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 AT-rich repeat (PATRR), which induces recurrent constitutional translocations in humans. Here, we established a plasmid-based model that promotes frequent intermolecular rearrangements between two PATRRs in HEK293 cells. In this model system, the proportion of PATRR plasmid that extrudes a cruciform structure correlates to the levels of rearrangement. Our data suggest that PATRR-mediated translocations are attributable to unusual DNA conformations that confer a common pathway for chromosomal rearrangements in humans.

journal_name

Genome Res

journal_title

Genome research

authors

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

doi

10.1101/gr.079244.108

subject

Has Abstract

pub_date

2009-02-01 00:00:00

pages

191-8

issue

2

eissn

1088-9051

issn

1549-5469

pii

gr.079244.108

journal_volume

19

pub_type

杂志文章
  • Genomics and hearing impairment.

    abstract::Hearing impairment is clinically and genetically heterogeneous. There are >400 disorders in which hearing impairment is a characteristic of the syndrome, and family studies demonstrate that there are at least 30 autosomal loci for nonsyndromic hearing impairment. The genes that have been identified encode diaphanous (...

    journal_title:Genome research

    pub_type: 历史文章,杂志文章,评审

    doi:

    authors: Keats BJ,Berlin CI

    更新日期:1999-01-01 00:00:00

  • An assessment of gene prediction accuracy in large DNA sequences.

    abstract::One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human health and medicine. Though progress has been made on computational gene identification in terms of ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.122800

    authors: Guigó R,Agarwal P,Abril JF,Burset M,Fickett JW

    更新日期:2000-10-01 00:00:00

  • The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint.

    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

    pub_type: 杂志文章

    doi:10.1101/gr.2195604

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

    更新日期:2004-05-01 00:00:00

  • Analysis of 5' junctions of human LINE-1 and Alu retrotransposons suggests an alternative model for 5'-end attachment requiring microhomology-mediated end-joining.

    abstract::Insertion of the human non-LTR retrotransposon LINE-1 (L1) into chromosomal DNA is thought to be initiated by a mechanism called target-primed reverse transcription (TPRT). This mechanism readily accounts for the attachment of the 3'-end of an L1 copy to the genomic target, but the subsequent integration steps leading...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.3421505

    authors: Zingler N,Willhoeft U,Brose HP,Schoder V,Jahns T,Hanschmann KM,Morrish TA,Löwer J,Schumann GG

    更新日期:2005-06-01 00:00:00

  • Prokaryotic phylogenies inferred from protein structural domains.

    abstract::The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.3033805

    authors: Deeds EJ,Hennessey H,Shakhnovich EI

    更新日期:2005-03-01 00:00:00

  • Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays.

    abstract::The exponential growth of pathogen nucleic acid sequences available in public domain databases has invited their direct use in pathogen detection, identification, and surveillance strategies. DNA microarray technology has offered the potential for the direct DNA sequence analysis of a broad spectrum of pathogens of in...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.4337206

    authors: Lin B,Wang Z,Vora GJ,Thornton JA,Schnur JM,Thach DC,Blaney KM,Ligler AG,Malanoski AP,Santiago J,Walter EA,Agan BK,Metzgar D,Seto D,Daum LT,Kruzelock R,Rowley RK,Hanson EH,Tibbetts C,Stenger DA

    更新日期:2006-04-01 00:00:00

  • Determinants of CpG islands: expression in early embryo and isochore structure.

    abstract::In an attempt to understand the origin of CpG islands (CGIs) in mammalian genomes, we have studied their location and structure according to the expression pattern of genes and to the G + C content of isochores in which they are embedded. We show that CGIs located over the transcription start site (named start CGIs) a...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.174501

    authors: Ponger L,Duret L,Mouchiroud D

    更新日期:2001-11-01 00:00:00

  • Alternative approach to a heavy weight problem.

    abstract::Obesity is reaching epidemic proportions in developed countries and represents a significant risk factor for hypertension, heart disease, diabetes, and dyslipidemia. Splicing mutations constitute at least 14% of disease-causing mutations, thus implicating polymorphisms that affect splicing as likely candidates for dis...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.6661308

    authors: Goren A,Kim E,Amit M,Bochner R,Lev-Maor G,Ahituv N,Ast G

    更新日期:2008-02-01 00:00:00

  • Construction of a genome-scale structural map at single-nucleotide resolution.

    abstract::Few methods are available for mapping the local structure of DNA throughout a genome. The hydroxyl radical cleavage pattern is a measure of the local variation in solvent-accessible surface area of duplex DNA, and thus provides information on the local shape and structure of DNA. We report the construction of a relati...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.6073107

    authors: Greenbaum JA,Pang B,Tullius TD

    更新日期:2007-06-01 00:00:00

  • Transcription factor binding and modified histones in human bidirectional promoters.

