DOCSLIB.ORG

Recurrent Evolution of DNA-Binding Motifs in the Drosophila Centromeric Histone

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone Harmit S. Malik*, Danielle Vermaak*, and Steven Henikoff*†‡ †Howard Hughes Medical Institute, *Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109 Communicated by Stanley M. Gartler, University of Washington, Seattle, WA, December 12, 2001 (received for review October 29, 2001) All eukaryotes contain centromere-specific histone H3 variants being one of the most evolutionarily constrained classes of (CenH3s), which replace H3 in centromeric chromatin. We have eukaryotic proteins. Second, CenH3s are evolving adaptively, previously documented the adaptive evolution of the Drosophila presumably in concert with centromeres, which consist of the CenH3 (Cid) in comparisons of Drosophila melanogaster and Dro- most rapidly evolving DNA in the genome. sophila simulans, a divergence of Ϸ2.5 million years. We have Chromosomes (and their centromeres) may compete at mei- proposed that rapidly changing centromeric DNA may be driving osis I for inclusion into the oocyte (11). A centromeric satellite CenH3’s altered DNA-binding specificity. Here, we compare Cid expansion could bias centromeric strength, leading to preferred sequences from a phylogenetically broader group of Drosophila inclusion in the oocyte, but also to increased nondisjunction. A species to suggest that Cid has been evolving adaptively for at least subsequent alteration of CenH3’s DNA-binding preferences 25 million years. Our analysis also reveals conserved blocks not could restore parity among different chromosomes (2), thereby only in the histone-fold domain but also in the N-terminal tail. In alleviating the deleterious consequences of satellite drive. Suc- several lineages, the N-terminal tail of Cid is characterized by cessive rounds of satellite and CenH3 drive are detected as an subgroup-specific oligopeptide expansions. These expansions re- excess of replacement changes in CenH3. Adaptive evolution of semble minor groove DNA binding motifs found in various histone CenH3 has been documented in the histone fold domain of tails. Remarkably, similar oligopeptides are also found in N-termi- Drosophila (10). The N-terminal tails of CenH3 in both Dro- nal tails of human and mouse CenH3 (Cenp-A). The recurrent sophila and Arabidopsis are also subject to adaptive evolution, evolution of these motifs in CenH3 suggests a packaging function consistent with their proposed role in contacting centromeric for the N-terminal tail, which results in a unique chromatin orga- DNA (10, 12). In addition, deletion studies in Saccharomyces nization at the primary constriction, the cytological marker of cerevisiae have revealed essential protein–protein interaction centromeres. sites encoded within the N-terminal tail of CenH3 (13). Al- though sequence divergence precludes aligning the N-terminal entromeres are the chromosomal loci responsible for pole- tails of CenH3s from different lineages, a comprehensive study Cward movement at meiosis and mitosis, and are essential for of the molecular evolution within a particular lineage of CenH3s could help elucidate function for this important feature of the faithful segregation of genetic information. Despite their GENETICS crucial role in the cell cycle, relatively little is known about how centromeric chromatin by revealing the architecture of evolu- most centromeres are organized at the molecular level. In tionary constraint. complex eukaryotes, centromeres contain large arrays of tan- To this end, we present a detailed analysis of the evolution of demly repeated satellite sequences, yet their inheritance appears the Drosophila centromeric histone (Cid) in the melanogaster to be largely sequence-independent (reviewed in refs. 1–3). group of species. Comparison of Cid genes across this 25-million- Instead, the presence of specialized centromeric histones is year divergence reveal highly conserved blocks in the histone thought to be a key determinant of centromere identity and fold domain, as expected, with the DNA-binding Loop 1 region maintenance. Centromeric histones (CenH3s) belong to the (14) evolving most rapidly. This analysis also revealed the histone H3 family of proteins, based on homology in the histone unexpected presence of oligopeptide repeats in the N-terminal fold domain, and can replace H3 in nucleosomes (4, 5). However, tail of at least three different lineages of Drosophila Cids. The centromeric chromatin is distinct from the rest of the genome, occurrence of these expansions in some vertebrate CenH3s and as demonstrated by nuclease accessibility studies in both budding their similarity to previously documented peptides that interact and fission yeast (6–8), as well as by topoisomerase II cleavage with the minor