当前位置： SCI文献检索 > GENOME RESEARCH期刊下所有文献 > Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity.

Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity.

Abstract：

:The acquisition of new genes, via horizontal transfer or gene duplication/diversification, has been the dominant mechanism thus far implicated in the evolution of microbial pathogenicity. In contrast, the role of many other modes of evolution--such as changes in gene expression regulation-remains unknown. A transition to a pathogenic lifestyle has recently taken place in some lineages of the budding yeast Saccharomyces cerevisiae. Here we identify a module of physically interacting proteins involved in endocytosis that has experienced selective sweeps for multiple cis-regulatory mutations that down-regulate gene expression levels in a pathogenic yeast. To test if these adaptations affect virulence, we created a panel of single-allele knockout strains whose hemizygous state mimics the genes' adaptive down-regulations, and measured their virulence in a mammalian host. Despite having no growth advantage in standard laboratory conditions, nearly all of the strains were more virulent than their wild-type progenitor, suggesting that these adaptations likely played a role in the evolution of pathogenicity. Furthermore, genetic variants at these loci were associated with clinical origin across 88 diverse yeast strains, suggesting the adaptations may have contributed to the virulence of a wide range of clinical isolates. We also detected pleiotropic effects of these adaptations on a wide range of morphological traits, which appear to have been mitigated by compensatory mutations at other loci. These results suggest that cis-regulatory adaptation can occur at the level of physically interacting modules and that one such polygenic adaptation led to increased virulence during the evolution of a pathogenic yeast.

journal_name

Genome Res

journal_title

Genome research

authors

Fraser HB,Levy S,Chavan A,Shah HB,Perez JC,Zhou Y,Siegal ML,Sinha H

doi

10.1101/gr.134080.111

subject

Has Abstract

pub_date

2012-10-01 00:00:00

pages

1930-9

issue

10

eissn

1088-9051

issn

1549-5469

pii

gr.134080.111

journal_volume

22

pub_type

杂志文章

相关文献

GENOME RESEARCH文献大全
  • Inferring tumor progression from genomic heterogeneity.

    abstract：:Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.099622.109

    authors： Navin N,Krasnitz A,Rodgers L,Cook K,Meth J,Kendall J,Riggs M,Eberling Y,Troge J,Grubor V,Levy D,Lundin P,Månér S,Zetterberg A,Hicks J,Wigler M

    更新日期：2010-01-01 00:00:00

  • A Plasmodium gene family encoding Maurer's cleft membrane proteins: structural properties and expression profiling.

    abstract：:Upon invasion of the erythrocyte cell, the malaria parasite remodels its environment; in particular, it establishes a complex membrane network, which connects the parasitophorous vacuole to the host plasma membrane and is involved in protein transport and trafficking. We have identified a novel subtelomeric gene famil...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.2126104

    authors： Sam-Yellowe TY,Florens L,Johnson JR,Wang T,Drazba JA,Le Roch KG,Zhou Y,Batalov S,Carucci DJ,Winzeler EA,Yates JR 3rd

    更新日期：2004-06-01 00:00:00

  • Long RT-PCR of the entire 8.5-kb NF1 open reading frame and mutation detection on agarose gels.

    abstract：:Previous approaches to mutation detection in mRNA from the neurofibromatosis 1 (NF1) locus have required the PCR amplification of five or more overlapping cDNA segments to screen the entire 8.5-kb open reading frame (ORF). Systematically, these assays do not detect deletions that span the region of overlap (usually 1-...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.6.1.58

    authors： Martinez JM,Breidenbach HH,Cawthon R

    更新日期：1996-01-01 00:00:00

  • Relationship between histone modifications and transcription factor binding is protein family specific.

    abstract：:The very small fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.220079.116

    authors： Xin B,Rohs R

    更新日期：2018-01-11 00:00:00

  • Eukaryotic regulatory element conservation analysis and identification using comparative genomics.

