Massive reshaping of genome-nuclear lamina interactions during oncogene-induced senescence.

abstract：:Yeasts and filamentous fungi do not have adenosine deaminase acting on RNA (ADAR) orthologs and are believed to lack A-to-I RNA editing, which is the most prevalent editing of mRNA in animals. However, during this study with the PUK1(FGRRES_01058) pseudokinase gene important for sexual reproduction in Fusarium gramine...

journal_title：Genome research

authors： Liu H,Wang Q,He Y,Chen L,Hao C,Jiang C,Li Y,Dai Y,Kang Z,Xu JR

更新日期：2016-04-01 00:00:00

abstract：:After completion of the Schizosaccharomyces pombe genome sequence, we have carried out a pilot gene deletion project to assess the feasibility of a genome-wide deletion project and to estimate the percentage of essential genes. Using a PCR-based gene deletion procedure, we investigated 100 genes within a 253-kb region...

journal_title：Genome research

authors： Decottignies A,Sanchez-Perez I,Nurse P

更新日期：2003-03-01 00:00:00

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

authors： Greenbaum JA,Pang B,Tullius TD

更新日期：2007-06-01 00:00:00

abstract：:Biophysical, chemical, and nanoscience approaches to the study of nuclear structure and activity have been developing recently and hold considerable promise. A selection of fundamental problems in genome organization and function are reviewed and discussed in the context of these new perspectives and approaches. Advan...

journal_title：Genome research

authors： O'Brien TP,Bult CJ,Cremer C,Grunze M,Knowles BB,Langowski J,McNally J,Pederson T,Politz JC,Pombo A,Schmahl G,Spatz JP,van Driel R

更新日期：2003-06-01 00:00:00

abstract：:Although changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. To systematically identify transcription factors (TFs) that can direct chromatin changes during cell fate decisions, we model t...

journal_title：Genome research

authors： Arnold P,Schöler A,Pachkov M,Balwierz PJ,Jørgensen H,Stadler MB,van Nimwegen E,Schübeler D

更新日期：2013-01-01 00:00:00

abstract：:Human tumors are comprised of heterogeneous cell populations that display diverse molecular and phenotypic features. To examine the extent to which epigenetic differences contribute to intratumoral cellular heterogeneity, we have developed a high-throughput method, termed MAPit-patch. The method uses multiplexed ampli...

journal_title：Genome research

authors： Nabilsi NH,Deleyrolle LP,Darst RP,Riva A,Reynolds BA,Kladde MP

更新日期：2014-02-01 00:00:00

abstract：:Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from...

journal_title：Genome research

authors： West PT,Probst AJ,Grigoriev IV,Thomas BC,Banfield JF

更新日期：2018-04-01 00:00:00

abstract：:We have cloned the human gene encoding the transcription factor T. T protein is vital for the formation of posterior mesoderm and axial development in all vertebrates. Brachyury mutant mice, which lack T protein, die in utero with abnormal notochord, posterior somites, and allantois. We have identified human T genomic...

journal_title：Genome research

authors： Edwards YH,Putt W,Lekoape KM,Stott D,Fox M,Hopkinson DA,Sowden J

更新日期：1996-03-01 00:00:00

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

authors： Slattery JP,Franchini G,Gessain A

更新日期：1999-06-01 00:00:00

abstract：:Human chromosomal regions enriched in segmental duplications are subject to extensive genomic reorganization. Such regions are particularly informative for illuminating the evolutionary history of a given chromosome. We have analyzed 866 kb of Y-chromosomal non-palindromic segmental duplications delineating four euchr...

journal_title：Genome research

authors： Kirsch S,Münch C,Jiang Z,Cheng Z,Chen L,Batz C,Eichler EE,Schempp W

更新日期：2008-07-01 00:00:00

abstract：:In addition to mediating sister chromatid cohesion during the cell cycle, the cohesin complex associates with CTCF and with active gene regulatory elements to form long-range interactions between its binding sites. Genome-wide chromosome conformation capture had shown that cohesin's main role in interphase genome orga...

journal_title：Genome research

authors： Ing-Simmons E,Seitan VC,Faure AJ,Flicek P,Carroll T,Dekker J,Fisher AG,Lenhard B,Merkenschlager M

更新日期：2015-04-01 00:00:00

abstract：:Large-scale sequencing of human and model organism genomes will have a profound impact on our ability to use sequence data base searching to predict the biochemical functions of sequences of interest. Despite the great value of more sequences in the data bases, a huge increase in data base size will also have adverse ...

journal_title：Genome research

authors： Smith RF

更新日期：1996-08-01 00:00:00

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

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

更新日期：2000-10-01 00:00:00

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

authors： Shuber AP,Grondin VJ,Klinger KW

更新日期：1995-12-01 00:00:00

abstract：:Double minutes (dmin) and homogeneously staining regions (hsr) are the cytogenetic hallmarks of genomic amplification in cancer. Different mechanisms have been proposed to explain their genesis. Recently, our group showed that the MYC-containing dmin in leukemia cases arise by excision and amplification (episome model...

journal_title：Genome research

authors： Storlazzi CT,Lonoce A,Guastadisegni MC,Trombetta D,D'Addabbo P,Daniele G,L'Abbate A,Macchia G,Surace C,Kok K,Ullmann R,Purgato S,Palumbo O,Carella M,Ambros PF,Rocchi M

