Variability of Sexual Phenotype in 46,XX(SRY+) Patients: the Influence of Spreading X Inactivation Versus Position Effects
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Nuclear and Mitochondrial Genome Defects in Autisms
UC Irvine UC Irvine Previously Published Works Title Nuclear and mitochondrial genome defects in autisms. Permalink https://escholarship.org/uc/item/8vq3278q Journal Annals of the New York Academy of Sciences, 1151(1) ISSN 0077-8923 Authors Smith, Moyra Spence, M Anne Flodman, Pamela Publication Date 2009 DOI 10.1111/j.1749-6632.2008.03571.x License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California THE YEAR IN HUMAN AND MEDICAL GENETICS 2009 Nuclear and Mitochondrial Genome Defects in Autisms Moyra Smith, M. Anne Spence, and Pamela Flodman Department of Pediatrics, University of California, Irvine, California In this review we will evaluate evidence that altered gene dosage and structure im- pacts neurodevelopment and neural connectivity through deleterious effects on synap- tic structure and function, and evidence that the latter are key contributors to the risk for autism. We will review information on alterations of structure of mitochondrial DNA and abnormal mitochondrial function in autism and indications that interactions of the nuclear and mitochondrial genomes may play a role in autism pathogenesis. In a final section we will present data derived using Affymetrixtm SNP 6.0 microar- ray analysis of DNA of a number of subjects and parents recruited to our autism spectrum disorders project. We include data on two sets of monozygotic twins. Col- lectively these data provide additional evidence of nuclear and mitochondrial genome imbalance in autism and evidence of specific candidate genes in autism. We present data on dosage changes in genes that map on the X chromosomes and the Y chro- mosome. -
Differences Between Human and Chimpanzee Genomes and Their Implications in Gene Expression, Protein Functions and Biochemical Properties of the Two Species Maria V
Suntsova and Buzdin BMC Genomics 2020, 21(Suppl 7):535 https://doi.org/10.1186/s12864-020-06962-8 REVIEW Open Access Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species Maria V. Suntsova1 and Anton A. Buzdin1,2,3,4* From 11th International Young Scientists School “Systems Biology and Bioinformatics”–SBB-2019 Novosibirsk, Russia. 24-28 June 2019 Abstract Chimpanzees are the closest living relatives of humans. The divergence between human and chimpanzee ancestors dates to approximately 6,5–7,5 million years ago. Genetic features distinguishing us from chimpanzees and making us humans are still of a great interest. After divergence of their ancestor lineages, human and chimpanzee genomes underwent multiple changes including single nucleotide substitutions, deletions and duplications of DNA fragments of different size, insertion of transposable elements and chromosomal rearrangements. Human-specific single nucleotide alterations constituted 1.23% of human DNA, whereas more extended deletions and insertions cover ~ 3% of our genome. Moreover, much higher proportion is made by differential chromosomal inversions and translocations comprising several megabase-long regions or even whole chromosomes. However, despite of extensive knowledge of structural genomic changes accompanying human evolution we still cannot identify with certainty the causative genes of human identity. Most structural gene-influential changes happened at the level of expression regulation, which in turn provoked larger alterations of interactome gene regulation networks. In this review, we summarized the available information about genetic differences between humans and chimpanzees and their potential functional impacts on differential molecular, anatomical, physiological and cognitive peculiarities of these species. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
"The Genecards Suite: from Gene Data Mining to Disease Genome Sequence Analyses". In: Current Protocols in Bioinformat
The GeneCards Suite: From Gene Data UNIT 1.30 Mining to Disease Genome Sequence Analyses Gil Stelzer,1,5 Naomi Rosen,1,5 Inbar Plaschkes,1,2 Shahar Zimmerman,1 Michal Twik,1 Simon Fishilevich,1 Tsippi Iny Stein,1 Ron Nudel,1 Iris Lieder,2 Yaron Mazor,2 Sergey Kaplan,2 Dvir Dahary,2,4 David Warshawsky,3 Yaron Guan-Golan,3 Asher Kohn,3 Noa Rappaport,1 Marilyn Safran,1 and Doron Lancet1,6 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel 2LifeMap Sciences Ltd., Tel Aviv, Israel 3LifeMap Sciences Inc., Marshfield, Massachusetts 4Toldot Genetics Ltd., Hod Hasharon, Israel 5These authors contributed equally to the paper 6Corresponding author GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It au- tomatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. Var- Elect’s capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. -
