Research, Oakland, California, USA.,Hjelt Institute, University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Dharambir K Sanghera
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Oklahoma Center for Neuroscience, Oklahoma City, Oklahoma, USA
| | - Joachim Thiery
- LIFE Research Center of Civilization Diseases, Leipzig, Germany.,Institute for Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Medical Faculty, Leipzig, Germany
| | - Hugh Watkins
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.,Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sekar Kathiresan
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK.,NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Heribert Schunkert
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, München, Germany.,Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Jeanette Erdmann
- DZHK (German Centre for Cardiovascular Research), partner site Hamburg-Lübeck-Kiel, Lübeck, Germany.,Institut für Integrative und Experimentelle Genomik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany and University Heart Center Luebeck, Campus Lübeck, Lübeck, Germany
| | - Inke R König
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Hamburg-Lübeck-Kiel, Lübeck, Germany
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Zhou QZ, Zhang B, Yu QY, Zhang Z. BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori. BMC Bioinformatics 2016; 17:370. [PMID: 27623959 PMCID: PMC5022206 DOI: 10.1186/s12859-016-1251-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 09/08/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori). DESCRIPTION In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA. CONCLUSIONS We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The BmncRNAdb is freely available at http://gene.cqu.edu.cn/BmncRNAdb/index.php .
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Affiliation(s)
- Qiu-Zhong Zhou
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Huxi Campus, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331 China
| | - Bindan Zhang
- School of Economics and Business Administration, Chongqing University, Campus A, No. 174 Shazheng Rd., Shapingba, Chongqing, 400044 China
| | - Quan-You Yu
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Huxi Campus, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331 China
| | - Ze Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Huxi Campus, No. 55 Daxuecheng South Rd., Shapingba, Chongqing, 401331 China
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32
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Casanova M, Liyakat Ali TM, Rougeulle C. Enlightening the contribution of the dark matter to the X chromosome inactivation process in mammals. Semin Cell Dev Biol 2016; 56:48-57. [PMID: 27174438 DOI: 10.1016/j.semcdb.2016.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 05/04/2016] [Accepted: 05/04/2016] [Indexed: 02/07/2023]
Abstract
X-chromosome inactivation (XCI) in mammals represents an exceptional example of transcriptional co-regulation occurring at the level of an entire chromosome. XCI is considered as a means to compensate for gene dosage imbalance between sexes, yet the largest part of the chromosome is composed of repeated elements of different nature and origins. Here we consider XCI from a repeat point of view, interrogating the mechanisms for inactivating X chromosome-derived repeated sequences and discussing the contribution of repetitive elements to the silencing process itself and to its evolution.
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Affiliation(s)
- Miguel Casanova
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, Université Paris Diderot, Paris, France
| | | | - Claire Rougeulle
- Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, Université Paris Diderot, Paris, France.
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33
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Long noncoding RNAs: a potent source of regulation in immunity and disease. Immunol Cell Biol 2016; 93:277-83. [PMID: 25776990 DOI: 10.1038/icb.2015.2] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/06/2014] [Indexed: 12/14/2022]
Abstract
The discovery of functional long noncoding RNAs (lncRNAs) coupled with the ever-increasing accessibility of genomic and transcriptomic technology has led to an explosion of functional and mechanistic investigation and discovery into what was once dismissed as junk DNA. Over the past decade, a significant number of lncRNAs have been found to be involved in a diverse array of processes: from epigenetic modulation, both repressive and activating; to protein scaffolding; to miRNA sequestration; to competitive inhibition; and more. The broad character of these mechanisms means that lncRNAs have the potential for regulation across all biological processes-not least of which are immunity and disease. A number of lncRNAs operating within these two contexts have already been identified and characterized, but untold more remain yet to be discovered. This review aims to provide an overview of the current state of research on lncRNAs involved in immune modulation and disease, with an emphasis on their mechanism and discovery.
