Birth and expression evolution of mammalian microRNA genes.

abstract：:In mammals, genetic recombination during meiosis is limited to a set of 1- to 2-kb regions termed hotspots. Their locations are predominantly determined by the zinc finger protein PRDM9, which binds to DNA in hotspots and subsequently uses its SET domain to locally trimethylate histone H3 at lysine 4 (H3K4me3). This s...

journal_title：Genome research

authors： Baker CL,Walker M,Kajita S,Petkov PM,Paigen K

更新日期：2014-05-01 00:00:00

abstract：:Little is known about the rate of emergence of de novo genes, what their initial properties are, and how they spread in populations. We examined wild yeast populations (Saccharomyces paradoxus) to characterize the diversity and turnover of intergenic ORFs over short evolutionary timescales. We find that hundreds of in...

journal_title：Genome research

authors： Durand É,Gagnon-Arsenault I,Hallin J,Hatin I,Dubé AK,Nielly-Thibault L,Namy O,Landry CR

更新日期：2019-06-01 00:00:00

abstract：:Centromeres pose an evolutionary paradox: strongly conserved in function but rapidly changing in sequence and structure. However, in the absence of damage, centromere locations are usually conserved within a species. We report here that isolates of the pathogenic yeast species Candida parapsilosis show within-species ...

journal_title：Genome research

authors： Ola M,O'Brien CE,Coughlan AY,Ma Q,Donovan PD,Wolfe KH,Butler G

更新日期：2020-05-01 00:00:00

abstract：:In mammals, genome-wide chromatin maps and immunofluorescence studies show that broad domains of repressive histone modifications are present on pericentromeric and telomeric repeats and on the inactive X chromosome. However, only a few autosomal loci such as silent Hox gene clusters have been shown to lie in broad do...

journal_title：Genome research

authors： Pauler FM,Sloane MA,Huang R,Regha K,Koerner MV,Tamir I,Sommer A,Aszodi A,Jenuwein T,Barlow DP

更新日期：2009-02-01 00:00:00

abstract：:We report the genome-wide mapping of ORC1 binding sites in mammals, by chromatin immunoprecipitation and parallel sequencing (ChIP-seq). ORC1 binding sites in HeLa cells were validated as active DNA replication origins (ORIs) using Repli-seq, a method that allows identification of ORI-containing regions by parallel se...

journal_title：Genome research

authors： Dellino GI,Cittaro D,Piccioni R,Luzi L,Banfi S,Segalla S,Cesaroni M,Mendoza-Maldonado R,Giacca M,Pelicci PG

更新日期：2013-01-01 00:00:00

abstract：:We compare the functional spectrum of protein evolution in two separate animal lineages with respect to two hypotheses: (1) rates of divergence are distributed similarly among functional classes within both lineages, indicating that selective pressure on the proteome is largely independent of organismic-level biologic...

journal_title：Genome research

authors： Castillo-Davis CI,Kondrashov FA,Hartl DL,Kulathinal RJ

更新日期：2004-05-01 00:00:00

abstract：:Long interspersed nuclear element-1 (LINE-1 or L1) retrotransposons are normally suppressed in somatic tissues mainly due to DNA methylation and antiviral defense. However, the mechanism to suppress L1s may be disrupted in cancers, thus allowing L1s to act as insertional mutagens and cause genomic rearrangement and in...

journal_title：Genome research

authors： Jung H,Choi JK,Lee EA

更新日期：2018-08-01 00:00:00

abstract：:Rhesus macaque is an Old World monkey that shared a common ancestor with human ∼25 Myr ago and is an important animal model for human disease studies. A deep understanding of its genetics is therefore required for both biomedical and evolutionary studies. Among structural variants, inversions represent a driving force...

journal_title：Genome research

authors： Maggiolini FAM,Sanders AD,Shew CJ,Sulovari A,Mao Y,Puig M,Catacchio CR,Dellino M,Palmisano D,Mercuri L,Bitonto M,Porubský D,Cáceres M,Eichler EE,Ventura M,Dennis MY,Korbel JO,Antonacci F

更新日期：2020-11-01 00:00:00

abstract：:The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipien...

journal_title：Genome research

authors： Aylor DL,Valdar W,Foulds-Mathes W,Buus RJ,Verdugo RA,Baric RS,Ferris MT,Frelinger JA,Heise M,Frieman MB,Gralinski LE,Bell TA,Didion JD,Hua K,Nehrenberg DL,Powell CL,Steigerwalt J,Xie Y,Kelada SN,Collins FS,Yang IV