groove of DNA suggest an attractive model for patterns of human centromeres (9). Instead of the regular the unique chromatin structure present at centromeres. nucleosomal arrays observed in surrounding heterochromatin, Methods centromeric DNA appears uniformly accessible to nucleases. These findings have led to suggestions that centromeric nucleo- Drosophila species (Table 1) were obtained from the Drosophila somes are randomly arranged (6, 7). A better understanding of Species Center (presently at Tucson, AZ) except for Drosophila this atypical chromatin might be gained by a closer examination trilutea (kind gift of Dr. M.T. Kimura, Hokkaido University, of CenH3 evolution. Japan). Genomic DNA was extracted from all flies and PCR was The structural organization of the C-terminal histone fold carried out to amplify the Cid gene and flanking regions as domain of CenH3 is believed to be very similar to that of H3 described in ref. 10. For more divergent species, additional itself, based on greater than 40% amino acid identity and analysis primers were designed to internal regions of Cid that are Ј Ј of reconstituted nucleosomes (2, 4). However, this domain relatively conserved, 5 -CGGCAGCTTGGGTATCAGTGT-3 evolves more rapidly in CenH3s than in canonical H3s. In addition, whereas H3 has a conserved 45-aa N-terminal tail, those of CenH3s vary in size from 20 to 200 aa, and cannot be Abbreviation: CenH3, centromeric histone H3. Data deposition: The sequences reported in this paper have been deposited in the GenBank aligned across different eukaryotic lineages (2). database (accession nos. AF435454–AF435467). This dichotomy in evolutionary rates between CenH3s and ‡To whom reprint requests should be addressed at: 1100 Fairview Avenue North A1-162, H3s is believed to have two causes. First, whereas the CenH3s are Seattle, WA 98109-1024. E-mail: [email protected]. only required to interact with centromeric DNA, conventional The publication costs of this article were defrayed in part by page charge payment. This H3 needs to interact with, and mediate the expression of, the rest article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. of the genome (10). This requirement results in the latter class §1734 solely to indicate this fact. www.pnas.org͞cgi͞doi͞10.1073͞pnas.032664299 PNAS ͉ February 5, 2002 ͉ vol. 99 ͉ no. 3 ͉ 1449–1454 Downloaded by guest on October 2, 2021 Table 1. Species used in the present study bio.psu.edu͞adaptivevol.html). Briefly, the alignment and phy- Drosophila GenBank logenetic tree are used to infer ancestral codons at all interior species Species group Stock center ID accession nos. nodes of the tree. Next, the total number of synonymous and nonsynonymous substitutions are calculated for each codon and melanogaster melanogaster ref. 3 AF259371 a global average is computed. Adaptive evolution is inferred simulans melanogaster ref. 3 AF321923 when the rate of nonsynonymous substitutions per nonsynony- sechellia melanogaster 14021-0248.0 AF321925 mous site (rN) exceeds that of synonymous substitutions per Ͻ mauritiana melanogaster 14021-0241.0 AF321924 synonymous site (rS) at a significant level. Conversely, if rS rN, yakuba melanogaster 14021-0261.0 AF435454 purifying selection is inferred. The 9-aa expansions in both the teissieri melanogaster 14021-0257.0 AF321926 takahashii and ananassae groups were examined for evidence of orena melanogaster 14021-0245.0 AF435456 natural selection. We used adaptsite-d (Poisson) to calculate rN erecta melanogaster 14021-0224.0 AF435455 and rS followed by adaptsite-t to evaluate statistical significance. takahashii takahashii 14022-0311.0 AF435460 PDB structures of the nucleosome core particle (1AOI, ref. trilutea takahashii Dr. M.T. Kimura AF435457 14) were displayed using the SWISSPDB VIEWER (Version 3.7b2, prostipennis takahashii 14022-0291.0 AF435354 http:͞͞www.expasy.ch͞spdbv). paralutea takahashii 14022-0281.0 AF435458 lutescens takahashii 14022-0271.0 AF435459 Results lucipennis suzukii 14023-0331.0 AF435356 To amplify a phylogenetic range of Cid sequences (Table 1), we mimetica suzukii 14023-0341.0 AF435461 used a PCR strategy using internal primers in conjunction with rajasekhari suzukii 14023-0361.0 AF435355 primers to upstream and downstream genes (10). In all 22 species ananassae ananassae 14024-0371.0 AF435466 studied, the Cid gene lacks introns and varies from 639 to 879 bipectinata ananassae 14024-0381.0* AF435462 nucleotides in length. Most of the length variation in Cid can be malerkotliana ananassae 14024-0391.0 AF435463 attributed to the N-terminal tail, whereas the histone fold pseudoananassae ananassae 14024-0411.0 AF435465 domain is nearly constant in length (schematized in Fig. 1A). parabipectinata ananassae 14024-0401.0
Recommended publications
  • (Pentatomidae) DISSERTATION Presented

