Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes.

abstract：:Many CpG islands have tissue-dependent and differentially methylated regions (T-DMRs) in normal cells and tissues. To elucidate how DNA methyltransferases (Dnmts) participate in methylation of the genomic components, we investigated the genome-wide DNA methylation pattern of the T-DMRs with Dnmt1-, Dnmt3a-, and/or Dnm...

journal_title：Genome research

authors： Hattori N,Abe T,Hattori N,Suzuki M,Matsuyama T,Yoshida S,Li E,Shiota K

更新日期：2004-09-01 00:00:00

abstract：:Transcript leaders (TLs) can have profound effects on mRNA translation and stability. To map TL boundaries genome-wide, we developed TL-sequencing (TL-seq), a technique combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. TL-seq identified mRNA start sites for the majority of yeast...

journal_title：Genome research

authors： Arribere JA,Gilbert WV

更新日期：2013-06-01 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：:Translocations are known to affect the expression of genes at the breakpoints and, in the case of unbalanced translocations, alter the gene copy number. However, a comprehensive understanding of the functional impact of this class of variation is lacking. Here, we have studied the effect of balanced chromosomal rearra...

journal_title：Genome research

authors： Harewood L,Schütz F,Boyle S,Perry P,Delorenzi M,Bickmore WA,Reymond A

更新日期：2010-05-01 00:00:00

abstract：:We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spannin...

journal_title：Genome research

authors： Sharim H,Grunwald A,Gabrieli T,Michaeli Y,Margalit S,Torchinsky D,Arielly R,Nifker G,Juhasz M,Gularek F,Almalvez M,Dufault B,Chandra SS,Liu A,Bhattacharya S,Chen YW,Vilain E,Wagner KR,Pevsner J,Reifenberger J,Lam

更新日期：2019-04-01 00:00:00

abstract：:The rate of transcription elongation plays an important role in the timing of expression of full-length transcripts as well as in the regulation of alternative splicing. In this study, we coupled Bru-seq technology with 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) to estimate the elongation rates of over 2000 ...

journal_title：Genome research

authors： Veloso A,Kirkconnell KS,Magnuson B,Biewen B,Paulsen MT,Wilson TE,Ljungman M

更新日期：2014-06-01 00:00:00

abstract：:Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. Gr...

journal_title：Genome research

authors： Zhou Z,Alikhan NF,Sergeant MJ,Luhmann N,Vaz C,Francisco AP,Carriço JA,Achtman M

更新日期：2018-09-01 00:00:00

abstract：:The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequen...

journal_title：Genome research

authors： Huang X,Feng Q,Qian Q,Zhao Q,Wang L,Wang A,Guan J,Fan D,Weng Q,Huang T,Dong G,Sang T,Han B

更新日期：2009-06-01 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：:Transposable elements (TEs) are an integral part of the host transcriptome. TE-containing noncoding RNAs (ncRNAs) show considerable tissue specificity and play important roles during development, including stem cell maintenance and cell differentiation. Recent advances in single-cell RNA-seq (scRNA-seq) revolutionized...

journal_title：Genome research

authors： Shao W,Wang T

更新日期：2021-01-01 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：:CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environ...

journal_title：Genome research

authors： Wang H,Maurano MT,Qu H,Varley KE,Gertz J,Pauli F,Lee K,Canfield T,Weaver M,Sandstrom R,Thurman RE,Kaul R,Myers RM,Stamatoyannopoulos JA

更新日期：2012-09-01 00:00:00

abstract：:Core promoters mediate transcription initiation by the integration of diverse regulatory signals encoded in the proximal promoter and enhancers. It has been suggested that genes under simple regulation may have low-complexity permissive promoters. For these genes, the core promoter may serve as the principal regulator...

journal_title：Genome research

authors： Grishkevich V,Hashimshony T,Yanai I

更新日期：2011-05-01 00:00:00

abstract：:The genomic alterations associated with cancers are numerous and varied, involving both isolated and large-scale complex genomic rearrangements (CGRs). Although the underlying mechanisms are not well understood, CGRs have been implicated in tumorigenesis. Here, we introduce CouGaR, a novel method for characterizing th...

