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The Interactome of KRAB Zinc Finger Proteins Reveals the Evolutionary History of Their Functional Diversification
Resource The interactome of KRAB zinc finger proteins reveals the evolutionary history of their functional diversification Pierre-Yves Helleboid1,†, Moritz Heusel2,†, Julien Duc1, Cécile Piot1, Christian W Thorball1, Andrea Coluccio1, Julien Pontis1, Michaël Imbeault1, Priscilla Turelli1, Ruedi Aebersold2,3,* & Didier Trono1,** Abstract years ago (MYA) (Imbeault et al, 2017). Their products harbor an N-terminal KRAB (Kru¨ppel-associated box) domain related to that of Krüppel-associated box (KRAB)-containing zinc finger proteins Meisetz (a.k.a. PRDM9), a protein that originated prior to the diver- (KZFPs) are encoded in the hundreds by the genomes of higher gence of chordates and echinoderms, and a C-terminal array of zinc vertebrates, and many act with the heterochromatin-inducing fingers (ZNF) with sequence-specific DNA-binding potential (Urru- KAP1 as repressors of transposable elements (TEs) during early tia, 2003; Birtle & Ponting, 2006; Imbeault et al, 2017). KZFP genes embryogenesis. Yet, their widespread expression in adult tissues multiplied by gene and segment duplication to count today more and enrichment at other genetic loci indicate additional roles. than 350 and 700 representatives in the human and mouse Here, we characterized the protein interactome of 101 of the ~350 genomes, respectively (Urrutia, 2003; Kauzlaric et al, 2017). A human KZFPs. Consistent with their targeting of TEs, most KZFPs majority of human KZFPs including all primate-restricted family conserved up to placental mammals essentially recruit KAP1 and members target sequences derived from TEs, that is, DNA trans- associated effectors. In contrast, a subset of more ancient KZFPs posons, ERVs (endogenous retroviruses), LINEs, SINEs (long and rather interacts with factors related to functions such as genome short interspersed nuclear elements, respectively), or SVAs (SINE- architecture or RNA processing. -
Association of a Matrix Metallopeptidase 1 Gene Polymorphism with Long-Term Outcome of Thoracic Aortic Aneurysm
INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 29: 125-132, 2012 Association of a matrix metallopeptidase 1 gene polymorphism with long-term outcome of thoracic aortic aneurysm KIMIHIKO KATO1,2, YOSHIYUKI TOKUDA3, NAOHIKO INAGAKI4, TETSURO YOSHIDA5, TETSUO FUJIMAKI5, MITSUTOSHI OGURI6, TAKESHI HIBINO4, KIYOSHI YOKOI4, TOYOAKI MUROHARA7 and YOSHIJI YAMADA2 1Meitoh Hospital, Nagoya; 2Department of Human Functional Genomics, Life Science Research Center, Mie University, Tsu, Mie 514-8507; 3Department of Cardiovascular Surgery, Chubu-Rosai Hospital, Nagoya; 4Department of Cardiovascular Medicine, Gifu Prefectural Tajimi Hospital, Tajimi; 5Department of Cardiovascular Medicine, Inabe General Hospital, Inabe; 6Department of Cardiology, Japanese Red Cross Nagoya First Hospital, Nagoya; 7Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan Received July 19, 2011; Accepted September 12, 2011 DOI: 10.3892/ijmm.2011.804 Abstract. Although genetic variants are thought to contribute Introduction to the development of thoracic aortic aneurysm including dissection (TAA), it remains unclear whether gene polymor- Thoracic aortic aneurysm including dissection (TAA) is a phisms are associated with the long-term outcome of TAA. The serious condition that results from aortic atherosclerosis and is purpose of the present study was to identify genetic variants a leading cause of mortality (1). Recent studies on the genetic associated with the long-term outcome of medically treated basis of familial TAA have focused on its relation to systemic patients with TAA. A total of 103 medically-treated patients connective tissue disorders such as the Marfan syndrome (2) with TAA (13 aneurysms and 90 dissections) were retrospec- and the Ehlers-Danlos syndrome (3). However, up to 19% tively studied for their outcomes (mean follow-up period, 24 of individuals with non-syndromic TAA referred for surgery months). -
Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus Dromedarius
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications from the Department of Electrical & Computer Engineering, Department Electrical and Computer Engineering of 2009 Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius Abdulaziz M. Al-Swailem King Abdulaziz City for Science and Technology Maher M. Shehata King Abdulaziz City for Science and Technology Faisel M. Abu-Duhier King Abdulaziz City for Science and Technology Essam J. Al-Yamani King Abdulaziz City for Science and Technology Khalid A. Al-Busadah King Faisal University See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/electricalengineeringfacpub Part of the Computer Engineering Commons, and the Electrical and Computer Engineering Commons Al-Swailem, Abdulaziz M.; Shehata, Maher M.; Abu-Duhier, Faisel M.; Al-Yamani, Essam J.; Al-Busadah, Khalid A.; Al-Arawi, Mohammed S.; Al-Khider, Ali Y.; Al-Muhaimeed, Abdullah N.; Al-Qahtani, Fahad H.; Manee, Manee M.; Al-Shomrani, Badr M.; Al-Qhtani, Saad M.; Al-Harthi, Amer S.; Akdemir, Kadir C.; Inan, Mehmet S.; and Otu, Hasan H., "Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius" (2009). Faculty Publications from the Department of Electrical and Computer Engineering. 426. https://digitalcommons.unl.edu/electricalengineeringfacpub/426 This Article is brought to you for free and open access by the Electrical & Computer Engineering, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications from the Department of Electrical and Computer Engineering by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Abdulaziz M. Al-Swailem, Maher M. -
Assignment of the Locus for Ichthyosis Prematurity Syndrome to Chromosome 9Q33.3–34.13
208 LETTER TO JMG J Med Genet: first published as 10.1136/jmg.2003.012567 on 1 March 2004. Downloaded from Assignment of the locus for ichthyosis prematurity syndrome to chromosome 9q33.3–34.13 J Klar, T Gedde-Dahl Jr, M Larsson, M Pigg, B Carlsson, D Tentler, A Vahlquist, N Dahl ............................................................................................................................... J Med Genet 2004;41:208–212. doi: 10.1136/jmg.2003.012567 utosomal recessive congenital ichthyosis (ARCI) is a clinically and genetically heterogeneous group of Key points inherited disorders of keratinisation, with an estimated A 1 incidence of one per 200 000 newborns. In Scandinavia, the N Autosomal recessive congenital ichthyosis (ARCI) is a prevalence is closer to one in 50 000.23 By electron micro- clinically and genetically heterogeneous group of scopy, ARCI can be classified into four subgroups—ichthyosis inherited disorders of keratinisation. To date, five congenita I–IV—and one so far undefined group. Six loci genes have been identified that underlie ARCI, and have been associated with ARCI: on chromosomes 2q34 (LI2 two additional gene loci for ARCI have been assigned. (MIM 601277)), 3p21 (NCIE2 (MIM 604780)), 14q11.2 (LI1 N Ichthyosis congenita IV is a rare form of ARCI that (MIM 242300) and NCIE1 (MIM 242100)), 17p13.1 (LI5 clinically is known as ichthyosis prematurity syndrome (MIM 606545)), 19p12–q12 (LI3 (MIM 190195)), and 4–9 (IPS). Key features are complications in the mid- 19p13.1–p13.2 (NNCI (MIM 604781)). trimester of pregnancy, with premature birth of a child Genes that correspond to four of these have been with thick caseous desquamating epidermis, respira- identified: the transglutaminase 1 gene (TGM1 (MIM tory complications, and eosinophilia that recovers into 190195)) on chromosome 14q11, the comparative gene a lifelong non-scaly ichthyosis with atopic manifesta- identification 58 (CGI-58 (MIM 604780)) on chromosome 3p21, two genes from the lipoxygenase (LOX) family— tions. -
