Repetitive Elements in Humans
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An Alu Element-Based Model of Human Genome Instability George Wyndham Cook, Jr
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2013 An Alu element-based model of human genome instability George Wyndham Cook, Jr. Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Cook, Jr., George Wyndham, "An Alu element-based model of human genome instability" (2013). LSU Doctoral Dissertations. 2090. https://digitalcommons.lsu.edu/gradschool_dissertations/2090 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. AN ALU ELEMENT-BASED MODEL OF HUMAN GENOME INSTABILITY A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by George Wyndham Cook, Jr. B.S., University of Arkansas, 1975 May 2013 TABLE OF CONTENTS LIST OF TABLES ...................................................................................................... iii LIST OF FIGURES .................................................................................................... iv LIST OF ABBREVIATIONS ...................................................................................... -
In Silico Prediction of High-Resolution Hi-C Interaction Matrices
ARTICLE https://doi.org/10.1038/s41467-019-13423-8 OPEN In silico prediction of high-resolution Hi-C interaction matrices Shilu Zhang1, Deborah Chasman 1, Sara Knaack1 & Sushmita Roy1,2* The three-dimensional (3D) organization of the genome plays an important role in gene regulation bringing distal sequence elements in 3D proximity to genes hundreds of kilobases away. Hi-C is a powerful genome-wide technique to study 3D genome organization. Owing to 1234567890():,; experimental costs, high resolution Hi-C datasets are limited to a few cell lines. Computa- tional prediction of Hi-C counts can offer a scalable and inexpensive approach to examine 3D genome organization across multiple cellular contexts. Here we present HiC-Reg, an approach to predict contact counts from one-dimensional regulatory signals. HiC-Reg pre- dictions identify topologically associating domains and significant interactions that are enri- ched for CCCTC-binding factor (CTCF) bidirectional motifs and interactions identified from complementary sources. CTCF and chromatin marks, especially repressive and elongation marks, are most important for HiC-Reg’s predictive performance. Taken together, HiC-Reg provides a powerful framework to generate high-resolution profiles of contact counts that can be used to study individual locus level interactions and higher-order organizational units of the genome. 1 Wisconsin Institute for Discovery, 330 North Orchard Street, Madison, WI 53715, USA. 2 Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53715, USA. *email: [email protected] NATURE COMMUNICATIONS | (2019) 10:5449 | https://doi.org/10.1038/s41467-019-13423-8 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-019-13423-8 he three-dimensional (3D) organization of the genome has Results Temerged as an important component of the gene regulation HiC-Reg for predicting contact count using Random Forests. -
Dynamics of Gene Silencing During X Inactivation Using Allele-Specific RNA-Seq Hendrik Marks1*, Hindrik H
Marks et al. Genome Biology (2015) 16:149 DOI 10.1186/s13059-015-0698-x RESEARCH Open Access Dynamics of gene silencing during X inactivation using allele-specific RNA-seq Hendrik Marks1*, Hindrik H. D. Kerstens1, Tahsin Stefan Barakat3, Erik Splinter4, René A. M. Dirks1, Guido van Mierlo1, Onkar Joshi1, Shuang-Yin Wang1, Tomas Babak5, Cornelis A. Albers2, Tüzer Kalkan6, Austin Smith6, Alice Jouneau7, Wouter de Laat4, Joost Gribnau3 and Hendrik G. Stunnenberg1* Abstract Background: During early embryonic development, one of the two X chromosomes in mammalian female cells is inactivated to compensate for a potential imbalance in transcript levels with male cells, which contain a single X chromosome. Here, we use mouse female embryonic stem cells (ESCs) with non-random X chromosome inactivation (XCI) and polymorphic X chromosomes to study the dynamics of gene silencing over the inactive X chromosome by high-resolution