Endogenous viral elements in animal genomes.


:Integration into the nuclear genome of germ line cells can lead to vertical inheritance of retroviral genes as host alleles. For other viruses, germ line integration has only rarely been documented. Nonetheless, we identified endogenous viral elements (EVEs) derived from ten non-retroviral families by systematic in silico screening of animal genomes, including the first endogenous representatives of double-stranded RNA, reverse-transcribing DNA, and segmented RNA viruses, and the first endogenous DNA viruses in mammalian genomes. Phylogenetic and genomic analysis of EVEs across multiple host species revealed novel information about the origin and evolution of diverse virus groups. Furthermore, several of the elements identified here encode intact open reading frames or are expressed as mRNA. For one element in the primate lineage, we provide statistically robust evidence for exaptation. Our findings establish that genetic material derived from all known viral genome types and replication strategies can enter the animal germ line, greatly broadening the scope of paleovirological studies and indicating a more significant evolutionary role for gene flow from virus to animal genomes than has previously been recognized.


PLoS Genet


PLoS genetics


Katzourakis A,Gifford RJ




Has Abstract


2010-11-18 00:00:00












  • A kinase-independent role for the Rad3(ATR)-Rad26(ATRIP) complex in recruitment of Tel1(ATM) to telomeres in fission yeast.

    abstract::ATM and ATR are two redundant checkpoint kinases essential for the stable maintenance of telomeres in eukaryotes. Previous studies have established that MRN (Mre11-Rad50-Nbs1) and ATRIP (ATR Interacting Protein) interact with ATM and ATR, respectively, and recruit their partner kinases to sites of DNA damage. Here, we...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Subramanian L,Nakamura TM

    更新日期:2010-02-05 00:00:00

  • The genomic landscape of undifferentiated embryonal sarcoma of the liver is typified by C19MC structural rearrangement and overexpression combined with TP53 mutation or loss.

    abstract::Undifferentiated embryonal sarcoma of the liver (UESL) is a rare and aggressive malignancy. Though the molecular underpinnings of this cancer have been largely unexplored, recurrent chromosomal breakpoints affecting a noncoding region on chr19q13, which includes the chromosome 19 microRNA cluster (C19MC), have been re...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Setty BA,Jinesh GG,Arnold M,Pettersson F,Cheng CH,Cen L,Yoder SJ,Teer JK,Flores ER,Reed DR,Brohl AS

    更新日期:2020-04-20 00:00:00

  • Learning the properties of adaptive regions with functional data analysis.

    abstract::Identifying regions of positive selection in genomic data remains a challenge in population genetics. Most current approaches rely on comparing values of summary statistics calculated in windows. We present an approach termed SURFDAWave, which translates measures of genetic diversity calculated in genomic windows to f...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Mughal MR,Koch H,Huang J,Chiaromonte F,DeGiorgio M

    更新日期:2020-08-27 00:00:00

  • Genetic analysis of variation in human meiotic recombination.

    abstract::The number of recombination events per meiosis varies extensively among individuals. This recombination phenotype differs between female and male, and also among individuals of each gender. In this study, we used high-density SNP genotypes of over 2,300 individuals and their offspring in two datasets to characterize r...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Chowdhury R,Bois PR,Feingold E,Sherman SL,Cheung VG

    更新日期:2009-09-01 00:00:00

  • Continent-wide decoupling of Y-chromosomal genetic variation from language and geography in native South Americans.

    abstract::Numerous studies of human populations in Europe and Asia have revealed a concordance between their extant genetic structure and the prevailing regional pattern of geography and language. For native South Americans, however, such evidence has been lacking so far. Therefore, we examined the relationship between Y-chromo...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Roewer L,Nothnagel M,Gusmão L,Gomes V,González M,Corach D,Sala A,Alechine E,Palha T,Santos N,Ribeiro-Dos-Santos A,Geppert M,Willuweit S,Nagy M,Zweynert S,Baeta M,Núñez C,Martínez-Jarreta B,González-Andrade F,Fagunde

    更新日期:2013-04-01 00:00:00

  • Allele frequency matching between SNPs reveals an excess of linkage disequilibrium in genic regions of the human genome.

    abstract::Significant interest has emerged in mapping genetic susceptibility for complex traits through whole-genome association studies. These studies rely on the extent of association, i.e., linkage disequilibrium (LD), between single nucleotide polymorphisms (SNPs) across the human genome. LD describes the nonrandom associat...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Eberle MA,Rieder MJ,Kruglyak L,Nickerson DA

