Alu-mediated acquisition of unstable ATTCT pentanucleotide repeats in the human ATXN10 gene.

Abstract:

:Spinocerebellar ataxia type 10 is caused by ATTCT repeat expansion in the ATXN10 gene in humans. We studied the evolutionary history of the human genome to determine the time and mechanism of the acquisition of unstable ATTCT repeats in the genome. We found that long interspersed element-1 (LINE-1) was inserted into ATXN10 intron 9; Alu was then inserted in the middle of LINE-1; and endogenous retrovilcus K was lastly retrotransposed in the middle of Alu. The ATTCT repeat was located on the boundary between the 3'-end of the Alu element and the direct repeat arising from LINE-1. We determined nucleotide sequences of the orthologous region of 50 individuals representing 33 primate species and compared them with the human sequence. The analysis revealed that the ATTCT repeat is present only in human and apes. Old World monkeys also possess pentanucleotide repeats, but their motifs are TGTCT and GGTCT. New World monkeys and prosimians are not informative because they lack the corresponding region in ATXN10 intron 9. Our studies dictate two parsimonious scenarios of evolution. First, a TTTCT motif arose from a TTTTT motif at the junction of Alu and LINE-1, which was followed by introduction of A to make an ATTCT motif in hominoids. Second, an ATTCT motif was directly generated from an ancestral ATTTT motif in the common ancestor of catarrhines. We also demonstrate that orangutan uniquely introduced G to make a GTTCT motif and later C to make a GTTCC motif, where newly introduced nucleotides are underlined. Our studies reveal that nucleotide substitutions in a poly(A) tail of the Alu element and the following amplification of pentanucleotides occurred in the lineages of Old World monkeys and hominoids and that unstable ATTCT pentanucleotide repeats originated in the common ancestor of hominoids. These findings also highlight a new aspect of the role of retrotransposons in human disease and evolution, which might be useful in investigating the mystery of human uniqueness.

journal_name

Mol Biol Evol

authors

Kurosaki T,Matsuura T,Ohno K,Ueda S

doi

10.1093/molbev/msp172

subject

Has Abstract

pub_date

2009-11-01 00:00:00

pages

2573-9

issue

11

eissn

0737-4038

issn

1537-1719

pii

msp172

journal_volume

26

pub_type

杂志文章
  • The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi.

    abstract::Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or "specialized" metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and cha...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa122

    authors: Gluck-Thaler E,Haridas S,Binder M,Grigoriev IV,Crous PW,Spatafora JW,Bushley K,Slot JC

    更新日期:2020-10-01 00:00:00

  • Nonneutral evolution of the transcribed pseudogene Makorin1-p1 in mice.

    abstract::Pseudogenes are nonfunctional relics of formerly functional genes and are thought to evolve neutrally. In some pseudogenes, however, the molecular evolutionary patterns are atypical of neutrally evolving sequences, exhibiting sequence conservation, codon-usage bias, and other features associated with functional genes....

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msh230

    authors: Podlaha O,Zhang J

    更新日期:2004-12-01 00:00:00

  • Evolution of the T1 retroposon family in the Anopheles gambiae complex.

    abstract::The T1 family of retrotransposable elements is interspersed and moderately repeated in five member species of the Anopheles gambiae sibling-species complex and has diverged little since the radiation of the complex. T1 includes two closely related but independent subfamilies, defined by the presence or absence of link...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a040599

    authors: Besansky NJ

    更新日期:1990-05-01 00:00:00

  • Splicing and transcription differ between spore and intracellular life stages in the parasitic microsporidia.

    abstract::Microsporidia are a diverse group of highly derived fungal relatives that are intracellular parasites of many animals. Both transcription and introns have been shown to be unusual in microsporidia: The complete genome of the human parasite Encephalitozoon cuniculi has only a few very short introns, and two distantly r...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq050

    authors: Gill EE,Lee RC,Corradi N,Grisdale CJ,Limpright VO,Keeling PJ,Fast NM

    更新日期:2010-07-01 00:00:00

  • Proteomic Analysis of Histones H2A/H2B and Variant Hv1 in Tetrahymena thermophila Reveals an Ancient Network of Chaperones.

