Genome-wide map of regulatory interactions in the human genome.

abstract：:Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering ...

journal_title：Genome research

authors： Ayele M,Haas BJ,Kumar N,Wu H,Xiao Y,Van Aken S,Utterback TR,Wortman JR,White OR,Town CD

更新日期：2005-04-01 00:00:00

abstract：:X-linked Mental Retardation (XLMR) occurs in 1 in 600 males and is highly genetically heterogeneous. We used a novel human X chromosome cDNA microarray (XCA) to survey the expression profile of X-linked genes in lymphoblasts of XLMR males. Genes with altered expression verified by Northern blot and/or quantitative PCR...

journal_title：Genome research

authors： Zhang L,Jie C,Obie C,Abidi F,Schwartz CE,Stevenson RE,Valle D,Wang T

更新日期：2007-05-01 00:00:00

abstract：:Single-cell sequencing (SCS) is a powerful new tool for investigating evolution and diversity in cancer and understanding the role of rare cells in tumor progression. These methods have begun to unravel key questions in cancer biology that have been difficult to address with bulk tumor measurements. Over the past five...

journal_title：Genome research

authors： Navin NE

更新日期：2015-10-01 00:00:00

abstract：:DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover <2% of the genome and cannot account...

journal_title：Genome research

authors： Kaplow IM,MacIsaac JL,Mah SM,McEwen LM,Kobor MS,Fraser HB

更新日期：2015-06-01 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：:The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is ...

journal_title：Genome research

authors： Yáñez-Cuna JO,Dinh HQ,Kvon EZ,Shlyueva D,Stark A

更新日期：2012-10-01 00:00:00

abstract：:During meiosis, chromatin undergoes extensive changes to facilitate recombination, homolog pairing, and chromosome segregation. To investigate the relationship between chromatin organization and meiotic processes, we used formaldehyde-assisted isolation of regulatory elements (FAIRE) to map open chromatin during the t...

journal_title：Genome research

authors： Berchowitz LE,Hanlon SE,Lieb JD,Copenhaver GP

更新日期：2009-12-01 00:00:00

abstract：:We assessed the content, structure, and distribution of segmental duplications (> or =90% sequence identity, > or =5 kb length) within the published version of the Rattus norvegicus genome assembly (v.3.1). The overall fraction of duplicated sequence within the rat assembly (2.92%) is greater than that of the mouse (1...

journal_title：Genome research

authors： Tuzun E,Bailey JA,Eichler EE

更新日期：2004-04-01 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：:We describe a new method, Tag-seq, which employs ultra high-throughput sequencing of 21 base pair cDNA tags for sensitive and cost-effective gene expression profiling. We compared Tag-seq data to LongSAGE data and observed improved representation of several classes of rare transcripts, including transcription factors,...

journal_title：Genome research

authors： Morrissy AS,Morin RD,Delaney A,Zeng T,McDonald H,Jones S,Zhao Y,Hirst M,Marra MA

更新日期：2009-10-01 00:00:00

abstract：:Disturbance of DNA methylation leading to aberrant gene expression has been implicated in the etiology of many diseases. Whereas variation at the genetic level has been studied extensively, less is known about the extent and function of epigenetic variation. To explore variation and heritability of DNA methylation, we...

journal_title：Genome research

authors： Gervin K,Hammerø M,Akselsen HE,Moe R,Nygård H,Brandt I,Gjessing HK,Harris JR,Undlien DE,Lyle R

更新日期：2011-11-01 00:00:00

abstract：:We developed a high-throughput technique for the generation of cDNA libraries in the yeast Saccharomyces cerevisiae which enables the selection of cloned cDNA inserts containing open reading frames (ORFs). For direct screening of random-primed cDNA libraries, we have constructed a yeast shuttle/expression vector, the ...

journal_title：Genome research

authors： Holz C,Lueking A,Bovekamp L,Gutjahr C,Bolotina N,Lehrach H,Cahill DJ

更新日期：2001-10-01 00:00:00

abstract：:PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree ...

journal_title：Genome research

authors： Schwartz S,Zhang Z,Frazer KA,Smit A,Riemer C,Bouck J,Gibbs R,Hardison R,Miller W