    abstract::Bidirectional promoters have received considerable attention because of their ability to regulate two downstream genes (divergent genes). They are also highly abundant, directing the transcription of approximately 11% of genes in the human genome. We categorized the presence of DNA sequence motifs, binding of transcri...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.5623407

    authors: Lin JM,Collins PJ,Trinklein ND,Fu Y,Xi H,Myers RM,Weng Z

    更新日期:2007-06-01 00:00:00

  • Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale.

    abstract::Many thousands of proteins encoded by the genome of Plasmodium falciparum, the causal organism of the deadliest form of human malaria, are of unknown function. It is of utmost importance that these proteins be characterized if we are to develop combative strategies against malaria based on the biology of the parasite....

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.4573206

    authors: Date SV,Stoeckert CJ Jr

    更新日期:2006-04-01 00:00:00

  • Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions.

    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

    pub_type: 杂志文章

    doi:10.1101/gr.088922.108

    authors: Kvikstad EM,Chiaromonte F,Makova KD

    更新日期:2009-07-01 00:00:00

  • A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast.

    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

    pub_type: 杂志文章

    doi:10.1101/gr.6341207

    authors: Scannell DR,Wolfe KH

    更新日期:2008-01-01 00:00:00

  • A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness.

    abstract::Animal microRNA sequences are subject to 3' nucleotide addition. Through detailed analysis of deep-sequenced short RNA data sets, we show adenylation and uridylation of miRNA is globally present and conserved across Drosophila and vertebrates. To better understand 3' adenylation function, we deep-sequenced RNA after k...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.106054.110

    authors: Burroughs AM,Ando Y,de Hoon MJ,Tomaru Y,Nishibu T,Ukekawa R,Funakoshi T,Kurokawa T,Suzuki H,Hayashizaki Y,Daub CO

    更新日期:2010-10-01 00:00:00

  • Antisense transcripts with FANTOM2 clone set and their implications for gene regulation.

    abstract::We have used the FANTOM2 mouse cDNA set (60,770 clones), public mRNA data, and mouse genome sequence data to identify 2481 pairs of sense-antisense transcripts and 899 further pairs of nonantisense bidirectional transcription based upon genomic mapping. The analysis greatly expands the number of known examples of sens...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.982903

    authors: Kiyosawa H,Yamanaka I,Osato N,Kondo S,Hayashizaki Y,RIKEN GER Group.,GSL Members.

    更新日期:2003-06-01 00:00:00

  • Gene expression profiling in human fetal liver and identification of tissue- and developmental-stage-specific genes through compiled expression profiles and efficient cloning of full-length cDNAs.

    abstract::Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functi...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.175501

    authors: Yu Y,Zhang C,Zhou G,Wu S,Qu X,Wei H,Xing G,Dong C,Zhai Y,Wan J,Ouyang S,Li L,Zhang S,Zhou K,Zhang Y,Wu C,He F

    更新日期:2001-08-01 00:00:00

  • Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.

    abstract::DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and tissue-specific gene expression. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA methylomes. This ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.156539.113

    authors: Zhang B,Zhou Y,Lin N,Lowdon RF,Hong C,Nagarajan RP,Cheng JB,Li D,Stevens M,Lee HJ,Xing X,Zhou J,Sundaram V,Elliott G,Gu J,Shi T,Gascard P,Sigaroudinia M,Tlsty TD,Kadlecek T,Weiss A,O'Geen H,Farnham PJ,Maire

    更新日期:2013-09-01 00:00:00

  • Detecting genetic variation in microarray expression data.

    abstract::The use of high-density oligonucleotide arrays to measure the expression levels of thousands of genes in parallel has become commonplace. To take further advantage of the growing body of data, we developed a method, termed "GeSNP," to mine the detailed hybridization patterns in oligonucleotide array expression data fo...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.6307307

    authors: Greenhall JA,Zapala MA,Cáceres M,Libiger O,Barlow C,Schork NJ,Lockhart DJ

    更新日期:2007-08-01 00:00:00

  • Global analysis of protein homomerization in Saccharomyces cerevisiae.

    abstract::In vivo analyses of the occurrence, subcellular localization, and dynamics of protein-protein interactions (PPIs) are important issues in functional proteomic studies. The bimolecular fluorescence complementation (BiFC) assay has many advantages in that it provides a reliable way to detect PPIs in living cells with mi...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.231860.117

    authors: Kim Y,Jung JP,Pack CG,Huh WK

    更新日期:2019-01-01 00:00:00

  • Genomic evolution, patterns of global dissemination, and interspecies transmission of human and simian T-cell leukemia/lymphotropic viruses.