更新日期：2011-08-01 00:00:00

abstract：:Gene order in prokaryotes is conserved to a much lesser extent than protein sequences. Only several operons, primarily those that code for physically interacting proteins, are conserved in all or most of the bacterial and archaeal genomes. Nevertheless, even the limited conservation of operon organization that is obse...

journal_title：Genome research

authors： Wolf YI,Rogozin IB,Kondrashov AS,Koonin EV

更新日期：2001-03-01 00:00:00

abstract：:Chromosome 21 represents approximately 1% of the human genome, and its long arm has been estimated to contain 600-1000 genes. A dense linkage map and almost complete physical maps based on yeast artificial chromosomes (YACs) and cosmids have been developed. We have used exon trapping to identify portions of genes from...

journal_title：Genome research

authors： Chen H,Chrast R,Rossier C,Morris MA,Lalioti MD,Antonarakis SE

更新日期：1996-08-01 00:00:00

abstract：:The primate-specific multisequence family chAB4 is represented with approximately 40 copies within the haploid human genome. Former analyis revealed that unusually long repetition units ( > 35 kb) are distributed to at least eight different chromosomal loci. Remarkably varying copy-numbers within the genomes of closel...

journal_title：Genome research

authors： Wöhr G,Fink T,Assum G

更新日期：1996-04-01 00:00:00

abstract：:Genome-wide association studies (GWAS) are identifying genetic predisposition to various diseases. The 17q24.3 locus harbors the single nucleotide polymorphism (SNP) rs1859962 that is statistically associated with prostate cancer (PCa). It defines a 130-kb linkage disequilibrium (LD) block that lies in an ∼2-Mb gene d...

journal_title：Genome research

authors： Zhang X,Cowper-Sal lari R,Bailey SD,Moore JH,Lupien M

更新日期：2012-08-01 00:00:00

abstract：:Identifying genes in the genomic context is central to a cell's ability to interpret the genome. Yet, in general, the signals used to define eukaryotic genes are poorly described. Here, we derived simple classifiers that identify where transcription will initiate and terminate using nucleic acid sequence features dete...

journal_title：Genome research

authors： de Boer CG,van Bakel H,Tsui K,Li J,Morris QD,Nislow C,Greenblatt JF,Hughes TR

更新日期：2014-01-01 00:00:00

abstract：:Double anal fin (Da) is a medaka with an autosomal semidominant mutation that causes mirror image duplication of the ventral region concentrating on the caudal region. The chromosomal location of the Da gene and its sequence have remained unknown. We constructed a medaka linkage map as a first step to approach positio...

journal_title：Genome research

authors： Ohtsuka M,Makino S,Yoda K,Wada H,Naruse K,Mitani H,Shima A,Ozato K,Kimura M,Inoko H

更新日期：1999-12-01 00:00:00

abstract：:Integration of DNA viruses into the human genome plays an important role in various types of tumors, including hepatitis B virus (HBV)-related hepatocellular carcinoma. However, the molecular details and clinical impact of HBV integration on either human or HBV epigenomes are unknown. Here, we show that methylation of...

journal_title：Genome research

authors： Watanabe Y,Yamamoto H,Oikawa R,Toyota M,Yamamoto M,Kokudo N,Tanaka S,Arii S,Yotsuyanagi H,Koike K,Itoh F

更新日期：2015-03-01 00:00:00

abstract：:The reported human genome sequence includes about 400 gaps of unknown sequence that were not found in the bacterial artificial chromosome (BAC) and cosmid libraries used for sequencing of the genome. These missing sequences correspond to approximately 1% of euchromatic regions of the human genome. Gap filling is a lab...

journal_title：Genome research

authors： Leem SH,Kouprina N,Grimwood J,Kim JH,Mullokandov M,Yoon YH,Chae JY,Morgan J,Lucas S,Richardson P,Detter C,Glavina T,Rubin E,Barrett JC,Larionov V

更新日期：2004-02-01 00:00:00

abstract：:Primate pericentromeric regions recently have been shown to exhibit extraordinary evolutionary plasticity. In this paper we report an additional peculiar feature of these regions that we discovered while analyzing, by FISH, the evolutionary conservation of primate phylogenetic chromosome IX. If the position of the cen...

journal_title：Genome research

authors： Montefalcone G,Tempesta S,Rocchi M,Archidiacono N

更新日期：1999-12-01 00:00:00

abstract：:Using AP-PCR-based DNA profiling we examined some structural features of B chromosomes from yellow-necked mice Apodemus flavicollis. Mice harboring one, two, or three or lacking B chromosomes were examined. Chromosomal structure was scanned for variant bands by using a series of arbitrary primers and from these, infor...

