Abstract:
:We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different transposable elements. We show that an interval between bands 3A2 and 3C2, believed in the 1970s to show a correlation between the number of bands on the polytene chromosomes and the 20 genes identified by conventional genetics, is predicted to contain 45 genes from its DNA sequence. We have determined the insertion sites of P-elements from 111 mutant lines, about half of which are in a position likely to affect the expression of novel predicted genes, thus representing a resource for subsequent functional genomic analysis. We compare the European Drosophila Genome Project sequence with the corresponding part of the independently assembled and annotated Joint Sequence determined through "shotgun" sequencing. Discounting differences in the distribution of known transposable elements between the strains sequenced in the two projects, we detected three major sequence differences, two of which are probably explained by errors in assembly; the origin of the third major difference is unclear. In addition there are eight sequence gaps within the Joint Sequence. At least six of these eight gaps are likely to be sites of transposable elements; the other two are complex. Of the 275 genes in common to both projects, 60% are identical within 1% of their predicted amino-acid sequence and 31% show minor differences such as in choice of translation initiation or termination codons; the remaining 9% show major differences in interpretation.
journal_name
Genome Resjournal_title
Genome researchauthors
Benos PV,Gatt MK,Murphy L,Harris D,Barrell B,Ferraz C,Vidal S,Brun C,Demaille J,Cadieu E,Dreano S,Gloux S,Lelaure V,Mottier S,Galibert F,Borkova D,Miñana B,Kafatos FC,Bolshakov S,Sidén-Kiamos I,Papagiannakis G,Sdoi
10.1101/gr.173801subject
Has Abstractpub_date
2001-05-01 00:00:00pages
710-30issue
5eissn
1088-9051issn
1549-5469journal_volume
11pub_type
杂志文章相关文献
GENOME RESEARCH文献大全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
pub_type: 杂志文章
doi:10.1101/gr.215160.116
更新日期:2017-07-01 00:00:00
abstract::Network "guilt by association" (GBA) is a proven approach for identifying novel disease genes based on the observation that similar mutational phenotypes arise from functionally related genes. In principle, this approach could account even for nonadditive genetic interactions, which underlie the synergistic combinatio...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.118992.110
更新日期:2011-07-01 00:00:00
abstract::The most widely appreciated role of DNA is to encode protein, yet the exact portion of the human genome that is translated remains to be ascertained. We previously developed PhyloCSF, a widely used tool to identify evolutionary signatures of protein-coding regions using multispecies genome alignments. Here, we present...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.246462.118
更新日期:2019-12-01 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::Orthologous genes that maintain a single-copy status in a broad range of species may indicate a selection against gene duplication. If this is the case, then duplicates of such genes that do survive may have escaped the dosage control by rapid and sizable changes in their function. To test this hypothesis and to devel...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3266405
更新日期:2005-03-01 00:00:00
abstract::In the search for common genetic variants that contribute to prevalent human diseases, patterns of linkage disequilibrium (LD) among linked markers should be considered when selecting SNPs. Genotyping efficiency can be increased by choosing tagging SNPs (tagSNPs) in LD with other SNPs. However, it remains to be seen w...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4138406
更新日期:2006-03-01 00:00:00
abstract::Oncoviral infection is responsible for 12%-15% of cancer in humans. Convergent evidence from epidemiology, pathology, and oncology suggests that new viral etiologies for cancers remain to be discovered. Oncoviral profiles can be obtained from cancer genome sequencing data; however, widespread viral sequence contaminat...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.242529.118
更新日期:2019-05-01 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::Transcription factors (TFs) are key mediators that propagate extracellular and intracellular signals through to changes in gene expression profiles. However, the rules by which promoters decode the amount of active TF into target gene expression are not well understood. To determine the mapping between promoter DNA se...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212316.116
更新日期:2017-01-01 00:00:00
abstract::Genome-wide association studies (GWAS) are identifying genetic predisposition to various diseases. The 17q24.3 locus harbors the single nucleotide polymorphism (SNP) rs1859962 that is statistically associated with prostate cancer (PCa). It defines a 130-kb linkage disequilibrium (LD) block that lies in an ∼2-Mb gene d...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.135665.111
更新日期:2012-08-01 00:00:00
abstract::Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.109678.110
更新日期:2011-04-01 00:00:00
abstract::Hammerhead ribozymes previously were found in satellite RNAs from plant viroids and in repetitive DNA from certain species of newts and schistosomes. To determine if this catalytic RNA motif has a wider distribution, we decided to scrutinize the GenBank database for RNAs that contain hammerhead or hammerhead-like moti...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.7.1011
更新日期:2000-07-01 00:00:00
abstract::Theory is developed for the process of sequencing randomly selected large-insert clones. Genome size, library depth, clone size, and clone distribution are considered relevant properties and perfect overlap detection for contig assembly is assumed. Genome-specific and nonrandom effects are neglected. Order of magnitud...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.gr-1339r
更新日期:2001-02-01 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
pub_type: 杂志文章
doi:10.1101/gr.2800104
