Abstract:
:UEV proteins are enzymatically inactive variants of the E2 ubiquitin-conjugating enzymes that regulate noncanonical elongation of ubiquitin chains. In Saccharomyces cerevisiae, UEV is part of the RAD6-mediated error-free DNA repair pathway. In mammalian cells, UEV proteins can modulate c-FOS transcription and the G2-M transition of the cell cycle. Here we show that the UEV genes from phylogenetically distant organisms present a remarkable conservation in their exon-intron structure. We also show that the human UEV1 gene is fused with the previously unknown gene Kua. In Caenorhabditis elegans and Drosophila melanogaster, Kua and UEV are in separated loci, and are expressed as independent transcripts and proteins. In humans, Kua and UEV1 are adjacent genes, expressed either as separate transcripts encoding independent Kua and UEV1 proteins, or as a hybrid Kua-UEV transcript, encoding a two-domain protein. Kua proteins represent a novel class of conserved proteins with juxtamembrane histidine-rich motifs. Experiments with epitope-tagged proteins show that UEV1A is a nuclear protein, whereas both Kua and Kua-UEV localize to cytoplasmic structures, indicating that the Kua domain determines the cytoplasmic localization of Kua-UEV. Therefore, the addition of a Kua domain to UEV in the fused Kua-UEV protein confers new biological properties to this regulator of variant polyubiquitination.
journal_name
Genome Resjournal_title
Genome researchauthors
Thomson TM,Lozano JJ,Loukili N,Carrió R,Serras F,Cormand B,Valeri M,Díaz VM,Abril J,Burset M,Merino J,Macaya A,Corominas M,Guigó Rdoi
10.1101/gr.gr-1405rsubject
Has Abstractpub_date
2000-11-01 00:00:00pages
1743-56issue
11eissn
1088-9051issn
1549-5469journal_volume
10pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Advanced prostate cancer can progress to systemic metastatic tumors, which are generally androgen insensitive and ultimately lethal. Here, we report a comprehensive genomic survey for somatic events in systemic metastatic prostate tumors using both high-resolution copy number analysis and targeted mutational survey of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.107961.110
更新日期:2011-01-01 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
pub_type: 杂志文章
doi:10.1101/gr.142521.112
更新日期:2013-04-01 00:00:00
abstract::Retrotransposons commonly encode a reverse transcriptase (RT), but other functional domains are variable. The acquisition of new domains is the dominant evolutionary force that brings structural variety to retrotransposons. Non-long-terminal-repeat (non-LTR) retrotransposons are classified into two groups by their str...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3271405
更新日期:2005-08-01 00:00:00
abstract::Interindividual variability in response to chemicals and drugs is a common regulatory concern. It is assumed that xenobiotic-induced adverse reactions have a strong genetic basis, but many mechanism-based investigations have not been successful in identifying susceptible individuals. While recent advances in pharmacog...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.090241.108
更新日期:2009-09-01 00:00:00
abstract::Despite considerable genetic heterogeneity underlying neurodevelopmental diseases, there is compelling evidence that many disease genes will map to a much smaller number of biological subnetworks. We developed a computational method, termed MAGI (merging affected genes into integrated networks), that simultaneously in...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.178855.114
更新日期:2015-01-01 00:00:00
abstract::The incorporation and creation of modified nucleobases in DNA have profound effects on genome function. We describe methods for mapping positions and local content of modified DNA nucleobases in genomic DNA. We combined in vitro nucleobase excision with massively parallel DNA sequencing (Excision-seq) to determine the...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.174052.114
更新日期:2014-09-01 00:00:00
abstract::Microsatellites are abundant in vertebrate genomes, but their sequence representation and length distributions vary greatly within each family of repeats (e.g., tetranucleotides). Biophysical studies of 82 synthetic single-stranded oligonucleotides comprising all tetra- and trinucleotide repeats revealed an inverse co...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.078303.108
更新日期:2008-10-01 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
pub_type: 杂志文章
doi:10.1101/gr.4303406
更新日期:2006-03-01 00:00:00
abstract::A machine that employs a novel reagent delivery technique for biomolecular synthesis has been developed. This machine separates the addressing of individual synthesis sites from the actual process of reagent delivery by using masks placed over the sites. Because of this separation, this machine is both cost-effective ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.359002
更新日期:2002-12-01 00:00:00
abstract::The association of subclasses of Alu repetitive elements with various classes of trinucleotide and tetranucleotide microsatellites was characterized as a first step toward advancing our understanding of the evolution of microsatellite repeats. In addition, information regarding the association of specific classes of m...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7.7.716
更新日期:1997-07-01 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
pub_type: 杂志文章
doi:10.1101/gr.113050.110