    更新日期:2006-09-08 00:00:00

  • Genetic analysis of floral symmetry in Van Gogh's sunflowers reveals independent recruitment of CYCLOIDEA genes in the Asteraceae.

    abstract::The genetic basis of floral symmetry is a topic of great interest because of its effect on pollinator behavior and, consequently, plant diversification. The Asteraceae, which is the largest family of flowering plants, is an ideal system in which to study this trait, as many species within the family exhibit a compound...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Chapman MA,Tang S,Draeger D,Nambeesan S,Shaffer H,Barb JG,Knapp SJ,Burke JM

    更新日期:2012-01-01 00:00:00

  • Supramolecular assembly of the beta-catenin destruction complex and the effect of Wnt signaling on its localization, molecular size, and activity in vivo.

    abstract::Wnt signaling provides a paradigm for cell-cell signals that regulate embryonic development and stem cell homeostasis and are inappropriately activated in cancers. The tumor suppressors APC and Axin form the core of the multiprotein destruction complex, which targets the Wnt-effector beta-catenin for phosphorylation, ...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Schaefer KN,Bonello TT,Zhang S,Williams CE,Roberts DM,McKay DJ,Peifer M

    更新日期:2018-04-11 00:00:00

  • Abnormal type I collagen post-translational modification and crosslinking in a cyclophilin B KO mouse model of recessive osteogenesis imperfecta.

    abstract::Cyclophilin B (CyPB), encoded by PPIB, is an ER-resident peptidyl-prolyl cis-trans isomerase (PPIase) that functions independently and as a component of the collagen prolyl 3-hydroxylation complex. CyPB is proposed to be the major PPIase catalyzing the rate-limiting step in collagen folding. Mutations in PPIB cause re...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Cabral WA,Perdivara I,Weis M,Terajima M,Blissett AR,Chang W,Perosky JE,Makareeva EN,Mertz EL,Leikin S,Tomer KB,Kozloff KM,Eyre DR,Yamauchi M,Marini JC

    更新日期:2014-06-26 00:00:00

  • Drosophila insulin-like peptide 2 mediates dietary regulation of sleep intensity.

    abstract::Sleep is a nearly universal behavior that is regulated by diverse environmental stimuli and physiological states. A defining feature of sleep is a homeostatic rebound following deprivation, where animals compensate for lost sleep by increasing sleep duration and/or sleep depth. The fruit fly, Drosophila melanogaster, ...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Brown EB,Shah KD,Faville R,Kottler B,Keene AC

    更新日期:2020-03-11 00:00:00

  • A comprehensive genetic characterization of bacterial motility.

    abstract::We have developed a powerful experimental framework that combines competitive selection and microarray-based genetic footprinting to comprehensively reveal the genetic basis of bacterial behaviors. Application of this method to Escherichia coli motility identifies 95% of the known flagellar and chemotaxis genes, and r...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Girgis HS,Liu Y,Ryu WS,Tavazoie S

    更新日期:2007-09-01 00:00:00

  • The nucleoside diphosphate kinase gene Nme3 acts as quantitative trait locus promoting non-Mendelian inheritance.

    abstract::The t-haplotype, a variant form of the t-complex region on mouse chromosome 17, acts as selfish genetic element and is transmitted at high frequencies (> 95%) from heterozygous (t/+) males to their offspring. This phenotype is termed transmission ratio distortion (TRD) and is caused by the interaction of the t-complex...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Bauer H,Schindler S,Charron Y,Willert J,Kusecek B,Herrmann BG

    更新日期:2012-01-01 00:00:00

  • An engineering approach to extending lifespan in C. elegans.

    abstract::We have taken an engineering approach to extending the lifespan of Caenorhabditis elegans. Aging stands out as a complex trait, because events that occur in old animals are not under strong natural selection. As a result, lifespan can be lengthened rationally using bioengineering to modulate gene expression or to add ...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Sagi D,Kim SK

    更新日期:2012-01-01 00:00:00

  • Binding of NF-κB to nucleosomes: effect of translational positioning, nucleosome remodeling and linker histone H1.

    abstract::NF-κB is a key transcription factor regulating the expression of inflammatory responsive genes. How NF-κB binds to naked DNA templates is well documented, but how it interacts with chromatin is far from being clear. Here we used a combination of UV laser footprinting, hydroxyl footprinting and electrophoretic mobility...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Lone IN,Shukla MS,Charles Richard JL,Peshev ZY,Dimitrov S,Angelov D

