Abstract：
:Somatic transposon expression in neural tissue is commonly considered as a measure of mobilization and has therefore been linked to neuropathology and organismal individuality. We combined genome sequencing data with single-cell mRNA sequencing of the same inbred fly strain to map transposon expression in the Drosophila midbrain and found that transposon expression patterns are highly stereotyped. Every detected transposon is resident in at least one cellular gene with a matching expression pattern. Bulk RNA sequencing from fly heads of the same strain revealed that coexpression is a physical link in the form of abundant chimeric transposon-gene mRNAs. We identified 264 genes where transposons introduce cryptic splice sites into the nascent transcript and thereby significantly expand the neural transcript repertoire. Some genes exclusively produce chimeric mRNAs with transposon sequence; on average, 11.6% of the mRNAs produced from a given gene are chimeric. Conversely, most transposon-containing transcripts are chimeric, which suggests that somatic expression of these transposons is largely driven by cellular genes. We propose that chimeric mRNAs produced by alternative splicing into polymorphic transposons, rather than transposon mobilization, may contribute to functional differences between individual cells and animals.
journal_name
Genome Resjournal_title
Genome researchauthors
Treiber CD,Waddell Sdoi
10.1101/gr.259200.119subject
Has Abstractpub_date
2020-11-01 00:00:00pages
1559-1569issue
11eissn
1088-9051issn
1549-5469pii
gr.259200.119journal_volume
30pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract：:In this study, we propose a system-theoretic approach to the analysis and quantitative modeling of the TNFalpha-mediated NF-kappaB-signaling pathway. Tumor necrosis factor alpha (TNFalpha) is a potent proinflammatory cytokine that plays an important role in immunity and inflammation, in the control of cell proliferati...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.1195703
更新日期：2003-11-01 00:00:00
abstract：:More than 25 loci have been linked to type 1 diabetes (T1D) in the nonobese diabetic (NOD) mouse, but identification of the underlying genes remains challenging. We describe here the positional cloning of a T1D susceptibility locus, Idd11, located on mouse chromosome 4. Sequence analysis of a series of congenic NOD mo...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.101881.109
更新日期：2010-12-01 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：: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：: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：:Phenotypic differences within populations and between closely related species are often driven by variation and evolution of gene expression. However, most analyses have focused on the effects of genomic variation at cis-regulatory elements such as promoters and enhancers that control transcriptional activity, and lit...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.212563.116
更新日期：2017-03-01 00:00:00
abstract：:We developed a microarray platform for PCR amplification-independent expression profiling of minute samples. A novel scanning system combined with specialized biochips enables detection down to individual fluorescent oligonucleotide molecules specifically hybridized to their complementary sequence over the entire bioc...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.4999906
更新日期：2006-08-01 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
abstract：:Differences in gene repertoire among bacterial genomes are usually ascribed to gene loss or to lateral gene transfer from unrelated cellular organisms. However, most bacteria contain large numbers of ORFans, that is, annotated genes that are restricted to a particular genome and that possess no known homologs. The uni...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.2231904
更新日期：2004-06-01 00:00:00
abstract：:Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat S...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.135780.111
更新日期：2012-06-01 00:00:00
abstract：:Genome-scale metabolic models promise important insights into cell function. However, the definition of pathways and functional network modules within these models, and in the biochemical literature in general, is often based on intuitive reasoning. Although mathematical methods have been proposed to identify modules,...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.5662207
更新日期：2007-04-01 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：: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 Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a ch...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.253435.119
更新日期：2019-11-01 00:00:00
abstract：:To accelerate the molecular analysis of behavior in the honey bee (Apis mellifera), we created expressed sequence tag (EST) and cDNA microarray resources for the bee brain. Over 20,000 cDNA clones were partially sequenced from a normalized (and subsequently subtracted) library generated from adult A. mellifera brains....
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.5302
更新日期：2002-04-01 00:00:00
abstract：:Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-base...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.235820.118
更新日期：2018-12-01 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：:Genomic comparisons provide evidence for ancient genome-wide duplications in a diverse array of animals and plants. We developed a birth-death model to identify evidence for genome duplication in EST data, and applied a mixture model to estimate the age distribution of paralogous pairs identified in EST sets for speci...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.4825606
更新日期：2006-06-01 00:00:00
abstract：:Integrating the genotype with epigenetic marks holds the promise of better understanding the biology that underlies the complex interactions of inherited and environmental components that define the developmental origins of a range of disorders. The quality of the in utero environment significantly influences health o...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.171439.113
更新日期：2014-07-01 00:00:00
abstract：:A subset of colorectal cancers was postulated to have the CpG island methylator phenotype (CIMP), a higher propensity for CpG island DNA methylation. The validity of CIMP, its molecular basis, and its prognostic value remain highly controversial. Using MBD-isolated genome sequencing, we mapped and compared genome-wide...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.122788.111
更新日期：2012-02-01 00:00:00
abstract：:Human chromosomal regions enriched in segmental duplications are subject to extensive genomic reorganization. Such regions are particularly informative for illuminating the evolutionary history of a given chromosome. We have analyzed 866 kb of Y-chromosomal non-palindromic segmental duplications delineating four euchr...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.076711.108
更新日期：2008-07-01 00:00:00
abstract：:Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.111765.110
更新日期：2010-12-01 00:00:00
abstract：:The most polymorphic part of the human genome, the MHC, encodes over 160 proteins of diverse function. Half of them, including the HLA class I and II genes, are directly involved in immune responses. Consequently, the MHC region strongly associates with numerous diseases and clinical therapies. Notoriously, the MHC re...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.213538.116
更新日期：2017-05-01 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：: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：:Many CpG islands have tissue-dependent and differentially methylated regions (T-DMRs) in normal cells and tissues. To elucidate how DNA methyltransferases (Dnmts) participate in methylation of the genomic components, we investigated the genome-wide DNA methylation pattern of the T-DMRs with Dnmt1-, Dnmt3a-, and/or Dnm...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.2431504
更新日期：2004-09-01 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：: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：:In vivo analyses of the occurrence, subcellular localization, and dynamics of protein-protein interactions (PPIs) are important issues in functional proteomic studies. The bimolecular fluorescence complementation (BiFC) assay has many advantages in that it provides a reliable way to detect PPIs in living cells with mi...
journal_title：Genome research
pub_type： 杂志文章
doi：10.1101/gr.231860.117
更新日期：2019-01-01 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