    abstract：:Comparative genomics is a promising approach to the challenging problem of eukaryotic regulatory element identification, because functional noncoding sequences may be conserved across species from evolutionary constraints. We systematically analyzed known human and Saccharomyces cerevisiae regulatory elements and disc...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.1327604

    authors： Liu Y,Liu XS,Wei L,Altman RB,Batzoglou S

    更新日期：2004-03-01 00:00:00

  • Utilization of FISH in positional cloning: an example on 13q22.

    abstract：:In positional cloning the initial assignment of a gene to a specific chromosomal locus is followed by physical mapping of the critical region. The construction of a high-resolution physical map still involves considerable effort. However, new high-resolution fluorescence in situ hybridization (FISH) techniques have fa...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.6.10.1002

    authors： Laan M,Isosomppi J,Klockars T,Peltonen L,Palotie A

    更新日期：1996-10-01 00:00:00

  • Rapid comparative genomic analysis for clinical microbiology: the Francisella tularensis paradigm.

    abstract：:It is critical to avoid delays in detecting strain manipulations, such as the addition/deletion of a gene or modification of genes for increased virulence or antibiotic resistance, using genome analysis during an epidemic outbreak or a bioterrorist attack. Our objective was to evaluate the efficiency of genome analysi...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.071266.107

    authors： La Scola B,Elkarkouri K,Li W,Wahab T,Fournous G,Rolain JM,Biswas S,Drancourt M,Robert C,Audic S,Löfdahl S,Raoult D

    更新日期：2008-05-01 00:00:00

  • HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter.

    abstract：:Pigmentation of skin, eye, and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified. The SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the nonpigment gene HERC2, 21 kb upstream of...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.128652.111

    authors： Visser M,Kayser M,Palstra RJ

    更新日期：2012-03-01 00:00:00

  • Sequencing of cDNA clones from the genetic map of tomato (Lycopersicon esculentum).

    abstract：:The dense RFLP linkage map of tomato (Lycopersicon esculentum) contains >300 anonymous cDNA clones. Of those clones, 272 were partially or completely sequenced. The sequences were compared at the DNA and protein level to known genes in databases. For 57% of the clones, a significant match to previously described genes...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.8.8.842

    authors： Ganal MW,Czihal R,Hannappel U,Kloos DU,Polley A,Ling HQ

    更新日期：1998-08-01 00:00:00

  • Chromosomal instability mediated by non-B DNA: cruciform conformation and not DNA sequence is responsible for recurrent translocation in humans.

    abstract：:Chromosomal aberrations have been thought to be random events. However, recent findings introduce a new paradigm in which certain DNA segments have the potential to adopt unusual conformations that lead to genomic instability and nonrandom chromosomal rearrangement. One of the best-studied examples is the palindromic ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.079244.108

    authors： Inagaki H,Ohye T,Kogo H,Kato T,Bolor H,Taniguchi M,Shaikh TH,Emanuel BS,Kurahashi H

    更新日期：2009-02-01 00:00:00

  • Birth and expression evolution of mammalian microRNA genes.

    abstract：:MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species tha...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.140269.112

    authors： Meunier J,Lemoine F,Soumillon M,Liechti A,Weier M,Guschanski K,Hu H,Khaitovich P,Kaessmann H

    更新日期：2013-01-01 00:00:00

  • Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure.

    abstract：:The genetic positions of the five Arabidopsis thaliana centromere regions have been identified by mapping size polymorphisms in the centromeric 180-bp repeat arrays. Structural and genetic analysis indicates that 180-bp repeat arrays of up to 1000 kb are found in the centromere region of each chromosome. The genetic b...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.7.11.1045

    authors： Round EK,Flowers SK,Richards EJ

    更新日期：1997-11-01 00:00:00

  • Isolation of cDNAs from the Cri-du-chat critical region by direct screening of a chromosome 5-specific cDNA library.

    abstract：:Chromosome-specific cDNA libraries are new tools for the isolation of genes from specific genomic regions. We have used two YACs than span the approximately 2-Mb cri-du-chat critical region (CDCCR) of chromosome 5p to directly screen a chromosome 5-specific (CH5SP) fetal brain cDNA library. To compare this library wit...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.7.2.118

    authors： Simmons AD,Overhauser J,Lovett M

    更新日期：1997-02-01 00:00:00

  • Global survey of escape from X inactivation by RNA-sequencing in mouse.

