Transcriptional alterations in glioma result primarily from DNA methylation-independent mechanisms.

abstract：:The centromere is the structural unit responsible for the faithful segregation of chromosomes. Although regulation of centromeric function by epigenetic factors has been well-studied, the contributions of the underlying DNA sequences have been much less well defined, and existing methodologies for studying centromere ...

journal_title：Genome research

authors： Contreras-Galindo R,Fischer S,Saha AK,Lundy JD,Cervantes PW,Mourad M,Wang C,Qian B,Dai M,Meng F,Chinnaiyan A,Omenn GS,Kaplan MH,Markovitz DM

更新日期：2017-12-01 00:00:00

abstract：:Genomic imprinting is a developmentally important mechanism that involves both differential DNA methylation and allelic histone modifications. Through detailed comparative characterization, a large imprinted domain mapping to chromosome 7q21 in humans and proximal chromosome 6 in mice was redefined. This domain is org...

journal_title：Genome research

authors： Monk D,Wagschal A,Arnaud P,Müller PS,Parker-Katiraee L,Bourc'his D,Scherer SW,Feil R,Stanier P,Moore GE

更新日期：2008-08-01 00:00:00

abstract：:We report here a new mechanism for allelic discrimination--allele-specific Holliday Junction formation. The Holliday Junction (HJ) is a unique DNA structure that can be formed in a sequence-nonspecific manner by routine PCR. To cause the PCR-based HJ formation to occur in an allele-specific manner, the PCR primers are...

journal_title：Genome research

authors： Yang Q,Lishanski A,Yang W,Hatcher S,Seet H,Gregg JP

更新日期：2003-07-01 00:00:00

abstract：:Clusters of functionally related genes can be disrupted by a single copy number variant (CNV). We demonstrate that the simultaneous disruption of multiple functionally related genes is a frequent and significant characteristic of de novo CNVs in patients with developmental disorders (P = 1 × 10(-3)). Using three diffe...

journal_title：Genome research

authors： Andrews T,Honti F,Pfundt R,de Leeuw N,Hehir-Kwa J,Vulto-van Silfhout A,de Vries B,Webber C

更新日期：2015-06-01 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：:We compare several commonly used expression-based gene clustering algorithms using a figure of merit based on the mutual information between cluster membership and known gene attributes. By studying various publicly available expression data sets we conclude that enrichment of clusters for biological function is, in g...

journal_title：Genome research

authors： Gibbons FD,Roth FP

更新日期：2002-10-01 00:00:00

abstract：:Large copy number variants (CNVs) have been recently found as structural polymorphisms of the human genome of still unknown biological significance. CNVs are significantly enriched in regions with segmental duplications or low-copy repeats (LCRs). Williams-Beuren syndrome (WBS) is a neurodevelopmental disorder caused ...

journal_title：Genome research

authors： Cuscó I,Corominas R,Bayés M,Flores R,Rivera-Brugués N,Campuzano V,Pérez-Jurado LA

更新日期：2008-05-01 00:00:00

abstract：:As the Human Genome Project moves into its sequencing phase, a serious problem has arisen. The same problem has been increasingly vexing in the closing phase of the Caenorhabditis elegans project. The difficulty lies in sequencing efficiently through certain regions in which the templates (DNA substrates for the seque...

journal_title：Genome research

authors： McMurray AA,Sulston JE,Quail MA

更新日期：1998-05-01 00:00:00

abstract：:UEV proteins are enzymatically inactive variants of the E2 ubiquitin-conjugating enzymes that regulate noncanonical elongation of ubiquitin chains. In Saccharomyces cerevisiae, UEV is part of the RAD6-mediated error-free DNA repair pathway. In mammalian cells, UEV proteins can modulate c-FOS transcription and the G2-M...

journal_title：Genome research

authors： Thomson TM,Lozano JJ,Loukili N,Carrió R,Serras F,Cormand B,Valeri M,Díaz VM,Abril J,Burset M,Merino J,Macaya A,Corominas M,Guigó R

