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 algorithms of minimum evolution-neighbor joining, maximum parsimony, and maximum likelihood, we address overall levels of genetic diversity, specific rates of mutation within and between different regions of the viral genome, relatedness among viral strains from geographically diverse regions, and estimation of the pattern of divergence of the virus into extant lineages. Despite broad genomic similarities, type I and type II viruses do not share concordant evolutionary histories. HTLV-I/STLV-I are united through distinct phylogeographic patterns, infection of 20 primate species, multiple episodes of interspecies transmission, and exhibition of a range in levels of genetic divergence. In contrast, type II viruses are isolated from only two species (Homo sapiens and Pan paniscus) and are paradoxically endemic to both Amerindian tribes of the New World and human Pygmy villagers in Africa. Furthermore, HTLV-II is spreading rapidly through new host populations of intravenous drug users. Despite such clearly disparate host populations, the resultant HTLV-II/STLV-II phylogeny exhibits little phylogeographic concordance and indicates low levels of transcontinental genetic differentiation. Together, these patterns generate a model of HTLV/STLV emergence marked by an ancient ancestry, differential rates of divergence, and continued global expansion.
journal_name
Genome Resjournal_title
Genome researchauthors
Slattery JP,Franchini G,Gessain Asubject
Has Abstractpub_date
1999-06-01 00:00:00pages
525-40issue
6eissn
1088-9051issn
1549-5469journal_volume
9pub_type
杂志文章,评审相关文献
GENOME RESEARCH文献大全abstract::The dense RFLP linkage map of tomato (Lycopersicon esculentum) contains >300 anonymous cDNA clones. Of those clones, 272 were partially or completely sequenced. The sequences were compared at the DNA and protein level to known genes in databases. For 57% of the clones, a significant match to previously described genes...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.8.842
更新日期:1998-08-01 00:00:00
abstract::The genetic positions of the five Arabidopsis thaliana centromere regions have been identified by mapping size polymorphisms in the centromeric 180-bp repeat arrays. Structural and genetic analysis indicates that 180-bp repeat arrays of up to 1000 kb are found in the centromere region of each chromosome. The genetic b...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7.11.1045
更新日期:1997-11-01 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::Spatial organization of different epigenomic marks was used to infer functions of the epigenome. It remains unclear what can be learned from the temporal changes of the epigenome. Here, we developed a probabilistic model to cluster genomic sequences based on the similarity of temporal changes of multiple epigenomic ma...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.144949.112
更新日期:2013-02-01 00:00:00
abstract::Here we describe a high-throughput screen to isolate transcripts with spatially restricted patterns of expression in early embryos. Our approach utilizes robotic automation for rapid analysis of sequence-selected cDNAs in a whole-mount in situ hybridization assay. We determined the spatial distribution of a random col...
journal_title:Genome research
pub_type: 信件
doi:10.1101/gr.84402
更新日期:2002-07-01 00:00:00
abstract::Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells modulate gene expression in response to changing environments. Previous comparative studies focused on specific conditions, describing interspecies variation in expression levels,...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.261537.120
更新日期:2020-07-01 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::In an attempt to understand the origin of CpG islands (CGIs) in mammalian genomes, we have studied their location and structure according to the expression pattern of genes and to the G + C content of isochores in which they are embedded. We show that CGIs located over the transcription start site (named start CGIs) a...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.174501
更新日期:2001-11-01 00:00:00
abstract::Transcript leaders (TLs) can have profound effects on mRNA translation and stability. To map TL boundaries genome-wide, we developed TL-sequencing (TL-seq), a technique combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. TL-seq identified mRNA start sites for the majority of yeast...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.150342.112
更新日期:2013-06-01 00:00:00
abstract::Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes cont...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.904303
更新日期:2003-05-01 00:00:00
abstract::An important aspect of the development of systems biology approaches in metazoans is the characterization of expression patterns of nearly all genes predicted from genome sequences. Such "localizome" maps should provide information on where (in what cells or tissues) and when (at what stage of development or under wha...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2497604
更新日期:2004-10-01 00:00:00
abstract::Evolutionary constraints on gene regulatory elements are poorly understood: Little is known about how the strength of transcription factor binding correlates with DNA sequence conservation, and whether transcription factor binding sites can evolve rapidly while retaining their function. Here we use the model of the NF...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6490707
更新日期:2007-09-01 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
pub_type: 杂志文章
doi:10.1101/gr.5075706
