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, but providing limited information about variation across different conditions. To close this gap, we profiled mRNA levels of two related yeast species in hundreds of conditions and used coexpression analysis to distinguish variation in the dynamic pattern of gene expression from variation in expression levels. The majority of genes whose expression varied between the species maintained a conserved dynamic pattern. Cases of diverged dynamic pattern correspond to genes that were induced under distinct subsets of conditions in the two species. Profiling the interspecific hybrid allowed us to distinguish between genes with predominantly cis- or trans-regulatory variation. We find that trans-varying alleles are dominantly inherited, and that cis-variations are often complemented by variations in trans Based on these results, we suggest that gene expression diverges primarily through changes in expression levels, but does not alter the pattern by which these levels are dynamically regulated.
journal_name
Genome Resjournal_title
Genome researchauthors
Krieger G,Lupo O,Levy AA,Barkai Ndoi
10.1101/gr.261537.120subject
Has Abstractpub_date
2020-07-01 00:00:00pages
1000-1011issue
7eissn
1088-9051issn
1549-5469pii
gr.261537.120journal_volume
30pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Analysis procedures are needed to extract useful information from the large amount of gene expression data that is becoming available. This work describes a set of analytical tools and their application to yeast cell cycle data. The components of our approach are (1) a similarity measure that reduces the number of fal...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.9.11.1106
更新日期:1999-11-01 00:00:00
abstract::Transposable elements (TEs) proliferate within the genome of their host, which responds by silencing them epigenetically. Much is known about the mechanisms of silencing in plants, particularly the role of siRNAs in guiding DNA methylation. In contrast, little is known about siRNA targeting patterns along the length o...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.193763.115
更新日期:2016-02-01 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::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,...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.094482.109
更新日期:2009-10-01 00:00:00
abstract::Organisms with large genomes contain vast amounts of repetitive DNA sequences, much of which is composed of retrotransposons. Amplification of retrotransposons has been postulated to be a major mechanism increasing genome size and leading to "genomic obesity." To gain insights into the relation between retrotransposon...
journal_title:Genome research
pub_type: 评论,杂志文章
doi:10.1101/gr.10.7.908
更新日期:2000-07-01 00:00:00
abstract::Translocations are a common class of chromosomal aberrations and can cause disease by physically disrupting genes or altering their regulatory environment. Some translocations, apparently balanced at the microscopic level, include deletions, duplications, insertions, or inversions at the molecular level. Traditionally...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.122986.111
更新日期:2011-10-01 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::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
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::Comparative gene mapping in mammals typically involves identification of segments of conserved synteny in diverse genomes. The development of maps that permit comparison of gene order within conserved synteny has not advanced beyond the mouse map that takes advantage of linkage analysis in interspecific backcrosses. R...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.8.7.731
更新日期:1998-07-01 00:00:00
abstract::The higher-order structural organization and dynamics of the chromosomes play a central role in gene regulation. To explore this structure-function relationship, it is necessary to directly visualize genomic elements in living cells. Genome imaging based on the CRISPR system is a powerful approach but has limited appl...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.260018.119
更新日期:2020-09-01 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::Chicken B cells create their immunoglobulin repertoire within the Bursa of Fabricius by gene conversion. The high homologous recombination activity is shared by the bursal B-cell-derived DT40 cell line, which integrates transfected DNA constructs at high rates into its endogenous loci. Targeted integration in DT40 is ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.12.2062
更新日期:2000-12-01 00:00:00
abstract::Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of po...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.146084.112
更新日期:2013-05-01 00:00:00
abstract::Epigenetic modifications on chromatin play important roles in regulating gene expression. Although chromatin states are often governed by multilayered structure, how individual pathways contribute to gene expression remains poorly understood. For example, DNA methylation is known to regulate transcription factor bindi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.257576.119
更新日期:2020-10-01 00:00:00
abstract::To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the "2-n-way" software suite to provide a fundamental and innovative processing framework for revealing and compar...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.262261.120
更新日期:2020-10-01 00:00:00
abstract::The genome size of Pseudoalteromonas haloplanktis, a ubiquitous and easily cultured marine bacterium, was measured as a step toward estimating the genome complexity of marine bacterioplankton. To determine total genome size, we digested P. haloplanktis DNA with the restriction endonucleases Notl and Sfil, separated th...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.12.1160
更新日期:1996-12-01 00:00:00
abstract::Many thousands of proteins encoded by the genome of Plasmodium falciparum, the causal organism of the deadliest form of human malaria, are of unknown function. It is of utmost importance that these proteins be characterized if we are to develop combative strategies against malaria based on the biology of the parasite....
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.4573206
更新日期:2006-04-01 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::Gene expression can be regulated at multiple levels, but it is not known if and how there is broad coordination between regulation at the transcriptional and post-transcriptional levels. Transcription factors and chromatin regulate gene expression transcriptionally, whereas microRNAs (miRNAs) are small regulatory RNAs...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.238311.118
更新日期:2019-02-01 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::As more genomes are sequenced, there is an increasing need for automated first-pass annotation which allows timely access to important genomic information. The Ensembl gene-building system enables fast automated annotation of eukaryotic genomes. It annotates genes based on evidence derived from known protein, cDNA, an...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1858004
更新日期:2004-05-01 00:00:00
abstract::Differential methylation between the two alleles of a gene has been observed in imprinted regions, where the methylation of one allele occurs on a parent-of-origin basis, the inactive X-chromosome in females, and at those loci whose methylation is driven by genetic variants. We have extensively characterized imprinted...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.164913.113
更新日期:2014-04-01 00:00:00
abstract::Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3176505
更新日期:2005-04-01 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 last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incred...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.191684.115
更新日期:2015-10-01 00:00:00
abstract::We report on the development of a methylation analysis workflow for optical detection of fluorescent methylation profiles along chromosomal DNA molecules. In combination with Bionano Genomics genome mapping technology, these profiles provide a hybrid genetic/epigenetic genome-wide map composed of DNA molecules spannin...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.240739.118
更新日期:2019-04-01 00:00:00
abstract::The genomic alterations associated with cancers are numerous and varied, involving both isolated and large-scale complex genomic rearrangements (CGRs). Although the underlying mechanisms are not well understood, CGRs have been implicated in tumorigenesis. Here, we introduce CouGaR, a novel method for characterizing th...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.211201.116
更新日期:2017-01-01 00:00:00
abstract::The rate of transcription elongation plays an important role in the timing of expression of full-length transcripts as well as in the regulation of alternative splicing. In this study, we coupled Bru-seq technology with 5,6-dichlorobenzimidazole 1-β-D-ribofuranoside (DRB) to estimate the elongation rates of over 2000 ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.171405.113
更新日期:2014-06-01 00:00:00
abstract::Large-scale sequencing of human and model organism genomes will have a profound impact on our ability to use sequence data base searching to predict the biochemical functions of sequences of interest. Despite the great value of more sequences in the data bases, a huge increase in data base size will also have adverse ...
journal_title:Genome research
pub_type: 杂志文章,评审
doi:10.1101/gr.6.8.653
更新日期:1996-08-01 00:00:00