The New Genetics
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Genomic Response to the Social Environment: Implications for Health Outcomes
Genomic Response to the Social Environment: Implications for Health Outcomes June 24, 2020 Workshop Summary Workshop Goals Jessica M. Gill, PhD, RN, FAAN Acting Deputy Director, National Institute of Nursing Research (NINR) Dr. Gill welcomed participants and acknowledged funding support from the National Institutes of Health (NIH) Office of Disease Prevention (ODP) and the NIH Office of Behavioral and Social Sciences Research (OBSSR) as well as colleagues across NIH Institutes, Centers, and Offices who participated in planning the workshop. Although it has long been recognized that the social environment can influence the risk, manifestation, and trajectory of disease and associated symptoms, the underlying biological mechanisms remain largely understudied. This transdisciplinary event will address the relationship among genomics (e.g., epigenomics, gene expression, microbiome, telomeres), the social environment, and health outcomes across conditions, populations, and the lifespan. Discussions will include an exchange of ideas to advance a social genomics research strategy that illuminates genetic influences on disease burden and to inform future interventions. Overview of the Day and Introduction of Keynote Speakers Lois Tully, PhD Program Director, NINR Dr. Tully provided an overview of the workshop agenda and introduced the keynote speakers, Drs. Janice Kiecolt-Glaser and Steve Cole. She encouraged participants to engage in thoughtful discussion about potential next steps toward integrating a social genomics approach into personalized strategies that prevent, modify, or buffer adverse social environments and lead to better health outcomes. Lovesick: How Couples’ Relationships Influence Health Janice Kiecolt-Glaser, PhD Director, Institute for Behavioral Medicine Research Distinguished University Professor Institute for Behavioral Medicine Research The Ohio State University College of Medicine Dr. -
Intelligent Design, Abiogenesis, and Learning from History: Dennis R
Author Exchange Intelligent Design, Abiogenesis, and Learning from History: Dennis R. Venema A Reply to Meyer Dennis R. Venema Weizsäcker’s book The World View of Physics is still keeping me very busy. It has again brought home to me quite clearly how wrong it is to use God as a stop-gap for the incompleteness of our knowledge. If in fact the frontiers of knowledge are being pushed back (and that is bound to be the case), then God is being pushed back with them, and is therefore continually in retreat. We are to find God in what we know, not in what we don’t know; God wants us to realize his presence, not in unsolved problems but in those that are solved. Dietrich Bonhoeffer1 am thankful for this opportunity to nature, is the result of intelligence. More- reply to Stephen Meyer’s criticisms over, this assertion is proffered as the I 2 of my review of his book Signature logical basis for inferring design for the in the Cell (hereafter Signature). Meyer’s origin of biological information: if infor- critiques of my review fall into two gen- mation only ever arises from intelli- eral categories. First, he claims I mistook gence, then the mere presence of Signature for an argument against bio- information demonstrates design. A few logical evolution, rendering several of examples from Signature make the point my arguments superfluous. Secondly, easily: Meyer asserts that I have failed to refute … historical scientists can show that his thesis by not providing a “causally a presently acting cause must have adequate alternative explanation” for the been present in the past because the origin of life in that the few relevant cri- proposed candidate is the only known tiques I do provide are “deeply flawed.” cause of the effect in question. -
The Genetic Background of Anticipation P Teisberg MD