journal_title：Genome research

authors： Tanic N,Dedovic N,Vujosevic M,Dimitrijevic B

更新日期：2000-01-01 00:00:00

abstract：:The draft genome ( approximately 160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution of chordates as well as vertebrates. However, because this genomic data has not yet been mapped onto chromoso...

journal_title：Genome research

authors： Shoguchi E,Kawashima T,Satou Y,Hamaguchi M,Sin-I T,Kohara Y,Putnam N,Rokhsar DS,Satoh N

更新日期：2006-02-01 00:00:00

abstract：:Recent studies have revealed that insertions and deletions (indels) are more different in their formation than previously assumed. What remains enigmatic is how the local DNA sequence context contributes to these differences. To investigate the relative impact of various molecular mechanisms to indel formation, we ana...

journal_title：Genome research

authors： Kvikstad EM,Chiaromonte F,Makova KD

更新日期：2009-07-01 00:00:00

abstract：:Analysis procedures are needed to extract useful information from the large amount of gene expression data that is becoming available. This work describes a set of analytical tools and their application to yeast cell cycle data. The components of our approach are (1) a similarity measure that reduces the number of fal...

journal_title：Genome research

authors： Heyer LJ,Kruglyak S,Yooseph S

更新日期：1999-11-01 00:00:00

abstract：:Mammalian genomes contain many highly conserved nongenic sequences (CNGs) whose functional significance is poorly understood. Sets of CNGs have previously been identified by selecting the most conserved elements from a chromosome or genome, but in these highly selected samples, conservation may be unrelated to purifyi...

journal_title：Genome research

authors： Keightley PD,Kryukov GV,Sunyaev S,Halligan DL,Gaffney DJ

更新日期：2005-10-01 00:00:00

abstract：:We have conducted a phylogenetic analysis of the Ribonuclease HI (RNH) domains present in Eubacteria, Eukarya, all long-term repeat (LTR)-bearing retrotransposons, and several late-branching clades of non-LTR retrotransposons. Analysis of this simple yet highly conserved enzymatic domain from these disparate sources p...

journal_title：Genome research

authors： Malik HS,Eickbush TH

更新日期：2001-07-01 00:00:00

abstract：:Translocations are a common class of chromosomal aberrations and can cause disease by physically disrupting genes or altering their regulatory environment. Some translocations, apparently balanced at the microscopic level, include deletions, duplications, insertions, or inversions at the molecular level. Traditionally...

journal_title：Genome research

authors： Sobreira NL,Gnanakkan V,Walsh M,Marosy B,Wohler E,Thomas G,Hoover-Fong JE,Hamosh A,Wheelan SJ,Valle D

更新日期：2011-10-01 00:00:00

abstract：:The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we...

journal_title：Genome research

authors： Lee IY,Westaway D,Smit AF,Wang K,Seto J,Chen L,Acharya C,Ankener M,Baskin D,Cooper C,Yao H,Prusiner SB,Hood LE

更新日期：1998-10-01 00:00:00

abstract：:It is widely accepted that newly arisen duplicate gene pairs experience an altered selective regime that is often manifested as an increase in the rate of protein sequence evolution. Many details about the nature of the rate acceleration remain unknown, however, including its typical magnitude and duration, and whethe...

journal_title：Genome research

authors： Scannell DR,Wolfe KH

更新日期：2008-01-01 00:00:00

abstract：:Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering ...

journal_title：Genome research

authors： Ayele M,Haas BJ,Kumar N,Wu H,Xiao Y,Van Aken S,Utterback TR,Wortman JR,White OR,Town CD

更新日期：2005-04-01 00:00:00

abstract：:Single-nucleotide polymorphisms (SNPs) are the most frequently found DNA sequence variations in the human genome. It has been argued that a dense set of SNP markers can be used to identify genetic factors associated with complex disease traits. Because all high-throughput genotyping methods require precise sequence kn...

journal_title：Genome research

authors： Taillon-Miller P,Piernot EE,Kwok PY

更新日期：1999-05-01 00:00:00

abstract：:Custom-designed nucleases (CDNs) greatly facilitate genetic engineering by generating a targeted DNA double-strand break (DSB) in the genome. Once a DSB is created, specific modifications can be introduced around the breakage site during its repair by two major DNA damage repair (DDR) mechanisms: the dominant but erro...

journal_title：Genome research

authors： Maresca M,Lin VG,Guo N,Yang Y

更新日期：2013-03-01 00:00:00