The Diversity of Zinc-Finger Genes on Human Chromosome 19 Provides
Cell Death and Differentiation (2014) 21, 381–387 OPEN & 2014 Macmillan Publishers Limited All rights reserved 1350-9047/14 www.nature.com/cdd The diversity of zinc-finger genes on human chromosome 19 provides an evolutionary mechanism for defense against inherited endogenous retroviruses S Lukic*1, J-C Nicolas1 and AJ Levine1 Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections of the germ line that can remain capable of replication within the host genome. In the soma, DNA methylation and repressive chromatin keep the majority of this parasitic DNA transcriptionally silent. However, it is unclear how the host organism adapts to recognize and silence novel invading retroviruses that enter the germ line. Krueppel-Associated Box (KRAB)-associated protein 1 (KAP1) is a transcriptional regulatory factor that drives the epigenetic repression of many different loci in mammalian genomes. Here, we use published experimental data to provide evidence that human KAP1 is recruited to endogenous retroviral DNA by KRAB-containing zinc-finger transcription factors (TFs). Many of these zinc-finger genes exist in clusters associated with human chromosome 19. We demonstrate that these clusters are located at hotspots for copy number variation (CNV), generating a large and continuing diversity of zinc-finger TFs with new generations. These zinc-finger genes possess a wide variety of DNA binding affinities, but their role as transcriptional repressors is conserved. We also perform a computational study of the different ERVs that invaded the human genome during primate evolution. We find candidate zinc-finger repressors that arise in the genome for each ERV family that enters the genomes of primates. -
Identification of Functional Genetic Variants in Inflammatory Bowel Disease by Genome and Transcriptome Sequencing
Identification of Functional Genetic Variants in Inflammatory Bowel Disease by Genome and Transcriptome Sequencing Dissertation zur Erlangung des Doktorgrades der Mathematisch-Naturwissenschaftlichen Fakultät der Christian-Albrechts-Universität zu Kiel vorgelegt von Matthias Barann August, 2012 Kiel, Deutschland 1 2 Referent/in: Prof. Dr. Philip Rosenstiel Korreferent/in: Prof. Dr. Dr. h.c. Thomas Bosch Tag der mündlichen Prüfung: 31.10.2012 Zum Druck genehmigt: 31.10.2012 gez. Prof. Dr. Wolfgang J. Duschl, Dekan 3 Parts of this dissertation are contained in the following two manuscripts. Rosenstiel R, Barann M, Klostermeier UC, Sheth V, Ellinghaus D, Rausch T, Korbel J, Nothnagel M, Krawczak M, Gilissen C, Veltman J, Forster M, Stade B, McLaughlin S, Lee CC, Fritscher-Ravens A, Franke A, Schreiber S. Whole Genome Sequence of a Crohn disease trio Barann M, Klostermeier UC, Esser D, Ammerpohl O, Siebert R, Sudbrak R, Lehrach H, Schreiber S, Rosenstiel R. Janus – Investigating the two faces of transcription 4 Contents 1. Introduction ............................................................................................................................. 7 1.1. Pathogenesis of inflammatory bowel diseases ...................................................................................... 8 1.2. Physical barrier function of the gut ......................................................................................................... 11 1.3. Pathogen recognition .................................................................................................................................. -
