Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications.

abstract：:The Saccharomyces cerevisiae genome contains about 35 copies of dispersed retrotransposons called Ty1 elements. Ty1 elements target regions upstream of tRNA genes and other Pol III-transcribed genes when retrotransposing to new sites. We used deep sequencing of Ty1-flanking sequence amplicons to characterize Ty1 integ...

journal_title：Genome research

authors： Mularoni L,Zhou Y,Bowen T,Gangadharan S,Wheelan SJ,Boeke JD

更新日期：2012-04-01 00:00:00

abstract：:A genome-wide search for multiple loci influencing salt-loaded systolic blood pressure (NaSBP) variation among 188 F2 progeny from a cross between the Brown-Norway and spontaneously hypertensive rat strains was pursued in an effort to gain insight into the polygenic basis of blood pressure regulation. The results sugg...

journal_title：Genome research

authors： Schork NJ,Krieger JE,Trolliet MR,Franchini KG,Koike G,Krieger EM,Lander ES,Dzau VJ,Jacob HJ

更新日期：1995-09-01 00:00:00

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：:Primordial dwarfism (PD) is a disease in which severely impaired fetal growth persists throughout postnatal development and results in stunted adult size. The condition is highly heterogeneous clinically, but the use of certain phenotypic aspects such as head circumference and facial appearance has proven helpful in d...

journal_title：Genome research

authors： Shaheen R,Faqeih E,Ansari S,Abdel-Salam G,Al-Hassnan ZN,Al-Shidi T,Alomar R,Sogaty S,Alkuraya FS

更新日期：2014-02-01 00:00:00

abstract：:It appears that, for many genes, the two alleles possessed by an individual may produce different amounts of transcript. When such allelic differences in transcription are observed for some individuals but not others, a plausible explanation is genetic variation in the cis-acting elements that regulate the gene in que...

journal_title：Genome research

authors： Forton JT,Udalova IA,Campino S,Rockett KA,Hull J,Kwiatkowski DP

更新日期：2007-01-01 00:00:00

abstract：:Previous approaches to mutation detection in mRNA from the neurofibromatosis 1 (NF1) locus have required the PCR amplification of five or more overlapping cDNA segments to screen the entire 8.5-kb open reading frame (ORF). Systematically, these assays do not detect deletions that span the region of overlap (usually 1-...

journal_title：Genome research

authors： Martinez JM,Breidenbach HH,Cawthon R

更新日期：1996-01-01 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：: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 expression of most genes is regulated by multiple transcription factors. The interactions between transcription factors produce complex patterns of gene expression that are not always obvious from the arrangement of cis-regulatory elements in a promoter. One critical element of promoters is the TATA box, the docki...

journal_title：Genome research

authors： Mogno I,Vallania F,Mitra RD,Cohen BA

更新日期：2010-10-01 00:00:00

abstract：:Genes with sex-biased expression in Drosophila are thought to underlie sexually dimorphic phenotypes and have been shown to possess unique evolutionary properties. However, the forces and constraints governing the evolution of sex-biased genes in the somatic tissues of Drosophila are largely unknown. By using populati...

journal_title：Genome research

authors： Khodursky S,Svetec N,Durkin SM,Zhao L

更新日期：2020-06-01 00:00:00

abstract：:Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uni...

journal_title：Genome research

authors： Daubin V,Ochman H

更新日期：2004-06-01 00:00:00

abstract：:Quantification of mRNA levels in human cortical brain biopsies and autopsies was performed using a fluorogenic 5' nuclease assay. The reproducibility of the assay using replica plates was 97%-99%. Relative quantities of mRNA from 16 different genes were evaluated using a statistical approach based on ANCOVA analysis. ...

journal_title：Genome research

authors： Castensson A,Emilsson L,Preece P,Jazin EE

更新日期：2000-08-01 00:00:00

abstract：:Mirtrons are intronic hairpin substrates of the dicing machinery that generate functional microRNAs. In this study, we describe experimental assays that defined the essential requirements for entry of introns into the mirtron pathway. These data informed a bioinformatic screen that effectively identified functional mi...

journal_title：Genome research

authors： Chung WJ,Agius P,Westholm JO,Chen M,Okamura K,Robine N,Leslie CS,Lai EC

更新日期：2011-02-01 00:00:00

abstract：:Recent advances in genome research have accelerated the process of locating candidate genes and the variable sites within them and have simplified the task of genotype measurement. The development of statistical and computational strategies to utilize information on hundreds -- soon thousands -- of variable loci to in...

journal_title：Genome research

authors： Nelson MR,Kardia SL,Ferrell RE,Sing CF

更新日期：2001-03-01 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：:Fish-mammal genomic comparisons have proved powerful in identifying conserved noncoding elements likely to be cis-regulatory in nature, and the majority of those tested in vivo have been shown to act as tissue-specific enhancers associated with genes involved in transcriptional regulation of development. Although most...