Y Chromosome
G C A T T A C G G C A T genes Article An 8.22 Mb Assembly and Annotation of the Alpaca (Vicugna pacos) Y Chromosome Matthew J. Jevit 1 , Brian W. Davis 1 , Caitlin Castaneda 1 , Andrew Hillhouse 2 , Rytis Juras 1 , Vladimir A. Trifonov 3 , Ahmed Tibary 4, Jorge C. Pereira 5, Malcolm A. Ferguson-Smith 5 and Terje Raudsepp 1,* 1 Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458, USA; [email protected] (M.J.J.); [email protected] (B.W.D.); [email protected] (C.C.); [email protected] (R.J.) 2 Molecular Genomics Workplace, Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843-4458, USA; [email protected] 3 Laboratory of Comparative Genomics, Institute of Molecular and Cellular Biology, 630090 Novosibirsk, Russia; [email protected] 4 Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164-6610, USA; [email protected] 5 Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK; [email protected] (J.C.P.); [email protected] (M.A.F.-S.) * Correspondence: [email protected] Abstract: The unique evolutionary dynamics and complex structure make the Y chromosome the most diverse and least understood region in the mammalian genome, despite its undisputable role in sex determination, development, and male fertility. Here we present the first contig-level annotated draft assembly for the alpaca (Vicugna pacos) Y chromosome based on hybrid assembly of short- and long-read sequence data of flow-sorted Y. -
Replication Profile of PCDH11X and PCDH11Y, a Gene Pair Located In
Chromosome Research (2007) 15:485Y498 # Springer 2007 DOI: 10.1007/s10577-007-1153-y Replication profile of PCDH11X and PCDH11Y, a gene pair located in the non-pseudoautosomal homologous region Xq21.3/Yp11.2 N. D. Wilson1, L. J. N. Ross2, J. Close2, R. Mott1,T.J.Crow2 & E. V. Volpi1* 1Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK; Tel: +44-1865-287646; Fax: +44-1865-287533; E-mail: [email protected]; 2Prince of Wales International Centre for SANE Research, Warneford Hospital, Oxford, UK *Correspondence Received 4 November 2006. Received in revised form and accepted for publication by Wendy Bickmore 15 April 2007 Key words: PCDH11X/Y, replication asynchrony, replication timing, X-inactivation, Xq21.3/Yp11.2 homology block Abstract In order to investigate the replication timing properties of PCDH11X and PCDH11Y, a pair of protocadherin genes located in the hominid-specific non-pseudoautosomal homologous region Xq21.3/Yp11.2, we conducted a FISH-based comparative study in different human and non-human primate (Gorilla gorilla) cell types. The replication profiles of three genes from different regions of chromosome X (ZFX, XIST and ATRX) were used as terms of reference. Particular emphasis was given to the evaluation of allelic replication asynchrony in relation to the inactivation status of each gene. The human cell types analysed include neuronal cells and ICF syndrome cells, considered to be a model system for the study of X inactivation. PCDH11 appeared to be generally characterized by replication asynchrony in both male and female cells, and no significant differences were observed between human and gorilla, in which this gene lacks X-Y homologous status. -
Gender-Specific Expression of Ubiquitin-Specific Peptidase 9 Modulates Tau Expression and Phosphorylation: Possible Implications for Tauopathies
Mol Neurobiol DOI 10.1007/s12035-016-0299-z Gender-Specific Expression of Ubiquitin-Specific Peptidase 9 Modulates Tau Expression and Phosphorylation: Possible Implications for Tauopathies Sandra Köglsberger1 & Maria Lorena Cordero-Maldonado1 & Paul Antony1 & Julia Ilona Forster1 & Pierre Garcia 1 & Manuel Buttini1 & Alexander Crawford1 & Enrico Glaab1 Received: 22 May 2016 /Accepted: 14 November 2016 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract Public transcriptomic studies have shown that sev- literature, we derive a data-congruent model for a USP9-de- eral genes display pronounced gender differences in their ex- pendent regulatory mechanism modulating MAPT expression pression in the human brain, which may influence the mani- via BACH1 and SMAD4. Overall, the analyses suggest USP9 festations and risk for neuronal disorders. Here, we apply a may contribute to molecular gender differences observed in transcriptome-wide analysis to discover genes with gender- tauopathies and provide a new target for intervention strate- specific expression and significant alterations in public post- gies to modulate MAPT expression. mortem brain tissue from Alzheimer’s disease (AD) patients compared to controls. We identify the sex-linked ubiquitin- Keywords Transcriptomics .Tau .Tauopathies .Alzheimer’s specific peptidase 9 (USP9) as an outstanding candidate gene disease . Gender differences . Zebrafish with highly significant expression differences between the genders and male-specific underexpression in -