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34
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Ferfouri F, Bernicot I, Schneider A, Haquet E, Hédon B, Anahory T. Is the resulting phenotype of an embryo with balanced X-autosome translocation, obtained by means of preimplantation genetic diagnosis, linked to the X inactivation pattern? Fertil Steril 2016; 105:1035-46. [PMID: 26772789 DOI: 10.1016/j.fertnstert.2015.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 11/07/2015] [Accepted: 12/08/2015] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To examine if a balanced female embryo with X-autosome translocation could, during its subsequent development, express an abnormal phenotype. DESIGN Preimplantation genetic diagnosis (PGD) analysis on two female carriers with maternal inherited X-autosome translocations. SETTING Infertility center and genetic laboratory in a public hospital. PATIENT(S) Two female patients carriers undergoing PGD for a balanced X-autosome translocations: patient 1 with 46,X,t(X;2)(q27;p15) and patient 2 with 46,X,t(X;22)(q28;q12.3). INTERVENTION(S) PGD for balanced X-autosome translocations. MAIN OUTCOME MEASURE(S) PGD outcomes, fluorescence in situ hybridization in biopsied embryos and meiotic segregation patterns analysis of embryos providing from X-autosome translocation carriers. RESULT(S) Controlled ovarian stimulation facilitated retrieval of a correct number of oocytes. One balanced embryo per patient was transferred and one developed, but the patient miscarried after 6 weeks of amenorrhea. In X-autosome translocation carriers, balanced Y-bearing embryos are most often phenotypically normal and viable. An ambiguous phenotype exists in balanced X-bearing embryos owing to the X inactivation mechanism. In 46,XX embryos issued from an alternate segregation, der(X) may be inactivated and partially spread transcriptional silencing into a translocated autosomal segment. Thus, the structural unbalanced genotype could be turned into a viable functional balanced one. It is relevant that a discontinuous silencing is observed with a partial and unpredictable inactivation of autosomal regions. Consequently, the resulting phenotype remains a mystery and is considered to be at risk of being an abnormal phenotype in the field of PGD. CONCLUSION(S) It is necessary to be cautious regarding to PGD management for this type of translocation, particularly in transferred female embryos.
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Affiliation(s)
- Fatma Ferfouri
- Cytogenetic PGD Department, CHU Montpellier University Hospital, Montpellier, France
| | - Izabel Bernicot
- Cytogenetic PGD Department, CHU Montpellier University Hospital, Montpellier, France
| | - Anouck Schneider
- Cytogenetic PGD Department, CHU Montpellier University Hospital, Montpellier, France
| | - Emmanuelle Haquet
- ART-PGD Department, CHU Montpellier University Hospital, Montpellier, France
| | - Bernard Hédon
- ART-PGD Department, CHU Montpellier University Hospital, Montpellier, France
| | - Tal Anahory
- Cytogenetic PGD Department, CHU Montpellier University Hospital, Montpellier, France; ART-PGD Department, CHU Montpellier University Hospital, Montpellier, France; INSERM U487, Saint Eloi Hospital, Montpellier, France.
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35
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Elsässer SJ, Ernst RJ, Walker OS, Chin JW. Genetic code expansion in stable cell lines enables encoded chromatin modification. Nat Methods 2016; 13:158-64. [PMID: 26727110 DOI: 10.1038/nmeth.3701] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/25/2015] [Indexed: 12/15/2022]
Abstract
Genetically encoded unnatural amino acids provide powerful strategies for modulating the molecular functions of proteins in mammalian cells. However, this approach has not been coupled to genome-wide measurements, because efficient incorporation of unnatural amino acids is limited to transient expression settings that lead to very heterogeneous expression. We demonstrate that stable integration of the Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS)/tRNA(Pyl)CUA pair (and its derivatives) into the mammalian genome enables efficient, homogeneous incorporation of unnatural amino acids into target proteins in diverse mammalian cells, and we reveal the distinct transcriptional responses of embryonic stem cells and mouse embryonic fibroblasts to amber codon suppression. Genetically encoding N-ɛ-acetyl-lysine in place of six lysine residues in histone H3 enables deposition of pre-acetylated histones into cellular chromatin, via a pathway that is orthogonal to enzymatic modification. After synthetically encoding lysine-acetylation at natural modification sites, we determined the consequences of acetylation at specific amino acids in histones for gene expression.