JOURNAL OF THE ROYAL SOCIETY OF MEDICINE Volume 88 April 1995 The genetic background of anticipation P Teisberg MD J R Soc Med 1995;88:185-187 Keywords: genetics; anticipation; triplet repeats; neurological disorders Anticipation was controversial impairment and increased infant mortality were observed. Anticipation may be defined as the occurrence of a genetic The sequence of events often ends in congenital MD with its disorder at progressively earlier ages in successive severe clinical manifestation of mental retardation and generations. The disease moreover occurs with increasing muscular dystrophy. Later, clinical studies confirmed these severity. The concept emerged early in this century mainly observations and described a dominant inheritance pattern through descriptive dinical studies ofmyotonic dystrophy1'2. which could not be explained by classical Mendelian Later studies have added other disease entities to a list of mechanisms8. states showing anticipation, the most notable being Another phenomenon which did not fit easily into the Huntington's disease3. In one form of inherited mental concepts of genetics was the finding that congenital MD was retardation, the fragile X syndrome, the term 'the Sherman transmitted almost exclusively via affected mothers9. paradox' describes a very similar phenomenon4. In the fragile X syndrome, anticipation is manifested in a Towards the middle of this century, basic research in different manner. This is the most common cause of familial genetics had given us a much clearer understanding of mental retardation. It segregates in families as an X-linked Mendelian inheritance. It became increasingly difficult to dominant disorder with reduced penetrance. When reconcile the originally described phenomenon of chromosomes are stained a fragile site on the X anticipation with a concept of genes as stable elements chromosome may be seen in a proportion of cells taken only changed by the rare mutation. -
A Supergene-Linked Estrogen Receptor Drives Alternative Phenotypes in a Polymorphic Songbird
A supergene-linked estrogen receptor drives alternative phenotypes in a polymorphic songbird Jennifer R. Merritta,1, Kathleen E. Grogana, Wendy M. Zinzow-Kramera, Dan Sunb, Eric A. Ortlundc, Soojin V. Yib, and Donna L. Maneya aDepartment of Psychology, Emory University, Atlanta, GA 30322; bSchool of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332; and cDepartment of Biochemistry, Emory University, Atlanta, GA 30322 Edited by Gene E. Robinson, University of Illinois at Urbana–Champaign, Urbana, IL, and approved July 8, 2020 (received for review June 3, 2020) Behavioral evolution relies on genetic changes, yet few behaviors tan-striped (TS) morph are homozygous for the standard ar- can be traced to specific genetic sequences in vertebrates. Here we rangement, ZAL2 (13, 14) (Fig. 1A). The rearrangement is provide experimental evidence showing that differentiation of a maintained in the population because of the species’ unique dis- single gene has contributed to the evolution of divergent behav- assortative mating system; nearly every breeding pair consists of ioral phenotypes in the white-throated sparrow, a common back- one individual of each morph (15). Because almost all WS birds yard songbird. In this species, a series of chromosomal inversions are heterozygous for ZAL2m (15, 16), this mating system keeps has formed a supergene that segregates with an aggressive phe- ZAL2m in a near-constant state of heterozygosity (Fig. 1B), pro- notype. The supergene has captured ESR1, the gene that encodes foundly suppressing recombination and causing it to differentiate estrogen receptor α (ERα); as a result, this gene is accumulating from ZAL2 (15, 17). changes that now distinguish the supergene allele from the stan- The rearranged region of ZAL2m in white-throated sparrows dard allele. -
Original Articles Anticipation Resulting in Elimination of the Myotonic
J7 Med Genet 1994;31:595-601 595 Original articles J Med Genet: first published as 10.1136/jmg.31.8.595 on 1 August 1994. Downloaded from Anticipation resulting in elimination of the myotonic dystrophy gene: a follow up study of one extended family C E M de Die-Smulders, C J Howeler, J F Mirandolle, H G Brunner, V Hovers, H Bruggenwirth, H J M Smeets, J P M Geraedts Abstract muscular manifestations, it is characterised by We have re-examined an extended myo- multiple systemic effects including cataract, tonic dystrophy (DM) family, previously mental retardation, cardiac involvement, and described in 1955, in order to study the testicular atrophy. Extreme variability is one of long term effects of anticipation in DM the hallmarks of the disease; clinical studies and in particular the implications for have led to the recognition of four disease types families affected by this disease. This fol- on the basis of age at onset and core symptoms: low up study provides data on 35 gene late onset (mild) type, adult onset (classical) carriers and 46 asymptomatic at risk type, childhood, and congenital type.'"3 family members in five generations. Anticipation, increasing severity and earlier Clinical anticipation, defined as the cas- age at onset in successive generations, has been cade ofmild, adult, childhood, or congen- observed in DM since the beginning of this ital disease in subsequent generations, century, but remained unexplained and contro- appeared to be a relentless process, oc- versial until recently."- With the discovery of curring in all affected branches of the an unstable CTG trinucleotide repeat in the 3' family. -