allele-specific RNA-seq. Results: Induction of XCI by differentiation of female ESCs shows that genes proximal to the X-inactivation center are silenced earlier than distal genes, while lowly expressed genes show faster XCI dynamics than highly expressed genes. The active X chromosome shows a minor but significant increase in gene activity during differentiation, resulting in complete dosage compensation in differentiated cell types. Genes escaping XCI show little or no silencing during early propagation of XCI. Allele-specific RNA-seq of neural progenitor cells generated from the female ESCs identifies three regions distal to the X-inactivation center that escape XCI. These regions, which stably escape during propagation and maintenance of XCI, coincide with topologically associating domains (TADs) as present in the female ESCs. -
ABO (ISBT 001) Blood Group Alleles V1.1 171023
Names for ABO (ISBT 001) blood group alleles v1.1 171023 Names for ABO (ISBT 001) Blood Group Alleles General description: The ABO system was discovered as in 1900 and is considered the first and clinically most important system. The ABO gene and its 7 coding exons give rise to one of two principally different glycosyltransferases. The A glycosyltransferase (GTA) catalyzes the addition of a donor substrate, UDP-N-acetylgalactosamine, to an acceptor substrate known as the H antigen. The B glycosyltransferase (GTB) differs by only four amino-acid substitutions from GTA and performs the same enzymatic reaction but uses UDP-galactose as donor substrate. In this way, genetic polymorphism gives rise to two related antigens in this system. Any polymorphism or mutation that changes the activity or specificity of the encoded enzyme may therefore alter the ABO phenotype. Alterations that completely abolish enzymic activity give rise to the blood group O phenotype, in which the H antigen remains unconverted and no A or B antigen can be detected. If the genetic alteration decreases the activity of the enzyme, or alters its subcellular location and thereby decreases conversion of H to A or B, a weak A or B subgroup phenotype can result. Furthermore, certain polymorphisms result in promiscuous enzymes that can synthesize both A and B antigen, thereby resulting in the so-called cisAB or B(A) phenotypes. The A phenotype is divided into A1 and A2. The former is more prevalent in all populations and has approximately 5 times more A epitopes per red cell. The GTA1 is also better than GTA2 at synthesizing certain forms of A, .e.g. -
Interfering with Retrotransposition by Two Types of CRISPR Effectors
Zhang et al. Cell Discovery (2020) 6:30 Cell Discovery https://doi.org/10.1038/s41421-020-0164-0 www.nature.com/celldisc ARTICLE Open Access Interfering with retrotransposition by two types of CRISPR effectors: Cas12a and Cas13a Niubing Zhang1,2, Xinyun Jing1, Yuanhua Liu3, Minjie Chen1,2, Xianfeng Zhu2, Jing Jiang2, Hongbing Wang4, Xuan Li1 and Pei Hao3 Abstract CRISPRs are a promising tool being explored in combating exogenous retroviral pathogens and in disabling endogenous retroviruses for organ transplantation. The Cas12a and Cas13a systems offer novel mechanisms of CRISPR actions that have not been evaluated for retrovirus interference. Particularly, a latest study revealed that the activated Cas13a provided bacterial hosts with a “passive protection” mechanism to defend against DNA phage infection by inducing cell growth arrest in infected cells, which is especially significant as it endows Cas13a, a RNA-targeting CRISPR effector, with mount defense against both RNA and DNA invaders. Here, by refitting long terminal repeat retrotransposon Tf1 as a model system, which shares common features with retrovirus regarding their replication mechanism and life cycle, we repurposed CRISPR-Cas12a and -Cas13a to interfere with Tf1 retrotransposition, and evaluated their different mechanisms of action. Cas12a exhibited strong inhibition on retrotransposition, allowing marginal Tf1 transposition that was likely the result of a lasting pool of Tf1 RNA/cDNA intermediates protected within virus-like particles. The residual activities, however, were completely eliminated with new constructs for persistent crRNA targeting. On the other hand, targeting Cas13a to Tf1 RNA intermediates significantly inhibited Tf1 retrotransposition. However, unlike in bacterial hosts, the sustained activation of Cas13a by Tf1 transcripts did not cause cell growth arrest in S. -