    (Pentatomidae) DISSERTATION Presented

    Genome Evolution During Development of Symbiosis in Extracellular Mutualists of Stink Bugs (Pentatomidae) DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Alejandro Otero-Bravo Graduate Program in Evolution, Ecology and Organismal Biology The Ohio State University 2020 Dissertation Committee: Zakee L. Sabree, Advisor Rachelle Adams Norman Johnson Laura Kubatko Copyrighted by Alejandro Otero-Bravo 2020 Abstract Nutritional symbioses between bacteria and insects are prevalent, diverse, and have allowed insects to expand their feeding strategies and niches. It has been well characterized that long-term insect-bacterial mutualisms cause genome reduction resulting in extremely small genomes, some even approaching sizes more similar to organelles than bacteria. While several symbioses have been described, each provides a limited view of a single or few stages of the process of reduction and the minority of these are of extracellular symbionts. This dissertation aims to address the knowledge gap in the genome evolution of extracellular insect symbionts using the stink bug – Pantoea system. Specifically, how do these symbionts genomes evolve and differ from their free- living or intracellular counterparts? In the introduction, we review the literature on extracellular symbionts of stink bugs and explore the characteristics of this system that make it valuable for the study of symbiosis. We find that stink bug symbiont genomes are very valuable for the study of genome evolution due not only to their biphasic lifestyle, but also to the degree of coevolution with their hosts. i In Chapter 1 we investigate one of the traits associated with genome reduction, high mutation rates, for Candidatus ‘Pantoea carbekii’ the symbiont of the economically important pest insect Halyomorpha halys, the brown marmorated stink bug, and evaluate its potential for elucidating host distribution, an analysis which has been successfully used with other intracellular symbionts.
  • Topography of the Histone Octamer Surface: Repeating Structural Motifs Utilized in the Docking of Nucleosomal

    Topography of the Histone Octamer Surface: Repeating Structural Motifs Utilized in the Docking of Nucleosomal

    Proc. Natl. Acad. Sci. USA Vol. 90, pp. 10489-10493, November 1993 Biochemistry Topography of the histone octamer surface: Repeating structural motifs utilized in the docking of nucleosomal DNA (histone fold/helix-strand-helix motif/parallel fi bridge/binary DNA binding sites/nucleosome) GINA ARENTS* AND EVANGELOS N. MOUDRIANAKIS*t *Department of Biology, The Johns Hopkins University, Baltimore, MD 21218; and tDepartment of Biology, University of Athens, Athens, Greece Communicated by Christian B. Anfinsen, August 5, 1993 ABSTRACT The histone octamer core of the nucleosome is interactions. The model offers strong predictive criteria for a protein superhelix offour spirally arrayed histone dimers. The structural and genetic biology. cylindrical face of this superhelix is marked by intradimer and interdimer pseudodyad axes, which derive from the nature ofthe METHODS histone fold. The histone fold appears as the result of a tandem, parallel duplication of the "helix-strand-helix" motif. This The determination of the structure of the histone octamer at motif, by its occurrence in the four dimers, gives rise torepetitive 3.1 A has been described (3). The overall shape and volume structural elements-i.e., the "parallel 13 bridges" and the of this tripartite structure is in agreement with the results of "paired ends of helix I" motifs. A preponderance of positive three independent studies based on differing methodolo- charges on the surface of the octamer appears as a left-handed gies-i.e., x-ray diffraction, neutron diffraction, and electron spiral situated at the expected path of the DNA. We have microscopic image reconstruction (4-6). Furthermore, the matched a subset of DNA pseudodyads with the octamer identification of the histone fold, a tertiary structure motif of pseudodyads and thus have built a model of the nucleosome.
  • Differential Evolvability Along Lines of Least Resistance of Upper and Lower Molars in Island House Mice