The Human Y Chromosome and Its Role in the Developing Male Nervous System
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1285 The Human Y chromosome and its role in the developing male nervous system MARTIN M. JOHANSSON ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 ISBN 978-91-554-9331-8 UPPSALA urn:nbn:se:uu:diva-261789 2015 Dissertation presented at Uppsala University to be publicly examined in Zootissalen (EBC 01.01006), Evolutionsbiologiskt centrum, EBC, Villavägen 9, Uppsala, Friday, 23 October 2015 at 13:15 for the degree of Doctor of Philosophy. The examination will be conducted in English. Faculty examiner: David Skuse (University College London Behavioural Sciences Unit). Abstract Johansson, M. M. 2015. The Human Y chromosome and its role in the developing male nervous system. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 1285. 63 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9331-8. Recent research demonstrated that besides a role in sex determination and male fertility, the Y chromosome is involved in additional functions including prostate cancer, sex-specific effects on the brain and behaviour, graft-versus-host disease, nociception, aggression and autoimmune diseases. The results presented in this thesis include an analysis of sex-biased genes encoded on the X and Y chromosomes of rodents. Expression data from six different somatic tissues was analyzed and we found that the X chromosome is enriched in female biased genes and depleted of male biased ones. The second study described copy number variation (CNV) patterns in a world-wide collection of human Y chromosome samples. Contrary to expectations, duplications and not deletions were the most frequent variations. -
The Y Chromosome: a Blueprint for Men’S Health?
European Journal of Human Genetics (2017) 25, 1181–1188 Official journal of The European Society of Human Genetics www.nature.com/ejhg REVIEW The Y chromosome: a blueprint for men’s health? Akhlaq A Maan1, James Eales1, Artur Akbarov1, Joshua Rowland1, Xiaoguang Xu1, Mark A Jobling2, Fadi J Charchar3 and Maciej Tomaszewski*,1,4 The Y chromosome has long been considered a ‘genetic wasteland’ on a trajectory to completely disappear from the human genome. The perception of its physiological function was restricted to sex determination and spermatogenesis. These views have been challenged in recent times with the identification of multiple ubiquitously expressed Y-chromosome genes and the discovery of several unexpected associations between the Y chromosome, immune system and complex polygenic traits. The collected evidence suggests that the Y chromosome influences immune and inflammatory responses in men, translating into genetically programmed susceptibility to diseases with a strong immune component. Phylogenetic studies reveal that carriers of a common European lineage of the Y chromosome (haplogroup I) possess increased risk of coronary artery disease. This occurs amidst upregulation of inflammation and suppression of adaptive immunity in this Y lineage, as well as inferior outcomes in human immunodeficiency virus infection. From structural analysis and experimental data, the UTY (Ubiquitously Transcribed Tetratricopeptide Repeat Containing, Y-Linked) gene is emerging as a promising candidate underlying the associations between Y-chromosome variants and the immunity-driven susceptibility to complex disease. This review synthesises the recent structural, experimental and clinical insights into the human Y chromosome in the context of men’s susceptibility to disease (with a particular emphasis on cardiovascular disease) and provides an overview of the paradigm shift in the perception of the Y chromosome. -
Regulatory Effects of the Uty/Ddx3y Locus on Neighboring Chromosome Y Genes and Autosomal Mrna Transcripts in Adult Mouse Non-Reproductive Cells
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.30.180232; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Regulatory effects of the Uty/Ddx3y locus on neighboring chromosome Y genes and autosomal mRNA transcripts in adult mouse non-reproductive cells Christian F. Deschepper Cardiovascular Biology Research Unit, Institut de recherches cliniques de Montréal (IRCM) and Université de Montréal Address : 100 Pine Ave West Montréal (QC) Canada H2W 1R7 E-mail : [email protected] Phone : 514 987 5759 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.30.180232; this version posted July 1, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 2 ABSTRACT In addition to sperm-related genes, the male-specific chromosome Y (chrY) contains a class of ubiquitously expressed and evolutionary conserved dosage-sensitive regulator genes that include the neighboring Uty, Ddx3y and (in mice) Eif2s3y genes. However, no study to date has investigated the functional impact of targeted mutations of any of these genes within adult non-reproductive somatic cells. We thus compared adult male mice carrying a gene trap within their Uty gene (UtyGT) to their wild-type (WT) isogenic controls, and performed deep sequencing of RNA and genome-wide profiling of chromatin features in extracts from either cardiac tissue, cardiomyocyte-specific nuclei or purified cardiomyocytes. The apparent impact of UtyGT on gene transcription concentrated mostly on chrY genes surrounding the locus of insertion, i.e. -