更新日期：2000-11-01 00:00:00

abstract：:The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipien...

journal_title：Genome research

authors： Aylor DL,Valdar W,Foulds-Mathes W,Buus RJ,Verdugo RA,Baric RS,Ferris MT,Frelinger JA,Heise M,Frieman MB,Gralinski LE,Bell TA,Didion JD,Hua K,Nehrenberg DL,Powell CL,Steigerwalt J,Xie Y,Kelada SN,Collins FS,Yang IV

更新日期：2011-08-01 00:00:00

abstract：:Telomeres shorten with each cell division and can ultimately become substrates for nonhomologous end-joining repair, leading to large-scale genomic rearrangements of the kind frequently observed in human cancers. We have characterized more than 1400 telomere fusion events at the single-molecule level, using a combinat...

journal_title：Genome research

authors： Liddiard K,Ruis B,Takasugi T,Harvey A,Ashelford KE,Hendrickson EA,Baird DM

更新日期：2016-05-01 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：:We have identified previously a putative tumor suppressor gene (TSG) locus at human chromosome (hchr) 7q31 showing that it is altered in a variety of human epithelial tumors. To determine whether this TSG is conserved in mice, we studied loss of heterozygosity (LOH) in chemically induced mouse liver adenomas. The LOH ...

journal_title：Genome research

authors： Zenklusen JC,Rodriguez LV,LaCava M,Wang Z,Goldstein LS,Conti CJ

更新日期：1996-11-01 00:00:00

abstract：:To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and compar...

journal_title：Genome research

authors： Churakov G,Zhang F,Grundmann N,Makalowski W,Noll A,Doronina L,Schmitz J

更新日期：2020-10-01 00:00:00

abstract：:Short insertions and deletions (indels) are the second most abundant form of human genetic variation, but our understanding of their origins and functional effects lags behind that of other types of variants. Using population-scale sequencing, we have identified a high-quality set of 1.6 million indels from 179 indivi...

journal_title：Genome research

authors： Montgomery SB,Goode DL,Kvikstad E,Albers CA,Zhang ZD,Mu XJ,Ananda G,Howie B,Karczewski KJ,Smith KS,Anaya V,Richardson R,Davis J,1000 Genomes Project Consortium.,MacArthur DG,Sidow A,Duret L,Gerstein M,Makova KD,Marc

更新日期：2013-05-01 00:00:00

abstract：:Interferons and interleukin-10 are involved in key aspects of the host defence mechanisms. Human chromosome 21 harbors the interferon/interleukin-10 receptor gene cluster linked to the GART gene. This cluster includes both components of the interferon alpha/beta-receptor (IFNAR1 and IFNAR2) and the second components o...

journal_title：Genome research

authors： Reboul J,Gardiner K,Monneron D,Uzé G,Lutfalla G

更新日期：1999-03-01 00:00:00

abstract：:Recent evidence from proteomics and deep massively parallel sequencing studies have revealed that eukaryotic genomes contain substantial numbers of as-yet-uncharacterized open reading frames (ORFs). We define these uncharacterized ORFs as novel ORFs (nORFs). nORFs in humans are mostly under 100 codons and are found in...

journal_title：Genome research

authors： Neville MDC,Kohze R,Erady C,Meena N,Hayden M,Cooper DN,Mort M,Prabakaran S

更新日期：2021-01-19 00:00:00

abstract：:Long interspersed nuclear element-1 (LINE-1 or L1) retrotransposons are normally suppressed in somatic tissues mainly due to DNA methylation and antiviral defense. However, the mechanism to suppress L1s may be disrupted in cancers, thus allowing L1s to act as insertional mutagens and cause genomic rearrangement and in...