Sequence Tags for Camelus Dromedarius
Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius Abdulaziz M. Al-Swailem1, Maher M. Shehata1, Faisel M. Abu-Duhier1, Essam J. Al-Yamani1, Khalid A. Al-Busadah2, Mohammed S. Al-Arawi1, Ali Y. Al-Khider1, Abdullah N. Al-Muhaimeed1, Fahad H. Al-Qahtani1, Manee M. Manee1, Badr M. Al-Shomrani1, Saad M. Al-Qhtani1, Amer S. Al-Harthi1, Kadir C. Akdemir3, Mehmet S. Inan1{, Hasan H. Otu1,3* 1 Biotechnology Research Center, Natural Resources and Environment Research Institute, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia, 2 Faculty of Veterinary Medicine and Animal Resources, King Faisal University, Al-Hassa, Saudi Arabia, 3 Department of Medicine, BIDMC Genomics Center, Harvard Medical School, Boston, Massachusetts, United States of America Abstract Despite its economical, cultural, and biological importance, there has not been a large scale sequencing project to date for Camelus dromedarius. With the goal of sequencing complete DNA of the organism, we first established and sequenced camel EST libraries, generating 70,272 reads. Following trimming, chimera check, repeat masking, cluster and assembly, we obtained 23,602 putative gene sequences, out of which over 4,500 potentially novel or fast evolving gene sequences do not carry any homology to other available genomes. Functional annotation of sequences with similarities in nucleotide and protein databases has been obtained using Gene Ontology classification. Comparison to available full length cDNA sequences and Open Reading Frame (ORF) analysis of camel sequences that exhibit homology to known genes show more than 80% of the contigs with an ORF.300 bp and ,40% hits extending to the start codons of full length cDNAs suggesting successful characterization of camel genes. -
Genome-Wide Association Study and Pathway Analysis for Female Fertility Traits in Iranian Holstein Cattle
Ann. Anim. Sci., Vol. 20, No. 3 (2020) 825–851 DOI: 10.2478/aoas-2020-0031 GENOME-WIDE ASSOCIATION STUDY AND PATHWAY ANALYSIS FOR FEMALE FERTILITY TRAITS IN IRANIAN HOLSTEIN CATTLE Ali Mohammadi1, Sadegh Alijani2♦, Seyed Abbas Rafat2, Rostam Abdollahi-Arpanahi3 1Department of Genetics and Animal Breeding, University of Tabriz, Tabriz, Iran 2Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran 3Department of Animal Science, University College of Abureyhan, University of Tehran, Tehran, Iran ♦Corresponding author: [email protected] Abstract Female fertility is an important trait that contributes to cow’s profitability and it can be improved by genomic information. The objective of this study was to detect genomic regions and variants affecting fertility traits in Iranian Holstein cattle. A data set comprised of female fertility records and 3,452,730 pedigree information from Iranian Holstein cattle were used to predict the breed- ing values, which were then employed to estimate the de-regressed proofs (DRP) of genotyped animals. A total of 878 animals with DRP records and 54k SNP markers were utilized in the ge- nome-wide association study (GWAS). The GWAS was performed using a linear regression model with SNP genotype as a linear covariate. The results showed that an SNP on BTA19, ARS-BFGL- NGS-33473, was the most significant SNP associated with days from calving to first service. In total, 69 significant SNPs were located within 27 candidate genes. Novel potential candidate genes include OSTN, DPP6, EphA5, CADPS2, Rfc1, ADGRB3, Myo3a, C10H14orf93, KIAA1217, RBPJL, SLC18A2, GARNL3, NCALD, ASPH, ASIC2, OR3A1, CHRNB4, CACNA2D2, DLGAP1, GRIN2A and ME3. -