    Differential Evolvability Along Lines of Least Resistance of Upper and Lower Molars in Island House Mice

    Differential Evolvability Along Lines of Least Resistance of Upper and Lower Molars in Island House Mice Sabrina Renaud1*, Sophie Pantalacci2, Jean-Christophe Auffray3 1 Laboratoire de Biome´trie et Biologie Evolutive, Universite´ Lyon 1, CNRS, Villeurbanne, France, 2 Molecular Zoology Team, Institut de Ge´nomique Fonctionnelle de Lyon, Universite´ de Lyon, CNRS, Ecole Normale Supe´rieure de Lyon, Lyon, France, 3 Institut des Sciences de l’Evolution, Universite´ Montpellier 2, CNRS, Montpellier, France Abstract Variation within a population is a key feature in evolution, because it can increase or impede response to selection, depending on whether or not the intrapopulational variance is correlated to the change under selection. Hence, main directions of genetic variance have been proposed to constitute ‘‘lines of least resistance to evolution’’ along which evolution would be facilitated. Yet, the screening of selection occurs at the phenotypic level, and the phenotypic variance is not only the product of the underlying genetic variance, but also of developmental processes. It is thus a key issue for interpreting short and long term evolutionary patterns to identify whether main directions of phenotypic variance indeed constitute direction of facilitated evolution, and whether this is favored by developmental processes preferably generating certain phenotypes. We tackled these questions by a morphometric quantification of the directions of variance, compared to the direction of evolution of the first upper and lower molars of wild continental and insular house mice. The main phenotypic variance indeed appeared as channeling evolution between populations. The upper molar emerged as highly evolvable, because a strong allometric component contributed to its variance.
  • (Non)Parallel Evolution 3 4 Daniel I. Bolnick1,2*, Rowan Barrett3, Krista

    (Non)Parallel Evolution 3 4 Daniel I. Bolnick1,2*, Rowan Barrett3, Krista

    1 2 3 (Non)Parallel Evolution 4 5 Daniel I. Bolnick1,2*, Rowan Barrett3, Krista Oke3,4 , Diana J. Rennison5 , Yoel E. Stuart1 6 7 1 Department of Integrative Biology, University of Texas at Austin, Austin TX 78712, USA; 8 [email protected]; [email protected] 9 2 Department of Ecology and Evolution, University of Connecticut, Storrs CT 06268, USA (as of 10 07/2018) 11 3 Redpath Museum, McGill University, Montreal, Quebec, Canada; [email protected] 12 4 Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa 13 Cruz, CA, 95060, USA; [email protected] 14 5 Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland; 15 [email protected] 16 17 * Corresponding author: Email: [email protected] Telephone: +011 (512) 471-2824 18 19 20 Running title: “(Non)Parallel Evolution” 21 22 1 23 Abstract 24 Parallel evolution across replicate populations has provided evolutionary biologists with iconic 25 examples of adaptation. When multiple populations colonize seemingly similar habitats, they 26 may evolve similar genes, traits, or functions. Yet, replicated evolution in nature or in the lab 27 often yields inconsistent outcomes: some replicate populations evolve along highly similar 28 trajectories, whereas other replicate populations evolve to different extents or in atypical 29 directions. To understand these heterogeneous outcomes, biologists are increasingly treating 30 parallel evolution not as a binary phenomenon but rather as a quantitative continuum ranging 31 from nonparallel to parallel. By measuring replicate populations’ positions along this 32 “(non)parallel” continuum, we can test hypotheses about evolutionary and ecological factors that 33 influence the likelihood of repeatable evolution.
  • Functional Domains for Assembly of Histones H3 and H4 Into the Chromatin of Xenopus Embryos

    Functional Domains for Assembly of Histones H3 and H4 Into the Chromatin of Xenopus Embryos