Genomics and Its Impact on Science and Society: the Human Genome Project and Beyond
DOE/SC-0083 Genomics and Its Impact on Science and Society The Human Genome Project and Beyond U.S. Department of Energy Genome Research Programs: genomics.energy.gov A Primer ells are the fundamental working units of every living system. All the instructions Cneeded to direct their activities are contained within the chemical DNA (deoxyribonucleic acid). DNA from all organisms is made up of the same chemical and physical components. The DNA sequence is the particular side-by-side arrangement of bases along the DNA strand (e.g., ATTCCGGA). This order spells out the exact instruc- tions required to create a particular organism with protein complex its own unique traits. The genome is an organism’s complete set of DNA. Genomes vary widely in size: The smallest known genome for a free-living organism (a bac- terium) contains about 600,000 DNA base pairs, while human and mouse genomes have some From Genes to Proteins 3 billion (see p. 3). Except for mature red blood cells, all human cells contain a complete genome. Although genes get a lot of attention, the proteins DNA in each human cell is packaged into 46 chro- perform most life functions and even comprise the mosomes arranged into 23 pairs. Each chromosome is majority of cellular structures. Proteins are large, complex a physically separate molecule of DNA that ranges in molecules made up of chains of small chemical com- length from about 50 million to 250 million base pairs. pounds called amino acids. Chemical properties that A few types of major chromosomal abnormalities, distinguish the 20 different amino acids cause the including missing or extra copies or gross breaks and protein chains to fold up into specific three-dimensional rejoinings (translocations), can be detected by micro- structures that define their particular functions in the cell. -
Genomic and Transcriptomic Analyses of the Subterranean Termite
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.11.451559; this version posted July 12, 2021. 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 Genomic and transcriptomic analyses of the 2 subterranean termite Reticulitermes speratus: gene 3 duplication facilitates social evolution 4 5 Shuji Shigenobu*+1,2, Yoshinobu Hayashi+3, Dai Watanabe 4,5, Gaku Tokuda6, 6 Masaru Y Hojo6,19, Kouhei Toga5,7, Ryota Saiki5, Hajime Yaguchi5,8, Yudai 7 Masuoka5,9, Ryutaro Suzuki5,10, Shogo Suzuki5, Moe Kimura11, Masatoshi 8 Matsunami4,12, Yasuhiro Sugime4, Kohei Oguchi4,10,13, Teruyuki Niimi2,14, Hiroki 9 Gotoh15,20, Masaru K Hojo8, Satoshi Miyazaki16, Atsushi Toyoda17, Toru Miura*4,13, 10 Kiyoto Maekawa*18 11 12 1) NIBB Research Core Facilities, National Institute for Basic Biology, Okazaki, 13 444-8585 Japan 14 2) Department of Basic Biology, School of Life Science, The Graduate University for 15 Advanced Studies, SOKENDAI, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444- 16 8585, Japan 17 3) Department of Biology, Keio University, Hiyoshi, Yokohama, 223-8521, Japan 18 4) Faculty of Environmental Earth Science, Hokkaido University, Sapporo, 19 Hokkaido, 060-0810, Japan 20 5) Graduate School of Science and Engineering, University of Toyama, Toyama, 21 930-8555, Japan 22 6) Tropical Biosphere Research Center, COMB, University of the Ryukyus, 23 Nishihara, Okinawa 903-0213, Japan 24 7) Department of Biosciences, College of Humanities and Sciences, -
Fact Sheet 54| FRAGILE X SYNDROME This Fact Sheet