journal_title：Genome research

authors： Dzamba M,Ramani AK,Buczkowicz P,Jiang Y,Yu M,Hawkins C,Brudno M

更新日期：2017-01-01 00:00:00

abstract：:The world of noncoding RNAs (ncRNAs) is composed of an enormous and growing number of transcripts, ranging in length from tens of bases to tens of kilobases, involved in all biological processes and altered in expression and/or function in many types of human disorders. The premise of this review is the concept that n...

journal_title：Genome research

authors： Fabbri M,Girnita L,Varani G,Calin GA

更新日期：2019-09-01 00:00:00

abstract：:DNA transposons, or class 2 transposable elements, have successfully propagated in a wide variety of genomes. However, it is widely believed that DNA transposon activity has ceased in mammalian genomes for at least the last 40 million years. We recently reported evidence for the relatively recent activity of hAT and H...

journal_title：Genome research

authors： Ray DA,Feschotte C,Pagan HJ,Smith JD,Pritham EJ,Arensburger P,Atkinson PW,Craig NL

更新日期：2008-05-01 00:00:00

abstract：:Long noncoding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics, and cell differentiation. They serve as a platform for RNA interference (RNAi)-mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe that heterochro...

journal_title：Genome research

authors： Brönner C,Salvi L,Zocco M,Ugolini I,Halic M

更新日期：2017-07-01 00:00:00

abstract：:Genome-wide association studies (GWAS) have consistently implicated noncoding variation within the TCF7L2 locus with type 2 diabetes (T2D) risk. While this locus represents the strongest genetic determinant for T2D risk in humans, it remains unclear how these noncoding variants affect disease etiology. To test the hyp...

journal_title：Genome research

authors： Savic D,Ye H,Aneas I,Park SY,Bell GI,Nobrega MA

更新日期：2011-09-01 00:00:00

abstract：:Changes in gene order between the genomes of two related yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus var. uvarum were studied. From the dataset of a previous low coverage sequencing of the S. bayanus var. uvarum genome, 35 different synteny breakpoints between neighboring genes and two cases of l...

journal_title：Genome research

authors： Fischer G,Neuvéglise C,Durrens P,Gaillardin C,Dujon B

更新日期：2001-12-01 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：:While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus stifling biological discoveries. Moreover, recent studies revealed that complex bacterial populations may be composed from dozens of related strains, thus further amp...

journal_title：Genome research

authors： Nurk S,Meleshko D,Korobeynikov A,Pevzner PA

更新日期：2017-05-01 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：: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

authors： Vibranovski MD,Zhang Y,Long M

更新日期：2009-05-01 00:00:00

abstract：:Dystroglycan is a laminin binding protein, which provides a structural link between the subsarcolemmal cytoskeleton and the extracellular matrix. It is also involved in the organization of basement membranes. So far the genomic organization of the dystroglycan gene DAG1 has not been completely investigated. Here we re...

journal_title：Genome research

authors： Leeb T,Neumann S,Deppe A,Breen M,Brenig B

更新日期：2000-03-01 00:00:00

abstract：:WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment. Sequence logos provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive. Ea...

journal_title：Genome research

authors： Crooks GE,Hon G,Chandonia JM,Brenner SE

更新日期：2004-06-01 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：: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：: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：:Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy u...

journal_title：Genome research

authors： He B,Caudy A,Parsons L,Rosebrock A,Pane A,Raj S,Wieschaus E

更新日期：2012-12-01 00:00:00

abstract：:Chronic neuropathic pain is affected by specifics of the precipitating neural pathology, psychosocial factors, and by genetic predisposition. Little is known about the identity of predisposing genes. Using an integrative approach, we discovered that CACNG2 significantly affects susceptibility to chronic pain following...

journal_title：Genome research

authors： Nissenbaum J,Devor M,Seltzer Z,Gebauer M,Michaelis M,Tal M,Dorfman R,Abitbul-Yarkoni M,Lu Y,Elahipanah T,delCanho S,Minert A,Fried K,Persson AK,Shpigler H,Shabo E,Yakir B,Pisanté A,Darvasi A

更新日期：2010-09-01 00:00:00