Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.

abstract：:MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3'-UTR, which interacts mainly with the 5'-end of miRNA in animals. Here we identify many endogenous motifs within human 5'-UTRs specific to the 3'-ends of miRNAs. The 3'-end of conserved miRNAs in particular has significant inter...

journal_title：Genome research

authors： Lee I,Ajay SS,Yook JI,Kim HS,Hong SH,Kim NH,Dhanasekaran SM,Chinnaiyan AM,Athey BD

更新日期：2009-07-01 00:00:00

abstract：:The determination of the phylogenetic relationships among microorganisms has long relied primarily on gene sequence information. Given that prokaryotic organisms often lack morphological characteristics amenable to phylogenetic analysis, prokaryotic phylogenies, in particular, are often based on sequence data. In this...

journal_title：Genome research

authors： Deeds EJ,Hennessey H,Shakhnovich EI

更新日期：2005-03-01 00:00:00

abstract：:Chromosomal aberrations have been thought to be random events. However, recent findings introduce a new paradigm in which certain DNA segments have the potential to adopt unusual conformations that lead to genomic instability and nonrandom chromosomal rearrangement. One of the best-studied examples is the palindromic ...

journal_title：Genome research

authors： Inagaki H,Ohye T,Kogo H,Kato T,Bolor H,Taniguchi M,Shaikh TH,Emanuel BS,Kurahashi H

更新日期：2009-02-01 00:00:00

abstract：:Comparative genomics provides a general methodology for discovering functional DNA elements and understanding their evolution. The availability of many related genomes enables more powerful analyses, but requires rigorous phylogenetic methods to resolve orthologous genes and regions. Here, we use 12 recently sequenced...

journal_title：Genome research

authors： Rasmussen MD,Kellis M

更新日期：2007-12-01 00:00:00

abstract：:Epigenetic mechanisms are believed to play key roles in the establishment of cell-specific transcription programs. Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten-e...

journal_title：Genome research

authors： Mahé EA,Madigou T,Sérandour AA,Bizot M,Avner S,Chalmel F,Palierne G,Métivier R,Salbert G

更新日期：2017-06-01 00:00:00

abstract：:We have developed a novel quantitative method for rapidly assessing the CpG methylation density of a DNA region in mammalian cells. After bisulfite modification of genomic DNA, the region of interest is PCR amplified with primers containing two dam sites (GATC). The purified PCR products are then incubated with 14C-la...

journal_title：Genome research

authors： Galm O,Rountree MR,Bachman KE,Jair KW,Baylin SB,Herman JG

更新日期：2002-01-01 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：:We have used the FANTOM2 mouse cDNA set (60,770 clones), public mRNA data, and mouse genome sequence data to identify 2481 pairs of sense-antisense transcripts and 899 further pairs of nonantisense bidirectional transcription based upon genomic mapping. The analysis greatly expands the number of known examples of sens...

journal_title：Genome research

authors： Kiyosawa H,Yamanaka I,Osato N,Kondo S,Hayashizaki Y,RIKEN GER Group.,GSL Members.

更新日期：2003-06-01 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：:Using both env and long terminal repeat (LTR) sequences, with maximal representation of genetic diversity within primate strains, we revise and expand the unique evolutionary history of human and simian T-cell leukemia/lymphotropic viruses (HTLV/STLV). Based on the robust application of three different phylogenetic al...

journal_title：Genome research

authors： Slattery JP,Franchini G,Gessain A

更新日期：1999-06-01 00:00:00

abstract：:The remarkable olfactory power of insect species is thought to be generated by a combinatorial action of two large protein families, G protein-coupled olfactory receptors (ORs) and odorant binding proteins (OBPs). In olfactory sensilla, OBPs deliver hydrophobic airborne molecules to ORs, but their expression in nonolf...

journal_title：Genome research

authors： Forêt S,Maleszka R

更新日期：2006-11-01 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：:By applying graph representations to biochemical pathways, a new computational pipeline is proposed to find potential operons in microbial genomes. The algorithm relies on the fact that enzyme genes in operons tend to catalyze successive reactions in metabolic pathways. We applied this algorithm to 42 microbial genome...

journal_title：Genome research

authors： Zheng Y,Szustakowski JD,Fortnow L,Roberts RJ,Kasif S

更新日期：2002-08-01 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

abstract：:We have cloned the human gene encoding the transcription factor T. T protein is vital for the formation of posterior mesoderm and axial development in all vertebrates. Brachyury mutant mice, which lack T protein, die in utero with abnormal notochord, posterior somites, and allantois. We have identified human T genomic...

