Characterization of the RNA content of chromatin.

abstract：:Somatic L1 retrotransposition events have been shown to occur in epithelial cancers. Here, we attempted to determine how early somatic L1 insertions occurred during the development of gastrointestinal (GI) cancers. Using L1-targeted resequencing (L1-seq), we studied different stages of four colorectal cancers arising ...

journal_title：Genome research

authors： Ewing AD,Gacita A,Wood LD,Ma F,Xing D,Kim MS,Manda SS,Abril G,Pereira G,Makohon-Moore A,Looijenga LH,Gillis AJ,Hruban RH,Anders RA,Romans KE,Pandey A,Iacobuzio-Donahue CA,Vogelstein B,Kinzler KW,Kazazian HH Jr,Sol

更新日期：2015-10-01 00:00:00

abstract：:Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora t...

journal_title：Genome research

authors： Corcoran P,Anderson JL,Jacobson DJ,Sun Y,Ni P,Lascoux M,Johannesson H

更新日期：2016-04-01 00:00:00

abstract：:The recently identified mouse obese (ob) gene apparently encodes a secreted protein that may function in the signaling pathway of adipose tissue. Mutations in the mouse ob gene are associated with the early development of gross obesity. A detailed knowledge concerning the RNA expression pattern and precise genomic loc...

journal_title：Genome research

authors： Green ED,Maffei M,Braden VV,Proenca R,DeSilva U,Zhang Y,Chua SC Jr,Leibel RL,Weissenbach J,Friedman JM

更新日期：1995-08-01 00:00:00

abstract：:Alternative splicing (AS) creates multiple mRNA transcripts from a single gene. While AS is known to contribute to gene regulation and proteome diversity in animals, the study of its importance in plants is in its early stages. However, recently available plant genome and transcript sequence data sets are enabling a g...

journal_title：Genome research

authors： Barbazuk WB,Fu Y,McGinnis KM

更新日期：2008-09-01 00:00:00

abstract：:All individuals in a finite population are related if traced back long enough and will, therefore, share regions of their genomes identical by descent (IBD). Detection of such regions has several important applications-from answering questions about human evolution to locating regions in the human genome containing di...

journal_title：Genome research

authors： Moltke I,Albrechtsen A,Hansen TV,Nielsen FC,Nielsen R

更新日期：2011-07-01 00:00:00

abstract：:We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales linearly with the number of samples, enabling analysis of whole-genome data in large cohorts. Our approach is based on ...

journal_title：Genome research

authors： Gusev A,Lowe JK,Stoffel M,Daly MJ,Altshuler D,Breslow JL,Friedman JM,Pe'er I

更新日期：2009-02-01 00:00:00

abstract：:Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the dominant technique for mapping transcription factor (TF) binding regions genome-wide. We performed an integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium. We ident...

journal_title：Genome research

authors： Wang J,Zhuang J,Iyer S,Lin X,Whitfield TW,Greven MC,Pierce BG,Dong X,Kundaje A,Cheng Y,Rando OJ,Birney E,Myers RM,Noble WS,Snyder M,Weng Z

更新日期：2012-09-01 00:00:00

abstract：:Gene expression levels can be an important link DNA between variation and phenotypic manifestations. Our previous map of global gene expression, based on ~400K single nucleotide polymorphisms (SNPs) and 50K transcripts in 400 sib pairs from the MRCA family panel, has been widely used to interpret the results of genome...

journal_title：Genome research

authors： Liang L,Morar N,Dixon AL,Lathrop GM,Abecasis GR,Moffatt MF,Cookson WO

更新日期：2013-04-01 00:00:00

abstract：:An important aspect of understanding a biological pathway is to delineate the transcriptional regulatory mechanisms of the genes involved. Two important tasks are often encountered when studying transcription regulation, i.e., (1) the identification of common transcriptional regulators of a set of coexpressed genes; (...

journal_title：Genome research

authors： Chang LW,Nagarajan R,Magee JA,Milbrandt J,Stormo GD

更新日期：2006-03-01 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：:Most new genes arise by duplication of existing gene structures, after which relaxed selection on the new copy frequently leads to mutational inactivation of the duplicate; only rarely will a new gene with modified function emerge. Here we describe a unique mechanism of gene creation, whereby new combinations of funct...

journal_title：Genome research

authors： Babushok DV,Ohshima K,Ostertag EM,Chen X,Wang Y,Mandal PK,Okada N,Abrams CS,Kazazian HH Jr

更新日期：2007-08-01 00:00:00

abstract：:CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during development than previously appreciated. Here, we set out to understand the extent to which shifts in genome-wide CTCF occ...

journal_title：Genome research

authors： Beagan JA,Duong MT,Titus KR,Zhou L,Cao Z,Ma J,Lachanski CV,Gillis DR,Phillips-Cremins JE

更新日期：2017-07-01 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：:It is believed that most modern mammalian lineages arose from a series of rapid speciation events near the Cretaceous-Tertiary boundary. It is shown that such a phylogeny makes the common ancestral genome sequence an ideal target for reconstruction. Simulations suggest that with methods currently available, we can exp...