更新日期:2006-11-01 00:00:00
abstract::After completion of the Schizosaccharomyces pombe genome sequence, we have carried out a pilot gene deletion project to assess the feasibility of a genome-wide deletion project and to estimate the percentage of essential genes. Using a PCR-based gene deletion procedure, we investigated 100 genes within a 253-kb region...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.636103
更新日期:2003-03-01 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::Trace Recalling is a novel method for deconvoluting double traces that result from simultaneously sequencing two DNA templates. Trace Recalling identifies up to two bases at each position of such a trace. The resulting ambiguity sequence is aligned to the genome, identifying one template sequence. A second template se...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5661407
更新日期:2007-02-01 00:00:00
abstract::The draft genome ( approximately 160 Mb) of the urochordate ascidian Ciona intestinalis has been sequenced by the whole-genome shotgun method and should provide important insights into the origin and evolution of chordates as well as vertebrates. However, because this genomic data has not yet been mapped onto chromoso...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4156606
更新日期:2006-02-01 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
pub_type: 杂志文章
doi:10.1101/gr.6252107
更新日期:2007-08-01 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
pub_type: 杂志文章
doi:10.1101/gr.196238.115
更新日期:2015-10-01 00:00:00
abstract::CLONEPICKER is a software pipeline that integrates sequence data with BAC clone fingerprints to dynamically select a minimal overlapping clone set covering the whole genome. In the Rat Genome Sequencing Project (RGSP), a hybrid strategy of "clone by clone" and "whole genome shotgun" approaches was used to maximize the...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2171704
更新日期:2004-04-01 00:00:00
abstract::Obtaining high-quality sequence continuity of complex regions of recent segmental duplication remains one of the major challenges of finishing genome assemblies. In the human and mouse genomes, this was achieved by targeting large-insert clones using costly and laborious capillary-based sequencing approaches. Sanger s...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.168450.113
更新日期:2014-04-01 00:00:00
abstract::Interactions mediated by cell surface receptors initiate important instructive signaling cues but can be difficult to detect in biochemical assays because they are often highly transient and membrane-embedded receptors are difficult to solubilize in their native conformation. Here, we address these biochemical challen...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.231183.117
更新日期:2018-09-01 00:00:00
abstract::Pre-mRNA processing often occurs in coordination with transcription thereby coupling these two key regulatory events. As such, many proteins involved in mRNA processing associate with the transcriptional machinery and are in proximity to DNA. This proximity allows for the mapping of the genomic associations of RNA bin...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.5211806
更新日期:2006-07-01 00:00:00
abstract::The phenotypic variation of living organisms is shaped by genetics, environment, and their interaction. Understanding phenotypic plasticity under natural conditions is hindered by the apparently complex environment and the interacting genes and pathways. Herein, we report findings from the dissection of rice flowering...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.255703.119
更新日期:2020-05-01 00:00:00
abstract::The very small fraction of putative binding sites (BSs) that are occupied by transcription factors (TFs) in vivo can be highly variable across different cell types. This observation has been partly attributed to changes in chromatin accessibility and histone modification (HM) patterns surrounding BSs. Previous studies...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.220079.116
更新日期:2018-01-11 00:00:00
abstract::The centromere is the structural unit responsible for the faithful segregation of chromosomes. Although regulation of centromeric function by epigenetic factors has been well-studied, the contributions of the underlying DNA sequences have been much less well defined, and existing methodologies for studying centromere ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.219709.116
更新日期:2017-12-01 00:00:00
abstract::DNA methylation is an epigenetic modification that plays a key role in gene regulation. Previous studies have investigated its genetic basis by mapping genetic variants that are associated with DNA methylation at specific sites, but these have been limited to microarrays that cover <2% of the genome and cannot account...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.183749.114
更新日期:2015-06-01 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::By analyzing 1,780,295 5'-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites (TSSs) for 14,628 human RefSeq genes. These TSSs were clustered into 30,964 clusters that were separated from each other by m...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4039406
更新日期:2006-01-01 00:00:00
abstract::Retrotransposons have proliferated extensively in eukaryotic lineages; the genomes of many animals and plants comprise 50% or more retrotransposon sequences by weight. There are several persuasive arguments that the enzymatic lynchpin of retrotransposon replication, reverse transcriptase (RT), is an ancient enzyme. Mo...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.1392003
更新日期:2003-09-01 00:00:00