    abstract::Using both env and long terminal repeat (LTR) sequences, with maximal representation of genetic diversity within primate strains, we revise and expand the unique evolutionary history of human and simian T-cell leukemia/lymphotropic viruses (HTLV/STLV). Based on the robust application of three different phylogenetic al...

    journal_title:Genome research

    pub_type: 杂志文章,评审

    doi:

    authors: Slattery JP,Franchini G,Gessain A

    更新日期:1999-06-01 00:00:00

  • A fine scale phenotype-genotype virulence map of a bacterial pathogen.

    abstract::A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We desc...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.137430.112

    authors: van Opijnen T,Camilli A

    更新日期:2012-12-01 00:00:00

  • Theories and applications for sequencing randomly selected clones.

    abstract::Theory is developed for the process of sequencing randomly selected large-insert clones. Genome size, library depth, clone size, and clone distribution are considered relevant properties and perfect overlap detection for contig assembly is assumed. Genome-specific and nonrandom effects are neglected. Order of magnitud...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.gr-1339r

    authors: Wendl MC,Marra MA,Hillier LW,Chinwalla AT,Wilson RK,Waterston RH

    更新日期:2001-02-01 00:00:00

  • CG dinucleotides enhance promoter activity independent of DNA methylation.

    abstract::Most mammalian RNA polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address this question, we determined the tra...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.241653.118

    authors: Hartl D,Krebs AR,Grand RS,Baubec T,Isbel L,Wirbelauer C,Burger L,Schübeler D

    更新日期:2019-04-01 00:00:00

  • A model for postzygotic mosaicisms quantifies the allele fraction drift, mutation rate, and contribution to de novo mutations.

    abstract::The allele fraction (AF) distribution, occurrence rate, and evolutionary contribution of postzygotic single-nucleotide mosaicisms (pSNMs) remain largely unknown. In this study, we developed a mathematical model to describe the accumulation and AF drift of pSNMs during the development of multicellular organisms. By app...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.230003.117

    authors: Ye AY,Dou Y,Yang X,Wang S,Huang AY,Wei L

    更新日期:2018-07-01 00:00:00

  • Rescue of targeted regions of mammalian chromosomes by in vivo recombination in yeast.

    abstract::In contrast to other animal cell lines, the chicken pre-B cell lymphoma line, DT40, exhibits a high level of homologous recombination, which can be exploited to generate site-specific alterations in defined target genes or regions. In addition, the ability to generate human/chicken monochromosomal hybrids in the DT40 ...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.8.6.666

    authors: Kouprina N,Kawamoto K,Barrett JC,Larionov V,Koi M

    更新日期:1998-06-01 00:00:00

  • lobSTR: A short tandem repeat profiler for personal genomes.

    abstract::Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat S...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.135780.111

    authors: Gymrek M,Golan D,Rosset S,Erlich Y

    更新日期:2012-06-01 00:00:00

  • Telomeric organization of a variable and inducible toxin gene family in the ancient eukaryote Giardia duodenalis.

    abstract::Giardia duodenalis is the best-characterized example of the most ancient eukaryotes, which are primitively amitochondrial and anaerobic. The surface of Giardia is coated with cysteine-rich proteins. One family of these proteins, CRP136, varies among isolates and upon environmental stress. A repeat region within the CR...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.7.1.37

    authors: Upcroft P,Chen N,Upcroft JA

    更新日期:1997-01-01 00:00:00

  • Phenotypically distinct female castes in honey bees are defined by alternative chromatin states during larval development.

    abstract::The capacity of the honey bee to produce three phenotypically distinct organisms (two female castes; queens and sterile workers, and haploid male drones) from one genotype represents one of the most remarkable examples of developmental plasticity in any phylum. The queen-worker morphological and reproductive divide is...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.236497.118

    authors: Wojciechowski M,Lowe R,Maleszka J,Conn D,Maleszka R,Hurd PJ

    更新日期:2018-10-01 00:00:00

  • 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

  • Transcriptional alterations in glioma result primarily from DNA methylation-independent mechanisms.

    abstract::In cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution of DNA methylat...

    journal_title:Genome research

    pub_type: 杂志文章

    doi:10.1101/gr.249219.119

    authors: Court F,Le Boiteux E,Fogli A,Müller-Barthélémy M,Vaurs-Barrière C,Chautard E,Pereira B,Biau J,Kemeny JL,Khalil T,Karayan-Tapon L,Verrelle P,Arnaud P

    更新日期:2019-10-01 00:00:00