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Affiliation(s)
- Simon J Elsässer
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Department of Chemistry, Cambridge University, Cambridge, UK.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Russell J Ernst
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Olivia S Walker
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Department of Chemistry, Cambridge University, Cambridge, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Department of Chemistry, Cambridge University, Cambridge, UK
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36
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Yang SX, Guo C, Zhang YK, Sun JT, Hong XY. Expression level and immunolocalization of de novo methyltransferase 3 protein (TuDNMT3) in adult females and males of the two-spotted spider mite, Tetranychus urticae. EXPERIMENTAL & APPLIED ACAROLOGY 2015; 67:381-392. [PMID: 26246190 DOI: 10.1007/s10493-015-9957-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/22/2015] [Indexed: 06/04/2023]
Abstract
DNA methylation is an epigenetic mechanism for regulating developmental and other important processes in eukaryotes. Several essential components of the DNA methylation machinery have been identified, such as DNA methyltransferases. In the two-spotted spider mite, Tetranychus urticae Koch, we have identified one DNA methyltransferase 3 gene (Tudnmt3) and tentatively investigated its potential role in adult females and males. Here, to better elucidate the functional role of Tudnmt3, its protein structure, expression and localization were subjected to more detailed analyses. Bioinformatic analyses clearly showed that the structure of TuDNMT3 was highly conserved, with several vital amino acid residues for the activation and stabilization of its confirmation. Western blot analyses revealed that this protein was expressed in both genders, with higher expression in adult females, which was inconsistent with the gene expression, suggesting translational regulation of Tudnmt3. Subsequent immunodetection provided supportive evidence for higher expression of the TuDNMT3 protein in adult females and indicated that this protein was generally localized in the cytoplasm and that its expression was predominantly confined to the genital region of spider mites, strengthening the hypothesis that de novo methylation mediated by Tudnmt3 in gonad development or gametogenesis has a different mechanism from maintenance methyltransferase.
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Affiliation(s)
- Si-Xia Yang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Chao Guo
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yan-Kai Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China.
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37
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LAKHOTIA SUBHASHC. Divergent actions of long noncoding RNAs on X-chromosome remodelling in mammals and Drosophila achieve the same end result: dosage compensation. J Genet 2015; 94:575-84. [DOI: 10.1007/s12041-015-0566-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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38
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Li W, Zhang T, Ding J. Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi. Nucleic Acids Res 2015; 43:10026-38. [PMID: 26429971 PMCID: PMC4787775 DOI: 10.1093/nar/gkv979] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/18/2015] [Indexed: 12/17/2022] Open
Abstract
TET proteins play a vital role in active DNA demethylation in mammals and thus have important functions in many essential cellular processes. The chemistry for the conversion of 5mC to 5hmC, 5fC and 5caC catalysed by TET proteins is similar to that of T to 5hmU, 5fU and 5caU catalysed by thymine-7-hydroxylase (T7H) in the nucleotide anabolism in fungi. Here, we report the crystal structures and biochemical properties of Neurospora crassa T7H. T7H can bind the substrates only in the presence of cosubstrate, and binding of different substrates does not induce notable conformational changes. T7H exhibits comparable binding affinity for T and 5hmU, but 3-fold lower affinity for 5fU. Residues Phe292, Tyr217 and Arg190 play critical roles in substrate binding and catalysis, and the interactions of the C5 modification group of substrates with the cosubstrate and enzyme contribute to the slightly varied binding affinity and activity towards different substrates. After the catalysis, the products are released and new cosubstrate and substrate are reloaded to conduct the next oxidation reaction. Our data reveal the molecular basis for substrate specificity and catalytic mechanism of T7H and provide new insights into the molecular mechanism of substrate recognition and catalysis of TET proteins.
