Complex genomic rearrangements lead to novel primate gene function.

abstract：:Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotation...

journal_title：Genome research

authors： Lunardon A,Johnson NR,Hagerott E,Phifer T,Polydore S,Coruh C,Axtell MJ

更新日期：2020-03-01 00:00:00

abstract：:We have developed a mutation-scanning approach suitable for whole population screening for unknown mutations. The method, meltMADGE, combines thermal ramp electrophoresis with MADGE to achieve suitable cost efficiency and throughput. The sensitivity was tested in blind trials using 54 amplicons representing the BRCA1 ...

journal_title：Genome research

authors： Alharbi KK,Aldahmesh MA,Spanakis E,Haddad L,Whittall RA,Chen XH,Rassoulian H,Smith MJ,Sillibourne J,Ball NJ,Graham NJ,Briggs PJ,Simpson IA,Phillips DI,Lawlor DA,Ye S,Humphries SE,Cooper C,Smith GD,Ebrahim S,Eccles

更新日期：2005-07-01 00:00:00

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：:Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencin...

journal_title：Genome research

authors： Heidari N,Phanstiel DH,He C,Grubert F,Jahanbani F,Kasowski M,Zhang MQ,Snyder MP

更新日期：2014-12-01 00:00:00

abstract：:We compared the genome of the nematode Caenorhabditis elegans to 13% of that of Caenorhabditis briggsae, identifying 252 conserved segments along their chromosomes. We detected 517 chromosomal rearrangements, with the ratio of translocations to inversions to transpositions being approximately 1:1:2. We estimate that t...

journal_title：Genome research

authors： Coghlan A,Wolfe KH

更新日期：2002-06-01 00:00:00

abstract：:The newly sequenced genome of Monodelphis domestica not only provides the out-group necessary to better understand our own eutherian lineage, but it enables insights into the innovative biology of metatherians. Here, we compare Monodelphis with Homo sequences from alignments of single nucleotides, genes, and whole chr...

journal_title：Genome research

authors： Goodstadt L,Heger A,Webber C,Ponting CP

更新日期：2007-07-01 00:00:00

abstract：:The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the ...

journal_title：Genome research

authors： Kvikstad EM,Makova KD

更新日期：2010-05-01 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：:Much of the available human genomic sequence data exist in a fragmentary draft state following the completion of the initial high-volume sequencing performed by the International Human Genome Sequencing Consortium (IHGSC) and Celera Genomics (CG). We compared six draft genome assemblies over a region of chromosome 4p ...

journal_title：Genome research

authors： Semple CA,Morris SW,Porteous DJ,Evans KL

更新日期：2002-03-01 00:00:00

abstract：:Here we use a chromosome-level genome assembly of a prairie rattlesnake (Crotalus viridis), together with Hi-C, RNA-seq, and whole-genome resequencing data, to study key features of genome biology and evolution in reptiles. We identify the rattlesnake Z Chromosome, including the recombining pseudoautosomal region, and...

journal_title：Genome research

authors： Schield DR,Card DC,Hales NR,Perry BW,Pasquesi GM,Blackmon H,Adams RH,Corbin AB,Smith CF,Ramesh B,Demuth JP,Betrán E,Tollis M,Meik JM,Mackessy SP,Castoe TA

更新日期：2019-04-01 00:00:00

abstract：:Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward thi...

journal_title：Genome research

authors： Tranchevent LC,Aubé F,Dulaurier L,Benoit-Pilven C,Rey A,Poret A,Chautard E,Mortada H,Desmet FO,Chakrama FZ,Moreno-Garcia MA,Goillot E,Janczarski S,Mortreux F,Bourgeois CF,Auboeuf D

更新日期：2017-06-01 00:00:00

abstract：:Next-generation sequencing technologies have made it possible to sequence targeted regions of the human genome in hundreds of individuals. Deep sequencing represents a powerful approach for the discovery of the complete spectrum of DNA sequence variants in functionally important genomic intervals. Current methods for ...

journal_title：Genome research

authors： Bansal V,Harismendy O,Tewhey R,Murray SS,Schork NJ,Topol EJ,Frazer KA

更新日期：2010-04-01 00:00:00

abstract：:The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes (cis-eQTLs). More research is needed to identify effects of genetic variation on distant genes (trans-eQTLs) and understand their...

journal_title：Genome research

authors： Yang F,Wang J,GTEx Consortium.,Pierce BL,Chen LS

更新日期：2017-11-01 00:00:00

abstract：:DNA microarrays produced by deposition (or 'spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted oligonucleotide arrays using two large collections of approximately 70-mer probes, and used these arrays to analyze gene expression i...

journal_title：Genome research

authors： Barczak A,Rodriguez MW,Hanspers K,Koth LL,Tai YC,Bolstad BM,Speed TP,Erle DJ

更新日期：2003-07-01 00:00:00

abstract：:Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for disease-gene discovery in cancer and developmental disorders as well as numerous other applications. However, widespread utilizati...

