Abstract:
BACKGROUND:In eukaryotic organisms, gene expression is regulated at multiple levels during the processes of transcription and translation. The absence of a tight regulatory network for transcription in the human malaria parasite suggests that gene expression may largely be controlled at post-transcriptional and translational levels. RESULTS:In this study, we compare steady-state mRNA and polysome-associated mRNA levels of Plasmodium falciparum at different time points during its asexual cell cycle. For more than 30% of its genes, we observe a delay in peak transcript abundance in the polysomal fraction as compared to the steady-state mRNA fraction, suggestive of strong translational control. Our data show that key regulatory mechanisms could include inhibitory activity of upstream open reading frames and translational repression of the major virulence gene family by intronic transcripts. In addition, we observe polysomal mRNA-specific alternative splicing events and widespread transcription of non-coding transcripts. CONCLUSIONS:These different layers of translational regulation are likely to contribute to a complex network that controls gene expression in this eukaryotic pathogen. Disrupting the mechanisms involved in such translational control could provide novel anti-malarial strategies.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Bunnik EM,Chung DW,Hamilton M,Ponts N,Saraf A,Prudhomme J,Florens L,Le Roch KGdoi
10.1186/gb-2013-14-11-r128subject
Has Abstractpub_date
2013-11-22 00:00:00pages
R128issue
11eissn
1474-7596issn
1474-760Xpii
gb-2013-14-11-r128journal_volume
14pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:One way in which the accuracy of gene structure prediction in vertebrate DNA sequences can be improved is by analyzing alignments with multiple related species, since functional regions of genes tend to be more conserved. RESULTS:We describe DOGFISH, a vertebrate gene finder consisting of a cleanly separate...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-s1-s6
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Francisella tularensis subspecies tularensis and holarctica are pathogenic to humans, whereas the two other subspecies, novicida and mediasiatica, rarely cause disease. To uncover the factors that allow subspecies tularensis and holarctica to be pathogenic to humans, we compared their genome sequences with t...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-6-r102
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out func...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-9-r50
更新日期:2012-09-26 00:00:00
abstract::Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/s13059-014-0516-x
更新日期:2014-11-08 00:00:00
abstract:BACKGROUND:Retrotransposons play a central role in plant evolution and could be a powerful endogenous source of genetic and epigenetic variability for crop breeding. To ensure genome integrity several silencing mechanisms have evolved to repress retrotransposon mobility. Even though retrotransposons fully depend on tra...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1265-4
更新日期:2017-07-07 00:00:00
abstract:BACKGROUND:The direct examination of large, unbiased samples of young gene duplicates in their early stages of evolution is crucial to understanding the origin, divergence and preservation of new genes. Furthermore, comparative analysis of multiple genomes is necessary to determine whether patterns of gene duplication ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-7-r75
更新日期:2009-01-01 00:00:00
abstract::Piwi-interacting RNAs (piRNAs) originate from genomic regions dubbed piRNA clusters. How cluster transcripts are selected for processing into piRNAs is not understood. We discuss evidence for the involvement of chromatin structure and maternally inherited piRNAs in determining their fate. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb4154
更新日期:2014-01-27 00:00:00
abstract:BACKGROUND:The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-11-r112
更新日期:2006-01-01 00:00:00
abstract::The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-D...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1138-2
更新日期:2017-01-18 00:00:00
abstract::Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA. ...
journal_title:Genome biology
pub_type: 历史文章,杂志文章,评审
doi:10.1186/s13059-015-0866-z
更新日期:2016-01-11 00:00:00
abstract:BACKGROUND:Estrogens and their receptors are important in human development, physiology and disease. In this study, we utilized an integrated genome-wide molecular and computational approach to characterize the interaction between the activated estrogen receptor (ER) and the regulatory elements of candidate target gene...