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Affiliation(s)
- Wenjing Li
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Tianlong Zhang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Jianping Ding
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China Collaborative Innovation Center for Genetics and Development, Fudan University, 2005 Song-Hu Road, Shanghai 200438, China
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39
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Jayakodi M, Jung JW, Park D, Ahn YJ, Lee SC, Shin SY, Shin C, Yang TJ, Kwon HW. Genome-wide characterization of long intergenic non-coding RNAs (lincRNAs) provides new insight into viral diseases in honey bees Apis cerana and Apis mellifera. BMC Genomics 2015; 16:680. [PMID: 26341079 PMCID: PMC4559890 DOI: 10.1186/s12864-015-1868-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 08/19/2015] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are a class of RNAs that do not encode proteins. Recently, lncRNAs have gained special attention for their roles in various biological process and diseases. RESULTS In an attempt to identify long intergenic non-coding RNAs (lincRNAs) and their possible involvement in honey bee development and diseases, we analyzed RNA-seq datasets generated from Asian honey bee (Apis cerana) and western honey bee (Apis mellifera). We identified 2470 lincRNAs with an average length of 1011 bp from A. cerana and 1514 lincRNAs with an average length of 790 bp in A. mellifera. Comparative analysis revealed that 5 % of the total lincRNAs derived from both species are unique in each species. Our comparative digital gene expression analysis revealed a high degree of tissue-specific expression among the seven major tissues of honey bee, different from mRNA expression patterns. A total of 863 (57 %) and 464 (18 %) lincRNAs showed tissue-dependent expression in A. mellifera and A. cerana, respectively, most preferentially in ovary and fat body tissues. Importantly, we identified 11 lincRNAs that are specifically regulated upon viral infection in honey bees, and 10 of them appear to play roles during infection with various viruses. CONCLUSIONS This study provides the first comprehensive set of lincRNAs for honey bees and opens the door to discover lincRNAs associated with biological and hormone signaling pathways as well as various diseases of honey bee.
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Affiliation(s)
- Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Je Won Jung
- WCU Biomodulation Major, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Doori Park
- WCU Biomodulation Major, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Young-Joon Ahn
- WCU Biomodulation Major, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Sang-Yoon Shin
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Chanseok Shin
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
| | - Hyung Wook Kwon
- WCU Biomodulation Major, Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
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40
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D'Amico F, Skarmoutsou E, Mazzarino MC. The sex bias in systemic sclerosis: on the possible mechanisms underlying the female disease preponderance. Clin Rev Allergy Immunol 2015; 47:334-43. [PMID: 24126759 DOI: 10.1007/s12016-013-8392-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Systemic sclerosis is a multifactorial and heterogeneous disease. Genetic and environmental factors are known to interplay in the onset and progression of systemic sclerosis. Sex plays an important and determinant role in the development of such a disorder. Systemic sclerosis shows a significant female preponderance. However, the reason for this female preponderance is incompletely understood. Hormonal status, genetic and epigenetic differences, and lifestyle have been considered in order to explain female preponderance in systemic sclerosis. Sex chromosomes play a determinant role in contributing to systemic sclerosis onset and progression, as well as in its sex-biased prevalence. It is known, in fact, that X chromosome contains many sex- and immuno-related genes, thus contributing to immuno tolerance and sex hormone status. This review focuses mainly on the recent progress on epigenetic mechanisms--exclusively linked to the X chromosome--which would contribute to the development of systemic sclerosis. Furthermore, we report also some hypotheses (dealing with skewed X chromosome inactivation, X gene reactivation, acquired monosomy) that have been proposed in order to justify the female preponderance in autoimmune diseases. However, despite the intensive efforts in elucidating the mechanisms involved in the pathogenesis of systemic sclerosis, many questions remain still unanswered.
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Affiliation(s)
- Fabio D'Amico
- Department of Bio-medical Sciences, University of Catania, via Androne 83, 95124, Catania, Italy,
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41
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Gardner PP, Fasold M, Burge SW, Ninova M, Hertel J, Kehr S, Steeves TE, Griffiths-Jones S, Stadler PF. Conservation and losses of non-coding RNAs in avian genomes. PLoS One 2015; 10:e0121797. [PMID: 25822729 PMCID: PMC4378963 DOI: 10.1371/journal.pone.0121797] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/03/2015] [Indexed: 11/21/2022] Open
Abstract
Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We identify 34 lncRNA-associated loci that are conserved between birds and mammals and validate 12 of these in chicken. We report several intriguing cases where a reported mammalian lncRNA, but not its function, is conserved. We also demonstrate extensive conservation of classical ncRNAs (e.g., tRNAs) and more recently discovered ncRNAs (e.g., snoRNAs and miRNAs) in birds. Furthermore, we describe numerous “losses” of several RNA families, and attribute these to either genuine loss, divergence or missing data. In particular, we show that many of these losses are due to the challenges associated with assembling avian microchromosomes. These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.