journal_title：Genome research

authors： Greshock J,Naylor TL,Margolin A,Diskin S,Cleaver SH,Futreal PA,deJong PJ,Zhao S,Liebman M,Weber BL

更新日期：2004-01-01 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：: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：:To investigate whether and how CRISPR-Cas9 on-target and off-target activities are affected by chromatin in eukaryotic cells, we first identified a series of identical endogenous DNA sequences present in both open and closed chromatin regions and then measured mutation frequencies at these sites in human cells using C...

journal_title：Genome research

authors： Kim D,Kim JS

更新日期：2018-12-01 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：:Inbred strains of the laboratory rat are widely used for identifying genetic regions involved in the control of complex quantitative phenotypes of biomedical importance. The draft genomic sequence of the rat now provides essential information for annotating rat quantitative trait locus (QTL) maps. Following the survey...

journal_title：Genome research

authors： Wilder SP,Bihoreau MT,Argoud K,Watanabe TK,Lathrop M,Gauguier D

更新日期：2004-04-01 00:00:00

abstract：:RNA-seq protocols that focus on transcript termini are well suited for applications in which template quantity is limiting. Here we show that, when applied to end-sequencing data, analytical methods designed for global RNA-seq produce computational artifacts. To remedy this, we created the End Sequence Analysis Toolki...

journal_title：Genome research

authors： Derr A,Yang C,Zilionis R,Sergushichev A,Blodgett DM,Redick S,Bortell R,Luban J,Harlan DM,Kadener S,Greiner DL,Klein A,Artyomov MN,Garber M

更新日期：2016-10-01 00:00:00

abstract：:Human tumors are comprised of heterogeneous cell populations that display diverse molecular and phenotypic features. To examine the extent to which epigenetic differences contribute to intratumoral cellular heterogeneity, we have developed a high-throughput method, termed MAPit-patch. The method uses multiplexed ampli...

journal_title：Genome research

authors： Nabilsi NH,Deleyrolle LP,Darst RP,Riva A,Reynolds BA,Kladde MP

更新日期：2014-02-01 00:00:00

abstract：:Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-base...

journal_title：Genome research

authors： Lv J,Jiao W,Guo H,Liu P,Wang R,Zhang L,Zeng Q,Hu X,Bao Z,Wang S

更新日期：2018-12-01 00:00:00

abstract：:In vivo analyses of the occurrence, subcellular localization, and dynamics of protein-protein interactions (PPIs) are important issues in functional proteomic studies. The bimolecular fluorescence complementation (BiFC) assay has many advantages in that it provides a reliable way to detect PPIs in living cells with mi...

journal_title：Genome research

authors： Kim Y,Jung JP,Pack CG,Huh WK

更新日期：2019-01-01 00:00:00

abstract：:Initially thought to play a restricted role in calcium homeostasis, the pleiotropic actions of vitamin D in biology and their clinical significance are only now becoming apparent. However, the mode of action of vitamin D, through its cognate nuclear vitamin D receptor (VDR), and its contribution to diverse disorders, ...

journal_title：Genome research

authors： Ramagopalan SV,Heger A,Berlanga AJ,Maugeri NJ,Lincoln MR,Burrell A,Handunnetthi L,Handel AE,Disanto G,Orton SM,Watson CT,Morahan JM,Giovannoni G,Ponting CP,Ebers GC,Knight JC

更新日期：2010-10-01 00:00:00

abstract：:Insertion of the human non-LTR retrotransposon LINE-1 (L1) into chromosomal DNA is thought to be initiated by a mechanism called target-primed reverse transcription (TPRT). This mechanism readily accounts for the attachment of the 3'-end of an L1 copy to the genomic target, but the subsequent integration steps leading...

journal_title：Genome research

authors： Zingler N,Willhoeft U,Brose HP,Schoder V,Jahns T,Hanschmann KM,Morrish TA,Löwer J,Schumann GG

更新日期：2005-06-01 00:00:00

abstract：:A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We desc...

journal_title：Genome research

authors： van Opijnen T,Camilli A

更新日期：2012-12-01 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：:Aberrations of protein-coding genes are a focus of cancer genomics; however, the impact of oncogenes on expression of the ~50% of transcripts without protein-coding potential, including long noncoding RNAs (lncRNAs), has been largely uncharacterized. Activating mutations in the BRAF oncogene are present in >70% of mel...

journal_title：Genome research

authors： Flockhart RJ,Webster DE,Qu K,Mascarenhas N,Kovalski J,Kretz M,Khavari PA

更新日期：2012-06-01 00:00:00

abstract：:Recent accumulation of microbial genome data has demonstrated that lateral gene transfers constitute an important and universal evolutionary process in prokaryotes, while those in multicellular eukaryotes are still regarded as unusual, except for endosymbiotic gene transfers from mitochondria and plastids. Here we tho...

journal_title：Genome research

authors： Nikoh N,Tanaka K,Shibata F,Kondo N,Hizume M,Shimada M,Fukatsu T

更新日期：2008-02-01 00:00:00