journal_title：Genome research

authors： Blanchette M,Green ED,Miller W,Haussler D

更新日期：2004-12-01 00:00:00

abstract：:We report the development of a simplified cap analysis of gene expression (CAGE) protocol adapted for single-molecule sequencers that avoids second strand synthesis, ligation, digestion, and PCR. HeliScopeCAGE directly sequences the 3' end of cap trapped first-strand cDNAs. As with previous versions of CAGE, we better...

journal_title：Genome research

authors： Kanamori-Katayama M,Itoh M,Kawaji H,Lassmann T,Katayama S,Kojima M,Bertin N,Kaiho A,Ninomiya N,Daub CO,Carninci P,Forrest AR,Hayashizaki Y

更新日期：2011-07-01 00:00:00

abstract：:Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. B...

journal_title：Genome research

authors： Kent WJ

更新日期：2002-04-01 00:00:00

abstract：:CBX5, CBX1, and CBX3 (HP1α, β, and γ, respectively) play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, CBX5, CBX1, and CBX3 may also participate in transcriptional regulation of genes. Recently, CBX3 binding to the bodies of a subset of genes has been observed in hu...

journal_title：Genome research

authors： Smallwood A,Hon GC,Jin F,Henry RE,Espinosa JM,Ren B

更新日期：2012-08-01 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：:As part of a recent high-density linkage disequilibrium (LD) study of chromosome 20, we obtained genotypes for approximately 30,000 SNPs at a density of 1 SNP/2 kb on four different population samples (47 CEPH founders; 91 UK unrelateds [unrelated white individuals of western European ancestry]; 97 African Americans; ...

journal_title：Genome research

authors： Lawrence R,Evans DM,Morris AP,Ke X,Hunt S,Paolucci M,Ragoussis J,Deloukas P,Bentley D,Cardon LR

更新日期：2005-11-01 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：:In plants there are several classes of 21-24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific species. We used high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato frui...

journal_title：Genome research

authors： Moxon S,Jing R,Szittya G,Schwach F,Rusholme Pilcher RL,Moulton V,Dalmay T

更新日期：2008-10-01 00:00:00

abstract：:Meiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here, we sequenced Arabidopsis Landsberg erecta (Ler) and two set...

journal_title：Genome research

authors： Lu P,Han X,Qi J,Yang J,Wijeratne AJ,Li T,Ma H

更新日期：2012-03-01 00:00:00

abstract：:Comparative analysis of the protein sequences encoded in the four euryarchaeal species whose genomes have been sequenced completely (Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Pyrococcus horikoshii) revealed 1326 orthologous sets, of which 543 are represented in all fou...

journal_title：Genome research

authors： Makarova KS,Aravind L,Galperin MY,Grishin NV,Tatusov RL,Wolf YI,Koonin EV

更新日期：1999-07-01 00:00:00

abstract：:ClinSeq is a pilot project to investigate the use of whole-genome sequencing as a tool for clinical research. By piloting the acquisition of large amounts of DNA sequence data from individual human subjects, we are fostering the development of hypothesis-generating approaches for performing research in genomic medicin...

journal_title：Genome research

authors： Biesecker LG,Mullikin JC,Facio FM,Turner C,Cherukuri PF,Blakesley RW,Bouffard GG,Chines PS,Cruz P,Hansen NF,Teer JK,Maskeri B,Young AC,NISC Comparative Sequencing Program.,Manolio TA,Wilson AF,Finkel T,Hwang P,Arai A

更新日期：2009-09-01 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：: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：:In mammals, genome-wide chromatin maps and immunofluorescence studies show that broad domains of repressive histone modifications are present on pericentromeric and telomeric repeats and on the inactive X chromosome. However, only a few autosomal loci such as silent Hox gene clusters have been shown to lie in broad do...

journal_title：Genome research

authors： Pauler FM,Sloane MA,Huang R,Regha K,Koerner MV,Tamir I,Sommer A,Aszodi A,Jenuwein T,Barlow DP

更新日期：2009-02-01 00:00:00

abstract：:Cephalochordates, urochordates, and vertebrates evolved from a common ancestor over 520 million years ago. To improve our understanding of chordate evolution and the origin of vertebrates, we intensively searched for particular genes, gene families, and conserved noncoding elements in the sequenced genome of the cepha...

journal_title：Genome research

authors： Holland LZ,Albalat R,Azumi K,Benito-Gutiérrez E,Blow MJ,Bronner-Fraser M,Brunet F,Butts T,Candiani S,Dishaw LJ,Ferrier DE,Garcia-Fernàndez J,Gibson-Brown JJ,Gissi C,Godzik A,Hallböök F,Hirose D,Hosomichi K,Ikuta T,I

更新日期：2008-07-01 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：:Biophysical, chemical, and nanoscience approaches to the study of nuclear structure and activity have been developing recently and hold considerable promise. A selection of fundamental problems in genome organization and function are reviewed and discussed in the context of these new perspectives and approaches. Advan...

journal_title：Genome research

authors： O'Brien TP,Bult CJ,Cremer C,Grunze M,Knowles BB,Langowski J,McNally J,Pederson T,Politz JC,Pombo A,Schmahl G,Spatz JP,van Driel R

更新日期：2003-06-01 00:00:00