更新日期：2010-09-01 00:00:00

abstract：:Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP ass...

journal_title：Genome research

authors： Hardenbol P,Yu F,Belmont J,Mackenzie J,Bruckner C,Brundage T,Boudreau A,Chow S,Eberle J,Erbilgin A,Falkowski M,Fitzgerald R,Ghose S,Iartchouk O,Jain M,Karlin-Neumann G,Lu X,Miao X,Moore B,Moorhead M,Namsaraev E,

更新日期：2005-02-01 00:00:00

abstract：:We have performed detrended DNA walks on whole prokaryotic genomes, on noncoding sequences and, separately, on each position in codons of coding sequences. Our method enables us to distinguish between the mutational pressure associated with replication and the mutational pressure associated with transcription and othe...

journal_title：Genome research

authors： MackiewiczP,Gierlik A,Kowalczuk M,Dudek MR,Cebrat S

更新日期：1999-05-01 00:00:00

abstract：:We developed a high-throughput technique for the generation of cDNA libraries in the yeast Saccharomyces cerevisiae which enables the selection of cloned cDNA inserts containing open reading frames (ORFs). For direct screening of random-primed cDNA libraries, we have constructed a yeast shuttle/expression vector, the ...

journal_title：Genome research

authors： Holz C,Lueking A,Bovekamp L,Gutjahr C,Bolotina N,Lehrach H,Cahill DJ

更新日期：2001-10-01 00:00:00

abstract：:Phenotypic differences within populations and between closely related species are often driven by variation and evolution of gene expression. However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and lit...

journal_title：Genome research

authors： Ma L,Zhao B,Chen K,Thomas A,Tuteja JH,He X,He C,White KP

更新日期：2017-03-01 00:00:00

abstract：:Remnants of more than 3 million transposable elements, primarily retroelements, comprise nearly half of the human genome and have generated much speculation concerning their evolutionary significance. We have exploited the draft human genome sequence to examine the distributions of retroelements on a genome-wide scale...

journal_title：Genome research

authors： Medstrand P,van de Lagemaat LN,Mager DL

更新日期：2002-10-01 00:00:00

abstract：:DNA microarrays produced by deposition (or 'spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted oligonucleotide arrays using two large collections of approximately 70-mer probes, and used these arrays to analyze gene expression i...

journal_title：Genome research

authors： Barczak A,Rodriguez MW,Hanspers K,Koth LL,Tai YC,Bolstad BM,Speed TP,Erle DJ

更新日期：2003-07-01 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：: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

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

abstract：:The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research. The challenges for the informatics community are how to integrat...

journal_title：Genome research

authors： Baldarelli RM,Hill DP,Blake JA,Adachi J,Furuno M,Bradt D,Corbani LE,Cousins S,Frazer KS,Qi D,Yang L,Ramachandran S,Reed D,Zhu Y,Kasukawa T,Ringwald M,King BL,Maltais LJ,McKenzie LM,Schriml LM,Maglott D,Church DM

更新日期：2003-06-01 00:00:00

abstract：:Gene duplication and alternative splicing are important sources of proteomic diversity. Despite research indicating that gene duplication and alternative splicing are negatively correlated, the evolutionary relationship between the two remains unclear. One manner in which alternative splicing and gene duplication may ...

journal_title：Genome research

authors： Lambert MJ,Cochran WO,Wilde BM,Olsen KG,Cooper CD

更新日期：2015-05-01 00:00:00

abstract：:Low-copy repeats, or segmental duplications, are highly dynamic regions in the genome. The low-copy repeats on chromosome 22q11.2 (LCR22) are a complex mosaic of genes and pseudogenes formed by duplication processes; they mediate chromosome rearrangements associated with velo-cardio-facial syndrome/DiGeorge syndrome, ...

journal_title：Genome research

authors： Babcock M,Pavlicek A,Spiteri E,Kashork CD,Ioshikhes I,Shaffer LG,Jurka J,Morrow BE

更新日期：2003-12-01 00:00:00

abstract：:Nucleosomes containing the CenH3 (CENPA or CENP-A) histone variant replace H3 nucleosomes at centromeres to provide a foundation for kinetochore assembly. CENPA nucleosomes are part of the constitutive centromere associated network (CCAN) that forms the inner kinetochore on which outer kinetochore proteins assemble. T...

journal_title：Genome research

authors： Thakur J,Henikoff S

更新日期：2016-09-01 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：:Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth-death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for speci...

journal_title：Genome research

authors： Cui L,Wall PK,Leebens-Mack JH,Lindsay BG,Soltis DE,Doyle JJ,Soltis PS,Carlson JE,Arumuganathan K,Barakat A,Albert VA,Ma H,dePamphilis CW

更新日期：2006-06-01 00:00:00

abstract：:Developments in microarray and high-throughput sequencing (HTS) technologies have resulted in a rapid expansion of research into epigenomic changes that occur in normal development and in the progression of disease, such as cancer. Not surprisingly, copy number variation (CNV) has a direct effect on HTS read densities...

journal_title：Genome research

authors： Robinson MD,Strbenac D,Stirzaker C,Statham AL,Song J,Speed TP,Clark SJ

更新日期：2012-12-01 00:00:00