Leveraging Mouse Chromatin Data for Heritability Enrichment Informs Common Disease Architecture and Reveals Cortical Layer Contributions to Schizophrenia
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Autism Multiplex Family with 16P11.2P12.2 Microduplication Syndrome in Monozygotic Twins and Distal 16P11.2 Deletion in Their Brother
European Journal of Human Genetics (2012) 20, 540–546 & 2012 Macmillan Publishers Limited All rights reserved 1018-4813/12 www.nature.com/ejhg ARTICLE Autism multiplex family with 16p11.2p12.2 microduplication syndrome in monozygotic twins and distal 16p11.2 deletion in their brother Anne-Claude Tabet1,2,3,4, Marion Pilorge2,3,4, Richard Delorme5,6,Fre´de´rique Amsellem5,6, Jean-Marc Pinard7, Marion Leboyer6,8,9, Alain Verloes10, Brigitte Benzacken1,11,12 and Catalina Betancur*,2,3,4 The pericentromeric region of chromosome 16p is rich in segmental duplications that predispose to rearrangements through non-allelic homologous recombination. Several recurrent copy number variations have been described recently in chromosome 16p. 16p11.2 rearrangements (29.5–30.1 Mb) are associated with autism, intellectual disability (ID) and other neurodevelopmental disorders. Another recognizable but less common microdeletion syndrome in 16p11.2p12.2 (21.4 to 28.5–30.1 Mb) has been described in six individuals with ID, whereas apparently reciprocal duplications, studied by standard cytogenetic and fluorescence in situ hybridization techniques, have been reported in three patients with autism spectrum disorders. Here, we report a multiplex family with three boys affected with autism, including two monozygotic twins carrying a de novo 16p11.2p12.2 duplication of 8.95 Mb (21.28–30.23 Mb) characterized by single-nucleotide polymorphism array, encompassing both the 16p11.2 and 16p11.2p12.2 regions. The twins exhibited autism, severe ID, and dysmorphic features, including a triangular face, deep-set eyes, large and prominent nasal bridge, and tall, slender build. The eldest brother presented with autism, mild ID, early-onset obesity and normal craniofacial features, and carried a smaller, overlapping 16p11.2 microdeletion of 847 kb (28.40–29.25 Mb), inherited from his apparently healthy father. -
047605V1.Full.Pdf
bioRxiv preprint doi: https://doi.org/10.1101/047605; this version posted April 8, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Assembly and Activation of Dynein-Dynactin by the Cargo Adaptor Protein Hook3 Courtney M. Schroeder1,2 and Ronald D. Vale1,2 1The Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, USA 2Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA. Corresponding Author: Ronald D. Vale Dept. of Cellular and Molecular Pharmacology University of California, San Francisco Genentech Hall, MC 2200, Room N312A 600-16th Street San Francisco, CA 94158-2517 E-mail: [email protected] Phone: 415-476-6380 Fax: 415-514-4412 bioRxiv preprint doi: https://doi.org/10.1101/047605; this version posted April 8, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 2 Abstract Metazoan cytoplasmic dynein moves processively along microtubules with the aid of dynactin and an adaptor protein that joins dynein and dynactin into a stable ternary complex. Here, we have examined how Hook3, a cargo adaptor involved in Golgi and endosome transport, forms a motile dynein-dynactin complex. We show that the conserved Hook domain interacts directly with the dynein light intermediate chain 1 (LIC1). -
Identification of Genetic Variants in CFAP221 As a Cause of Primary Ciliary Dyskinesia
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author J Hum Genet Manuscript Author . Author manuscript; Manuscript Author available in PMC 2020 April 21. Published in final edited form as: J Hum Genet. 2020 January ; 65(2): 175–180. doi:10.1038/s10038-019-0686-1. Identification of Genetic Variants in CFAP221 as a Cause of Primary Ciliary Dyskinesia Ximena M. Bustamante-Marin1,#, Adam Shapiro2,#, Patrick R. Sears1, Wu-Lin Charng3, Donald F. Conrad3,4, Margaret W. Leigh5, Michael R. Knowles1, Lawrence E. Ostrowski1,*, Maimoona A. Zariwala6,* 1Department of Medicine, Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina., NC 27599, USA. 2Department of Pediatrics, Division of Pediatric Respiratory Medicine, McGill University Health Centre Research Institute, Montreal, Quebec. 