Preference of DNA methyltransferases for CpG islands in mouse embryonic stem cells.

abstract：:The identification and interpretation of the regulatory signals within the human genome remain among the greatest goals and most difficult challenges in genome analysis. The ability to predict the temporal and spatial control of transcription is likely to require a combination of methods to address the contribution of...

journal_title：Genome research

authors： Krivan W,Wasserman WW

更新日期：2001-09-01 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：:In mammals, genetic recombination during meiosis is limited to a set of 1- to 2-kb regions termed hotspots. Their locations are predominantly determined by the zinc finger protein PRDM9, which binds to DNA in hotspots and subsequently uses its SET domain to locally trimethylate histone H3 at lysine 4 (H3K4me3). This s...

journal_title：Genome research

authors： Baker CL,Walker M,Kajita S,Petkov PM,Paigen K

更新日期：2014-05-01 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：: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：:MicroRNAs (miRNAs) are critical regulators of gene expression, and their role in a wide variety of biological processes, including host antimicrobial defense, is increasingly well described. Consistent with their diverse functional effects, miRNA expression is highly context dependent and shows marked changes upon cel...

journal_title：Genome research

authors： Siddle KJ,Deschamps M,Tailleux L,Nédélec Y,Pothlichet J,Lugo-Villarino G,Libri V,Gicquel B,Neyrolles O,Laval G,Patin E,Barreiro LB,Quintana-Murci L

更新日期：2014-05-01 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：:Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around n...

journal_title：Genome research

authors： Schep AN,Buenrostro JD,Denny SK,Schwartz K,Sherlock G,Greenleaf WJ

更新日期：2015-11-01 00:00:00

abstract：:The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions and local content of modified DNA nucleobases in genomic DNA. We combined in vitro nucleobase excision with massively parallel DNA sequencing (Excision-seq) to determine the...

journal_title：Genome research

authors： Bryan DS,Ransom M,Adane B,York K,Hesselberth JR

更新日期：2014-09-01 00:00:00

abstract：:Genes with sex-biased expression in Drosophila are thought to underlie sexually dimorphic phenotypes and have been shown to possess unique evolutionary properties. However, the forces and constraints governing the evolution of sex-biased genes in the somatic tissues of Drosophila are largely unknown. By using populati...

journal_title：Genome research

authors： Khodursky S,Svetec N,Durkin SM,Zhao L

更新日期：2020-06-01 00:00:00

abstract：:Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. ...

journal_title：Genome research

authors： Castensson A,Emilsson L,Preece P,Jazin EE

更新日期：2000-08-01 00:00:00

abstract：:The human genome is estimated to contain 23,000 to 33,000 retropseudogenes. To study the properties of genes giving rise to these retroelements, we compared the structure and expression of genes with or without known retropseudogenes. Four main features have emerged from the analysis of 181 genes associated to retrops...

journal_title：Genome research

authors： Gonçalves I,Duret L,Mouchiroud D

更新日期：2000-05-01 00:00:00

abstract：:The expression of most genes is regulated by multiple transcription factors. The interactions between transcription factors produce complex patterns of gene expression that are not always obvious from the arrangement of cis-regulatory elements in a promoter. One critical element of promoters is the TATA box, the docki...

journal_title：Genome research

authors： Mogno I,Vallania F,Mitra RD,Cohen BA

更新日期：2010-10-01 00:00:00

abstract：:Single-nucleotide polymorphisms (SNPs) are the most frequently found DNA sequence variations in the human genome. It has been argued that a dense set of SNP markers can be used to identify genetic factors associated with complex disease traits. Because all high-throughput genotyping methods require precise sequence kn...

journal_title：Genome research

authors： Taillon-Miller P,Piernot EE,Kwok PY

更新日期：1999-05-01 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：:Highly overlapping patterns of genome-wide binding of many distinct transcription factors have been observed in worms, insects, and mammals, but the origins and consequences of this overlapping binding remain unclear. While analyzing chromatin immunoprecipitation data sets from 21 sequence-specific transcription facto...

journal_title：Genome research

authors： Satija R,Bradley RK

更新日期：2012-04-01 00:00:00

abstract：:Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the two complete STEC O157 genomes (Sakai and EDL933) revealed a strikingly high level of sequence identity in orthologous pr...

journal_title：Genome research

authors： Zhang W,Qi W,Albert TJ,Motiwala AS,Alland D,Hyytia-Trees EK,Ribot EM,Fields PI,Whittam TS,Swaminathan B

