当前位置： SCI文献检索 > GENOME RESEARCH期刊下所有文献 > Unique DNA methylome profiles in CpG island methylator phenotype colon cancers.

Unique DNA methylome profiles in CpG island methylator phenotype colon cancers.

Abstract：

:A subset of colorectal cancers was postulated to have the CpG island methylator phenotype (CIMP), a higher propensity for CpG island DNA methylation. The validity of CIMP, its molecular basis, and its prognostic value remain highly controversial. Using MBD-isolated genome sequencing, we mapped and compared genome-wide DNA methylation profiles of normal, non-CIMP, and CIMP colon specimens. Multidimensional scaling analysis revealed that each specimen could be clearly classified as normal, non-CIMP, and CIMP, thus signifying that these three groups have distinctly different global methylation patterns. We discovered 3780 sites in various genomic contexts that were hypermethylated in both non-CIMP and CIMP colon cancers when compared with normal colon. An additional 2026 sites were found to be hypermethylated in CIMP tumors only; and importantly, 80% of these sites were located in CpG islands. These data demonstrate on a genome-wide level that the additional hypermethylation seen in CIMP tumors occurs almost exclusively at CpG islands and support definitively that these tumors were appropriately named. When these sites were examined more closely, we found that 25% were adjacent to sites that were also hypermethylated in non-CIMP tumors. Thus, CIMP is also characterized by more extensive methylation of sites that are already prone to be hypermethylated in colon cancer. These observations indicate that CIMP tumors have specific defects in controlling both DNA methylation seeding and spreading and serve as an important first step in delineating molecular mechanisms that control these processes.

journal_name

Genome Res

journal_title

Genome research

authors

Xu Y,Hu B,Choi AJ,Gopalan B,Lee BH,Kalady MF,Church JM,Ting AH

doi

10.1101/gr.122788.111

subject

Has Abstract

pub_date

2012-02-01 00:00:00

pages

283-91

issue

2

eissn

1088-9051

issn

1549-5469

pii

gr.122788.111

journal_volume

22

pub_type

杂志文章

相关文献

GENOME RESEARCH文献大全
  • PipMaker--a web server for aligning two genomic DNA sequences.

    abstract：:PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.10.4.577

    authors： Schwartz S,Zhang Z,Frazer KA,Smit A,Riemer C,Bouck J,Gibbs R,Hardison R,Miller W

    更新日期：2000-04-01 00:00:00

  • High-resolution landmark framework for the sequence-ready mapping of Xq23-q26.1.

    abstract：:We have established a landmark framework map over 20-25 Mb of the long arm of the human X chromosome using yeast artificial chromosome (YAC) clones. The map has approximately one landmark per 45 kb of DNA and stretches from DXS7531 in proximal Xq23 to DXS895 in proximal Xq26, connecting to published framework maps on ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：

    authors： Steingruber HE,Dunham A,Coffey AJ,Clegg SM,Howell GR,Maslen GL,Scott CE,Gwilliam R,Hunt PJ,Sotheran EC,Huckle EJ,Hunt SE,Dhami P,Soderlund C,Leversha MA,Bentley DR,Ross MT

    更新日期：1999-08-01 00:00:00

  • Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera).

    abstract：:The remarkable olfactory power of insect species is thought to be generated by a combinatorial action of two large protein families, G protein-coupled olfactory receptors (ORs) and odorant binding proteins (OBPs). In olfactory sensilla, OBPs deliver hydrophobic airborne molecules to ORs, but their expression in nonolf...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.5075706

    authors： Forêt S,Maleszka R

    更新日期：2006-11-01 00:00:00

  • Genetically indistinguishable SNPs and their influence on inferring the location of disease-associated variants.