3Department of Genetics and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA 4Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, 97006, USA 5Department of Pediatrics, Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, 27599. 6Department of Pathology and Laboratory Medicine, Marsico Lung Institute University of North Carolina, Chapel Hill, NC 27599, USA. Abstract Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms * Corresponding Author: Lawrence E. Ostrowski, 104 Manning Dr Room 6021, [email protected], Phone: 919-8437177, Maimoona A. Zariwala, 7219 A Marsico Hall, [email protected], Phone: 919-966-7050, Fax: 919-966-5178. #Ximena M. Bustamante-Marin and Adam Shapiro are co-first authors. -
Microtubular Dysfunction and Male Infertility
Review Article pISSN: 2287-4208 / eISSN: 2287-4690 World J Mens Health Published online Oct 22, 2018 https://doi.org/10.5534/wjmh.180066 Microtubular Dysfunction and Male Infertility Sezgin Gunes1,7 , Pallav Sengupta2,7 , Ralf Henkel3,7 , Aabed Alguraigari4,7 , Mariana Marques Sinigaglia5,7 , Malik Kayal6,7 , Ahmad Joumah6,7 , Ashok Agarwal7 1Department of Medical Biology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey, 2Department of Physiology, Faculty of Medicine, MAHSA University, Selangor, Malaysia, 3Department of Medical Bioscience, University of the Western Cape, Bellville, South Africa, 4Batterjee Medical College, Jeddah, Saudi Arabia, 5University of Sao Paulo, Sao Paulo, Brazil, 6Alfaisal University Medical School, Riyadh, Saudi Arabia, 7American Center for Reproductive Medicine, Cleveland Clinic, Cleveland, OH, USA Microtubules are the prime component of the cytoskeleton along with microfilaments. Being vital for organelle transport and cellular divisions during spermatogenesis and sperm motility process, microtubules ascertain functional capacity of sperm. Also, microtubule based structures such as axoneme and manchette are crucial for sperm head and tail formation. This review (a) presents a concise, yet detailed structural overview of the microtubules, (b) analyses the role of microtubule structures in various male reproductive functions, and (c) presents the association of microtubular dysfunctions with male infertility. Consid- ering the immense importance of microtubule structures in the formation and maintenance -
Cargo Specific Regulation of Cytoplasmic Dynein by Effector Proteins
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2018 Cargo Specific Regulation Of Cytoplasmic Dynein By Effector Proteins Mara Olenick University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Biochemistry Commons, Biophysics Commons, and the Cell Biology Commons Recommended Citation Olenick, Mara, "Cargo Specific Regulation Of Cytoplasmic Dynein By Effector Proteins" (2018). Publicly Accessible Penn Dissertations. 3167. https://repository.upenn.edu/edissertations/3167 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/3167 For more information, please contact [email protected]. Cargo Specific Regulation Of Cytoplasmic Dynein By Effector Proteins Abstract Axonal transport is vital for the development and survival of neurons. The transport of cargo and organelles from the axon to the cell body is driven almost completely by the molecular motor, cytoplasmic dynein. Yet, it remains unclear how dynein is spatially and temporally regulated given the variety of cargo that must be properly localized to maintain cellular function. Previous work has suggested that adaptor proteins provide a mechanism for cargo-specific egulationr of motors. During my thesis work, I have investigated the role of mammalian Hook proteins, Hook1 and Hook3, as potential motor adaptors. Using optogenetic and single molecule assays, I found that Hook proteins interact with both dynein and dynactin, to effectively activate dynein motility, inducing longer run lengths and higher velocities than the previously characterized dynein activator, BICD2. In addition, I found that complex formation requires the N-terminal domain of Hook proteins, which resembles the calponin-homology domain of EB proteins yet cannot bind directly to microtubules. -
Aristaless-Like Homeobox Protein 1 (ALX1) Variant Associated with Craniofacial Structure and Frontonasal Dysplasia in Burmese Cats
