Abstract:
BACKGROUND:Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. RESULTS:In the model legume Medicago truncatula, we analyze the small RNA transcriptome of roots submitted to symbiotic and pathogenic interactions. Genome mapping and a computational pipeline identify 416 miRNA candidates, including known and novel variants of 78 miRNA families present in miRBase. Stringent criteria of pre-miRNA prediction yield 52 new mtr-miRNAs, including 27 miRtrons. Analyzing miRNA precursor polymorphisms in 26 M. truncatula ecotypes identifies higher sequence polymorphism in conserved rather than Medicago-specific miRNA precursors. An average of 19 targets, mainly involved in environmental responses and signalling, is predicted per novel miRNA. We identify miRNAs responsive to bacterial and fungal pathogens or symbionts as well as their related Nod and Myc-LCO symbiotic signals. Network analyses reveal modules of new and conserved co-expressed miRNAs that regulate distinct sets of targets, highlighting potential miRNA-regulated biological pathways relevant to pathogenic and symbiotic interactions. CONCLUSIONS:We identify 52 novel genuine miRNAs and large plasticity of the root miRNAome in response to the environment, and also in response to purified Myc/Nod signaling molecules. The new miRNAs identified and their sequence variation across M. truncatula ecotypes may be crucial to understand the adaptation of root growth to the soil environment, notably in the agriculturally important legume crops.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Formey D,Sallet E,Lelandais-Brière C,Ben C,Bustos-Sanmamed P,Niebel A,Frugier F,Combier JP,Debellé F,Hartmann C,Poulain J,Gavory F,Wincker P,Roux C,Gentzbittel L,Gouzy J,Crespi Mdoi
10.1186/s13059-014-0457-4subject
Has Abstractpub_date
2014-09-24 00:00:00pages
457issue
9eissn
1474-7596issn
1474-760Xpii
s13059-014-0457-4journal_volume
15pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:As a biomarker of cellular activities, the transcriptome of a specific tissue or cell type during development and disease is of great biomedical interest. We have generated and analyzed 10,000 expressed sequence tags (ESTs) from three mouse eye tissue cDNA libraries: embryonic day 15.5 (M15E) eye, postnatal ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2003-4-10-r65
更新日期:2003-01-01 00:00:00
abstract::A combined approach of whole genome shotgun sequencing and ultra-high density linkage mapping using skim sequencing of a segregating population is effective for assembling allopolyploid genomes. ...
journal_title:Genome biology
pub_type: 信件
doi:10.1186/s13059-015-0585-5
更新日期:2015-01-31 00:00:00
abstract:BACKGROUND:Protein domains are protein regions that are shared among different proteins and are frequently functionally and structurally independent from the rest of the protein. Novel domain combinations have a major role in evolutionary innovation. However, the relative contributions of the different molecular mechan...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-7-r74
更新日期:2010-01-01 00:00:00
abstract::A report on the Keystone symposium 'Non-coding RNAs' held at Snowbird, Utah, USA, 31 March to 5 April 2012. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2012-13-5-315
更新日期:2012-05-25 00:00:00
abstract::A new generation of DNA-sequencing platforms will become commercially available over the next few years. These instruments will enable re-sequencing of human genomes at a previously unimagined throughput and low cost. Here, I examine why the 1,000 dollar human genome is an important goal for research and clinical diag...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-7-112
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications mus...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02190-1
更新日期:2020-11-25 00:00:00
abstract::A report on the 2004 meeting on Molecular Genetics of Bacteria and Bacteriophages, Cold Spring Harbor, USA, 25-29 August 2004. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2004-5-12-357
更新日期:2004-01-01 00:00:00
abstract:BACKGROUND:Chronic psychological stress is associated with accelerated aging and increased risk for aging-related diseases, but the underlying molecular mechanisms are unclear. RESULTS:We examined the effect of lifetime stressors on a DNA methylation-based age predictor, epigenetic clock. After controlling for blood c...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0828-5
更新日期:2015-12-17 00:00:00
abstract:BACKGROUND:We have constructed Bayesian prior-based, amino-acid sequence profiles for the complete yeast mitochondrial proteome and used them to develop methods for identifying and characterizing the context of protein mutations that give rise to human mitochondrial diseases. (Bayesian priors are conditional probabilit...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2001-2-6-research0021
更新日期:2001-01-01 00:00:00
abstract:BACKGROUND:Maps depicting binary interactions between proteins can be powerful starting points for understanding biological systems. A proven technology for generating such maps is high-throughput yeast two-hybrid screening. In the most extensive screen to date, a Gal4-based two-hybrid system was used recently to detec...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-12-r96
更新日期:2004-01-01 00:00:00
abstract::The mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a novel, compositional approach to this problem which combines core ontologies from a variety of sou...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-6-1-r8
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:Growth rate is central to the development of cells in all organisms. However, little is known about the impact of changing growth rates. We used continuous cultures to control growth rate and studied the transcriptional program of the model eukaryote Saccharomyces cerevisiae, with generation times varying be...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-11-r107
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified. RESULTS:To investi...