更新日期:2004-12-01 00:00:00
abstract::Sequencing of the human Y chromosome has uncovered the peculiarities of the genomic organization of a heterogametic sex chromosome of old evolutionary age, and has led to many insights into the evolutionary changes that occurred during its long history. We have studied the genomic organization of the medaka fish Y chr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5016106
更新日期:2006-07-01 00:00:00
abstract::The human pseudoautosomal region 1 (PAR1) is essential for meiotic pairing and recombination, and its deletion causes male sterility. Comparative studies of human and mouse pseudoautosomal genes are valuable in charting the evolution of this interesting region, but have been limited by the paucity of genes conserved b...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.197001
更新日期:2001-12-01 00:00:00
abstract::We have conducted a phylogenetic analysis of the Ribonuclease HI (RNH) domains present in Eubacteria, Eukarya, all long-term repeat (LTR)-bearing retrotransposons, and several late-branching clades of non-LTR retrotransposons. Analysis of this simple yet highly conserved enzymatic domain from these disparate sources p...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.185101
更新日期:2001-07-01 00:00:00
abstract::We have developed a new tool to visualize expression data on metabolic pathways and to evaluate which metabolic pathways are most affected by transcriptional changes in whole-genome expression experiments. Using the Fisher Exact Test, the method scores biochemical pathways according to the probability that as many or ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.226602
更新日期:2002-07-01 00:00:00
abstract::Integration of DNA viruses into the human genome plays an important role in various types of tumors, including hepatitis B virus (HBV)-related hepatocellular carcinoma. However, the molecular details and clinical impact of HBV integration on either human or HBV epigenomes are unknown. Here, we show that methylation of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.175240.114
更新日期:2015-03-01 00:00:00
abstract::Chromosome-specific cDNA libraries are new tools for the isolation of genes from specific genomic regions. We have used two YACs than span the approximately 2-Mb cri-du-chat critical region (CDCCR) of chromosome 5p to directly screen a chromosome 5-specific (CH5SP) fetal brain cDNA library. To compare this library wit...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7.2.118
更新日期:1997-02-01 00:00:00
abstract::Repetitive DNA is a significant component of eukaryotic genomes. We have developed a strategy to efficiently and accurately sequence repetitive DNA in the nematode Caenorhabditis elegans using integrated artificial transposons and automated fluorescent sequencing. Mapping and assembly tools represent important compone...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7.5.551
更新日期:1997-05-01 00:00:00
abstract::Annotation transfer is a principal process in genome annotation. It involves "transferring" structural and functional annotation to uncharacterized open reading frames (ORFs) in a newly completed genome from experimentally characterized proteins similar in sequence. To prevent errors in genome annotation, it is import...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.183801
更新日期:2001-10-01 00:00:00
abstract::Mutations in the human AIRE gene (hAIRE) result in the development of an autoimmune disease named APECED (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy; OMIM 240300). Previously, we have cloned hAIRE and shown that it codes for a putative transcription-associated factor. Here we report the cloning and...
journal_title:Genome research
pub_type: 杂志文章
doi:
更新日期:1999-02-01 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
pub_type: 杂志文章
doi:10.1101/gr.103622.109
更新日期:2010-05-01 00:00:00
abstract::Extracellular cues play critical roles in the establishment of the epigenome during development and may also contribute to epigenetic perturbations found in disease states. The direct role of the local tissue environment on the post-development human epigenome, however, remains unclear due to limitations in studies of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.166439.113
更新日期:2014-04-01 00:00:00
abstract::Clusters of functionally related genes can be disrupted by a single copy number variant (CNV). We demonstrate that the simultaneous disruption of multiple functionally related genes is a frequent and significant characteristic of de novo CNVs in patients with developmental disorders (P = 1 × 10(-3)). Using three diffe...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.184325.114
更新日期:2015-06-01 00:00:00
abstract::Cellular senescence is a mechanism that virtually irreversibly suppresses the proliferative capacity of cells in response to various stress signals. This includes the expression of activated oncogenes, which causes Oncogene-Induced Senescence (OIS). A body of evidence points to the involvement in OIS of chromatin reor...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.225763.117
更新日期:2017-10-01 00:00:00
abstract::Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced th...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.121137.111
更新日期:2011-11-01 00:00:00
abstract::Custom-designed nucleases (CDNs) greatly facilitate genetic engineering by generating a targeted DNA double-strand break (DSB) in the genome. Once a DSB is created, specific modifications can be introduced around the breakage site during its repair by two major DNA damage repair (DDR) mechanisms: the dominant but erro...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.145441.112
更新日期:2013-03-01 00:00:00
abstract::Diversity in the antigen-binding receptors of the immune system has long been a primary interest of biologists. Recently it has been suggested that polymorphism in regulatory (noncoding) gene segments is of substantial importance as well. Here, we survey the level of variation in MHC class II gene promoters in man and...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.2.124
更新日期:1998-02-01 00:00:00