更新日期：2006-06-01 00:00:00

abstract：:Large scale gene perturbation experiments generate information about the number of genes whose activity is directly or indirectly affected by a gene perturbation. From this information, one can numerically estimate coarse structural network features such as the total number of direct regulatory interactions and the nu...

journal_title：Genome research

authors： Wagner A

更新日期：2002-02-01 00:00:00

abstract：:Pollen, the male gametophyte of flowering plants, represents an ideal biological system to study developmental processes, such as cell polarity, tip growth, and morphogenesis. Upon hydration, the metabolically quiescent pollen rapidly switches to an active state, exhibiting extremely fast growth. This rapid switch req...

journal_title：Genome research

authors： Grobei MA,Qeli E,Brunner E,Rehrauer H,Zhang R,Roschitzki B,Basler K,Ahrens CH,Grossniklaus U

更新日期：2009-10-01 00:00:00

abstract：:Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessin...

journal_title：Genome research

authors： Yang T,Zhang F,Yardımcı GG,Song F,Hardison RC,Noble WS,Yue F,Li Q

更新日期：2017-11-01 00:00:00

abstract：:The genome size of Pseudoalteromonas haloplanktis, a ubiquitous and easily cultured marine bacterium, was measured as a step toward estimating the genome complexity of marine bacterioplankton. To determine total genome size, we digested P. haloplanktis DNA with the restriction endonucleases Notl and Sfil, separated th...

journal_title：Genome research

authors： Lanoil BD,Ciuffetti LM,Giovannoni SJ

更新日期：1996-12-01 00:00:00

abstract：:Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify 23,849 anthropoid-specific constrained (ASC) regions and confirmed their robust functional signatures. Of the ASC base pairs, 99.7% were noncoding, suggesting tha...

journal_title：Genome research

authors： del Rosario RC,Rayan NA,Prabhakar S

更新日期：2014-09-01 00:00:00

abstract：:Genomics data introduce a substantial computational burden as well as data privacy and ownership issues. Data sets generated by high-throughput sequencing platforms require immense amounts of computational resources to align to reference genomes and to call and annotate genomic variants. This problem is even more pron...

journal_title：Genome research

authors： Ozercan HI,Ileri AM,Ayday E,Alkan C

更新日期：2018-09-01 00:00:00

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

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

abstract：:Genomic structural variation (SV) is a major determinant for phenotypic variation. Although it has been extensively studied in humans, the nucleotide resolution structure of SVs within the widely used model organism Drosophila remains unknown. We report a highly accurate, densely validated map of unbalanced SVs compri...

journal_title：Genome research

authors： Zichner T,Garfield DA,Rausch T,Stütz AM,Cannavó E,Braun M,Furlong EE,Korbel JO

更新日期：2013-03-01 00:00:00

abstract：:Giardia duodenalis is the best-characterized example of the most ancient eukaryotes, which are primitively amitochondrial and anaerobic. The surface of Giardia is coated with cysteine-rich proteins. One family of these proteins, CRP136, varies among isolates and upon environmental stress. A repeat region within the CR...

journal_title：Genome research

authors： Upcroft P,Chen N,Upcroft JA

更新日期：1997-01-01 00:00:00

abstract：:X inactivation equalizes the dosage of gene expression between the sexes, but some genes escape silencing and are thus expressed from both alleles in females. To survey X inactivation and escape in mouse, we performed RNA sequencing in Mus musculus x Mus spretus cells with complete skewing of X inactivation, relying o...

journal_title：Genome research

authors： Yang F,Babak T,Shendure J,Disteche CM

更新日期：2010-05-01 00:00:00

abstract：:To gauge the complexity of gene regulation in yeast, it is essential to know how much promoter sequence is functional. Conservation across species can be a sensitive means of detecting functional sequences, provided that the significance of conservation can be accurately calibrated with the local neutral mutation rate...

journal_title：Genome research

authors： Chin CS,Chuang JH,Li H

更新日期：2005-02-01 00:00:00

abstract：:Gene expression can be regulated at multiple levels, but it is not known if and how there is broad coordination between regulation at the transcriptional and post-transcriptional levels. Transcription factors and chromatin regulate gene expression transcriptionally, whereas microRNAs (miRNAs) are small regulatory RNAs...

journal_title：Genome research

authors： Shivram H,Le SV,Iyer VR

更新日期：2019-02-01 00:00:00

abstract：:Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosa...

journal_title：Genome research

authors： Naqvi S,Bellott DW,Lin KS,Page DC

更新日期：2018-04-01 00:00:00