journal_title：Genome research

authors： Jung H,Choi JK,Lee EA

更新日期：2018-08-01 00:00:00

abstract：:As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables fast automated annotation of eukaryotic genomes. It annotates genes based on evidence derived from known protein, cDNA, an...

journal_title：Genome research

authors： Curwen V,Eyras E,Andrews TD,Clarke L,Mongin E,Searle SM,Clamp M

更新日期：2004-05-01 00:00:00

abstract：:Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important compone...

journal_title：Genome research

authors： Devine SE,Chissoe SL,Eby Y,Wilson RK,Boeke JD

更新日期：1997-05-01 00:00:00

abstract：:Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functi...

journal_title：Genome research

authors： Yu Y,Zhang C,Zhou G,Wu S,Qu X,Wei H,Xing G,Dong C,Zhai Y,Wan J,Ouyang S,Li L,Zhang S,Zhou K,Zhang Y,Wu C,He F

更新日期：2001-08-01 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：: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：:Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells modulate gene expression in response to changing environments. Previous comparative studies focused on specific conditions, describing interspecies variation in expression levels,...

journal_title：Genome research

authors： Krieger G,Lupo O,Levy AA,Barkai N

更新日期：2020-07-01 00:00:00

abstract：:Elucidating the pathophysiology and molecular attributes of common disorders as well as developing targeted and effective treatments hinges on the study of the relevant cell type and tissues. Pancreatic beta cells within the islets of Langerhans are centrally involved in the pathogenesis of both type 1 and type 2 diab...

journal_title：Genome research

authors： Nica AC,Ongen H,Irminger JC,Bosco D,Berney T,Antonarakis SE,Halban PA,Dermitzakis ET

更新日期：2013-09-01 00:00:00

abstract：:A rigorous analysis of the Merck-sponsored EST data with respect to known gene sequences increases the utility of the data set and helps refine methods for building a gene index. A highly curated human transcript data base was used as a reference data set of known genes. A detailed analysis of EST sequences derived fr...

journal_title：Genome research

authors： Aaronson JS,Eckman B,Blevins RA,Borkowski JA,Myerson J,Imran S,Elliston KO

更新日期：1996-09-01 00:00:00

abstract：:Early embryogenesis is characterized by the maternal to zygotic transition (MZT), in which maternally deposited messenger RNAs are degraded while zygotic transcription begins. Before the MZT, post-transcriptional gene regulation by RNA-binding proteins (RBPs) is the dominant force in embryo patterning. We used two mRN...

journal_title：Genome research

authors： Wessels HH,Imami K,Baltz AG,Kolinski M,Beldovskaya A,Selbach M,Small S,Ohler U,Landthaler M

更新日期：2016-07-01 00:00:00

abstract：:We have conducted a phylogenetic analysis of the Ribonuclease HI (RNH) domains present in Eubacteria, Eukarya, all long-term repeat (LTR)-bearing retrotransposons, and several late-branching clades of non-LTR retrotransposons. Analysis of this simple yet highly conserved enzymatic domain from these disparate sources p...

journal_title：Genome research

authors： Malik HS,Eickbush TH

更新日期：2001-07-01 00:00:00

abstract：:DNA methylation plays key roles in diverse biological processes such as X chromosome inactivation, transposable element repression, genomic imprinting, and tissue-specific gene expression. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA methylomes. This ...

journal_title：Genome research

authors： Zhang B,Zhou Y,Lin N,Lowdon RF,Hong C,Nagarajan RP,Cheng JB,Li D,Stevens M,Lee HJ,Xing X,Zhou J,Sundaram V,Elliott G,Gu J,Shi T,Gascard P,Sigaroudinia M,Tlsty TD,Kadlecek T,Weiss A,O'Geen H,Farnham PJ,Maire

更新日期：2013-09-01 00:00:00

abstract：:Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of po...

journal_title：Genome research

authors： Wang Y,Lu J,Yu J,Gibbs RA,Yu F

更新日期：2013-05-01 00:00:00