Novel noncoding RNA from human Y distal heterochromatic block (Yq12) generates testis-specific chimeric CDC2L2.

abstract：:Plasticity of gene regulatory encryption can permit DNA sequence divergence without loss of function. Functional information is preserved through conservation of the composition of transcription factor binding sites (TFBS) in a regulatory element. We have developed a method that can accurately identify pairs of functi...

journal_title：Genome research

authors： Taher L,McGaughey DM,Maragh S,Aneas I,Bessling SL,Miller W,Nobrega MA,McCallion AS,Ovcharenko I

更新日期：2011-07-01 00:00:00

abstract：:Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these hu...

journal_title：Genome research

authors： Peyrégne S,Boyle MJ,Dannemann M,Prüfer K

更新日期：2017-09-01 00:00:00

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：: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

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：: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：:Recent studies have analyzed large-scale data sets of gene expression to identify genes associated with interindividual variation in phenotypes ranging from cancer subtypes to drug sensitivity, promising new avenues of research in personalized medicine. However, gene expression data alone is limited in its ability to ...

journal_title：Genome research

authors： Hanson C,Cairns J,Wang L,Sinha S

更新日期：2018-08-01 00:00:00

abstract：:Tissue development and function are exquisitely dependent on proper regulation of gene expression, but it remains controversial whether the genomic signals controlling this process are subject to strong selective constraint. While some studies show that highly constrained noncoding regions act to enhance transcription...

journal_title：Genome research

authors： Cheng Y,King DC,Dore LC,Zhang X,Zhou Y,Zhang Y,Dorman C,Abebe D,Kumar SA,Chiaromonte F,Miller W,Green RD,Weiss MJ,Hardison RC

更新日期：2008-12-01 00:00:00

abstract：:Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length o...

journal_title：Genome research

authors： Bousios A,Diez CM,Takuno S,Bystry V,Darzentas N,Gaut BS

更新日期：2016-02-01 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：:Evolutionary constraints on gene regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NF...

journal_title：Genome research

authors： Copley RR,Totrov M,Linnell J,Field S,Ragoussis J,Udalova IA

更新日期：2007-09-01 00:00:00

abstract：:Whole-genome sequencing using massively parallel sequencing technologies enables accurate detection of somatic rearrangements in cancer. Pinpointing large numbers of rearrangement breakpoints to base-pair resolution allows analysis of rearrangement microhomology and genomic location for every sample. Here we analyze 9...

journal_title：Genome research

authors： Drier Y,Lawrence MS,Carter SL,Stewart C,Gabriel SB,Lander ES,Meyerson M,Beroukhim R,Getz G

更新日期：2013-02-01 00:00:00

abstract：:Integration of DNA viruses into the human genome plays an important role in various types of tumors, including hepatitis B virus (HBV)-related hepatocellular carcinoma. However, the molecular details and clinical impact of HBV integration on either human or HBV epigenomes are unknown. Here, we show that methylation of...

journal_title：Genome research

authors： Watanabe Y,Yamamoto H,Oikawa R,Toyota M,Yamamoto M,Kokudo N,Tanaka S,Arii S,Yotsuyanagi H,Koike K,Itoh F

更新日期：2015-03-01 00:00:00

abstract：:In positional cloning the initial assignment of a gene to a specific chromosomal locus is followed by physical mapping of the critical region. The construction of a high-resolution physical map still involves considerable effort. However, new high-resolution fluorescence in situ hybridization (FISH) techniques have fa...

journal_title：Genome research

authors： Laan M,Isosomppi J,Klockars T,Peltonen L,Palotie A

更新日期：1996-10-01 00:00:00

abstract：:DNA methylation is found in many eukaryotes, but its function is still controversial. We have studied the methylation of plant and animal genomes using a PCR-based technique amenable for high throughput. Repetitive elements are methylated in both organisms, but whereas most mammalian exons are methylated, plant exons ...

journal_title：Genome research

authors： Rabinowicz PD,Palmer LE,May BP,Hemann MT,Lowe SW,McCombie WR,Martienssen RA

