Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex.

abstract：:A small set of core transcription factors (TFs) dominates control of the gene expression program in embryonic stem cells and other well-studied cellular models. These core TFs collectively regulate their own gene expression, thus forming an interconnected auto-regulatory loop that can be considered the core transcript...

journal_title：Genome research

authors： Saint-André V,Federation AJ,Lin CY,Abraham BJ,Reddy J,Lee TI,Bradner JE,Young RA

更新日期：2016-03-01 00:00:00

abstract：:LSH, a member of the SNF2 family of chromatin remodeling ATPases encoded by the Hells gene, is essential for normal levels of DNA methylation in the mammalian genome. While the role of LSH in the methylation of repetitive DNA sequences is well characterized, its contribution to the regulation of DNA methylation and th...

journal_title：Genome research

authors： Myant K,Termanis A,Sundaram AY,Boe T,Li C,Merusi C,Burrage J,de Las Heras JI,Stancheva I

更新日期：2011-01-01 00:00:00

abstract：:The development of high-throughput sequencing (HTS) technologies has opened the door to novel methods for detecting copy number variants (CNVs) in the human genome. While in the past CNVs have been detected based on array CGH data, recent studies have shown that depth-of-coverage information from HTS technologies can ...

journal_title：Genome research

authors： Medvedev P,Fiume M,Dzamba M,Smith T,Brudno M

更新日期：2010-11-01 00:00:00

abstract：:Maize (Zea mays L. ssp. mays), one of the most important agricultural crops in the world, originated by hybridization of two closely related progenitors. To investigate the fate of its genes after tetraploidization, we analyzed the sequence of five duplicated regions from different chromosomal locations. We also compa...

journal_title：Genome research

authors： Lai J,Ma J,Swigonová Z,Ramakrishna W,Linton E,Llaca V,Tanyolac B,Park YJ,Jeong OY,Bennetzen JL,Messing J

更新日期：2004-10-01 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：:Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium, leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitati...

journal_title：Genome research

authors： Gao AW,Sterken MG,Uit de Bos J,van Creij J,Kamble R,Snoek BL,Kammenga JE,Houtkooper RH

更新日期：2018-09-01 00:00:00

abstract：:The acquisition of new genes, via horizontal transfer or gene duplication/diversification, has been the dominant mechanism thus far implicated in the evolution of microbial pathogenicity. In contrast, the role of many other modes of evolution--such as changes in gene expression regulation-remains unknown. A transition...

journal_title：Genome research

authors： Fraser HB,Levy S,Chavan A,Shah HB,Perez JC,Zhou Y,Siegal ML,Sinha H

更新日期：2012-10-01 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：:C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether ...

journal_title：Genome research

authors： Schmitges FW,Radovani E,Najafabadi HS,Barazandeh M,Campitelli LF,Yin Y,Jolma A,Zhong G,Guo H,Kanagalingam T,Dai WF,Taipale J,Emili A,Greenblatt JF,Hughes TR

更新日期：2016-12-01 00:00:00

abstract：:Eukaryotic translation initiation involves preinitiation ribosomal complex 5'-to-3' directional probing of mRNA for codons suitable for starting protein synthesis. The recognition of codons as starts depends on the codon identity and on its immediate nucleotide context known as Kozak context. When the context is weak ...

journal_title：Genome research

authors： Benitez-Cantos MS,Yordanova MM,O'Connor PBF,Zhdanov AV,Kovalchuk SI,Papkovsky DB,Andreev DE,Baranov PV

更新日期：2020-07-01 00:00:00

abstract：:The main objectives of the study reported here were to construct a molecular map of wild emmer wheat, Triticum dicoccoides, to characterize the marker-related anatomy of the genome, and to evaluate segregation and recombination patterns upon crossing T. dicoccoides with its domesticated descendant Triticum durum (cult...

journal_title：Genome research

authors： Peng J,Korol AB,Fahima T,Röder MS,Ronin YI,Li YC,Nevo E

更新日期：2000-10-01 00:00:00

abstract：:High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classi...

journal_title：Genome research

authors： Corvelo A,Clarke WE,Robine N,Zody MC

更新日期：2018-05-01 00:00:00

abstract：:How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectiv...

journal_title：Genome research

authors： Arimizu Y,Kirino Y,Sato MP,Uno K,Sato T,Gotoh Y,Auvray F,Brugere H,Oswald E,Mainil JG,Anklam KS,Döpfer D,Yoshino S,Ooka T,Tanizawa Y,Nakamura Y,Iguchi A,Morita-Ishihara T,Ohnishi M,Akashi K,Hayashi T,Ogura Y