更新日期:2011-02-01 00:00:00
abstract::The study of genetic variability within natural populations of pathogens may provide insight into their evolution and pathogenesis. We used a Mycobacterium tuberculosis high-density oligonucleotide microarray to detect small-scale genomic deletions among 19 clinically and epidemiologically well-characterized isolates ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.166401
更新日期:2001-04-01 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
pub_type: 杂志文章
doi:10.1101/gr.6.9.829
更新日期:1996-09-01 00:00:00
abstract::Core promoters mediate transcription initiation by the integration of diverse regulatory signals encoded in the proximal promoter and enhancers. It has been suggested that genes under simple regulation may have low-complexity permissive promoters. For these genes, the core promoter may serve as the principal regulator...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.113381.110
更新日期:2011-05-01 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
pub_type: 杂志文章
doi:10.1101/gr.103663.109
更新日期:2010-04-01 00:00:00
abstract::Thousands of long noncoding RNAs (lncRNAs) have been found in vertebrate animals, a few of which have known biological roles. To better understand the genomics and features of lncRNAs in invertebrates, we used available RNA-seq, poly(A)-site, and ribosome-mapping data to identify lncRNAs of Caenorhabditis elegans. We ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.140475.112
更新日期:2012-12-01 00:00:00
abstract::In this communication, we describe the use of specialized transposons (Tn5 derivatives) to create deletions in the Escherichia coli K-12 chromosome. These transposons are essentially rearranged composite transposons that have been assembled to promote the use of the internal transposon ends, resulting in intramolecula...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.611403
更新日期:2003-04-01 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
pub_type: 信件
doi:10.1101/gr.2433104
更新日期:2004-11-01 00:00:00
abstract::Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here, we present sequential ChIP-bisulfite-sequencing (ChIP-BS-seq) as an approach to quantitatively assess DNA methylat...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.133728.111
更新日期:2012-06-01 00:00:00
abstract::Interferons and interleukin-10 are involved in key aspects of the host defence mechanisms. Human chromosome 21 harbors the interferon/interleukin-10 receptor gene cluster linked to the GART gene. This cluster includes both components of the interferon alpha/beta-receptor (IFNAR1 and IFNAR2) and the second components o...
journal_title:Genome research
pub_type: 杂志文章
doi:
更新日期:1999-03-01 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
pub_type: 杂志文章
doi:10.1101/gr.982903
更新日期:2003-06-01 00:00:00
abstract::The current Caenorhabditis elegans genomic annotation has many genes organized in operons. Using directionally stitched promoterGFP methodology, we have conducted the largest survey to date on the regulatory regions of annotated C. elegans operons and identified 65, over 25% of those studied, with internal promoters. ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6824707
更新日期:2007-10-01 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
pub_type: 杂志文章
doi:10.1101/gr.10.8.1219
更新日期:2000-08-01 00:00:00
abstract::We have developed a simplified method for multiplex PCR based on the use of chimeric primers. Each primer contains a 3' region complementary to sequence-specific recognition sites and a 5' region made up of an unrelated 20-nucleotide sequence. Identical reaction conditions, cycling times, and annealing temperatures ha...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5.5.488
更新日期:1995-12-01 00:00:00
abstract::A contiguous high-resolution map of 44 loci from a 35-Mb portion of the distal region of the long arm of human chromosome 5, q21-q35, was produced using radiation hybrid (RH) mapping in conjunction with a natural deletion mapping panel. The map includes 30 genes, four sequence-tagged site (STS) loci, and 10 DNA marker...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.7.628
更新日期:1996-07-01 00:00:00
abstract::Most mammalian RNA polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address this question, we determined the tra...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.241653.118
更新日期:2019-04-01 00:00:00
abstract::The capacity of the honey bee to produce three phenotypically distinct organisms (two female castes; queens and sterile workers, and haploid male drones) from one genotype represents one of the most remarkable examples of developmental plasticity in any phylum. The queen-worker morphological and reproductive divide is...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.236497.118
更新日期:2018-10-01 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
pub_type: 杂志文章
doi:10.1101/gr.6093907
更新日期:2007-07-01 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
pub_type: 杂志文章
doi:10.1101/gr.204784.116
更新日期:2016-09-01 00:00:00
abstract::Careful titration of Vent polymerase activity allows efficient amplification of full-length plasmids (12 kb). The high processivity and fidelity of this enzyme made oligonucleotide-directed site-specific mutagenesis of plasmids a straight-forward process. Using only two primers, a mutagenic and a complementary, single...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5.4.404
更新日期:1995-11-01 00:00:00