    更新日期:2013-01-01 00:00:00

  • Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals.

    abstract::Detection and validation of the RNA degradation signals controlling transcriptome stability are essential steps for understanding how cells regulate gene expression. Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) a...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Gagnon J,Lavoie M,Catala M,Malenfant F,Elela SA

    更新日期:2015-02-13 00:00:00

  • Mitochondrial 2,4-dienoyl-CoA reductase deficiency in mice results in severe hypoglycemia with stress intolerance and unimpaired ketogenesis.

    abstract::The mitochondrial beta-oxidation system is one of the central metabolic pathways of energy metabolism in mammals. Enzyme defects in this pathway cause fatty acid oxidation disorders. To elucidate the role of 2,4-dienoyl-CoA reductase (DECR) as an auxiliary enzyme in the mitochondrial beta-oxidation of unsaturated fatt...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Miinalainen IJ,Schmitz W,Huotari A,Autio KJ,Soininen R,Ver Loren van Themaat E,Baes M,Herzig KH,Conzelmann E,Hiltunen JK

    更新日期:2009-07-01 00:00:00

  • Analysis of the genetic basis of disease in the context of worldwide human relationships and migration.

    abstract::Genetic diversity across different human populations can enhance understanding of the genetic basis of disease. We calculated the genetic risk of 102 diseases in 1,043 unrelated individuals across 51 populations of the Human Genome Diversity Panel. We found that genetic risk for type 2 diabetes and pancreatic cancer d...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Corona E,Chen R,Sikora M,Morgan AA,Patel CJ,Ramesh A,Bustamante CD,Butte AJ

    更新日期:2013-05-01 00:00:00

  • Interaction of HP1 and Brg1/Brm with the globular domain of histone H3 is required for HP1-mediated repression.

    abstract::The heterochromatin-enriched HP1 proteins play a critical role in regulation of transcription. These proteins contain two related domains known as the chromo- and the chromoshadow-domain. The chromo-domain binds histone H3 tails methylated on lysine 9. However, in vivo and in vitro experiments have shown that the affi...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Lavigne M,Eskeland R,Azebi S,Saint-André V,Jang SM,Batsché E,Fan HY,Kingston RE,Imhof A,Muchardt C

    更新日期:2009-12-01 00:00:00

  • The rate of nonallelic homologous recombination in males is highly variable, correlated between monozygotic twins and independent of age.

    abstract::Nonallelic homologous recombination (NAHR) between highly similar duplicated sequences generates chromosomal deletions, duplications and inversions, which can cause diverse genetic disorders. Little is known about interindividual variation in NAHR rates and the factors that influence this. We estimated the rate of del...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: MacArthur JA,Spector TD,Lindsay SJ,Mangino M,Gill R,Small KS,Hurles ME

    更新日期:2014-03-06 00:00:00

  • Glycine promotes longevity in Caenorhabditis elegans in a methionine cycle-dependent fashion.

    abstract::The deregulation of metabolism is a hallmark of aging. As such, changes in the expression of metabolic genes and the profiles of amino acid levels are features associated with aging animals. We previously reported that the levels of most amino acids decline with age in Caenorhabditis elegans (C. elegans). Glycine, in ...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Liu YJ,Janssens GE,McIntyre RL,Molenaars M,Kamble R,Gao AW,Jongejan A,Weeghel MV,MacInnes AW,Houtkooper RH

    更新日期:2019-03-07 00:00:00

  • Identification of a genomic reservoir for new TRIM genes in primate genomes.

    abstract::Tripartite Motif (TRIM) ubiquitin ligases act in the innate immune response against viruses. One of the best characterized members of this family, TRIM5α, serves as a potent retroviral restriction factor with activity against HIV. Here, we characterize what are likely to be the youngest TRIM genes in the human genome....