    Proc. Natl. Acad. Sci. USA Vol. 93, pp. 12780–12785, November 1996 Biochemistry Functional domains for assembly of histones H3 and H4 into the chromatin of Xenopus embryos LITA FREEMAN,HITOSHI KURUMIZAKA, AND ALAN P. WOLFFE* Laboratory of Molecular Embryology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-2710 Communicated by Stuart L. Schreiber, Harvard University, Cambridge, MA, September 3, 1996 (received for review May 31, 1996) ABSTRACT Histones H3 and H4 have a well defined Modification of the N-terminal tail of H4 by acetylation has structural role in the nucleosome and an established role in been correlated with both transcription (25, 26) and nucleo- the regulation of transcription. We have made use of a some assembly (27, 28). Direct evidence for a causal role for microinjection strategy using Xenopus embryos to define the H4 acetylation in these events is, however, yet to be estab- minimal structural components of H3 and H4 necessary for lished. Tryptic removal of the N-terminal tail of histone H4 nucleosome assembly into metazoan chromosomes in vivo.We from the nucleosome or acetylation of the tail does not find that both the N-terminal tail of H4, including all sites of influence the helical periodicity of DNA in the nucleosome but acetylation, and the C-terminal a-helix of the H4 histone fold might influence the exact path taken by the double helix as it domain are dispensable for chromatin assembly. The N- wraps around the histone fold domains of the core histones (29, terminal tail and an N-terminal a-helix of H3 are also 30).
  • Johnson Stander 2020

    Johnson Stander 2020

    Gene Regulatory Network Homoplasy Underlies Recurrent Sexually Dimorphic Fruit Fly Pigmentation Jesse Hughes, Rachel Johnson, and Thomas M. Williams The Department of Biology at the University of Dayton; 300 College Park, Dayton, OH 45469 ABSTRACT Widespread Dimorphism in Sophophora and Beyond Pigment Metabolic Pathway Utilization in H. duncani Species with dimorphic tergite pigmentation are Traits that appear discontinuously along phylogenies may be explained by independent ori- widespread throughout the Drosophila genus. (A-E) Female and (A’-E’) male expressions of H. duncani gins (homoplasy) or repeated loss (homology). While discriminating between these models Sophophora subgenus species groups and species pigment metabolic pathway genes, and (F and F’) cartoon is difficult, the dissection of gene regulatory networks (GRNs) which drive the development are indicated by the gray background. D. busckii and representation of the pigmentation phenotype. (G) of such repeatedly occurring traits can offer a mechanistic window on this fundamental Summary of the H. duncani pathway use includes robust D. funebris are included as non-Sophophora species problem. The GRN responsible for the male-specific pattern of Drosophila (D.) melano- expression of all genes, with dimorphic expressions of Ddc, from the Drosophila genus that respectively exhibit gaster melanic tergite pigmentation has received considerable attention. In this system, a ebony, tan, and yellow. (A, A’) pale, (B, B’) Ddc, (C, C’) monomorphic and dimorphic patterns of tergite metabolic pathway of pigmentation enzyme genes is expressed in spatial and sex-specific ebony, (D, D’) tan, and (E, E’) yellow. Red arrowheads pigmentation. The homologous A5 and A6 segment (i.e., dimorphic) patterns. The dimorphic expression of several genes is regulated by the indicate robust patterns of dimorphic expression in the tergites are indicated for each species, the segments Bab transcription factors, which suppress pigmentation enzyme expression in females, by dorsal abdominal epidermis.
  • 1 Recurrent Evolution of Two Competing Haplotypes in An

    1 Recurrent Evolution of Two Competing Haplotypes in An

    bioRxiv preprint doi: https://doi.org/10.1101/2020.05.14.096024; this version posted May 19, 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-NC-ND 4.0 International license. Recurrent evolution of two competing haplotypes in an insect DNA virus Tom Hill1*, Robert L. Unckless1 1. 4055 Haworth Hall, The Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045. * Corresponding author - Email: [email protected] Keywords: nudivirus, Drosophila innubila, DiNV, virulence, coevolution 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.14.096024; this version posted May 19, 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-NC-ND 4.0 International license. 1 Abstract 2 Hosts and viruses are constantly evolving in response to each other: as hosts attempt to suppress the virus, 3 the virus attempts to evade and suppress the host’s immune system. This arms race results in the evolution 4 of novel pathways in both the host and virus to gain the upper hand. Here we describe the coevolution 5 between Drosophila species and a common and virulent DNA virus. We identify two distinct viral types 6 that differ 100-fold in viral titer in infected individuals, with similar effects across multiple species.
  • Rapid and Widespread De Novo Evolution of Kin Discrimination

