Abstract:
:The reported human genome sequence includes about 400 gaps of unknown sequence that were not found in the bacterial artificial chromosome (BAC) and cosmid libraries used for sequencing of the genome. These missing sequences correspond to approximately 1% of euchromatic regions of the human genome. Gap filling is a laborious process because it relies on analysis of random clones of numerous genomic BAC or cosmid libraries. In this work we demonstrate that closing the gaps can be accelerated by a selective recombinational capture of missing chromosomal segments in yeast. The use of both methodologies allowed us to close the four remaining gaps on the human chromosome 19. Analysis of the gap sequences revealed that they contain several abnormalities that could result in instability of the sequences in microbe hosts, including large blocks of micro- and minisatellites and a high density of Alu repeats. Sequencing of the gap regions, in both BAC and YAC forms, allowed us to generate a complete sequence of four genes, including the neuronal cell signaling gene SCK1/SLI. The SCK1/SLI gene contains a record number of minisatellites, most of which are polymorphic and transmitted through meiosis following a Mendelian inheritance. In conclusion, the use of the alternative recombinational cloning system in yeast may greatly accelerate work on closing the remaining gaps in the human genome (as well as in other complex genomes) to achieve the goal of annotation of all human genes.
journal_name
Genome Resjournal_title
Genome researchauthors
Leem SH,Kouprina N,Grimwood J,Kim JH,Mullokandov M,Yoon YH,Chae JY,Morgan J,Lucas S,Richardson P,Detter C,Glavina T,Rubin E,Barrett JC,Larionov Vdoi
10.1101/gr.1929904subject
Has Abstractpub_date
2004-02-01 00:00:00pages
239-46issue
2eissn
1088-9051issn
1549-5469pii
1929904journal_volume
14pub_type
杂志文章相关文献
GENOME RESEARCH文献大全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::Up-frameshift protein 1 (UPF1) is an ATP-dependent RNA helicase that has essential roles in RNA surveillance and in post-transcriptional gene regulation by promoting the degradation of mRNAs. Previous studies revealed that UPF1 is associated with the 3' untranslated region (UTR) of target mRNAs via as-yet-unknown sequ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.206060.116
更新日期:2017-03-01 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
pub_type: 杂志文章
doi:10.1101/gr.6.1.58
更新日期:1996-01-01 00:00:00
abstract::The need to translate genes to function has positioned the rat as an invaluable animal model for genomic research. The significant increase in genomic resources in recent years has had an immediate functional application in the rat. Many of the resources for translational research are already in place and are ready to...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.3744005
更新日期:2005-12-01 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
pub_type: 杂志文章
doi:10.1101/gr.132811.111
更新日期:2012-10-01 00:00:00
abstract::The maternal and paternal copies of the genome are both required for mammalian development, and this is primarily due to imprinted genes, those that are monoallelically expressed based on parent-of-origin. Typically, this pattern of expression is regulated by differentially methylated regions (DMRs) that are establish...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.196139.115
更新日期:2016-06-01 00:00:00
abstract::Transcriptomic genome-wide analyses demonstrate massive variation of alternative splicing in many physiological and pathological situations. One major challenge is now to establish the biological contribution of alternative splicing variation in physiological- or pathological-associated cellular phenotypes. Toward thi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.212696.116
更新日期:2017-06-01 00:00:00
abstract::Despite claims that the mammalian Y Chromosome is on a path to extinction, comparative sequence analysis of primate Y Chromosomes has shown the decay of the ancestral single-copy genes has all but ceased in this eutherian lineage. The suite of single-copy Y-linked genes is highly conserved among the majority of euther...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.237586.118
更新日期:2018-12-01 00:00:00
abstract::Although changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. To systematically identify transcription factors (TFs) that can direct chromatin changes during cell fate decisions, we model t...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.142661.112
更新日期:2013-01-01 00:00:00
abstract::The world of noncoding RNAs (ncRNAs) is composed of an enormous and growing number of transcripts, ranging in length from tens of bases to tens of kilobases, involved in all biological processes and altered in expression and/or function in many types of human disorders. The premise of this review is the concept that n...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.247239.118
更新日期:2019-09-01 00:00:00
abstract::DNA transposons, or class 2 transposable elements, have successfully propagated in a wide variety of genomes. However, it is widely believed that DNA transposon activity has ceased in mammalian genomes for at least the last 40 million years. We recently reported evidence for the relatively recent activity of hAT and H...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.071886.107
更新日期:2008-05-01 00:00:00