    abstract：:X inactivation equalizes the dosage of gene expression between the sexes, but some genes escape silencing and are thus expressed from both alleles in females. To survey X inactivation and escape in mouse, we performed RNA sequencing in Mus musculus x Mus spretus cells with complete skewing of X inactivation, relying o...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.103200.109

    authors： Yang F,Babak T,Shendure J,Disteche CM

    更新日期：2010-05-01 00:00:00

  • A complexity reduction algorithm for analysis and annotation of large genomic sequences.

    abstract：:DNA is a universal language encrypted with biological instruction for life. In higher organisms, the genetic information is preserved predominantly in an organized exon/intron structure. When a gene is expressed, the exons are spliced together to form the transcript for protein synthesis. We have developed a complexit...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.313703

    authors： Chuang TJ,Lin WC,Lee HC,Wang CW,Hsiao KL,Wang ZH,Shieh D,Lin SC,Ch'ang LY

    更新日期：2003-02-01 00:00:00

  • Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains.

    abstract：:How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectiv...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.249268.119

    authors： Arimizu Y,Kirino Y,Sato MP,Uno K,Sato T,Gotoh Y,Auvray F,Brugere H,Oswald E,Mainil JG,Anklam KS,Döpfer D,Yoshino S,Ooka T,Tanizawa Y,Nakamura Y,Iguchi A,Morita-Ishihara T,Ohnishi M,Akashi K,Hayashi T,Ogura Y

    更新日期：2019-09-01 00:00:00

  • Random mutagenesis of proximal mouse chromosome 5 uncovers predominantly embryonic lethal mutations.

    abstract：:A region-specific ENU mutagenesis screen was conducted to elucidate the functional content of proximal mouse Chr 5. We used the visibly marked, recessive, lethal inversion Rump White (Rw) as a balancer in a three-generation breeding scheme to identify recessive mutations within the approximately 50 megabases spanned b...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.3826505

    authors： Wilson L,Ching YH,Farias M,Hartford SA,Howell G,Shao H,Bucan M,Schimenti JC

    更新日期：2005-08-01 00:00:00

  • Detecting ancient positive selection in humans using extended lineage sorting.

    abstract：:Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these hu...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.219493.116

    authors： Peyrégne S,Boyle MJ,Dannemann M,Prüfer K

    更新日期：2017-09-01 00:00:00

  • Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms.

    abstract：:Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the two complete STEC O157 genomes (Sakai and EDL933) revealed a strikingly high level of sequence identity in orthologous pr...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.4759706

    authors： Zhang W,Qi W,Albert TJ,Motiwala AS,Alland D,Hyytia-Trees EK,Ribot EM,Fields PI,Whittam TS,Swaminathan B

    更新日期：2006-06-01 00:00:00

  • Species-specific class I gene expansions formed the telomeric 1 mb of the mouse major histocompatibility complex.

    abstract：:We have determined the complete sequence of 951,695 bp from the class I region of H2, the mouse major histocompatibility complex (Mhc) from strain 129/Sv (haplotype bc). The sequence contains 26 genes. The sequence spans from the last 50 kb of the H2-T region, including 2 class I genes and 3 class I pseudogenes, and i...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.975303

    authors： Takada T,Kumánovics A,Amadou C,Yoshino M,Jones EP,Athanasiou M,Evans GA,Fischer Lindahl K

    更新日期：2003-04-01 00:00:00

  • Investigations into the analysis and modeling of the TNF alpha-mediated NF-kappa B-signaling pathway.

    abstract：:In this study, we propose a system-theoretic approach to the analysis and quantitative modeling of the TNFalpha-mediated NF-kappaB-signaling pathway. Tumor necrosis factor alpha (TNFalpha) is a potent proinflammatory cytokine that plays an important role in immunity and inflammation, in the control of cell proliferati...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.1195703

    authors： Cho KH,Shin SY,Lee HW,Wolkenhauer O

    更新日期：2003-11-01 00:00:00

  • Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood.