Developmental Biology 409 (2016) 451–458 Contents lists available at ScienceDirect Developmental Biology journal homepage: www.elsevier.com/locate/developmentalbiology Aristaless-Like Homeobox protein 1 (ALX1) variant associated with craniofacial structure and frontonasal dysplasia in Burmese cats Leslie A. Lyons a,f,n, Carolyn A. Erdman b,f, Robert A. Grahn c,f, Michael J. Hamilton d,f, Michael J. Carter e,f, Christopher R. Helps g, Hasan Alhaddad h, Barbara Gandolfi a,f a Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, MO 65211, USA b Department of Psychiatry, University of California-San Francisco, San Francisco, CA 94143, USA c Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA 96516, USA d Department of Cell Biology and Neuroscience, Institute for Integrative Genome Biology, Center for Disease Vector Research, University of California-Riv- erside, Riverside, CA 92521, USA e MDxHealth Inc, 15279 Alton Parkway, Suite #100, Irvine, CA 92618, USA f Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95776, USA g Langford Veterinary Services, University of Bristol, Bristol BS40 5DU, UK h College of Science, Kuwait University, Safat, Kuwait article info abstract Article history: Frontonasal dysplasia (FND) can have severe presentations that are medically and socially debilitating. Received 2 October 2015 Several genes are implicated in FND conditions, including Aristaless-Like Homeobox 1 (ALX1), which is Received in revised form associated with FND3. Breeds of cats are selected and bred for extremes in craniofacial morphologies. In 3 November 2015 particular, a lineage of Burmese cats with severe brachycephyla is extremely popular and is termed Accepted 20 November 2015 Contemporary Burmese. -
Dynein Activators and Adaptors at a Glance Mara A
© 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs227132. doi:10.1242/jcs.227132 CELL SCIENCE AT A GLANCE Dynein activators and adaptors at a glance Mara A. Olenick and Erika L. F. Holzbaur* ABSTRACT ribonucleoprotein particles for BICD2, and signaling endosomes for Cytoplasmic dynein-1 (hereafter dynein) is an essential cellular motor Hook1. In this Cell Science at a Glance article and accompanying that drives the movement of diverse cargos along the microtubule poster, we highlight the conserved structural features found in dynein cytoskeleton, including organelles, vesicles and RNAs. A long- activators, the effects of these activators on biophysical parameters, standing question is how a single form of dynein can be adapted to a such as motor velocity and stall force, and the specific intracellular wide range of cellular functions in both interphase and mitosis. functions they mediate. – Recent progress has provided new insights dynein interacts with a KEY WORDS: BICD2, Cytoplasmic dynein, Dynactin, Hook1, group of activating adaptors that provide cargo-specific and/or Microtubule motors, Trafficking function-specific regulation of the motor complex. Activating adaptors such as BICD2 and Hook1 enhance the stability of the Introduction complex that dynein forms with its required activator dynactin, leading Microtubule-based transport is vital to cellular development and to highly processive motility toward the microtubule minus end. survival. Microtubules provide a polarized highway to facilitate Furthermore, activating adaptors mediate specific interactions of the active transport by the molecular motors dynein and kinesin. While motor complex with cargos such as Rab6-positive vesicles or many types of kinesins drive transport toward microtubule plus- ends, there is only one major form of dynein, cytoplasmic dynein-1, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, which drives the trafficking of a wide array of minus-end-directed USA. -
The Transformation of the Centrosome Into the Basal Body: Similarities and Dissimilarities Between Somatic and Male Germ Cells and Their Relevance for Male Fertility