    abstract::Epigenetic information, which can be passed on independently of the DNA sequence, is stored in part in the form of histone posttranslational modifications and specific histone variants. Although complexes necessary for deposition have been identified for canonical and variant histones, information regarding the chroma...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msz039

    authors: Ashraf K,Nabeel-Shah S,Garg J,Saettone A,Derynck J,Gingras AC,Lambert JP,Pearlman RE,Fillingham J

    更新日期:2019-05-01 00:00:00

  • Ylli, a non-LTR retrotransposon L1 family in the dimorphic yeast Yarrowia lipolytica.

    abstract::During the course of a random sequencing project of the genome of the dimorphic yeast Yarrowia lipolytica, we have identified sequences that were repeated in the genome and that matched the reverse transcriptase (RT) sequence of non-long terminal repeat (non-LTR) retrotransposons. Extension of sequencing on each side ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a004125

    authors: Casaregola S,Neuvéglise C,Bon E,Gaillardin C

    更新日期:2002-05-01 00:00:00

  • The adaptation of enzymes to temperature: catalytic characterization of glucosephosphate isomerase homologues isolated from Mytilus edulis and Isognomon alatus, bivalve molluscs inhabiting different thermal environments.

    abstract::Homologues of glucosephosphate isomerase (GPI, EC 5.3.1.9) were purified to homogeneity and kinetically characterized from Mytilus edulis and Isognomon alatus, two bivalve molluscs experiencing contrasting thermal environments. The enzyme isolated from I. alatus functions at warmer temperatures (25-35 C) than GPI from...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a040346

    authors: Hall JG

    更新日期:1985-05-01 00:00:00

  • Nucleotide polymorphism in the acidic chitinase locus (ChiA) region of the wild plant Arabidopsis thaliana.

    abstract::To investigate DNA variation in natural plant populations, a 1.8-kb region of the acidic chitinase locus (ChiA)was analyzed for 17 ecotypes of Arabidopsis thaliana sampled worldwide and 3 Arabis species in Japan. As in the Adh region, dimorphism was detected throughout the investigated ChiA region, suggesting the poss...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025740

    authors: Kawabe A,Innan H,Terauchi R,Miyashita NT

    更新日期:1997-12-01 00:00:00

  • Molecular clocks do not support the Cambrian explosion.

    abstract::The fossil record has long supported the view that most animal phyla originated during a brief period approximately 520 MYA known as the Cambrian explosion. However, molecular data analyses over the past 3 decades have found deeper divergences among animals (approximately 800 to 1,200 MYA), with and without the assump...

    journal_title:Molecular biology and evolution

    pub_type: 信件

    doi:10.1093/molbev/msi039

    authors: Blair JE,Hedges SB

    更新日期:2005-03-01 00:00:00

  • Nucleotide sequence analysis of the human salivary protein genes HIS1 and HIS2, and evolution of the STATH/HIS gene family.

    abstract::Human histatins are a family of low-M(r), neutral to very basic, histidine-rich salivary polypeptides. They probably function as part of the nonimmune host defense system in the oral cavity. A 39-kb region of DNA containing the HIS1 and HIS2 genes was isolated from two human genomic phage libraries as a series of over...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a040022

    authors: Sabatini LM,Ota T,Azen EA

    更新日期:1993-05-01 00:00:00

  • Ancient origin of glycosyl hydrolase family 9 cellulase genes.

    abstract::While it is widely accepted that most animals (Metazoa) do not have endogenous cellulases, relying instead on intestinal symbionts for cellulose digestion, the glycosyl hydrolase family 9 (GHF9) cellulases found in the genomes of termites, abalone, and sea squirts could be an exception. Using information from expresse...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msi107

    authors: Davison A,Blaxter M

    更新日期:2005-05-01 00:00:00

  • Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes.

    abstract::Gene orders have been shown to be generally unstable by comprehensive analyses in several complete genomes. In this study, we examined instability of genome structures within operons, where functionally related genes are clustered. We compared gene orders of known operons obtained from Escherichia coli and Bacillus su...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a026114

    authors: Itoh T,Takemoto K,Mori H,Gojobori T

    更新日期:1999-03-01 00:00:00

  • Rapid R2 retrotransposition leads to the loss of previously inserted copies via large deletions of the rDNA locus.