Complete Article
The EMBO Journal Vol. I No. 12 pp. 1539-1544, 1982 Long terminal repeat-like elements flank a human immunoglobulin epsilon pseudogene that lacks introns Shintaro Ueda', Sumiko Nakai, Yasuyoshi Nishida, lack the entire IVS have been found in the gene families of the Hiroshi Hisajima, and Tasuku Honjo* mouse a-globin (Nishioka et al., 1980; Vanin et al., 1980), the lambda chain (Hollis et al., 1982), Department of Genetics, Osaka University Medical School, Osaka 530, human immunoglobulin Japan and the human ,B-tubulin (Wilde et al., 1982a, 1982b). The mouse a-globin processed gene is flanked by long terminal Communicated by K.Rajewsky Received on 30 September 1982 repeats (LTRs) of retrovirus-like intracisternal A particles on both sides, although their orientation is opposite to each There are at least three immunoglobulin epsilon genes (C,1, other (Lueders et al., 1982). The human processed genes CE2, and CE) in the human genome. The nucleotide sequences described above have poly(A)-like tails -20 bases 3' to the of the expressed epsilon gene (CE,) and one (CE) of the two putative poly(A) addition signal and are flanked by direct epsilon pseudogenes were compared. The results show that repeats of several bases on both sides (Hollis et al., 1982; the CE3 gene lacks the three intervening sequences entirely and Wilde et al., 1982a, 1982b). Such direct repeats, which were has a 31-base A-rich sequence 16 bases 3' to the putative also found in human small nuclear RNA pseudogenes poly(A) addition signal, indicating that the CE3 gene is a pro- (Arsdell et al., 1981), might have been formed by repair of cessed gene. -
NPRL3 Gene NPR3 Like, GATOR1 Complex Subunit
NPRL3 gene NPR3 like, GATOR1 complex subunit Normal Function The NPRL3 gene provides instructions for making a protein that is one piece of a group of proteins (complex) called GATOR1. This complex is found in cells throughout the body, where it regulates a signaling pathway called the mTOR pathway. The mTOR pathway is involved in cell growth and division (proliferation), the survival of cells, and the creation (synthesis) of new proteins. The role of the GATOR1 complex is to block this pathway by inhibiting (stopping) the activity of a complex called mTOR complex 1 ( mTORC1) that is integral to the mTOR pathway. In the brain, the mTOR pathway regulates many processes, including the growth and development of nerve cells and their ability to change and adapt over time (plasticity). Health Conditions Related to Genetic Changes Familial focal epilepsy with variable foci At least ten NPRL3 gene mutations have been found to cause familial focal epilepsy with variable foci (FFEVF), which is an uncommon form of recurrent seizures (epilepsy) that runs in families. Most of these mutations lead to the production of an abnormally short, nonfunctional protein. As a result, formation of normal GATOR1 complex is reduced, leading to overactivity of mTORC1 and excessive signaling of the mTOR pathway. It is not clear how an abnormally active mTOR pathway leads to the seizures of FFEVF. Research suggests that increased mTOR pathway signaling in the brain leads to changes in the connections between nerve cells (synapses) and increased activation (excitation) -
Retrotransposon Long Interspersed Nucleotide Element1 (LINE1) Is