Disruption of ROBO2 Is Associated with Urinary Tract Anomalies and Confers Risk of Vesicoureteral Reflux
ARTICLE Disruption of ROBO2 Is Associated with Urinary Tract Anomalies and Confers Risk of Vesicoureteral Reflux Weining Lu, Albertien M. van Eerde, Xueping Fan, Fabiola Quintero-Rivera,* Shashikant Kulkarni, Heather Ferguson, Hyung-Goo Kim, Yanli Fan, Qiongchao Xi, Qing-gang Li, Damien Sanlaville, William Andrews, Vasi Sundaresan, Weimin Bi, Jiong Yan, Jacques C. Giltay, Cisca Wijmenga, Tom P. V. M. de Jong, Sally A. Feather, Adrian S. Woolf, Yi Rao, James R. Lupski, Michael R. Eccles, Bradley J. Quade, James F. Gusella, Cynthia C. Morton,† and Richard L. Maas Congenital anomalies of the kidney and urinary tract (CAKUT) include vesicoureteral reflux (VUR). VUR is a complex, genetically heterogeneous developmental disorder characterized by the retrograde flow of urine from the bladder into the ureter and is associated with reflux nephropathy, the cause of 15% of end-stage renal disease in children and young adults. We investigated a man with a de novo translocation, 46,X,t(Y;3)(p11;p12)dn, who exhibits multiple congenital abnormalities, including severe bilateral VUR with ureterovesical junction defects. This translocation disrupts ROBO2, which encodes a transmembrane receptor for SLIT ligand, and produces dominant-negative ROBO2 proteins that abrogate SLIT-ROBO signaling in vitro. In addition, we identified two novel ROBO2 intracellular missense variants that segregate with CAKUT and VUR in two unrelated families. Adult heterozygous and mosaic mutant mice with reduced Robo2 gene dosage also exhibit striking CAKUT-VUR phenotypes. Collectively, these results implicate the SLIT-ROBO signaling path- way in the pathogenesis of a subset of human VUR. Congenital anomalies of the kidney and urinary tract offspring of affected patients, the prevalence is as high as (CAKUT) make up a family of diseases with a diverse an- 50%.9,10 Despite its high incidence in the pediatric pop- atomical spectrum, including kidney anomalies (e.g., re- ulation, the genetic basis of VUR remains to be elucidated. -
Name Aliases Binding Partner Physiology / Oncology References
Name Aliases Binding partner Physiology / Oncology References AJAP1 Adherens junction associated protein 1, ? PHY : Expressed in uterus and pancreas. [1] http://www.uniprot.org/uniprot/Q9UKB5. [2] SHREW1 Plays a role in cell adhesion and migration. McDonald JM, Cancer Biol Ther 2006, 5:300-4 Forms a complex with CDH1 and beta-catenin at adherens junctions [1] ONC : Frequently deleted in oligodendrogliomas, functions to inhibit cell adhesion and migration [2] ALCAM Activated leukocyte cell adhesion CD6 PHY : Adhesion of activated leukocytes and [1] Ofori-Acquah SF, Transl Res 2008, 151:122- molecule, CD166, MEMD (melanoma neurons 8. [2] van Kilsdonk JW, Cancer Res 2008, metastasis clone D) 68:3671-9 ONC : Expressed by different tumor types including melanoma; mediates cancer/ melanoma invasiveness [1,2] AMICA1 Adhesion molecule interacting with CXADR PHY : Expression is restricted to the [1] http://www.uniprot.org/uniprot/Q86YT9. [2] CXADR antigen 1, JAML (junctional hematopoietic tissues with the exception of Moog-Lutz C, Blood 2003, 102:3371-8 adhesion molecule-like) liver. May function in transmigration of leukocytes through epithelial and endothelial tissues. Mediates adhesive interactions with CXADR, a protein of the junctional complex of epithelial cells [1] ONC : Enhances myeloid leukemia cell adhesion to endothelial cells [2] AMIGO1 Amphoterin-induced gene and open AMIGO PHY : May be involved in fasciculation as well [1] http://www.uniprot.org/uniprot/Q86WK6 reading frame 1, Alivin-2 as myelination of developing neural axons. May have a role in regeneration as well as neural plasticity in the adult nervous system. May mediate homophilic as well as heterophilic cell-cell interaction and contribute to signal transduction through its intracellular domain [1] ONC : - AMIGO2 Amphoterin-induced gene and open AMIGO PHY : Highest levels in breast, ovary, cervix, [1] http://www.uniprot.org/uniprot/Q86SJ2.