Multi-Omics Integration Analysis Identifies Novel Genes for Alcoholism with Potential Link to Neurodegenerative Diseases
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.15.341750; this version posted October 16, 2020. 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 4.0 International license. Multi-omics integration analysis identifies novel genes for alcoholism with potential link to neurodegenerative diseases Manav Kapoor1*, Michael Chao1, Emma C. Johnson2, Gloriia Novikova1, Dongbing Lai3, Jacquelyn Meyers5, Jessica Schulman1, John I Nurnberger Jr4, Bernice Porjesz5, Yunlong Liu3, COGA collaborators, Tatiana Foroud3,4, Howard J. Edenberg3,6, Edoardo Marcora1, Arpana Agrawal2 and Alison Goate1 1Dept. of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 2Dept. of Psychiatry, Washington University School of Medicine, St. Louis, MO 3Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 4Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 5Department of Psychiatry, State University of New York, Downstate Medical Center, Brooklyn, NY, USA 6Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN *Corresponding Author Manav Kapoor, PhD Assistant Professor Dept. of Neuroscience Dept. of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue, Room 10-75B Box #1065 New York, NY 10029 Tel: (212) 659-5967 email: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.10.15.341750; this version posted October 16, 2020. 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. -
Reverse Engineering of Ewing Sarcoma Regulatory Network Uncovers PAX7 and RUNX3 As Master Regulators Associated with Good Prognosis
cancers Article Reverse Engineering of Ewing Sarcoma Regulatory Network Uncovers PAX7 and RUNX3 as Master Regulators Associated with Good Prognosis Marcel da Câmara Ribeiro-Dantas 1,2 , Danilo Oliveira Imparato 1 , Matheus Gibeke Siqueira Dalmolin 3 , Caroline Brunetto de Farias 3,4 , André Tesainer Brunetto 3 , Mariane da Cunha Jaeger 3,4 , Rafael Roesler 4,5 , Marialva Sinigaglia 3 and Rodrigo Juliani Siqueira Dalmolin 1,6,* 1 Bioinformatics Multidisciplinary Environment—IMD, Federal University of Rio Grande do Norte, Natal 59078-400, Brazil; [email protected] (M.d.C.R.-D.); [email protected] (D.O.I.) 2 Laboratoire Physico Chimie Curie, UMR168, Institut Curie, Université PSL, Sorbonne Université, 75005 Paris, France 3 Children’s Cancer Institute, Porto Alegre 90620-110, Brazil; [email protected] (M.G.S.D.); [email protected] (C.B.d.F.); [email protected] (A.T.B.); [email protected] (M.d.C.J.); [email protected] (M.S.) 4 Cancer and Neurobiology Laboratory, Experimental Research Center, Clinical Hospital (CPE HCPA), Porto Alegre 90035-903, Brazil; [email protected] 5 Department of Pharmacology, Institute for Basic Health Sciences, Federal University of Rio Grande do Sul, Citation: Ribeiro-Dantas, M.d.C.; Porto Alegre 90050-170, Brazil 6 Imparato, D.O.; Dalmolin, M.G.S.; Department of Biochemistry—CB, Federal University of Rio Grande do Norte, Natal 59078-970, Brazil * Correspondence: [email protected] de Farias, C.B.; Brunetto, A.T.; da Cunha Jaeger, M.; Roesler, R.; Sinigaglia, M.; Siqueira Dalmolin, R.J. Simple Summary: Ewing Sarcoma is a rare cancer that, when localized, has an overall five-year Reverse Engineering of Ewing survival rate of 70%. -
Table of Contents