    abstract::R2 non-long terminal repeat retrotransposable elements insert specifically into the 28S rRNA genes of a wide range of animals. These elements maintain long-term stable relationships with the host genome. By scoring the variation present at the 5' ends of individual R2 copies, lines of Drosophila simulans have been ide...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msm250

    authors: Zhang X,Zhou J,Eickbush TH

    更新日期:2008-01-01 00:00:00

  • High rate of large-scale hemizygous deletions in asexually propagating Daphnia: implications for the evolution of sex.

    abstract::The origin and maintenance of sex remains one of the most debated topics in evolutionary biology. Investigations of the molecular genetic consequences of asexuality, such as direct estimation of mutation and recombination rates in asexual lineages, are critical for explaining the prevalence of sex in nature. In this s...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq199

    authors: Xu S,Omilian AR,Cristescu ME

    更新日期:2011-01-01 00:00:00

  • Recurrent positive selection of the Drosophila hybrid incompatibility gene Hmr.

    abstract::Lethality in hybrids between Drosophila melanogaster and its sibling species Drosophila simulans is caused in part by the interaction of the genes Hybrid male rescue (Hmr) and Lethal hybrid rescue (Lhr). Hmr and Lhr have diverged under positive selection in the hybridizing species. Here we test whether positive select...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msn190

    authors: Maheshwari S,Wang J,Barbash DA

    更新日期:2008-11-01 00:00:00

  • Maximum-likelihood phylogenetic analysis under a covarion-like model.

    abstract::Here, a model allowing covarion-like evolution of DNA sequences is introduced. In contrast to standard representation of the distribution of evolutionary rates, this model allows the site-specific rate to vary between lineages. This is achieved by adding as few as two parameters to the widely used among-site rate vari...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a003868

    authors: Galtier N

    更新日期:2001-05-01 00:00:00

  • Nineteenth century seeds reveal the population genetics of landrace barley (Hordeum vulgare).

    abstract::Barley (Hordeum vulgare) is a major crop, grown worldwide and in a wide range of climatic conditions. Despite its importance as a crop species, little is known about the population genetics of barley and the effects of bottlenecks, adaptation, and gene flow on genetic diversity within and between landrace populations....

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msp308

    authors: Leino MW,Hagenblad J

    更新日期:2010-04-01 00:00:00

  • Recent Out-of-Africa Migration of Human Herpes Simplex Viruses.

    abstract::Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results ind...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa001

    authors: Forni D,Pontremoli C,Clerici M,Pozzoli U,Cagliani R,Sironi M

    更新日期:2020-05-01 00:00:00

  • SPIn: model selection for phylogenetic mixtures via linear invariants.

    abstract::In phylogenetic inference, an evolutionary model describes the substitution processes along each edge of a phylogenetic tree. Misspecification of the model has important implications for the analysis of phylogenetic data. Conventionally, however, the selection of a suitable evolutionary model is based on heuristics or...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msr259

    authors: Kedzierska AM,Drton M,Guigó R,Casanellas M

    更新日期:2012-03-01 00:00:00

  • Mitochondrial genomic rearrangements in songbirds.

    abstract::The organization of the mitochondrial genome is generally very conserved among vertebrates. Because of this, examination of the rare rearrangements which do occur has been suggested as offering a powerful alternative to phylogenetic analyses of mitochondrial DNA sequences. Here, we report on an avian mitochondrial rea...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a026223

    authors: Bensch S,Härlid A

    更新日期:2000-01-01 00:00:00

  • Phylogenomic analysis of the uracil-DNA glycosylase superfamily.

    abstract::The spontaneous deamination of cytosine produces uracil mispaired with guanine in DNA, which will produce a mutation, unless repaired. In all domains of life, uracil-DNA glycosylases (UDGs) are responsible for the elimination of uracil from DNA. Thus, UDGs contribute to the integrity of the genetic information and the...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq318

    authors: Lucas-Lledó JI,Maddamsetti R,Lynch M

    更新日期:2011-03-01 00:00:00

  • Molecular distance and divergence time in carnivores and primates.