11111 Fact Sheet 54| FRAGILE X SYNDROME This fact sheet describes the condition Fragile X and includes a discussion of the symptoms, causes and available testing. In summary Fragile X is a condition caused by a change in the FMR-1 gene, on the X chromosome It is characterised by particular physical features, varying degrees of learning difficulties and behavioural and emotional problems Fragile X affects around 1 in 4,000 males and between 1 in 5,000 and 1 in 8,000 females. WHAT IS FRAGILE X SYNDROME? WHAT CAUSES FRAGILE X SYNDROME? Fragile X syndrome is the most common known Fragile X syndrome is caused by a variation in the cause of inherited intellectual disability. genetic information in the FMR-1 gene. Genes are Intellectual problems in people with fragile X made up of a string of three letter ‘words’, or syndrome can vary from mild learning difficulties triplets, using the letters A,T, C & G. The FMR-1 through to severe intellectual disability. gene codes for a protein called FMRP that is necessary for usual brain development and/or Emotional and behavioural problems may also be function. In the FMR-1 gene, the triplet word present. ‘CGG’ can be repeated many times. When the Females with fragile X syndrome show varying number of ‘CGG’ repeats in the FMR-1 gene degrees of the condition, but are usually less increases over a critical number, the gene severely affected than males. becomes so long that it becomes faulty and the production of the FMRP is disrupted. The features of the condition, and their severity, are related to the genetic information in the faulty gene causing the condition. -
RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases
G C A T T A C G G C A T genes Review RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases Amber Willbanks, Shaun Wood and Jason X. Cheng * Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL 60637, USA; [email protected] (A.W.); [email protected] (S.W.) * Correspondence: [email protected] Abstract: Chromatin structure plays an essential role in eukaryotic gene expression and cell identity. Traditionally, DNA and histone modifications have been the focus of chromatin regulation; however, recent molecular and imaging studies have revealed an intimate connection between RNA epigenetics and chromatin structure. Accumulating evidence suggests that RNA serves as the interplay between chromatin and the transcription and splicing machineries within the cell. Additionally, epigenetic modifications of nascent RNAs fine-tune these interactions to regulate gene expression at the co- and post-transcriptional levels in normal cell development and human diseases. This review will provide an overview of recent advances in the emerging field of RNA epigenetics, specifically the role of RNA modifications and RNA modifying proteins in chromatin remodeling, transcription activation and RNA processing, as well as translational implications in human diseases. Keywords: 5’ cap (5’ cap); 7-methylguanosine (m7G); R-loops; N6-methyladenosine (m6A); RNA editing; A-to-I; C-to-U; 2’-O-methylation (Nm); 5-methylcytosine (m5C); NOL1/NOP2/sun domain Citation: Willbanks, A.; Wood, S.; (NSUN); MYC Cheng, J.X. RNA Epigenetics: Fine-Tuning Chromatin Plasticity and Transcriptional Regulation, and the Implications in Human Diseases. Genes 2021, 12, 627. -
RNA Interference with Sirna
CANCER GENOMICS & PROTEOMICS 3: 127-136 (2006) Review RNA Interference with siRNA HELENA JOYCE*, ISABELLA BRAY* and MARTIN CLYNES National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland Abstract. Over the last decade, RNA interference has RNAs (13). Twenty-one different gene products with emerged as an effective mechanism for silencing gene different functions and subcellular localizations were expression. This ancient cellular antiviral response can be used studied. Knockdown experiments, monitored by to allow specific inhibition of the function of any chosen target immunofluorescence and immunoblotting, showed that even gene, including those involved in diseases such as cancer, major cellular proteins such as actin and vimentin could be AIDS and hepatitis. It has become an invaluable research tool silenced efficiently. Previous work had discovered that these to aid in the identification of novel genes involved in disease 22-nucleotide sequences served as guide sequences that processes. It has advanced from the use of synthetic RNA for instruct a multicomponent nuclease, RNA-induced silencing the endogenous production of small hairpin RNA by plasmid complex (RISC), to destroy specific messenger RNAs (7). and viral vectors, and from transient inhibition in vitro to It was then found that, in response to dsRNA, cells trigger longer-lasting effects in vivo. However, as with antisense and a two-step reaction. In the first step, long dsRNA is ribozymes, the efficient delivery of siRNA into cells is currently processed by a ribonuclease (RNase) III enzyme, called the limiting factor to successful gene expression inhibition in Dicer, into small interfering RNAs (siRNAs); these vivo. This review gives an overview of the mechanism of action subsequently serve as the sequence determinants of the of siRNA and its use in cancer research. -