    abstract：:As part of a recent high-density linkage disequilibrium (LD) study of chromosome 20, we obtained genotypes for approximately 30,000 SNPs at a density of 1 SNP/2 kb on four different population samples (47 CEPH founders; 91 UK unrelateds [unrelated white individuals of western European ancestry]; 97 African Americans; ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.4217605

    authors： Lawrence R,Evans DM,Morris AP,Ke X,Hunt S,Paolucci M,Ragoussis J,Deloukas P,Bentley D,Cardon LR

    更新日期：2005-11-01 00:00:00

  • The human obese (OB) gene: RNA expression pattern and mapping on the physical, cytogenetic, and genetic maps of chromosome 7.

    abstract：:The recently identified mouse obese (ob) gene apparently encodes a secreted protein that may function in the signaling pathway of adipose tissue. Mutations in the mouse ob gene are associated with the early development of gross obesity. A detailed knowledge concerning the RNA expression pattern and precise genomic loc...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.5.1.5

    authors： Green ED,Maffei M,Braden VV,Proenca R,DeSilva U,Zhang Y,Chua SC Jr,Leibel RL,Weissenbach J,Friedman JM

    更新日期：1995-08-01 00:00:00

  • The clustering of functionally related genes contributes to CNV-mediated disease.

    abstract：:Clusters of functionally related genes can be disrupted by a single copy number variant (CNV). We demonstrate that the simultaneous disruption of multiple functionally related genes is a frequent and significant characteristic of de novo CNVs in patients with developmental disorders (P = 1 × 10(-3)). Using three diffe...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.184325.114

    authors： Andrews T,Honti F,Pfundt R,de Leeuw N,Hehir-Kwa J,Vulto-van Silfhout A,de Vries B,Webber C

    更新日期：2015-06-01 00:00:00

  • Integration of the rat recombination and EST maps in the rat genomic sequence and comparative mapping analysis with the mouse genome.

    abstract：:Inbred strains of the laboratory rat are widely used for identifying genetic regions involved in the control of complex quantitative phenotypes of biomedical importance. The draft genomic sequence of the rat now provides essential information for annotating rat quantitative trait locus (QTL) maps. Following the survey...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.2001604

    authors： Wilder SP,Bihoreau MT,Argoud K,Watanabe TK,Lathrop M,Gauguier D

    更新日期：2004-04-01 00:00:00

  • Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells.

    abstract：:Duplication of the genome in mammalian cells occurs in a defined temporal order referred to as its replication-timing (RT) program. RT changes dynamically during development, regulated in units of 400-800 kb referred to as replication domains (RDs). Changes in RT are generally coordinated with transcriptional competen...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.187989.114

    authors： Rivera-Mulia JC,Buckley Q,Sasaki T,Zimmerman J,Didier RA,Nazor K,Loring JF,Lian Z,Weissman S,Robins AJ,Schulz TC,Menendez L,Kulik MJ,Dalton S,Gabr H,Kahveci T,Gilbert DM

    更新日期：2015-08-01 00:00:00

  • A simplified procedure for developing multiplex PCRs.

    abstract：:We have developed a simplified method for multiplex PCR based on the use of chimeric primers. Each primer contains a 3' region complementary to sequence-specific recognition sites and a 5' region made up of an unrelated 20-nucleotide sequence. Identical reaction conditions, cycling times, and annealing temperatures ha...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.5.5.488

    authors： Shuber AP,Grondin VJ,Klinger KW

    更新日期：1995-12-01 00:00:00

  • Selective enrichment of damaged DNA molecules for ancient genome sequencing.

    abstract：:Contamination by present-day human and microbial DNA is one of the major hindrances for large-scale genomic studies using ancient biological material. We describe a new molecular method, U selection, which exploits one of the most distinctive features of ancient DNA--the presence of deoxyuracils--for selective enrichm...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.174201.114

    authors： Gansauge MT,Meyer M

    更新日期：2014-09-01 00:00:00

  • Dynamic building of a BAC clone tiling path for the Rat Genome Sequencing Project.