更新日期：2003-12-01 00:00:00

abstract：:Pre-mRNA processing often occurs in coordination with transcription thereby coupling these two key regulatory events. As such, many proteins involved in mRNA processing associate with the transcriptional machinery and are in proximity to DNA. This proximity allows for the mapping of the genomic associations of RNA bin...

journal_title：Genome research

authors： Swinburne IA,Meyer CA,Liu XS,Silver PA,Brodsky AS

更新日期：2006-07-01 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：: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：: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 allele fraction (AF) distribution, occurrence rate, and evolutionary contribution of postzygotic single-nucleotide mosaicisms (pSNMs) remain largely unknown. In this study, we developed a mathematical model to describe the accumulation and AF drift of pSNMs during the development of multicellular organisms. By app...

journal_title：Genome research

authors： Ye AY,Dou Y,Yang X,Wang S,Huang AY,Wei L

更新日期：2018-07-01 00:00:00

abstract：:RNA interference is a powerful tool for studying gene function and for drug target discovery in diverse organisms and cell types. In mammalian systems, small interfering RNAs (siRNAs), or DNA plasmids expressing these siRNAs, have been used to down-modulate gene expression. However, inefficient transfection protocols,...

journal_title：Genome research

authors： Arts GJ,Langemeijer E,Tissingh R,Ma L,Pavliska H,Dokic K,Dooijes R,Mesić E,Clasen R,Michiels F,van der Schueren J,Lambrecht M,Herman S,Brys R,Thys K,Hoffmann M,Tomme P,van Es H

更新日期：2003-10-01 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：:Nucleosomes in active chromatin are dynamic, but whether they have distinct structural conformations is unknown. To identify nucleosomes with alternative structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed that 5% of budding yeast (Saccharomyces cerevisiae) nucleosome positions have asymme...

journal_title：Genome research

authors： Ramachandran S,Zentner GE,Henikoff S

更新日期：2015-03-01 00:00:00

abstract：:Regulatory sequences in higher genomes can map large distances from gene coding regions, and cannot yet be identified by simple inspection of primary DNA sequence information. Here we describe an efficient method of surveying large genomic regions for gene regulatory information, and subdividing complex sets of distan...

journal_title：Genome research

authors： Mortlock DP,Guenther C,Kingsley DM

更新日期：2003-09-01 00:00:00

abstract：:Essential genes refer to those whose null mutation leads to lethality or sterility. Theoretical reasoning and empirical data both suggest that the fatal effect of inactivating an essential gene can be attributed to either the loss of indispensable core cellular function (Type I), or the gain of fatal side effects afte...

journal_title：Genome research

authors： Chen P,Wang D,Chen H,Zhou Z,He X

更新日期：2016-10-01 00:00:00

abstract：:Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the p...

journal_title：Genome research

authors： Blanchette M,Tompa M

更新日期：2002-05-01 00:00:00

abstract：:Organisms with large genomes contain vast amounts of repetitive DNA sequences, much of which is composed of retrotransposons. Amplification of retrotransposons has been postulated to be a major mechanism increasing genome size and leading to "genomic obesity." To gain insights into the relation between retrotransposon...

journal_title：Genome research

authors： Shirasu K,Schulman AH,Lahaye T,Schulze-Lefert P

更新日期：2000-07-01 00:00:00

abstract：:Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance suggests that their genes may have been subject to adaptive evolution. We have estimated the consequences of selection on ro...

journal_title：Genome research

authors： Emes RD,Beatson SA,Ponting CP,Goodstadt L

更新日期：2004-04-01 00:00:00

abstract：:In-gel competitive reassociation (IGCR) is a method of differential subtraction to enrich polymorphic DNA restriction fragments between two DNA samples without probes or specific sequence information. Here, we show that by combining IGCR and expressed sequence tags (EST) array hybridization, polymorphic DNA fragments ...

journal_title：Genome research

authors： Gotoh K,Oishi M

更新日期：2003-03-01 00:00:00

abstract：:The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonr...

journal_title：Genome research

authors： Bi X,Cheng YJ,Hu B,Ma X,Wu R,Wang JW,Liu C

更新日期：2017-07-01 00:00:00