Table of Contents Comparison Page Numbers RF vs Static 2-231 HSS vs Static 232-507 LSS vs Static 508-715 RF vs HSS 716-746 RF vs LSS 747-751 HSS vs LSS 752-764 Fold change Regulation ([RF] vs ([RF] vs Probe Name [Static]) [Static]) Common name Gene Symbol Description Genbank Accession Homo sapiens apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B (APOBEC3B), A_24_P66027 2.741304 down NM_004900 APOBEC3B mRNA [NM_004900] NM_004900 Homo sapiens vasohibin 1 (VASH1), mRNA A_23_P77000 3.932838 down NM_014909 VASH1 [NM_014909] NM_014909 Homo sapiens transmembrane protein 97 A_24_P151920 2.292691 down NM_014573 TMEM97 (TMEM97), mRNA [NM_014573] NM_014573 CN479126 UI-CF-FN0-afv-i-22-0-UI.s1 UI-CF-FN0 Homo sapiens cDNA clone UI-CF-FN0-afv-i-22-0-UI A_32_P149011 3.661964 up CN479126 CN479126 3', mRNA sequence [CN479126] CN479126 Homo sapiens notchless homolog 1 (Drosophila) (NLE1), transcript variant 2, mRNA A_23_P141315 1.785076 down NM_001014445 NLE1 [NM_001014445] NM_001014445 Homo sapiens ribonucleotide reductase M1 A_23_P87351 1.519893 down NM_001033 RRM1 polypeptide (RRM1), mRNA [NM_001033] NM_001033 AT_ssH_PC_3 2.387579 down AT_ssH_PC_3 AT_ssH_PC_3 Homo sapiens huntingtin interacting protein 2 A_23_P155677 1.640733 up NM_005339 HIP2 (HIP2), mRNA [NM_005339] NM_005339 Homo sapiens chromosome 1 open reading frame A_24_P131173 3.527582 down NM_024709 C1orf115 115 (C1orf115), mRNA [NM_024709] NM_024709 Homo sapiens CCR4-NOT transcription complex, A_23_P110846 1.616577 up NM_004779 CNOT8 subunit 8 (CNOT8), mRNA [NM_004779] NM_004779 Homo sapiens protein kinase, AMP-activated, alpha A_23_P60811 3.629454 down NM_006252 PRKAA2 2 catalytic subunit (PRKAA2), mRNA [NM_006252] NM_006252 Homo sapiens pannexin 1 (PANX1), mRNA A_23_P47155 2.378446 up NM_015368 PANX1 [NM_015368] NM_015368 Homo sapiens chemokine (C-X-C motif) ligand 2 A_23_P315364 11.12551 down NM_002089 CXCL2 (CXCL2), mRNA [NM_002089] NM_002089 Centromere protein P (CENP-P). -
De Novo Mutations in the Gene Encoding STXBP1 (MUNC18-1) Cause Early Infantile Epileptic Encephalopathy
LETTERS De novo mutations in the gene encoding STXBP1 (MUNC18-1) cause early infantile epileptic encephalopathy Hirotomo Saitsu1, Mitsuhiro Kato2, Takeshi Mizuguchi1, Keisuke Hamada3, Hitoshi Osaka4, Jun Tohyama5, Katsuhisa Uruno6, Satoko Kumada7, Kiyomi Nishiyama1, Akira Nishimura1, Ippei Okada1, Yukiko Yoshimura1, Syu-ichi Hirai8, Tatsuro Kumada9, Kiyoshi Hayasaka2, Atsuo Fukuda9, Kazuhiro Ogata3 & Naomichi Matsumoto1 http://www.nature.com/naturegenetics Early infantile epileptic encephalopathy with suppression-burst syndromes has been suggested. Consistent with this idea, specific (EIEE), also known as Ohtahara syndrome, is one of the most mutations of the ARX (aristaless-related homeobox) gene at Xp22.13 severe and earliest forms of epilepsy1. Using array-based have been recently found in male subjects with EIEE and West comparative genomic hybridization, we found a de novo syndrome7,8. In most cryptogenic EIEE cases, however, the genetic 2.0-Mb microdeletion at 9q33.3–q34.11 in a girl with EIEE. cause remains to be elucidated. Mutation analysis of candidate genes mapped to the deletion Microarray technologies detect genomic copy number alterations, revealed that four unrelated individuals with EIEE had which may be related to disease phenotypes, at a submicroscopic heterozygous missense mutations in the gene encoding syntaxin level9,10. In a BAC array-based comparative genomic hybridization bindingprotein1(STXBP1). STXBP1 (also known as MUNC18- (aCGH) analysis (containing 4,219 clones with 0.7-Mb resolution for 1) is an evolutionally conserved neuronal Sec1/Munc-18 (SM) genome-wide analysis) of individuals with mental retardation, we Nature Publishing Group Group Nature Publishing found a microdeletion at 9q33.3–q34.11 in a girl with EIEE (subject 1) 8 protein that is essential in synaptic vesicle release in several species2–4.