    abstract：:CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome Sequencing Project (RGSP), a hybrid strategy of "clone by clone" and "whole genome shotgun" approaches was used to maximize the...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.2171704

    authors： Chen R,Sodergren E,Weinstock GM,Gibbs RA

    更新日期：2004-04-01 00:00:00

  • Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.

    abstract：:Accurate gene tree-species tree reconciliation is fundamental to inferring the evolutionary history of a gene family. However, although it has long been appreciated that population-related effects such as incomplete lineage sorting (ILS) can dramatically affect the gene tree, many of the most popular reconciliation me...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.161968.113

    authors： Wu YC,Rasmussen MD,Bansal MS,Kellis M

    更新日期：2014-03-01 00:00:00

  • General gene movement off the X chromosome in the Drosophila genus.

    abstract：:In Drosophila melanogaster, there is an excess of genes duplicated by retroposition from the X chromosome to the autosomes. Most of those retrogenes that originated on the X chromosome have testis expression pattern. These observations could be explained by natural selection favoring genes that avoided spermatogenesis...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.088609.108

    authors： Vibranovski MD,Zhang Y,Long M

    更新日期：2009-05-01 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

  • Two breakpoint clusters at fragile site FRA3B form phased nucleosomes.

    abstract：:Fragile sites are gaps and breaks in metaphase chromosomes generated by specific culture conditions. Fragile site FRA3B is the most unstable site and is directly involved in the breakpoints of deletion and translocation in a wide spectrum of cancers. To learn about the general characteristics of common fragile sites, ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.2304404

    authors： Mulvihill DJ,Wang YH

    更新日期：2004-07-01 00:00:00

  • Immune signatures correlate with L1 retrotransposition in gastrointestinal cancers.

    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

    pub_type： 杂志文章

    doi：10.1101/gr.231837.117

    authors： Jung H,Choi JK,Lee EA

    更新日期：2018-08-01 00:00:00

  • The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes.

    abstract：:Integrating the genotype with epigenetic marks holds the promise of better understanding the biology that underlies the complex interactions of inherited and environmental components that define the developmental origins of a range of disorders. The quality of the in utero environment significantly influences health o...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.171439.113

    authors： Teh AL,Pan H,Chen L,Ong ML,Dogra S,Wong J,MacIsaac JL,Mah SM,McEwen LM,Saw SM,Godfrey KM,Chong YS,Kwek K,Kwoh CK,Soh SE,Chong MF,Barton S,Karnani N,Cheong CY,Buschdorf JP,Stünkel W,Kobor MS,Meaney MJ,Gluckma

    更新日期：2014-07-01 00:00:00

  • Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.

    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

    pub_type： 杂志文章

    doi：10.1101/gr.gr-1619r

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

    更新日期：2001-03-01 00:00:00

  • Evolution and comparative genomics of odorant- and pheromone-associated genes in rodents.

    abstract：:Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance suggests that their genes may have been subject to adaptive evolution. We have estimated the consequences of selection on ro...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.1940604

    authors： Emes RD,Beatson SA,Ponting CP,Goodstadt L

    更新日期：2004-04-01 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

  • A platform for curated products from novel open reading frames prompts reinterpretation of disease variants.

    abstract：:Recent evidence from proteomics and deep massively parallel sequencing studies have revealed that eukaryotic genomes contain substantial numbers of as-yet-uncharacterized open reading frames (ORFs). We define these uncharacterized ORFs as novel ORFs (nORFs). nORFs in humans are mostly under 100 codons and are found in...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.263202.120

    authors： Neville MDC,Kohze R,Erady C,Meena N,Hayden M,Cooper DN,Mort M,Prabakaran S

    更新日期：2021-01-19 00:00:00

  • The repetitive landscape of the chicken genome.

    abstract：:Cot-based cloning and sequencing (CBCS) is a powerful tool for isolating and characterizing the various repetitive components of any genome, combining the established principles of DNA reassociation kinetics with high-throughput sequencing. CBCS was used to generate sequence libraries representing the high, middle, an...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.2438004

    authors： Wicker T,Robertson JS,Schulze SR,Feltus FA,Magrini V,Morrison JA,Mardis ER,Wilson RK,Peterson DG,Paterson AH,Ivarie R