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Affiliation(s)
- Paul P. Gardner
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand
- * E-mail:
| | - Mario Fasold
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
- ecSeq Bioinformatics, Brandvorwerkstr.43, D-04275 Leipzig, Germany
| | - Sarah W. Burge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Ninova
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Jana Hertel
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Stephanie Kehr
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
| | - Tammy E. Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Sam Griffiths-Jones
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
- Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany
- Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria
- Center for RNA in Technology and Health, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, USA
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany
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Wang X, Guan Z, Chen Y, Dong Y, Niu Y, Wang J, Zhang T, Niu B. Genomic DNA hypomethylation is associated with neural tube defects induced by methotrexate inhibition of folate metabolism. PLoS One 2015; 10:e0121869. [PMID: 25822193 PMCID: PMC4379001 DOI: 10.1371/journal.pone.0121869] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 02/16/2015] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is thought to be involved in the etiology of neural tube defects (NTDs). However, the exact mechanism between DNA methylation and NTDs remains unclear. Herein, we investigated the change of methylation in mouse model of NTDs associated with folate dysmetabolism by use of ultraperformance liquid chromatography tandem mass spectrometry (UPLC/MS/MS), liquid chromatography-electrospray ionization tandem mass spectrometry (LC-MS/MS), microarray, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and Real time quantitative PCR. Results showed that NTD neural tube tissues had lower concentrations of 5-methyltetrahydrofolate (5-MeTHF, P = 0.005), 5-formyltetrahydrofolate (5-FoTHF, P = 0.040), S-adenosylmethionine (SAM, P = 0.004) and higher concentrations of folic acid (P = 0.041), homocysteine (Hcy, P = 0.006) and S-adenosylhomocysteine (SAH, P = 0.045) compared to control. Methylation levels of genomic DNA decreased significantly in the embryonic neural tube tissue of NTD samples. 132 differentially methylated regions (35 low methylated regions and 97 high methylated regions) were selected by microarray. Two genes (Siah1b, Prkx) in Wnt signal pathway demonstrated lower methylated regions (peak) and higher expression in NTDs (P<0.05; P<0.05). Results suggest that DNA hypomethylation was one of the possible epigenetic variations correlated with the occurrence of NTDs induced by folate dysmetabolism and that Siah1b, Prkx in Wnt pathway may be candidate genes for NTDs.
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Affiliation(s)
- Xiuwei Wang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Zhen Guan
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Yan Chen
- Department of Respiratory, the Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Yanting Dong
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Yuhu Niu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, China
| | - Jianhua Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- * E-mail: (BN); (TZ)
| | - Bo Niu
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, China
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
- * E-mail: (BN); (TZ)
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Kungulovski G, Nunna S, Thomas M, Zanger UM, Reinhardt R, Jeltsch A. Targeted epigenome editing of an endogenous locus with chromatin modifiers is not stably maintained. Epigenetics Chromatin 2015; 8:12. [PMID: 25901185 PMCID: PMC4404288 DOI: 10.1186/s13072-015-0002-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/09/2015] [Indexed: 01/23/2023] Open
Abstract
Background DNA methylation and histone 3 lysine 9 (H3K9) methylation are considered as epigenetic marks that can be inherited through cell divisions. To explore the functional consequences and stability of these modifications, we employed targeted installment of DNA methylation and H3K9 methylation in the vascular endothelial growth factor A (VEGF-A) promoter using catalytic domains of DNA or H3K9 methyltransferases that are fused to a zinc finger protein which binds a site in the VEGF-A promoter. Results Expression of the targeted DNA and H3K9 methyltransferases caused dense deposition of DNA methylation or H3K9 di- and trimethylation in the promoter of VEGF-A and downregulation of VEGF-A gene expression. We did not observe positive feedback between DNA methylation and H3K9 methylation. Upon loss of the targeted methyltransferases from the cells, the epigenetic marks, chromatin environment, and gene expression levels returned to their original state, indicating that both methylation marks were not stably propagated after their installment. Conclusions The clear anti-correlation between DNA or H3K9 methylation and gene expression suggests a direct role of these marks in transcriptional control. The lack of maintenance of the transiently induced silenced chromatin state suggests that the stability of epigenetic signaling is based on an epigenetic network consisting of several molecular marks. Therefore, for stable reprogramming, either multivalent deposition of functionally related epigenetic marks or longer-lasting trigger stimuli might be necessary. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0002-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Goran Kungulovski
- Institute of Biochemistry, Faculty of Chemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Suneetha Nunna