journal_title:Genome biology
pub_type: 杂志文章,meta分析
doi:10.1186/gb-2004-5-9-r66
更新日期:2004-01-01 00:00:00
abstract::We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide m...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1517-y
更新日期:2018-09-25 00:00:00
abstract::A report on the Plant Genomics European Meeting (Plant-GEMS2004), Lyon, France, 22-25 September 2004. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2004-6-1-302
更新日期:2005-01-01 00:00:00
abstract::Understanding the functional impact of genomic variants is a major goal of modern genetics and personalized medicine. Although many synonymous and non-coding variants act through altering the efficiency of pre-mRNA splicing, it is difficult to predict how these variants impact pre-mRNA splicing. Here, we describe a ma...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1437-x
更新日期:2018-06-01 00:00:00
abstract::Abhay Sharma brings two arguments in favor of transgenerational epigenetic inheritance (TGEI) in mammals when criticizing our work. He uses probability calculations and finds that the probability of obtaining the number of common changes in the in utero-exposed prospermatogonia and the same cells in the next generatio...
journal_title:Genome biology
pub_type: 评论,信件
doi:10.1186/s13059-016-0978-0
更新日期:2016-05-16 00:00:00
abstract::The iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP ( https://github....
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1364-2
更新日期:2017-12-28 00:00:00
abstract:BACKGROUND:Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an important opportunistic human pathogen. Generally, the acquisition of genes in the form of pathogenicity islands distinguishes pathogenic isolates from nonpathogens. We therefore sequenced a highly virulent strain of P. aeruginosa, PA14, a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-10-r90
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Obligate pathogenic bacteria lose more genes relative to facultative pathogens, which, in turn, lose more genes than free-living bacteria. It was suggested that the increased gene loss in obligate pathogens may be due to a reduction in the effectiveness of purifying selection. Less attention has been given t...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-8-r164
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:A key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02131-y
更新日期:2020-09-07 00:00:00
abstract::The use of DNA sequences to estimate the timing of evolutionary events is increasingly popular, although it is fraught with practical difficulties. But the exponential growth of relevant information and improved methods of analysis are providing increasingly reliable sequence-derived dates, and it may become possible ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2001-3-1-reviews0001
更新日期:2002-01-01 00:00:00
abstract:BACKGROUND:Long noncoding RNAs (lncRNAs) form an abundant class of transcripts, but the function of the majority of them remains elusive. While it has been shown that some lncRNAs are bound by ribosomes, it has also been convincingly demonstrated that these transcripts do not code for proteins. To obtain a comprehensiv...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-1-r6
更新日期:2014-01-07 00:00:00
abstract:BACKGROUND:Neisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequenc...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-12-r127
更新日期:2011-12-30 00:00:00
abstract:BACKGROUND:Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processe...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-5-r85
更新日期:2008-01-01 00:00:00
abstract::Genomic and proteomic studies have identified hundreds of proteins from mitochondria. A recent study has added a functional twist to these systematic approaches and identified novel mitochondrial modifiers and regulators. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2008-9-2-209
更新日期:2008-01-01 00:00:00
abstract::A report on the 23rd Fungal Genetics Conference, Pacific Grove, USA, 15-20 March 2005. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2005-6-8-336
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements lo...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1278-z
更新日期:2017-08-07 00:00:00
abstract:BACKGROUND:Many eukaryotic genomes encode cis-natural antisense transcripts (cis-NATs). Sense and antisense transcripts may form double-stranded RNAs that are processed by the RNA interference machinery into small interfering RNAs (siRNAs). A few so-called nat-siRNAs have been reported in plants, mammals, Drosophila, a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-3-r20
更新日期:2012-01-01 00:00:00
abstract::Gene expression analysis of microRNA molecules is becoming increasingly important. In this study we assess the use of the mean expression value of all expressed microRNAs in a given sample as a normalization factor for microRNA real-time quantitative PCR data and compare its performance to the currently adopted approa...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-6-r64
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis, perception of microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 and MPK6. Increasing information depicts the molecular events activated by MAMPs in plants, but th...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-6-r87
更新日期:2014-06-30 00:00:00
abstract:BACKGROUND:DNA damage leads to cellular responses that include the increased expression of DNA repair genes, repression of DNA replication and alterations in cellular metabolism. Archaeal information processing pathways resemble those in eukaryotes, but archaeal damage response pathways remain poorly understood. RESUL...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-10-r220
更新日期:2007-01-01 00:00:00