    更新日期：2005-01-01 00:00:00

  • Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding.

    abstract：:The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.132811.111

    authors： Yáñez-Cuna JO,Dinh HQ,Kvon EZ,Shlyueva D,Stark A

    更新日期：2012-10-01 00:00:00

  • Fusion of the human gene for the polyubiquitination coeffector UEV1 with Kua, a newly identified gene.

    abstract：:UEV proteins are enzymatically inactive variants of the E2 ubiquitin-conjugating enzymes that regulate noncanonical elongation of ubiquitin chains. In Saccharomyces cerevisiae, UEV is part of the RAD6-mediated error-free DNA repair pathway. In mammalian cells, UEV proteins can modulate c-FOS transcription and the G2-M...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.gr-1405r

    authors： Thomson TM,Lozano JJ,Loukili N,Carrió R,Serras F,Cormand B,Valeri M,Díaz VM,Abril J,Burset M,Merino J,Macaya A,Corominas M,Guigó R

    更新日期：2000-11-01 00:00:00

  • A periodic pattern of SNPs in the human genome.

    abstract：:By surveying a filtered, high-quality set of SNPs in the human genome, we have found that SNPs positioned 1, 2, 4, 6, or 8 bp apart are more frequent than SNPs positioned 3, 5, 7, or 9 bp apart. The observed pattern is not restricted to genomic regions that are known to cause sequencing or alignment errors, for exampl...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.6223207

    authors： Madsen BE,Villesen P,Wiuf C

    更新日期：2007-10-01 00:00:00

  • Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin.

    abstract：:In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining nucleolus-associated domains (NADs) and lamina-associated domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (M...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.247072.118

    authors： Vertii A,Ou J,Yu J,Yan A,Pagès H,Liu H,Zhu LJ,Kaufman PD

    更新日期：2019-08-01 00:00:00

  • Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle.

    abstract：:We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events in 25,332 female gametes. The average number of COs was found to be larger in males (23.3) than in females (21.4). T...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.204214.116

    authors： Kadri NK,Harland C,Faux P,Cambisano N,Karim L,Coppieters W,Fritz S,Mullaart E,Baurain D,Boichard D,Spelman R,Charlier C,Georges M,Druet T

    更新日期：2016-10-01 00:00:00

  • ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm.

    abstract：:Establishment of spatial coordinates during Drosophila embryogenesis relies on differential regulatory activity of axis patterning enhancers. Concentration gradients of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target ...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.242362.118

    authors： Bozek M,Cortini R,Storti AE,Unnerstall U,Gaul U,Gompel N

    更新日期：2019-05-01 00:00:00

  • The amphioxus genome illuminates vertebrate origins and cephalochordate biology.

    abstract：:Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cepha...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.073676.107

    authors： Holland LZ,Albalat R,Azumi K,Benito-Gutiérrez E,Blow MJ,Bronner-Fraser M,Brunet F,Butts T,Candiani S,Dishaw LJ,Ferrier DE,Garcia-Fernàndez J,Gibson-Brown JJ,Gissi C,Godzik A,Hallböök F,Hirose D,Hosomichi K,Ikuta T,I

    更新日期：2008-07-01 00:00:00

  • Distribution of hammerhead and hammerhead-like RNA motifs through the GenBank.

    abstract：:Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive DNA from certain species of newts and schistosomes. To determine if this catalytic RNA motif has a wider distribution, we decided to scrutinize the GenBank database for RNAs that contain hammerhead or hammerhead-like moti...

    journal_title：Genome research

    pub_type： 杂志文章

    doi：10.1101/gr.10.7.1011

    authors： Ferbeyre G,Bourdeau V,Pageau M,Miramontes P,Cedergren R

    更新日期：2000-07-01 00:00:00