Abstract:
:We describe a new method, Tag-seq, which employs ultra high-throughput sequencing of 21 base pair cDNA tags for sensitive and cost-effective gene expression profiling. We compared Tag-seq data to LongSAGE data and observed improved representation of several classes of rare transcripts, including transcription factors, antisense transcripts, and intronic sequences, the latter possibly representing novel exons or genes. We observed increases in the diversity, abundance, and dynamic range of such rare transcripts and took advantage of the greater dynamic range of expression to identify, in cancers and normal libraries, altered expression ratios of alternative transcript isoforms. The strand-specific information of Tag-seq reads further allowed us to detect altered expression ratios of sense and antisense (S-AS) transcripts between cancer and normal libraries. S-AS transcripts were enriched in known cancer genes, while transcript isoforms were enriched in miRNA targeting sites. We found that transcript abundance had a stronger GC-bias in LongSAGE than Tag-seq, such that AT-rich tags were less abundant than GC-rich tags in LongSAGE. Tag-seq also performed better in gene discovery, identifying >98% of genes detected by LongSAGE and profiling a distinct subset of the transcriptome characterized by AT-rich genes, which was expressed at levels below those detectable by LongSAGE. Overall, Tag-seq is sensitive to rare transcripts, has less sequence composition bias relative to LongSAGE, and allows differential expression analysis for a greater range of transcripts, including transcripts encoding important regulatory molecules.
journal_name
Genome Resjournal_title
Genome researchauthors
Morrissy AS,Morin RD,Delaney A,Zeng T,McDonald H,Jones S,Zhao Y,Hirst M,Marra MAdoi
10.1101/gr.094482.109subject
Has Abstractpub_date
2009-10-01 00:00:00pages
1825-35issue
10eissn
1088-9051issn
1549-5469pii
gr.094482.109journal_volume
19pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Identifying genes in the genomic context is central to a cell's ability to interpret the genome. Yet, in general, the signals used to define eukaryotic genes are poorly described. Here, we derived simple classifiers that identify where transcription will initiate and terminate using nucleic acid sequence features dete...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.164327.113
更新日期:2014-01-01 00:00:00
abstract::Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene orders. The progress in whole genome seque...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3002305
更新日期:2005-01-01 00:00:00
abstract::Drug development efforts against cancer are often hampered by the complex properties of signaling networks. Here we combined the results of an RNAi screen targeting the cellular signaling machinery, with graph theoretical analysis to extract the core modules that process both mitogenic and oncogenic signals to drive c...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.116145.110
更新日期:2011-12-01 00:00:00
abstract::Mammalian genomes contain many highly conserved nongenic sequences (CNGs) whose functional significance is poorly understood. Sets of CNGs have previously been identified by selecting the most conserved elements from a chromosome or genome, but in these highly selected samples, conservation may be unrelated to purifyi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3942005
更新日期:2005-10-01 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::A total of 202 genes were cytogenetically mapped to goat chromosomes, multiplying by five the total number of regional gene localizations in domestic ruminants (255). This map encompasses 249 and 173 common anchor loci regularly spaced along human and murine chromosomes, respectively, which makes it possible to perfor...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.9.901
更新日期:1998-09-01 00:00:00
abstract::GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.4.511
更新日期:2000-04-01 00:00:00
abstract::PipMaker (http://bio.cse.psu.edu) is a World-Wide Web site for comparing two long DNA sequences to identify conserved segments and for producing informative, high-resolution displays of the resulting alignments. One display is a percent identity plot (pip), which shows both the position in one sequence and the degree ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.4.577
更新日期:2000-04-01 00:00:00
abstract::Current methods struggle to reconstruct and visualize the genomic relationships of large numbers of bacterial genomes. GrapeTree facilitates the analyses of large numbers of allelic profiles by a static "GrapeTree Layout" algorithm that supports interactive visualizations of large trees within a web browser window. Gr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.232397.117
更新日期:2018-09-01 00:00:00
abstract::Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora t...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.197244.115
更新日期:2016-04-01 00:00:00
abstract::Dual channel imaging and warping of two-dimensional (2D) protein gels were used to visualize global changes of the gene expression patterns in growing Bacillus subtilis cells during entry into the stationary phase as triggered by glucose exhaustion. The 2D gels only depict single moments during the cells' growth cycle...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.905003
更新日期:2003-02-01 00:00:00
abstract::Gene duplication and alternative splicing are important sources of proteomic diversity. Despite research indicating that gene duplication and alternative splicing are negatively correlated, the evolutionary relationship between the two remains unclear. One manner in which alternative splicing and gene duplication may ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.184473.114
更新日期:2015-05-01 00:00:00
abstract::The development of high-throughput sequencing (HTS) technologies has opened the door to novel methods for detecting copy number variants (CNVs) in the human genome. While in the past CNVs have been detected based on array CGH data, recent studies have shown that depth-of-coverage information from HTS technologies can ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.106344.110
更新日期:2010-11-01 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::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::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
pub_type: 杂志文章
doi:10.1101/gr.10.5.672
更新日期:2000-05-01 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::Natural killer (NK) cells are innate lymphocytes important for early host defense against infectious pathogens and surveillance against malignant transformation. Resting murine NK cells regulate the translation of effector molecule mRNAs (e.g., granzyme B, GzmB) through unclear molecular mechanisms. MicroRNAs (miRNAs)...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.107995.110
更新日期:2010-11-01 00:00:00
abstract::Infections by Shiga toxin-producing Escherichia coli O157:H7 (STEC O157) are the predominant cause of bloody diarrhea and hemolytic uremic syndrome in the United States. In silico comparison of the two complete STEC O157 genomes (Sakai and EDL933) revealed a strikingly high level of sequence identity in orthologous pr...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4759706
更新日期:2006-06-01 00:00:00
abstract::High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.225276.117
更新日期:2018-05-01 00:00:00
abstract::Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.099622.109
更新日期:2010-01-01 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
pub_type: 杂志文章
doi:10.1101/gr.215160.116
更新日期:2017-07-01 00:00:00
abstract::The vomeronasal system of mice is thought to be specialized in the detection of pheromones. Two multigene families have been identified that encode proteins with seven putative transmembrane domains and that are expressed selectively in subsets of neurons of the vomeronasal organ. The products of these vomeronasal rec...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.12.1958
更新日期:2000-12-01 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::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
pub_type: 杂志文章
doi:10.1101/gr.259069.119
更新日期:2020-06-01 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::Little is known about novel genetic elements that drove the emergence of anthropoid primates. We exploited the sequencing of the marmoset genome to identify 23,849 anthropoid-specific constrained (ASC) regions and confirmed their robust functional signatures. Of the ASC base pairs, 99.7% were noncoding, suggesting tha...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.168963.113
更新日期:2014-09-01 00:00:00
abstract::An open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. The genus Campylobacter encompasses several important human a...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.089250.108
更新日期:2009-07-01 00:00:00
abstract::Contamination by present-day human and microbial DNA is one of the major hindrances for large-scale genomic studies using ancient biological material. We describe a new molecular method, U selection, which exploits one of the most distinctive features of ancient DNA--the presence of deoxyuracils--for selective enrichm...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.174201.114
更新日期:2014-09-01 00:00:00
abstract::We have cloned the human gene encoding the transcription factor T. T protein is vital for the formation of posterior mesoderm and axial development in all vertebrates. Brachyury mutant mice, which lack T protein, die in utero with abnormal notochord, posterior somites, and allantois. We have identified human T genomic...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.3.226
更新日期:1996-03-01 00:00:00