- Institute of Biochemistry, Faculty of Chemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Maria Thomas
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstraße 112, 70376 Stuttgart, Germany.,University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
| | - Ulrich M Zanger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstraße 112, 70376 Stuttgart, Germany.,University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
| | - Richard Reinhardt
- Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, Stuttgart University, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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Uh HW, Beekman M, Meulenbelt I, Houwing-Duistermaat JJ. Genotype-Based Score Test for Association Testing in Families. STATISTICS IN BIOSCIENCES 2015; 7:394-416. [PMID: 26473021 PMCID: PMC4596911 DOI: 10.1007/s12561-015-9128-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 11/20/2014] [Accepted: 02/17/2015] [Indexed: 11/29/2022]
Abstract
The multiplex-case and control design in which multiple cases are sampled from the same family is considered. In such studies phenotype information of the un-genotyped relatives might be available. We intend to use additional family information when performing genetic association tests. A score test is revisited to provide a flexible framework to accommodate various genetic models and to improve power of the association test by adding available family information. The proposed test accounts for correlations induced by multiple cases from the same pedigree, directly deals with X-linked SNPs in mixed-sex-related samples, and incorporates additional phenotypic information such as the number of (un-genotyped) siblings and parents with similar symptoms by assigning the weights to (genotyped) multiplex cases. In addition, the score test directly incorporates posterior probabilities of imputed genotypes, which leads to an efficiency measure that reflects imputation uncertainty on the test conducted. The proposed test is applied to real applications for illustration. Its efficiency is demonstrated via simulations.
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Affiliation(s)
- Hae-Won Uh
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, S-5-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Marian Beekman
- Department of Molecular Epidemiology, Leiden University Medical Center, S-5-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Ingrid Meulenbelt
- Department of Molecular Epidemiology, Leiden University Medical Center, S-5-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Jeanine J Houwing-Duistermaat
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, S-5-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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Borel C, Ferreira PG, Santoni F, Delaneau O, Fort A, Popadin KY, Garieri M, Falconnet E, Ribaux P, Guipponi M, Padioleau I, Carninci P, Dermitzakis ET, Antonarakis SE. Biased allelic expression in human primary fibroblast single cells. Am J Hum Genet 2015; 96:70-80. [PMID: 25557783 DOI: 10.1016/j.ajhg.2014.12.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/01/2014] [Indexed: 11/16/2022] Open
Abstract
The study of gene expression in mammalian single cells via genomic technologies now provides the possibility to investigate the patterns of allelic gene expression. We used single-cell RNA sequencing to detect the allele-specific mRNA level in 203 single human primary fibroblasts over 133,633 unique heterozygous single-nucleotide variants (hetSNVs). We observed that at the snapshot of analyses, each cell contained mostly transcripts from one allele from the majority of genes; indeed, 76.4% of the hetSNVs displayed stochastic monoallelic expression in single cells. Remarkably, adjacent hetSNVs exhibited a haplotype-consistent allelic ratio; in contrast, distant sites located in two different genes were independent of the haplotype structure. Moreover, the allele-specific expression in single cells correlated with the abundance of the cellular transcript. We observed that genes expressing both alleles in the majority of the single cells at a given time point were rare and enriched with highly expressed genes. The relative abundance of each allele in a cell was controlled by some regulatory mechanisms given that we observed related single-cell allelic profiles according to genes. Overall, these results have direct implications in cellular phenotypic variability.
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Affiliation(s)
- Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
| | - Pedro G Ferreira
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland; Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland; Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Federico Santoni
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
| | - Olivier Delaneau
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland; Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland; Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland
| | - Alexandre Fort
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Konstantin Y Popadin
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
| | - Marco Garieri
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
| | - Emilie Falconnet
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
| | - Pascale Ribaux
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1211 Geneva, Switzerland
| | - Ismael Padioleau
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland; Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland; Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland; Center of Excellence for Genomic Medicine Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Biomedical Research Foundation Academy of Athens, Athens 11527, Greece.