    abstract：:Variation in the composition of the human oral microbiome in health and disease has been observed. We have characterized inter- and intra-individual variation of microbial communities of 107 individuals in one of the largest cohorts to date (264 saliva samples), using culture-independent 16S rRNA pyrosequencing. We ex...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.140608.112

    authors： Stahringer SS,Clemente JC,Corley RP,Hewitt J,Knights D,Walters WA,Knight R,Krauter KS

    更新日期：2012-11-01 00:00:00

  • The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important.

    abstract：:The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.099044.109

    authors： Kvikstad EM,Makova KD

    更新日期：2010-05-01 00:00:00

  • The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes.

    abstract：:Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.240952.118

    authors： Schield DR,Card DC,Hales NR,Perry BW,Pasquesi GM,Blackmon H,Adams RH,Corbin AB,Smith CF,Ramesh B,Demuth JP,Betrán E,Tollis M,Meik JM,Mackessy SP,Castoe TA

    更新日期：2019-04-01 00:00:00

  • Parente2: a fast and accurate method for detecting identity by descent.

    abstract：:Identity-by-descent (IBD) inference is the problem of establishing a genetic connection between two individuals through a genomic segment that is inherited by both individuals from a recent common ancestor. IBD inference is an important preceding step in a variety of population genomic studies, ranging from demographi...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.173641.114

    authors： Rodriguez JM,Bercovici S,Huang L,Frostig R,Batzoglou S

    更新日期：2015-02-01 00:00:00

  • Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization.

    abstract：:The gastrointestinal microbiome undergoes shifts in species and strain abundances, yet dynamics involving closely related microorganisms remain largely unknown because most methods cannot resolve them. We developed new metagenomic methods and utilized them to track species and strain level variations in microbial comm...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.142315.112

    authors： Sharon I,Morowitz MJ,Thomas BC,Costello EK,Relman DA,Banfield JF

    更新日期：2013-01-01 00:00:00

  • Natural genetic variation in yeast longevity.

    abstract：:The genetics of aging in the yeast Saccharomyces cerevisiae has involved the manipulation of individual genes in laboratory strains. We have instituted a quantitative genetic analysis of the yeast replicative lifespan by sampling the natural genetic variation in a wild yeast isolate. Haploid segregants from a cross be...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.136549.111

    authors： Stumpferl SW,Brand SE,Jiang JC,Korona B,Tiwari A,Dai J,Seo JG,Jazwinski SM

    更新日期：2012-10-01 00:00:00

  • Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication.

    abstract：:Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced th...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.121137.111

    authors： Heidel AJ,Lawal HM,Felder M,Schilde C,Helps NR,Tunggal B,Rivero F,John U,Schleicher M,Eichinger L,Platzer M,Noegel AA,Schaap P,Glöckner G

    更新日期：2011-11-01 00:00:00

  • Reprogramming of the human intestinal epigenome by surgical tissue transposition.

    abstract：:Extracellular cues play critical roles in the establishment of the epigenome during development and may also contribute to epigenetic perturbations found in disease states. The direct role of the local tissue environment on the post-development human epigenome, however, remains unclear due to limitations in studies of...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.166439.113

    authors： Lay FD,Triche TJ Jr,Tsai YC,Su SF,Martin SE,Daneshmand S,Skinner EC,Liang G,Chihara Y,Jones PA

    更新日期：2014-04-01 00:00:00

  • A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity.

    abstract：:Histone modifications are now well-established mediators of transcriptional programs that distinguish cell states. However, the kinetics of histone modification and their role in mediating rapid, signal-responsive gene expression changes has been little studied on a genome-wide scale. Vascular endothelial growth facto...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.149674.112

    authors： Zhang B,Day DS,Ho JW,Song L,Cao J,Christodoulou D,Seidman JG,Crawford GE,Park PJ,Pu WT

    更新日期：2013-06-01 00:00:00