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 tran...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.173801
更新日期:2001-05-01 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::Coevolution maintains interactions between phenotypic traits through the process of reciprocal natural selection. Detecting molecular coevolution can expose functional interactions between molecules in the cell, generating insights into biological processes, pathways, and the networks of interactions important for cel...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.092452.109
更新日期:2009-10-01 00:00:00
abstract::Mutation rates of microsatellites vary greatly among loci. The causes of this heterogeneity remain largely enigmatic yet are crucial for understanding numerous human neurological diseases and genetic instability in cancer. In this first genome-wide study, the relative contributions of intrinsic features and regional g...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7113408
更新日期:2008-01-01 00:00:00
abstract::The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research. The challenges for the informatics community are how to integrat...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.991003
更新日期:2003-06-01 00:00:00
abstract::Array-based comparative genomic hybridization (aCGH) is a recently developed tool for genome-wide determination of DNA copy number alterations. This technology has tremendous potential for disease-gene discovery in cancer and developmental disorders as well as numerous other applications. However, widespread utilizati...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1847304
更新日期:2004-01-01 00:00:00
abstract::X-linked Mental Retardation (XLMR) occurs in 1 in 600 males and is highly genetically heterogeneous. We used a novel human X chromosome cDNA microarray (XCA) to survey the expression profile of X-linked genes in lymphoblasts of XLMR males. Genes with altered expression verified by Northern blot and/or quantitative PCR...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5336307
更新日期:2007-05-01 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::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
pub_type: 杂志文章
doi:10.1101/gr.172901
更新日期:2001-03-01 00:00:00
abstract::Natural killer (NK) cells contribute to the essential functions of innate immunity and reproduction. Various genes encode NK cell receptors that recognize the major histocompatibility complex (MHC) Class I molecules expressed by other cells. For primate NK cells, the killer-cell immunoglobulin-like receptors (KIR) are...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.085738.108
更新日期:2009-05-01 00:00:00
abstract::Here, we report that CRISPR guide RNAs (gRNAs) with a 5'-triphosphate group (5'-ppp gRNAs) produced via in vitro transcription trigger RNA-sensing innate immune responses in human and murine cells, leading to cytotoxicity. 5'-ppp gRNAs in the cytosol are recognized by DDX58, which in turn activates type I interferon r...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.231936.117
更新日期:2018-02-22 00:00:00
abstract::Although it is well understood that selection shapes the polymorphism pattern in Drosophila, signatures of classic selective sweeps are scarce. Here, we focus on Drosophila mauritiana, an island endemic, which is closely related to Drosophila melanogaster. Based on a new, annotated genome sequence, we characterized th...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.139873.112
更新日期:2013-01-01 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 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
pub_type: 杂志文章
doi:10.1101/gr.080861.108
更新日期:2009-02-01 00:00:00
abstract::Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to apparent completion. Although this assembly employed a standard C. elegans strain (N2), it used sequence data from several laboratories, with DNA propagated in bacteria and yeast. Thus, the N2 assembly has many differences from any C. el...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.244830.118
更新日期:2019-06-01 00:00:00
abstract::Inbred strains of the laboratory rat are widely used for identifying genetic regions involved in the control of complex quantitative phenotypes of biomedical importance. The draft genomic sequence of the rat now provides essential information for annotating rat quantitative trait locus (QTL) maps. Following the survey...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2001604
更新日期:2004-04-01 00:00:00
abstract::Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of inter...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.136739.111
更新日期:2013-01-01 00:00:00
abstract::Single-nucleotide polymorphisms (SNPs) are the most frequently found DNA sequence variations in the human genome. It has been argued that a dense set of SNP markers can be used to identify genetic factors associated with complex disease traits. Because all high-throughput genotyping methods require precise sequence kn...
journal_title:Genome research
pub_type: 杂志文章
doi:
更新日期:1999-05-01 00:00:00
abstract::Remnants of more than 3 million transposable elements, primarily retroelements, comprise nearly half of the human genome and have generated much speculation concerning their evolutionary significance. We have exploited the draft human genome sequence to examine the distributions of retroelements on a genome-wide scale...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.388902
更新日期:2002-10-01 00:00:00