cells Review The Transformation of the Centrosome into the Basal Body: Similarities and Dissimilarities between Somatic and Male Germ Cells and Their Relevance for Male Fertility Constanza Tapia Contreras and Sigrid Hoyer-Fender * Göttingen Center of Molecular Biosciences, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology-Developmental Biology, Faculty of Biology and Psychology, Georg-August University of Göttingen, 37077 Göttingen, Germany; [email protected] * Correspondence: [email protected] Abstract: The sperm flagellum is essential for the transport of the genetic material toward the oocyte and thus the transmission of the genetic information to the next generation. During the haploid phase of spermatogenesis, i.e., spermiogenesis, a morphological and molecular restructuring of the male germ cell, the round spermatid, takes place that includes the silencing and compaction of the nucleus, the formation of the acrosomal vesicle from the Golgi apparatus, the formation of the sperm tail, and, finally, the shedding of excessive cytoplasm. Sperm tail formation starts in the round spermatid stage when the pair of centrioles moves toward the posterior pole of the nucleus. The sperm tail, eventually, becomes located opposed to the acrosomal vesicle, which develops at the anterior pole of the nucleus. The centriole pair tightly attaches to the nucleus, forming a nuclear membrane indentation. An Citation: Tapia Contreras, C.; articular structure is formed around the centriole pair known as the connecting piece, situated in the Hoyer-Fender, S. The Transformation neck region and linking the sperm head to the tail, also named the head-to-tail coupling apparatus or, of the Centrosome into the Basal in short, HTCA. -
Bioinformatic Analysis Reveals the Importance of Epithelial-Mesenchymal Transition in the Development of Endometriosis
www.nature.com/scientificreports OPEN Bioinformatic analysis reveals the importance of epithelial- mesenchymal transition in the development of endometriosis Meihong Chen1,6, Yilu Zhou2,3,6, Hong Xu4, Charlotte Hill2, Rob M. Ewing2,3, Deming He1, Xiaoling Zhang1 ✉ & Yihua Wang2,3,5 ✉ Background: Endometriosis is a frequently occurring disease in women, which seriously afects their quality of life. However, its etiology and pathogenesis are still unclear. Methods: To identify key genes/ pathways involved in the pathogenesis of endometriosis, we recruited 3 raw microarray datasets (GSE11691, GSE7305, and GSE12768) from Gene Expression Omnibus database (GEO), which contain endometriosis tissues and normal endometrial tissues. We then performed in-depth bioinformatic analysis to determine diferentially expressed genes (DEGs), followed by gene ontology (GO), Hallmark pathway enrichment and protein-protein interaction (PPI) network analysis. The fndings were further validated by immunohistochemistry (IHC) staining in endometrial tissues from endometriosis or control patients. Results: We identifed 186 DEGs, of which 118 were up-regulated and 68 were down-regulated. The most enriched DEGs in GO functional analysis were mainly associated with cell adhesion, infammatory response, and extracellular exosome. We found that epithelial-mesenchymal transition (EMT) ranked frst in the Hallmark pathway enrichment. EMT may potentially be induced by infammatory cytokines such as CXCL12. IHC confrmed the down-regulation of E-cadherin (CDH1) and up-regulation of CXCL12 in endometriosis tissues. Conclusions: Utilizing bioinformatics and patient samples, we provide evidence of EMT in endometriosis. Elucidating the role of EMT will improve the understanding of the molecular mechanisms involved in the development of endometriosis. Endometriosis is a frequently occurring gynaecological disease characterised by chronic pelvic pain, dysmenor- rhea and infertility1. -
A KMT2A-AFF1 Gene Regulatory Network Highlights the Role of Core Transcription Factors and Reveals the Regulatory Logic of Key Downstream Target Genes
Downloaded from genome.cshlp.org on October 7, 2021 - Published by Cold Spring Harbor Laboratory Press Research A KMT2A-AFF1 gene regulatory network highlights the role of core transcription factors and reveals the regulatory logic of key downstream target genes Joe R. Harman,1,7 Ross Thorne,1,7 Max Jamilly,2 Marta Tapia,1,8 Nicholas T. Crump,1 Siobhan Rice,1,3 Ryan Beveridge,1,4 Edward Morrissey,5 Marella F.T.R. de Bruijn,1 Irene Roberts,3,6 Anindita Roy,3,6 Tudor A. Fulga,2,9 and Thomas A. Milne1,6 1MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom; 2MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom; 3MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 