The Japanese Society of Developmental Biologists Develop. Growth Differ. (2012) 54, 673–685 doi: 10.1111/j.1440-169X.2012.01368.x Original Article Retrotransposon long interspersed nucleotide element-1 (LINE-1) is activated during salamander limb regeneration Wei Zhu,1 Dwight Kuo,2 Jason Nathanson,3 Akira Satoh,4,5 Gerald M. Pao,1 Gene W. Yeo,3 Susan V. Bryant,5 S. Randal Voss,6 David M. Gardiner5*and Tony Hunter1* 1Molecular and Cell Biology Laboratory and Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, California 92037, Departments of 2Bioengineering and 3Cellular and Molecular Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA; 4Okayama University, R.C.I.S. Okayama-city, Okayama, 700-8530, Japan; 5Department of Developmental and Cell Biology, University of California at Irvine, Irvine, California 92697, and 6Department of Biology and Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40506, USA Salamanders possess an extraordinary capacity for tissue and organ regeneration when compared to mam- mals. In our effort to characterize the unique transcriptional fingerprint emerging during the early phase of sala- mander limb regeneration, we identified transcriptional activation of some germline-specific genes within the Mexican axolotl (Ambystoma mexicanum) that is indicative of cellular reprogramming of differentiated cells into a germline-like state. In this work, we focus on one of these genes, the long interspersed nucleotide element-1 (LINE-1) retrotransposon, which is usually active in germ cells and silent in most of the somatic tissues in other organisms. LINE-1 was found to be dramatically upregulated during regeneration. -
The Basic Karyotype of Rye Giemsa and Fluorescence
Heredity (1974) 33 (3), 403-408 THEBASIC KARYOTYPE OF RYE (SECALE CEREALE) ANALYSED WITH GIEMSA AND FLUORESCENCE METHODS CANIO G. VOSA Botany School, Oxford Received26.iii.74 SUMMARY The basic karyotype of Rye (Secale cereale L.) has been analysed with several fluorochromes and with a Giemsa staining technique. Only the fluoro- chrome Hoechst 33258 and the Giemsa technique were successful in differenti- ating the heterochromatic segments. Five cultivated varieties were studied. In the haploid set there are 11 large and two small terminally located bands, four small intercalary bands and a variable band adjacent to the nucleolar constriction on chromosome VII which are constant for all varieties. Five more very small intercalary bands occur sporadically in all the varieties. All the chromosomes possess thin centromeric bands. 1. INTRODUCTION RYE is the hardiest of the cereals and its cultivation reaches beyond the Arctic Circle. It is of considerable importance in Russia, Sweden, Poland, the Netherlands and Belgium. In Britain, Rye has ceased to be of any great importance since the change to wheaten bread in the eighteenth century. Compared with other cereals, Rye has fewer varieties and these are not very uniform because of cross-pollination which is the rule in Rye but the exception in other cereal crops. It probably occurred as a weed in fields before being accepted as a crop rather later in the history of civilisation.Its oldest archaeological records date from the first Iron Age (Halstatt period, c. 900-700 B.C.). Thefirst chromosome counts are those of Nemec (1910) as cited by Emme (1928), giving 18 chromosomes for endosperm cells. -
Extra Euchromatic Band in the Qh Region of Chromosome 9
J Med Genet: first published as 10.1136/jmg.22.2.156 on 1 April 1985. Downloaded from 156 Short reports two centromeres indicated by two distinct C bands but only I HANCKE AND K MILLER one primary constriction at the proximal C band. The two Department of Human Genetics, C bands were separated by chromosomal material staining Medizinische Hochschule Hannover, pale in G banding and intensely dark in R banding (fig 1). Hannover, Both NORs could be observed in satellite associations (fig Federal Republic of Germany. 2). The chromosome was therefore defined as pseudo- dicentric chromosome 21 (pseudic 21). The same chromo- References some was found in the proband's father and paternal Balicek P, Zizka, J. Intercalar satellites of human acrocentric grandmother. chromosomes as a cytological manifestation of polymorphisms Acrocentric chromosomes with a short arm morphology in GC-rich material? Hum Genet 1980;54:343-7. similar to that presented here have been reported by 2 Ing PS, Smith SD. Cytogenetic studies of a patient with Balicek and Zizka.' These authors paid no attention to the mosaicism of isochromosome 13q and a dicentric (Y;13) activity of the centromeres. The suppression of additional translocation showing differential centromeric activity. Clin centromeres is indicated by the presence of only one Genet 1983;24:194-9. primary constriction as shown by Ing and Smith2 in a 3 Passarge E. Analysis of chromosomes in mitosis and evaluation dicentric (Y;13) transtocation. Variants of acrocentric of cytogenetic data. 5. Variability of the karyotype. In: Schwarzacher HG, Wolf U, eds. Methods in human cytogene- chromosomes are often observed in patients with congen- tics. -