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, 1211 Geneva, Switzerland; Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1211 Geneva, Switzerland.
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Yang SX, Guo C, Xu M, Sun JT, Hong XY. Sex-dependent activity of de novo methyltransferase 3 (Tudnmt3) in the two-spotted mite, Tetranychus urticae Koch. INSECT MOLECULAR BIOLOGY 2014; 23:743-753. [PMID: 25055993 DOI: 10.1111/imb.12120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
DNA methylation is an epigenetic mechanism for regulating developmental and other important processes in eukaryotes. Several components of the DNA methylation machinery have been identified, such as DNA methyltransferases. However, little is known about DNA methyltransferases in chelicerates, which is the second largest arthropod group. Epigenetics are expected to have a crucial role in the metabolism and development of this group. Here, we investigated the role of DNA methyltransferase 3 in the development of Tetranychus urticae Koch. In silico analyses clearly showed that this enzyme possesses the necessary conserved motifs for the catalytic activity of de novo methylation of DNA. Real-time PCR revealed that T. urticae de novo methyltransferase 3 (Tudnmt3) is expressed ubiquitously and throughout the life cycle of the two-spotted spider mite. However, the pattern of Tudnmt3 expression was sex-dependent during the adult stage. Whole in situ hybridization provided supportive evidence that Tudnmt3 is linked to the differentiation of the gonads in adult females and males. Methylation-sensitive amplification polymorphism analyses of 119 loci showed that the status of DNA methylation is partially different between adult females and males, raising the possibility that this sex-dependent DNA methylation pattern is mediated by different methylation activity of Tudnmt3.
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Affiliation(s)
- S-X Yang
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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47
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Beerman I, Rossi DJ. Epigenetic regulation of hematopoietic stem cell aging. Exp Cell Res 2014; 329:192-9. [PMID: 25261778 DOI: 10.1016/j.yexcr.2014.09.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 09/11/2014] [Indexed: 12/27/2022]
Abstract
Aging is invariably associated with alterations of the hematopoietic stem cell (HSC) compartment, including loss of functional capacity, altered clonal composition, and changes in lineage contribution. Although accumulation of DNA damage occurs during HSC aging, it is unlikely such consistent aging phenotypes could be solely attributed to changes in DNA integrity. Another mechanism by which heritable traits could contribute to the changes in the functional potential of aged HSCs is through alterations in the epigenetic landscape of adult stem cells. Indeed, recent studies on hematopoietic stem cells have suggested that altered epigenetic profiles are associated with HSC aging and play a key role in modulating the functional potential of HSCs at different stages during ontogeny. Even small changes of the epigenetic landscape can lead to robustly altered expression patterns, either directly by loss of regulatory control or through indirect, additive effects, ultimately leading to transcriptional changes of the stem cells. Potential drivers of such changes in the epigenetic landscape of aged HSCs include proliferative history, DNA damage, and deregulation of key epigenetic enzymes and complexes. This review will focus largely on the two most characterized epigenetic marks - DNA methylation and histone modifications - but will also discuss the potential role of non-coding RNAs in regulating HSC function during aging.
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Affiliation(s)
- Isabel Beerman
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children׳s Hospital, MA 02116, USA.
| | - Derrick J Rossi
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Division of Hematology/Oncology, Boston Children׳s Hospital, MA 02116, USA
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Abstract
Epigenetics refers to long-term modifications of gene activity that can be inherited, either somatically or transgenerationally, but that are independent of alterations in the primary base sequence of the organism's DNA. These changes can include chemical modifications of both the DNA bases and the proteins that associate with the DNA helices to form chromatin, the nucleic acid:protein complex of which the chromosomes are comprised. Epigenetic modifications can affect the accessibility of the DNA for transcription factors (the DNA-binding proteins that specify which genes are to be active or silent by modulating the recruitment of the transcriptional machinery that reads the information encoded in the sequence) and thereby regulate the expression of genes and alter the phenotype of the organism. Epigenetic marks can also be re-established following mitosis, allowing patterns of differential gene expression to be transmitted from one cell generation to the next, and can even be maintained through meiosis, allowing transgenerational transfer of regulatory cues. Unlike the information encoded in the DNA sequence, which is invariant between most cell types and over time, epigenetic information is tissue specific and can change in response to exogenous and endogenous perturbations. This responsive capacity enables a sensitive and reactive system that can optimize gene expression in relevant tissue in response to environmental change. The realization that organisms are capable of genetically 'reprograming' themselves as well as 'preprograming' future cells, and even future offspring to optimize gene expression for a given environment may have tremendous ramifications on our understanding of both acclimatization and adaptation to hypoxia.
