Characterization and dynamics of pericentromere-associated domains in mice.

abstract：:In mammals, genome-wide chromatin maps and immunofluorescence studies show that broad domains of repressive histone modifications are present on pericentromeric and telomeric repeats and on the inactive X chromosome. However, only a few autosomal loci such as silent Hox gene clusters have been shown to lie in broad do...

journal_title：Genome research

authors： Pauler FM,Sloane MA,Huang R,Regha K,Koerner MV,Tamir I,Sommer A,Aszodi A,Jenuwein T,Barlow DP

更新日期：2009-02-01 00:00:00

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...

journal_title：Genome research

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

更新日期：2012-02-01 00:00:00

abstract：:We used a combination of cDNA selection, exon amplification, and computational prediction from genomic sequence to isolate transcribed sequences from genomic DNA surrounding the familial Mediterranean fever (FMF) locus. Eighty-seven kb of genomic DNA around D16S3370, a marker showing a high degree of linkage disequili...

journal_title：Genome research

authors： Centola M,Chen X,Sood R,Deng Z,Aksentijevich I,Blake T,Ricke DO,Chen X,Wood G,Zaks N,Richards N,Krizman D,Mansfield E,Apostolou S,Liu J,Shafran N,Vedula A,Hamon M,Cercek A,Kahan T,Gumucio D,Callen DF,Richards

更新日期：1998-11-01 00:00:00

abstract：:We generated high-resolution maps of histone H3 lysine 9/14 acetylation (H3ac), histone H4 lysine 5/8/12/16 acetylation (H4ac), and histone H3 at lysine 4 mono-, di-, and trimethylation (H3K4me1, H3K4me2, H3K4me3, respectively) across the ENCODE regions. Studying each modification in five human cell lines including th...

journal_title：Genome research

authors： Koch CM,Andrews RM,Flicek P,Dillon SC,Karaöz U,Clelland GK,Wilcox S,Beare DM,Fowler JC,Couttet P,James KD,Lefebvre GC,Bruce AW,Dovey OM,Ellis PD,Dhami P,Langford CF,Weng Z,Birney E,Carter NP,Vetrie D,Dunham I

更新日期：2007-06-01 00:00:00

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

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

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

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

更新日期：2004-04-01 00:00:00

abstract：:We report the construction of a dense linkage map of the rat genome integrating 767 simple sequence length polymorphism markers, combined over three crosses with high rates of polymorphism. F2 populations from WKY x S (n = 159), BN x S (n = 91), and BN x GK (n = 139) were selected and genotyped for combinations of mic...

journal_title：Genome research

authors： Bihoreau MT,Gauguier D,Kato N,Hyne G,Lindpaintner K,Rapp JP,James MR,Lathrop GM

更新日期：1997-05-01 00:00:00

abstract：:Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the z...

journal_title：Genome research

authors： Völker M,Backström N,Skinner BM,Langley EJ,Bunzey SK,Ellegren H,Griffin DK

更新日期：2010-04-01 00:00:00

abstract：:Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes cont...

journal_title：Genome research

authors： Fuhrmann DR,Krzywinski MI,Chiu R,Saeedi P,Schein JE,Bosdet IE,Chinwalla A,Hillier LW,Waterston RH,McPherson JD,Jones SJ,Marra MA

更新日期：2003-05-01 00:00:00

abstract：:Although mRNA decay rates are a key determinant of the steady-state concentration for any given mRNA species, relatively little is known, on a population level, about what factors influence turnover rates and how these rates are integrated into cellular decisions. We decided to measure mRNA decay rates in two human ce...

journal_title：Genome research

authors： Yang E,van Nimwegen E,Zavolan M,Rajewsky N,Schroeder M,Magnasco M,Darnell JE Jr

更新日期：2003-08-01 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

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 ...

journal_title：Genome research

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

更新日期：2009-02-01 00:00:00

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

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

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

authors： Madsen BE,Villesen P,Wiuf C

更新日期：2007-10-01 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：: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：: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：:Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here, we present sequential ChIP-bisulfite-sequencing (ChIP-BS-seq) as an approach to quantitatively assess DNA methylat...

journal_title：Genome research

authors： Brinkman AB,Gu H,Bartels SJ,Zhang Y,Matarese F,Simmer F,Marks H,Bock C,Gnirke A,Meissner A,Stunnenberg HG

更新日期：2012-06-01 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：:Custom-designed nucleases (CDNs) greatly facilitate genetic engineering by generating a targeted DNA double-strand break (DSB) in the genome. Once a DSB is created, specific modifications can be introduced around the breakage site during its repair by two major DNA damage repair (DDR) mechanisms: the dominant but erro...

journal_title：Genome research

authors： Maresca M,Lin VG,Guo N,Yang Y

更新日期：2013-03-01 00:00:00

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

authors： Simmons AD,Overhauser J,Lovett M

更新日期：1997-02-01 00:00:00

abstract：:Dual channel imaging and warping of two-dimensional (2D) protein gels were used to visualize global changes of the gene expression patterns in growing Bacillus subtilis cells during entry into the stationary phase as triggered by glucose exhaustion. The 2D gels only depict single moments during the cells' growth cycle...

journal_title：Genome research

authors： Bernhardt J,Weibezahn J,Scharf C,Hecker M

更新日期：2003-02-01 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：:Histone modifications are now well-established mediators of transcriptional programs that distinguish cell states. However, the kinetics of histone modification and their role in mediating rapid, signal-responsive gene expression changes has been little studied on a genome-wide scale. Vascular endothelial growth facto...

journal_title：Genome research

authors： Zhang B,Day DS,Ho JW,Song L,Cao J,Christodoulou D,Seidman JG,Crawford GE,Park PJ,Pu WT

更新日期：2013-06-01 00:00:00

abstract：:Retroposed copies (RPCs) of genes are functional (intronless paralogs) or nonfunctional (processed pseudogenes) copies derived from mRNA through a process of retrotransposition. Previous studies found that gene families involved in mRNA translation or nuclear function were more likely to have large numbers of RPCs. He...

journal_title：Genome research

authors： Strichman-Almashanu LZ,Bustin M,Landsman D

更新日期：2003-05-01 00:00:00

abstract：:MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species tha...

journal_title：Genome research

authors： Meunier J,Lemoine F,Soumillon M,Liechti A,Weier M,Guschanski K,Hu H,Khaitovich P,Kaessmann H

更新日期：2013-01-01 00:00:00

abstract：:It appears that, for many genes, the two alleles possessed by an individual may produce different amounts of transcript. When such allelic differences in transcription are observed for some individuals but not others, a plausible explanation is genetic variation in the cis-acting elements that regulate the gene in que...

journal_title：Genome research

authors： Forton JT,Udalova IA,Campino S,Rockett KA,Hull J,Kwiatkowski DP

更新日期：2007-01-01 00:00:00

abstract：:Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs...

journal_title：Genome research

authors： Feber A,Wilson GA,Zhang L,Presneau N,Idowu B,Down TA,Rakyan VK,Noon LA,Lloyd AC,Stupka E,Schiza V,Teschendorff AE,Schroth GP,Flanagan A,Beck S

更新日期：2011-04-01 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：: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

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