更新日期：2019-09-01 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：:Natural killer (NK) cells are innate lymphocytes important for early host defense against infectious pathogens and surveillance against malignant transformation. Resting murine NK cells regulate the translation of effector molecule mRNAs (e.g., granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs)...

journal_title：Genome research

authors： Fehniger TA,Wylie T,Germino E,Leong JW,Magrini VJ,Koul S,Keppel CR,Schneider SE,Koboldt DC,Sullivan RP,Heinz ME,Crosby SD,Nagarajan R,Ramsingh G,Link DC,Ley TJ,Mardis ER

更新日期：2010-11-01 00:00:00

abstract：:We have developed the CADLIVE (Computer-Aided Design of LIVing systEms) Simulator that provided a rule-based automatic way to convert biochemical network maps into dynamic models, which enables simulating their dynamics without going through all of the reactions down to the details of exact kinetic parameters. The sim...

journal_title：Genome research

authors： Kurata H,Masaki K,Sumida Y,Iwasaki R

更新日期：2005-04-01 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：:The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of m...

journal_title：Genome research

authors： Yandava CN,Gastier JM,Pulido JC,Brody T,Sheffield V,Murray J,Buetow K,Duyk GM

更新日期：1997-07-01 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：:A new algorithm, WABA, was developed for doing large-scale alignments between genomic DNA of different species. WABA was used to align 8 million bases of Caenorhabditis briggsae genomic DNA against the entire 97-million-base Caenorhabditis elegans genome. The alignment, including C. briggsae homologs of 154 geneticall...

journal_title：Genome research

authors： Kent WJ,Zahler AM

更新日期：2000-08-01 00:00:00

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

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

abstract：:Advanced prostate cancer can progress to systemic metastatic tumors, which are generally androgen insensitive and ultimately lethal. Here, we report a comprehensive genomic survey for somatic events in systemic metastatic prostate tumors using both high-resolution copy number analysis and targeted mutational survey of...

journal_title：Genome research

authors： Robbins CM,Tembe WA,Baker A,Sinari S,Moses TY,Beckstrom-Sternberg S,Beckstrom-Sternberg J,Barrett M,Long J,Chinnaiyan A,Lowey J,Suh E,Pearson JV,Craig DW,Agus DB,Pienta KJ,Carpten JD

更新日期：2011-01-01 00:00:00

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：: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

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

abstract：:The mammalian cell nucleus contains numerous discrete suborganelles named nuclear bodies. While recruitment of specific genomic regions into these large ribonucleoprotein (RNP) complexes critically contributes to higher-order functional chromatin organization, such regions remain ill-defined. We have developed the hig...

journal_title：Genome research

authors： Baudement MO,Cournac A,Court F,Seveno M,Parrinello H,Reynes C,Sabatier R,Bouschet T,Yi Z,Sallis S,Tancelin M,Rebouissou C,Cathala G,Lesne A,Mozziconacci J,Journot L,Forné T

更新日期：2018-11-01 00:00:00

abstract：:Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypot...

journal_title：Genome research

authors： Kelkar YD,Eckert KA,Chiaromonte F,Makova KD

更新日期：2011-12-01 00:00:00

abstract：:All individuals in a finite population are related if traced back long enough and will, therefore, share regions of their genomes identical by descent (IBD). Detection of such regions has several important applications-from answering questions about human evolution to locating regions in the human genome containing di...

journal_title：Genome research

authors： Moltke I,Albrechtsen A,Hansen TV,Nielsen FC,Nielsen R

更新日期：2011-07-01 00:00:00

abstract：:Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data al...

journal_title：Genome research

authors： Zimin AV,Puiu D,Luo MC,Zhu T,Koren S,Marçais G,Yorke JA,Dvořák J,Salzberg SL

更新日期：2017-05-01 00:00:00

abstract：:Extracellular cues play critical roles in the establishment of the epigenome during development and may also contribute to epigenetic perturbations found in disease states. The direct role of the local tissue environment on the post-development human epigenome, however, remains unclear due to limitations in studies of...

journal_title：Genome research

authors： Lay FD,Triche TJ Jr,Tsai YC,Su SF,Martin SE,Daneshmand S,Skinner EC,Liang G,Chihara Y,Jones PA

更新日期：2014-04-01 00:00:00

abstract：:The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show t...

journal_title：Genome research

authors： Bollenbach T,Vetsigian K,Kishony R

更新日期：2007-04-01 00:00:00