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Affiliation(s)
- Carolyn J Brown
- 1 Department of Medical Genetics, Molecular Epigenetics Group, University of British Columbia , Vancouver, British Columbia, Canada
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49
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Liu Z, Yang J, Xu H, Li C, Wang Z, Li Y, Dong X, Li Y. Comparing computational methods for identification of allele-specific expression based on next generation sequencing data. Genet Epidemiol 2014; 38:591-8. [PMID: 25183311 DOI: 10.1002/gepi.21846] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 05/15/2014] [Accepted: 06/16/2014] [Indexed: 11/07/2022]
Abstract
Allele-specific expression (ASE) studies have wide-ranging implications for genome biology and medicine. Whole transcriptome RNA sequencing (RNA-Seq) has emerged as a genome-wide tool for identifying ASE, but suffers from mapping bias favoring reference alleles. Two categories of methods are adopted nowadays, to reduce the effect of mapping bias on ASE identification-normalizing RNA allelic ratio with the parallel genomic allelic ratio (pDNAar) and modifying reference genome to make reads carrying both alleles with the same chance to be mapped (mREF). We compared the sensitivity and specificity of both methods with simulated data, and demonstrated that the pDNAar, though ideally practical, was lower in sensitivity, because of its lower mapping rate of reads carrying nonreference (alternative) alleles, although mREF achieved higher sensitivity and specificity for its efficiency in mapping reads carrying both alleles. Application of these two methods in real sequencing data showed that mREF were able to identify more ASE loci because of its higher mapping efficiency, and able to correcting some seemly incorrect ASE loci identified by pDNAar due to the inefficiency in mapping reads carrying alternative alleles of pDNAar. Our study provides useful information for RNA sequencing data processing in the identification of ASE.
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Affiliation(s)
- Zhi Liu
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academic of Science, Shanghai, P. R. China; University of Chinese Academic of Science, Beijing, P. R. China
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50
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Wang J, Yu R, Shete S. X-chromosome genetic association test accounting for X-inactivation, skewed X-inactivation, and escape from X-inactivation. Genet Epidemiol 2014; 38:483-93. [PMID: 25043884 PMCID: PMC4127090 DOI: 10.1002/gepi.21814] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/06/2014] [Accepted: 04/17/2014] [Indexed: 11/07/2022]
Abstract
X-chromosome inactivation (XCI) is the process in which one of the two copies of the X-chromosome in females is randomly inactivated to achieve the dosage compensation of X-linked genes between males and females. That is, 50% of the cells have one allele inactive and the other 50% of the cells have the other allele inactive. However, studies have shown that skewed or nonrandom XCI is a biological plausibility wherein more than 75% of cells have the same allele inactive. Also, some of the X-chromosome genes escape XCI, i.e., both alleles are active in all cells. Current statistical tests for X-chromosome association studies can either account for random XCI (e.g., Clayton's approach) or escape from XCI (e.g., PLINK software). Because the true XCI process is unknown and differs across different regions on the X-chromosome, we proposed a unified approach of maximizing likelihood ratio over all biological possibilities: random XCI, skewed XCI, and escape from XCI. A permutation-based procedure was developed to assess the significance of the approach. We conducted simulation studies to compare the performance of the proposed approach with Clayton's approach and PLINK regression. The results showed that the proposed approach has higher powers in the scenarios where XCI is skewed while losing some power in scenarios where XCI is random or XCI is escaped, with well-controlled type I errors. We also applied the approach to the X-chromosomal genetic association study of head and neck cancer.
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Affiliation(s)
- Jian Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, U.S.A
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, U.S.A
| | - Robert Yu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, U.S.A
| | - Sanjay Shete
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, U.S.A
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, U.S.A
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