更新日期：2000-04-01 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：: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：: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：: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：:There are numerous examples from the genomes of viruses, mitochondria, and chromosomes that adjacent genes can overlap, sharing at least one nucleotide. Overlaps have been hypothesized to be involved in genome size minimization and as a regulatory mechanism of gene expression. Here we show that overlapping genes are a...

journal_title：Genome research

authors： Johnson ZI,Chisholm SW

更新日期：2004-11-01 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：:Despite recent progress in genome topology knowledge, the role of repeats, which make up the majority of mammalian genomes, remains elusive. Satellite repeats are highly abundant sequences that cluster around centromeres, attract pericentromeric heterochromatin, and aggregate into nuclear chromocenters. These nuclear ...

journal_title：Genome research

authors： Wijchers PJ,Geeven G,Eyres M,Bergsma AJ,Janssen M,Verstegen M,Zhu Y,Schell Y,Vermeulen C,de Wit E,de Laat W

更新日期：2015-07-01 00:00:00

abstract：:The recent publication of the FANTOM mouse transcriptome has provided a unique opportunity to study the diversity of transcripts arising from a single gene locus. We have focused on the Gnas complex, as imprinting loci themselves provide unique insights into transcriptional regulation. Thirteen full-length cDNAs from ...

journal_title：Genome research

authors： Holmes R,Williamson C,Peters J,Denny P,Wells C,RIKEN GER Group.,GSL Members.

更新日期：2003-06-01 00:00:00

abstract：:Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into target gene expression are not well understood. To determine the mapping between promoter DNA se...

journal_title：Genome research

authors： van Dijk D,Sharon E,Lotan-Pompan M,Weinberger A,Segal E,Carey LB

更新日期：2017-01-01 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：:Establishment of spatial coordinates during Drosophila embryogenesis relies on differential regulatory activity of axis patterning enhancers. Concentration gradients of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target ...

journal_title：Genome research

authors： Bozek M,Cortini R,Storti AE,Unnerstall U,Gaul U,Gompel N

更新日期：2019-05-01 00:00:00

abstract：:Chronic bacterial infections of the lung are the leading cause of morbidity and mortality in cystic fibrosis patients. Tracking bacterial evolution during chronic infections can provide insights into how host selection pressures-including immune responses and therapeutic interventions-shape bacterial genomes. We carri...

journal_title：Genome research

authors： Lee AH,Flibotte S,Sinha S,Paiero A,Ehrlich RL,Balashov S,Ehrlich GD,Zlosnik JE,Mell JC,Nislow C

更新日期：2017-04-01 00:00:00

abstract：:Structured elements of RNA molecules are essential in, e.g., RNA stabilization, localization, and protein interaction, and their conservation across species suggests a common functional role. We computationally screened vertebrate genomes for conserved RNA structures (CRSs), leveraging structure-based, rather than seq...

journal_title：Genome research

authors： Seemann SE,Mirza AH,Hansen C,Bang-Berthelsen CH,Garde C,Christensen-Dalsgaard M,Torarinsson E,Yao Z,Workman CT,Pociot F,Nielsen H,Tommerup N,Ruzzo WL,Gorodkin J

更新日期：2017-08-01 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：:The genetics of aging in the yeast Saccharomyces cerevisiae has involved the manipulation of individual genes in laboratory strains. We have instituted a quantitative genetic analysis of the yeast replicative lifespan by sampling the natural genetic variation in a wild yeast isolate. Haploid segregants from a cross be...

journal_title：Genome research

authors： Stumpferl SW,Brand SE,Jiang JC,Korona B,Tiwari A,Dai J,Seo JG,Jazwinski SM

更新日期：2012-10-01 00:00:00

abstract：:Memory is a hallmark of adaptive immunity, wherein lymphocytes mount a superior response to a previously encountered antigen. It has been speculated that epigenetic alterations in memory lymphocytes contribute to their functional distinction from their naive counterparts. However, the nature and extent of epigenetic a...

journal_title：Genome research

authors： Lai AY,Mav D,Shah R,Grimm SA,Phadke D,Hatzi K,Melnick A,Geigerman C,Sobol SE,Jaye DL,Wade PA

更新日期：2013-12-01 00:00:00

abstract：:Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships po...

journal_title：Genome research

authors： Horvath JE,Weisrock DW,Embry SL,Fiorentino I,Balhoff JP,Kappeler P,Wray GA,Willard HF,Yoder AD

更新日期：2008-03-01 00:00:00