    abstract::Numerous studies have used indices of genetic distance between species to reconstruct evolutionary relationships and to estimate divergence time. However, the empirical relationship between molecular-based indices of genetic divergence and divergence time based on the fossil record is poorly known. To date, the result...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a040651

    authors: Wayne RK,Van Valkenburgh B,O'Brien SJ

    更新日期:1991-05-01 00:00:00

  • Estimation of genetic distance and coefficient of gene diversity from single-probe multilocus DNA fingerprinting data.

    abstract::DNA fingerprinting exhibits multilocus genotypes of individuals, detected by the use of a single multilocus probe. Consequently, population data on DNA fingerprinting do not provide a complete characterization of the genetic variation in terms of allele-frequency distributions, since neither the number of loci nor the...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a040086

    authors: Jin L,Chakraborty R

    更新日期:1994-01-01 00:00:00

  • Gene duplications and losses within the cyclooxygenase family of teleosts and other chordates.

    abstract::Cyclooxygenase (COX) produces prostaglandins in animals via the oxidation and reduction of arachidonic acid. Different types and numbers of COX genes have been found in corals, sea squirts, fishes, and tetrapods, but no study has used a comparative phylogenetic approach to investigate the evolutionary history of this ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msn183

    authors: Havird JC,Miyamoto MM,Choe KP,Evans DH

    更新日期:2008-11-01 00:00:00

  • Chordate Hox and ParaHox gene clusters differ dramatically in their repetitive element content.

    abstract::The ParaHox and Hox gene clusters control aspects of animal anterior-posterior development and are related as paralogous evolutionary sisters. Despite this relationship, it is not clear if the clusters operate in similar ways, with similar constraints. To compare clusters, we examined the transposable-element (TE) con...

    journal_title:Molecular biology and evolution

    pub_type: 信件

    doi:10.1093/molbev/msp235

    authors: Osborne PW,Ferrier DE

    更新日期:2010-02-01 00:00:00

  • Influence of mutational and sampling factors on the estimation of demographic parameters in a "continuous" population under isolation by distance.

    abstract::In numerous species, individual dispersal is restricted in space so that "continuous" populations evolve under isolation by distance. A method based on individual genotypes assuming a lattice population model was recently developed to estimate the product Dsigma2, where D is the population density and sigma2 is the av...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msg034

    authors: Leblois R,Estoup A,Rousset F

    更新日期:2003-04-01 00:00:00

  • Phylogenetic analysis of the 90 kD heat shock family of protein sequences and an examination of the relationship among animals, plants, and fungi species.

    abstract::The heat shock protein (Hsp) sequences, because of their ubiquity and high degree of conservation, provide useful models for phylogenetic analysis. In this paper I have carried out a global alignment of all available sequences (a total of 31) for the 90-kD heat shock protein (Hsp90) family. The minimum amino acid iden...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a040281

    authors: Gupta RS

    更新日期:1995-11-01 00:00:00

  • Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice.

    abstract::Varying degrees of reduction of genetic diversity in crops relative to their wild progenitors occurred during the process of domestication. Such information, however, has not been available for the Asian cultivated rice (Oryza sativa) despite its importance as a staple food and a model organism. To reveal levels and p...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msm005

    authors: Zhu Q,Zheng X,Luo J,Gaut BS,Ge S

    更新日期:2007-03-01 00:00:00

  • Alternative Evolutionary Paths to Bacterial Antibiotic Resistance Cause Distinct Collateral Effects.

    abstract::When bacteria evolve resistance against a particular antibiotic, they may simultaneously gain increased sensitivity against a second one. Such collateral sensitivity may be exploited to develop novel, sustainable antibiotic treatment strategies aimed at containing the current, dramatic spread of drug resistance. To da...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msx158

    authors: Barbosa C,Trebosc V,Kemmer C,Rosenstiel P,Beardmore R,Schulenburg H,Jansen G

    更新日期:2017-09-01 00:00:00

  • A Working Model of the Deep Relationships of Diverse Modern Human Genetic Lineages Outside of Africa.

    abstract::A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogen...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msw293

    authors: Lipson M,Reich D

    更新日期:2017-04-01 00:00:00