(Lcrs) in 22Q11 Mediate Deletions, Duplications, Translocations, and Genomic Instability: an Update and Literature Review Tamim H
review January/February 2001 ⅐ Vol. 3 ⅐ No. 1 Evolutionarily conserved low copy repeats (LCRs) in 22q11 mediate deletions, duplications, translocations, and genomic instability: An update and literature review Tamim H. Shaikh, PhD1, Hiroki Kurahashi, MD, PhD1, and Beverly S. Emanuel, PhD1,2 Several constitutional rearrangements, including deletions, duplications, and translocations, are associated with 22q11.2. These rearrangements give rise to a variety of genomic disorders, including DiGeorge, velocardiofacial, and conotruncal anomaly face syndromes (DGS/VCFS/CAFS), cat eye syndrome (CES), and the supernumerary der(22)t(11;22) syndrome associated with the recurrent t(11;22). Chromosome 22-specific duplications or low copy repeats (LCRs) have been directly implicated in the chromosomal rearrangements associated with 22q11.2. Extensive sequence analysis of the different copies of 22q11 LCRs suggests a complex organization. Examination of their evolutionary origin suggests that the duplications in 22q11.2 may predate the divergence of New World monkeys 40 million years ago. Based on the current data, a number of models are proposed to explain the LCR-mediated constitutional rearrangements of 22q11.2. Genetics in Medicine, 2001:3(1):6–13. Key Words: duplication, evolution, 22q11, deletion and translocation Although chromosome 22 represents only 2% of the haploid The 22q11.2 deletion syndrome, which includes DGS/ human genome,1 recurrent, clinically significant, acquired, VCFS/CAFS, is the most common microdeletion syndrome. and somatic -
Lncrna Jpx Induces Xist Expression in Mice Using Both Trans and Cis Mechanisms
RESEARCH ARTICLE LncRNA Jpx induces Xist expression in mice using both trans and cis mechanisms Sarah Carmona, Benjamin Lin, Tristan Chou, Katti Arroyo, Sha Sun* Department of Developmental and Cell Biology, Ayala School of Biological Sciences, University of California, Irvine, Irvine, CA, United States of America * [email protected] a1111111111 a1111111111 Abstract a1111111111 a1111111111 Mammalian X chromosome dosage compensation balances X-linked gene products a1111111111 between sexes and is coordinated by the long noncoding RNA (lncRNA) Xist. Multiple cis and trans-acting factors modulate Xist expression; however, the primary competence factor responsible for activating Xist remains a subject of dispute. The lncRNA Jpx is a proposed competence factor, yet it remains unknown if Jpx is sufficient to activate Xist expression in OPEN ACCESS mice. Here, we utilize a novel transgenic mouse system to demonstrate a dose-dependent relationship between Jpx copy number and ensuing Jpx and Xist expression. By localizing Citation: Carmona S, Lin B, Chou T, Arroyo K, Sun S (2018) LncRNA Jpx induces Xist expression in transcripts of Jpx and Xist using RNA Fluorescence in situ Hybridization (FISH) in mouse mice using both trans and cis mechanisms. PLoS embryonic cells, we provide evidence of Jpx acting in both trans and cis to activate Xist. Our Genet 14(5): e1007378. https://doi.org/10.1371/ data contribute functional and mechanistic insight for lncRNA activity in mice, and argue that journal.pgen.1007378 Jpx is a competence factor for Xist activation in vivo. Editor: Gregory S. Barsh, Stanford University School of Medicine, UNITED STATES Received: November 20, 2017 Accepted: April 24, 2018 Author summary Published: May 7, 2018 Long noncoding RNA (lncRNA) have been identified in all eukaryotes but mechanisms Copyright: © 2018 Carmona et al.