    Rapid and Widespread De Novo Evolution of Kin Discrimination

    Rapid and widespread de novo evolution of kin discrimination Olaya Renduelesa,1, Peter C. Zeeb,c, Iris Dinkelackerd, Michaela Amherda, Sébastien Wielgossa, and Gregory J. Velicera,b,d aInstitute for Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland; bDepartment of Biology, Indiana University, Bloomington, IN 47405; cDepartment of Biology, California State University-Northridge, Northridge, CA 91330; and dDepartment of Evolutionary Biology, Max-Planck Institute for Developmental Biology, 72076 Tübingen, Germany Edited by Richard E. Lenski, Michigan State University, East Lansing, MI, and approved June 1, 2015 (received for review February 3, 2015) Diverse forms of kin discrimination, broadly defined as alteration that formed between distinct nonmerging colonies of the bacterium of social behavior as a function of genetic relatedness among Proteus mirabilis (21) and has since been found in several other interactants, are common among social organisms from microbes species (20, 22). For example, a large number of such colony- to humans. However, the evolutionary origins and causes of kin- merger incompatibilities evolved among closely related genotypes of discriminatory behavior remain largely obscure. One form of kin the cooperative bacterium Myxococcus xanthus in a natural centi- discrimination observed in microbes is the failure of genetically meter-scale population (20). Irrespective of their original evolu- distinct colonies to merge freely upon encounter. Here, we first use tionary cause(s), the emergence of colony-merger incompatibilities natural isolates of the highly social bacterium Myxococcus xanthus to in nature is likely to have profound implications for the distribution show that colony-merger incompatibilities can be strong barriers to of social interactions among genotypes during cooperative pro- social interaction, particularly by reducing chimerism in multicellular cesses.
  • Crystal Structure of the Nucleosome Core Particle at 2.8Å Resolution Karolin Luger, Armin W

    Crystal Structure of the Nucleosome Core Particle at 2.8Å Resolution Karolin Luger, Armin W

    Crystal structure of the nucleosome core particle at 2.8Å resolution Karolin Luger, Armin W. Mader, Robin K. Richmond, David R Sargent & Timothy J. Richmond Institut fur Molekularbiologie und Biophysik ETHZ, ETH-Hönggerberg, CH-8093 Zürich, Switzerland Nature, Vol 389, pages 251-260 The X-ray crystal structure of the nucleosome core particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it. Both histone/histone and histone/DNA interactions depend on the histone fold domains and additional, well ordered structure elements extending from this motif. Histone amino-terminal tails pass over and between the gyros of the DNA superhelix to contact neighboring particles. The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry. DNA in chromatin is organized in arrays of nucleosomes (1). Two copies of each histone protein, H2A, H2B, H3 and H4, are assembled into an octamer that has 145-147 base pairs (bp) of DNA wrapped around it to form a nucleosome core (of relative molecular mass 206K). This highly conserved nucleoprotein complex occurs essentially every 200 ± 40 bp throughout all eukaryotic genomes (2). The repeating nucleosome cores further assemble into higher-order structures which are stabilized by the linker histone H1 and these compact linear DNA overall by a factor of 30-40. The nucleosome (nucleosome core, linker DNA and H1) thereby shapes the DNA molecule both at the atomic level through DNA bending, and on the much larger scale of genes by forming higher- order helices (3).
  • Predicting the Genetic Loci of Past Evolution

    Predicting the Genetic Loci of Past Evolution

    bioRxiv preprint doi: https://doi.org/10.1101/205153; this version posted October 19, 2017. 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 4.0 International license. Predicting the genetic loci of past evolution Virginie Courtier-Orgogozo1 and Arnaud Martin2 1CNRS UMR 7592, Institut Jacques Monod, Paris, France 2Department of Biological Sciences, The George Washington University, Washington, DC, USA *Correspondence to: [email protected] 34,941 characters excluding spaces (excluding tables) Abstract Repetitions in the mutations found to be responsible for independent evolution of similar phenotypes in various taxa have led some biologists to propose that for certain evolutionary changes the causal mutations are predictable. We examine here the nature of the predictions that have been made and their associated arguments. Predictions about the loci of past evolution are retrodictions, i.e. inferences about events that occurred in the past. They are not based on elaborate models and they derive mainly from the observation of repeated cases of genetic evolution. Predictions at the nucleotide level or at the gene level have a higher inference gain than those for broader categories of genetic changes such as cis-regulatory mutations. Introduction Evolution reveals itself by the changes in observable characteristics of biological populations over successive generations. Here we focus on the DNA mutations underlying phenotypic changes that have occurred during natural evolution of populations or species, as well as through domestication and experimental evolution.
  • Containing Protein That Replaces TAF6 in Drosophila SAGA Is Required for SAGA-Dependent Gene Expression