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Han K,Lou DI,Sawyer SL

    更新日期:2011-12-01 00:00:00

  • DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton.

    abstract::Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved reso...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Page JT,Liechty ZS,Alexander RH,Clemons K,Hulse-Kemp AM,Ashrafi H,Van Deynze A,Stelly DM,Udall JA

    更新日期:2016-05-11 00:00:00

  • The gene regulatory basis of genetic compensation during neural crest induction.

    abstract::The neural crest (NC) is a vertebrate-specific cell type that contributes to a wide range of different tissues across all three germ layers. The gene regulatory network (GRN) responsible for the formation of neural crest is conserved across vertebrates. Central to the induction of the NC GRN are AP-2 and SoxE transcri...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Dooley CM,Wali N,Sealy IM,White RJ,Stemple DL,Collins JE,Busch-Nentwich EM

    更新日期:2019-06-14 00:00:00

  • The zinc finger protein DCM1 is required for male meiotic cytokinesis by preserving callose in rice.

    abstract::Meiotic cytokinesis influences the fertility and ploidy of gametes. However, limited information is available on the genetic control of meiotic cytokinesis in plants. Here, we identified a rice mutant with low male fertility, defective callose in meiosis 1 (dcm1). The pollen grains of dcm1 are proved to be defective i...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Zhang C,Shen Y,Tang D,Shi W,Zhang D,Du G,Zhou Y,Liang G,Li Y,Cheng Z

    更新日期:2018-11-12 00:00:00

  • Translational control by the DEAD Box RNA helicase belle regulates ecdysone-triggered transcriptional cascades.

    abstract::Steroid hormones act, through their respective nuclear receptors, to regulate target gene expression. Despite their critical role in development, physiology, and disease, however, it is still unclear how these systemic cues are refined into tissue-specific responses. We identified a mutation in the evolutionarily cons...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Ihry RJ,Sapiro AL,Bashirullah A

    更新日期:2012-01-01 00:00:00

  • Genetic modifiers of muscular dystrophy act on sarcolemmal resealing and recovery from injury.

    abstract::Genetic disruption of the dystrophin complex produces muscular dystrophy characterized by a fragile muscle plasma membrane leading to excessive muscle degeneration. Two genetic modifiers of Duchenne Muscular Dystrophy implicate the transforming growth factor β (TGFβ) pathway, osteopontin encoded by the SPP1 gene and l...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Quattrocelli M,Capote J,Ohiri JC,Warner JL,Vo AH,Earley JU,Hadhazy M,Demonbreun AR,Spencer MJ,McNally EM

    更新日期:2017-10-24 00:00:00

  • Diversity of flowering responses in wild Arabidopsis thaliana strains.

    abstract::Although multiple environmental cues regulate the transition to flowering in Arabidopsis thaliana, previous studies have suggested that wild A. thaliana accessions fall primarily into two classes, distinguished by their requirement for vernalization (extended winter-like temperatures), which enables rapid flowering un...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Lempe J,Balasubramanian S,Sureshkumar S,Singh A,Schmid M,Weigel D

    更新日期:2005-07-01 00:00:00

  • A trans-acting protein effect causes severe eye malformation in the Mp mouse.

    abstract::Mp is an irradiation-induced mouse mutation associated with microphthalmia, micropinna and hind limb syndactyly. We show that Mp is caused by a 660 kb balanced inversion on chromosome 18 producing reciprocal 3-prime gene fusion events involving Fbn2 and Isoc1. The Isoc1-Fbn2 fusion gene (Isoc1(Mp)) mRNA has a frameshi...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Rainger J,Keighren M,Keene DR,Charbonneau NL,Rainger JK,Fisher M,Mella S,Huang JT,Rose L,van't Hof R,Sakai LY,Jackson IJ,Fitzpatrick DR

    更新日期:2013-01-01 00:00:00

  • Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution.

    abstract::Convergent phenotypic evolution is often caused by recurrent changes at particular nodes in the underlying gene regulatory networks (GRNs). The genes at such evolutionary 'hotspots' are thought to maximally affect the phenotype with minimal pleiotropic consequences. This has led to the suggestion that if a GRN is unde...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Kittelmann S,Buffry AD,Franke FA,Almudi I,Yoth M,Sabaris G,Couso JP,Nunes MDS,Frankel N,Gómez-Skarmeta JL,Pueyo-Marques J,Arif S,McGregor AP

    更新日期:2018-05-03 00:00:00

  • A genome-wide systematic analysis reveals different and predictive proliferation expression signatures of cancerous vs. non-cancerous cells.

    abstract::Understanding cell proliferation mechanisms has been a long-lasting goal of the scientific community and specifically of cancer researchers. Previous genome-scale studies of cancer proliferation determinants have mainly relied on knockdown screens aimed to gauge their effects on cancer growth. This powerful approach h...

    journal_title:PLoS genetics

    pub_type: 杂志文章


    authors: Waldman YY,Geiger T,Ruppin E

    更新日期:2013-01-01 00:00:00