9DS, United Kingdom; 4Virus Screening Facility, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, United Kingdom; 5Center for Computational Biology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom; 6NIHR Oxford Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, OX3 9DS, United Kingdom Regulatory interactions mediated by transcription factors (TFs) make up complex networks that control cellular behavior. Fully understanding these gene regulatory networks (GRNs) offers greater insight into the consequences of disease-causing perturbations than can be achieved by studying single TF binding events in isolation. Chromosomal translocations of the lysine methyltransferase 2A (KMT2A) gene produce KMT2A fusion proteins such as KMT2A-AFF1 (previously MLL-AF4), caus- ing poor prognosis acute lymphoblastic leukemias (ALLs) that sometimes relapse as acute myeloid leukemias (AMLs). -
A Rare Duplication on Chromosome 16P11.2 Is Identified in Patients with Psychosis in Alzheimer’S Disease
A Rare Duplication on Chromosome 16p11.2 Is Identified in Patients with Psychosis in Alzheimer’s Disease Xiaojing Zheng1,7*, F. Yesim Demirci2, M. Michael Barmada2, Gale A. Richardson3,6, Oscar L. Lopez4,5, Robert A. Sweet3,4,5, M. Ilyas Kamboh2,3,5, Eleanor Feingold1,2 1 Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, 2 Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, 3 Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, 4 Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, 5 VISN 4 Mental Illness Research, Education and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, United States of America, 6 Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, 7 Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America Abstract Epidemiological and genetic studies suggest that schizophrenia and autism may share genetic links. Besides common single nucleotide polymorphisms, recent data suggest that some rare copy number variants (CNVs) are risk factors for both disorders. Because we have previously found that schizophrenia and psychosis in Alzheimer’s disease (AD+P) share some genetic risk, we investigated whether CNVs reported in schizophrenia and autism are also linked to AD+P. We searched for CNVs associated with AD+P in 7 recurrent CNV regions that have been previously identified across autism and schizophrenia, using the Illumina HumanOmni1-Quad BeadChip. -
Transcriptomic and Epigenomic Characterization of the Developing Bat Wing
ARTICLES OPEN Transcriptomic and epigenomic characterization of the developing bat wing Walter L Eckalbar1,2,9, Stephen A Schlebusch3,9, Mandy K Mason3, Zoe Gill3, Ash V Parker3, Betty M Booker1,2, Sierra Nishizaki1,2, Christiane Muswamba-Nday3, Elizabeth Terhune4,5, Kimberly A Nevonen4, Nadja Makki1,2, Tara Friedrich2,6, Julia E VanderMeer1,2, Katherine S Pollard2,6,7, Lucia Carbone4,8, Jeff D Wall2,7, Nicola Illing3 & Nadav Ahituv1,2 Bats are the only mammals capable of powered flight, but little is known about the genetic determinants that shape their wings. Here we generated a genome for Miniopterus natalensis and performed RNA-seq and ChIP-seq (H3K27ac and H3K27me3) analyses on its developing forelimb and hindlimb autopods at sequential embryonic stages to decipher the molecular events that underlie bat wing development. Over 7,000 genes and several long noncoding RNAs, including Tbx5-as1 and Hottip, were differentially expressed between forelimb and hindlimb, and across different stages. ChIP-seq analysis identified thousands of regions that are differentially modified in forelimb and hindlimb. Comparative genomics found 2,796 bat-accelerated regions within H3K27ac peaks, several of which cluster near limb-associated genes. Pathway analyses highlighted multiple ribosomal proteins and known limb patterning signaling pathways as differentially regulated and implicated increased forelimb mesenchymal condensation in differential growth. In combination, our work outlines multiple genetic components that likely contribute to bat wing formation, providing insights into this morphological innovation. The order Chiroptera, commonly known as bats, is the only group of To characterize the genetic differences that underlie divergence in mammals to have evolved the capability of flight.