    Containing Protein That Replaces TAF6 in Drosophila SAGA Is Required for SAGA-Dependent Gene Expression

    Downloaded from genesdev.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH COMMUNICATION shown previously that Drosophila SAGA (dSAGA) in- A novel histone fold domain- cludes the orthologs of most components of the yeast containing protein that replaces SAGA (ySAGA) complex (Supplemental Table S1; Kusch et al. 2003; Muratoglu et al. 2003; Guelman et al. 2006; TAF6 in Drosophila SAGA is Kurshakova et al. 2007; Weake et al. 2008). In addition, required for SAGA-dependent dSAGA contains subunits that are unique to the fly com- plex, such as the WD repeat-containing protein WDA gene expression (Guelman et al. 2006). SAGA is essential for development in multicellular Vikki M. Weake,1 Selene K. Swanson,1 organisms, and Gcn5 is required for viability in both Arcady Mushegian,1,2 Laurence Florens,1 mice and Drosophila (Xu et al. 2000; Carre et al. 2005). Michael P. Washburn,1,3 Susan M. Abmayr,1,4 Furthermore, mutations that disrupt the HAT activity of and Jerry L. Workman1,5 dSAGA, such as ada2b and wda, result in lethality in flies (Qi et al. 2004; Pankotai et al. 2005; Guelman et al. 2006). 1Stowers Institute for Medical Research, Kansas City, Missouri Moreover, mutations that specifically affect the ubiquitin 64110, USA; 2Department of Microbiology, Molecular Genetics protease activity of dSAGA are lethal, and result in and Immunology, University of Kansas Medical Center, Kansas defects in axon targeting in the larval eye–brain complex City, Kansas 66160, USA; 3Department of Pathology and (Weake et al. 2008). To characterize dSAGA more fully, Laboratory Medicine, University of Kansas Medical Center, we sought to identify orthologs of all ySAGA compo- Kansas City, Kansas 66160, USA; 4Department of Anatomy and nents, as there are subunits present in the ySAGA and Cell Biology, University of Kansas Medical Center, Kansas City, human SAGA complexes for which orthologs have not Kansas 66160, USA yet been identified in flies (Rodriguez-Navarro 2009).
  • Histone Variants — Ancient Wrap Artists of the Epigenome

    Histone Variants — Ancient Wrap Artists of the Epigenome

    REVIEWS CHROMATIN DYNAMICS Histone variants — ancient wrap artists of the epigenome Paul B. Talbert and Steven Henikoff Abstract | Histones wrap DNA to form nucleosome particles that compact eukaryotic genomes. Variant histones have evolved crucial roles in chromosome segregation, transcriptional regulation, DNA repair, sperm packaging and other processes. ‘Universal’ histone variants emerged early in eukaryotic evolution and were later displaced for bulk packaging roles by the canonical histones (H2A, H2B, H3 and H4), the synthesis of which is coupled to DNA replication. Further specializations of histone variants have evolved in some lineages to perform additional tasks. Differences among histone variants in their stability, DNA wrapping, specialized domains that regulate access to DNA, and post-translational modifications, underlie the diverse functions that histones have acquired in evolution. Histone chaperone Nearly all eukaryotes wrap their DNA around histones to In this Review, we consider the diversity and evolution of An escort protein that form nucleosomes that compact the genome while still core histone variants, from archaeal ancestors to univer- performs a transfer reaction on allowing access for active processes such as trans cription, sal eukaryotic variants to lineage-specific variants and a histone, such as deposition replication and DNA repair. Each nucleosome core variant-specific post-translational modifications (PTMs). onto DNA, eviction from DNA, transfer to another chaperone particle comprises ~ 147 bp of DNA wrapped in 1.7 turns We summarize their diverse and dynamic interactions as or enzyme, or storage for later around a protein octamer of 2 molecules of each of the 4 ‘wrap artists’ of DNA and discuss recent developments use.