journal_title：Genome research

authors： Edwards YH,Putt W,Lekoape KM,Stott D,Fox M,Hopkinson DA,Sowden J

更新日期：1996-03-01 00:00:00

abstract：:Large-scale gene expression studies and genomic sequencing projects are providing vast amounts of information that can be used to identify or predict cellular regulatory processes. Genes can be clustered on the basis of the similarity of their expression profiles or function and these clusters are likely to contain ge...

journal_title：Genome research

authors： Jakt LM,Cao L,Cheah KS,Smith DK

更新日期：2001-01-01 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：:A-to-I RNA editing is a conserved widespread phenomenon in which adenosine (A) is converted to inosine (I) by adenosine deaminases (ADARs) in double-stranded RNA regions, mainly noncoding. Mutations in ADAR enzymes in Caenorhabditis elegans cause defects in normal development but are not lethal as in human and mouse. ...

journal_title：Genome research

authors： Goldstein B,Agranat-Tamir L,Light D,Ben-Naim Zgayer O,Fishman A,Lamm AT

更新日期：2017-03-01 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：:The lack of long-term evolutionary conservation of microRNA (miRNA) target sites appears to contradict many analyses of their functions. Several hypotheses have been offered, but an attractive one-that the conservation may be a function of taxonomic hierarchy (vertebrates, mammals, primates, etc.)-has rarely been disc...

journal_title：Genome research

authors： Xu J,Zhang R,Shen Y,Liu G,Lu X,Wu CI

更新日期：2013-11-01 00:00:00

abstract：:The need for expeditious and inexpensive methods for high-throughput DNA sequencing has been highlighted by the accelerated pace of genome DNA sequencing over the past year. At the Joint Genome Institute, the throughput in terms of high-quality bases per day has increased over 20-fold during the past 18 mo, reaching a...

journal_title：Genome research

authors： Elkin CJ,Richardson PM,Fourcade HM,Hammon NM,Pollard MJ,Predki PF,Glavina T,Hawkins TL

更新日期：2001-07-01 00:00:00

abstract：:In interphase eukaryotic cells, almost all heterochromatin is located adjacent to the nucleolus or to the nuclear lamina, thus defining nucleolus-associated domains (NADs) and lamina-associated domains (LADs), respectively. Here, we determined the first genome-scale map of murine NADs in mouse embryonic fibroblasts (M...

journal_title：Genome research

authors： Vertii A,Ou J,Yu J,Yan A,Pagès H,Liu H,Zhu LJ,Kaufman PD

更新日期：2019-08-01 00:00:00

abstract：:The human genome is estimated to contain 23,000 to 33,000 retropseudogenes. To study the properties of genes giving rise to these retroelements, we compared the structure and expression of genes with or without known retropseudogenes. Four main features have emerged from the analysis of 181 genes associated to retrops...

journal_title：Genome research

authors： Gonçalves I,Duret L,Mouchiroud D

更新日期：2000-05-01 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：: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：:Long sequencing reads generated by single-molecule sequencing technology offer the possibility of dramatically improving the contiguity of genome assemblies. The biggest challenge today is that long reads have relatively high error rates, currently around 15%. The high error rates make it difficult to use this data al...

journal_title：Genome research

authors： Zimin AV,Puiu D,Luo MC,Zhu T,Koren S,Marçais G,Yorke JA,Dvořák J,Salzberg SL

更新日期：2017-05-01 00:00:00

abstract：:Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We presen...

journal_title：Genome research

authors： Florea L,Di Francesco V,Miller J,Turner R,Yao A,Harris M,Walenz B,Mobarry C,Merkulov GV,Charlab R,Dew I,Deng Z,Istrail S,Li P,Sutton G

更新日期：2005-01-01 00:00:00

abstract：:GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored ...

journal_title：Genome research

authors： Parra G,Blanco E,Guigó R

更新日期：2000-04-01 00:00:00

abstract：:It is widely accepted that newly arisen duplicate gene pairs experience an altered selective regime that is often manifested as an increase in the rate of protein sequence evolution. Many details about the nature of the rate acceleration remain unknown, however, including its typical magnitude and duration, and whethe...

journal_title：Genome research

authors： Scannell DR,Wolfe KH

更新日期：2008-01-01 00:00:00

abstract：:The initial comparison of the human and chimpanzee genome sequences revealed 16 genomic regions with an unusually high density of rapidly evolving genes. One such region is the whey acidic protein (WAP) four-disulfide core domain locus (or WFDC locus), which contains 14 WFDC genes organized in two subloci on human chr...

journal_title：Genome research

authors： Hurle B,Swanson W,NISC Comparative Sequencing Program.,Green ED

更新日期：2007-03-01 00:00:00