journal_title：Genome research

authors： McEwen GK,Woolfe A,Goode D,Vavouri T,Callaway H,Elgar G

更新日期：2006-04-01 00:00:00

abstract：:In Drosophila melanogaster, there is an excess of genes duplicated by retroposition from the X chromosome to the autosomes. Most of those retrogenes that originated on the X chromosome have testis expression pattern. These observations could be explained by natural selection favoring genes that avoided spermatogenesis...

journal_title：Genome research

authors： Vibranovski MD,Zhang Y,Long M

更新日期：2009-05-01 00:00:00

abstract：:Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and co...

journal_title：Genome research

authors： Hoskins RA,Carlson JW,Wan KH,Park S,Mendez I,Galle SE,Booth BW,Pfeiffer BD,George RA,Svirskas R,Krzywinski M,Schein J,Accardo MC,Damia E,Messina G,Méndez-Lago M,de Pablos B,Demakova OV,Andreyeva EN,Boldyreva LV,Ma

更新日期：2015-03-01 00:00:00

abstract：:Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the z...

journal_title：Genome research

authors： Völker M,Backström N,Skinner BM,Langley EJ,Bunzey SK,Ellegren H,Griffin DK

更新日期：2010-04-01 00:00:00

abstract：:Genome-scale metabolic models promise important insights into cell function. However, the definition of pathways and functional network modules within these models, and in the biochemical literature in general, is often based on intuitive reasoning. Although mathematical methods have been proposed to identify modules,...

journal_title：Genome research

authors： Bundy JG,Papp B,Harmston R,Browne RA,Clayson EM,Burton N,Reece RJ,Oliver SG,Brindle KM

更新日期：2007-04-01 00:00:00

abstract：:We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, th...

journal_title：Genome research

authors： Buchan DW,Shepherd AJ,Lee D,Pearl FM,Rison SC,Thornton JM,Orengo CA

更新日期：2002-03-01 00:00:00

abstract：:Facio-scapulo-humeral dystrophy (FSHD), a muscular hereditary disease with a prevalence of 1 in 20,000, is caused by a partial deletion of a subtelomeric repeat array on chromosome 4q. Earlier, we demonstrated the existence in the vicinity of the D4Z4 repeat of a nuclear matrix attachment site, FR-MAR, efficient in no...

journal_title：Genome research

authors： Petrov A,Allinne J,Pirozhkova I,Laoudj D,Lipinski M,Vassetzky YS

更新日期：2008-01-01 00:00:00

abstract：:We have generated an improved assembly and gene annotation of the pig X Chromosome, and a first draft assembly of the pig Y Chromosome, by sequencing BAC and fosmid clones from Duroc animals and incorporating information from optical mapping and fiber-FISH. The X Chromosome carries 1033 annotated genes, 690 of which a...

journal_title：Genome research

authors： Skinner BM,Sargent CA,Churcher C,Hunt T,Herrero J,Loveland JE,Dunn M,Louzada S,Fu B,Chow W,Gilbert J,Austin-Guest S,Beal K,Carvalho-Silva D,Cheng W,Gordon D,Grafham D,Hardy M,Harley J,Hauser H,Howden P,Howe K,

更新日期：2016-01-01 00:00:00

abstract：:We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization...

journal_title：Genome research

authors： Wu ZJ,Meyer CA,Choudhury S,Shipitsin M,Maruyama R,Bessarabova M,Nikolskaya T,Sukumar S,Schwartzman A,Liu JS,Polyak K,Liu XS

更新日期：2010-12-01 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：: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：:The prion protein (PrP), first identified in scrapie-infected rodents, is encoded by a single exon of a single-copy chromosomal gene. In addition to the protein-coding exon, PrP genes in mammals contain one or two 5'-noncoding exons. To learn more about the genomic organization of regions surrounding the PrP exons, we...

journal_title：Genome research

authors： Lee IY,Westaway D,Smit AF,Wang K,Seto J,Chen L,Acharya C,Ankener M,Baskin D,Cooper C,Yao H,Prusiner SB,Hood LE

更新日期：1998-10-01 00:00:00

abstract：:Pollen, the male gametophyte of flowering plants, represents an ideal biological system to study developmental processes, such as cell polarity, tip growth, and morphogenesis. Upon hydration, the metabolically quiescent pollen rapidly switches to an active state, exhibiting extremely fast growth. This rapid switch req...

journal_title：Genome research

authors： Grobei MA,Qeli E,Brunner E,Rehrauer H,Zhang R,Roschitzki B,Basler K,Ahrens CH,Grossniklaus U

更新日期：2009-10-01 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：: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