Genetics and Genomics of Human Population Structure 20
Genetics and Genomics of Human Population Structure 20 Sohini Ramachandran , Hua Tang , Ryan N. Gutenkunst , and Carlos D. Bustamante Abstract Recent developments in sequencing technology have created a fl ood of new data on human genetic variation, and this data has yielded new insights into human popu- lation structure. Here we review what both early and more recent studies have taught us about human population structure and history. Early studies showed that most human genetic variation occurs within populations rather than between them, and that genetically related populations often cluster geographically. Recent studies based on much larger data sets have recapitulated these observations, but have also demonstrated that high-density genotyping allows individuals to be reliably assigned to their population of origin. In fact, for admixed individuals, even the ancestry of particular genomic regions can often be reli- ably inferred. Recent studies have also offered detailed information about the composition of specifi c populations from around the world, revealing how history has shaped their genetic makeup. We also briefl y review quantitative models of human genetic history, including the role natural selection has played in shaping human genetic variation. Contents 20.2.3 Characterizing Locus-Specifi c Ancestry ...................................................... 594 20.1 Introduction ............................................................... 590 20.3 Global Patterns of Human Population Structure ....... 595 20.1.1 Evolutionary Forces Shaping 20.3.1 The Apportionment of Human Human Genetic Variation ........................... 590 Diversity ..................................................... 595 20.2 Quantifying Population Structure ............................. 592 20.3.2 The History and Geography of Human Genes ......................................... 596 20.2.1 FST and Genetic Distance ............................ 592 20.2.2 Model-Based Clustering 20.3.3 Genetic Structure of Human Populations .. -
RNA Interference in the Nucleus: Roles for Small Rnas in Transcription, Epigenetics and Beyond
REVIEWS NON-CODING RNA RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond Stephane E. Castel1 and Robert A. Martienssen1,2 Abstract | A growing number of functions are emerging for RNA interference (RNAi) in the nucleus, in addition to well-characterized roles in post-transcriptional gene silencing in the cytoplasm. Epigenetic modifications directed by small RNAs have been shown to cause transcriptional repression in plants, fungi and animals. Additionally, increasing evidence indicates that RNAi regulates transcription through interaction with transcriptional machinery. Nuclear small RNAs include small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs) and are implicated in nuclear processes such as transposon regulation, heterochromatin formation, developmental gene regulation and genome stability. RNA interference Since the discovery that double-stranded RNAs (dsRNAs) have revealed a conserved nuclear role for RNAi in (RNAi). Silencing at both the can robustly silence genes in Caenorhabditis elegans and transcriptional gene silencing (TGS). Because it occurs post-transcriptional and plants, RNA interference (RNAi) has become a new para- in the germ line, TGS can lead to transgenerational transcriptional levels that is digm for understanding gene regulation. The mecha- inheritance in the absence of the initiating RNA, but directed by small RNA molecules. nism is well-conserved across model organisms and it is dependent on endogenously produced small RNA. uses short antisense RNA to inhibit translation or to Such epigenetic inheritance is familiar in plants but has Post-transcriptional gene degrade cytoplasmic mRNA by post-transcriptional gene only recently been described in metazoans. silencing silencing (PTGS). PTGS protects against viral infection, In this Review, we cover the broad range of nuclear (PTGS).