journal_title:Genome biology
pub_type: 杂志文章,随机对照试验
doi:10.1186/gb-2013-14-4-r34
更新日期:2013-04-29 00:00:00
abstract::The definition of cell identity is a central problem in biology. While single-cell RNA-seq provides a wealth of information regarding cell states, better methods are needed to map their identity, especially during developmental transitions. Here, we use repositories of cell type-specific transcriptomes to quantify ide...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0580-x
更新日期:2015-01-22 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::A report on the Genome-Based Pathogen Biology meeting, Hinxton, UK, 7-10 July 2002. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2002-3-9-reports4029
更新日期:2002-08-27 00:00:00
abstract:BACKGROUND:Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome se...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2013-14-6-r63
更新日期:2013-06-25 00:00:00
abstract::The key molecules involved in regulating the assembly and function of the mitotic spindle are shared by evolutionarily divergent species. Studies in different model systems are leading to convergent conclusions about the central role of microtubule nucleation and dynamics and of kinesin-related motor proteins in spind...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2000-1-1-reviews101
更新日期:2000-01-01 00:00:00
abstract::Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1238-7
更新日期:2017-05-22 00:00:00
abstract:BACKGROUND:Xanthomonas campestris pathovar campestris (Xcc) is the causal agent of black rot disease of crucifers worldwide. The molecular genetic diversity and host specificity of Xcc are poorly understood. RESULTS:We constructed a microarray based on the complete genome sequence of Xcc strain 8004 and investigated t...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-10-r218
更新日期:2007-01-01 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::The army of the men of death, in John Bunyan's memorable phrase, has a new recruit, and fear has a new face: a face wearing a surgical mask. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2003-4-7-113
更新日期:2003-01-01 00:00:00
abstract:BACKGROUND:Synthetic genetic interactions have recently been mapped on a genome scale in the budding yeast Saccharomyces cerevisiae, providing a functional view of the central processes of eukaryotic life. Currently, comprehensive genetic interaction networks have not been determined for other species, and we therefore...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-7-r57
更新日期:2012-07-02 00:00:00
abstract:BACKGROUND:Neuropsychiatric disorders are common forms of disability in humans. Despite recent progress in deciphering the genetics of these disorders, their phenotypic complexity continues to be a major challenge. Mendelian neuropsychiatric disorders are rare but their study has the potential to unravel novel mechanis...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1061-6
更新日期:2016-09-27 00:00:00
abstract::Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers from clinical array comparative genomic hybridization data. The tumor cell fraction is reliably e...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-5-r86
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:High-density oligonucleotide microarrays provide a powerful tool for assessing differential mRNA expression levels. Characterizing the noise resulting from the enzymatic and hybridization steps, called type I noise, is essential for attributing significance measures to the differential expression scores. We ...
journal_title:Genome biology
pub_type: 杂志文章
doi:
更新日期:2002-01-01 00:00:00
abstract:BACKGROUND:In microarray data analysis, the comparison of gene-expression profiles with respect to different conditions and the selection of biologically interesting genes are crucial tasks. Multivariate statistical methods have been applied to analyze these large datasets. Less work has been published concerning the a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-4-research0019
更新日期:2002-01-01 00:00:00
abstract::Key components of the programmed cell death pathway are conserved between Caenorhabditis elegans, Drosophila melanogaster and humans. The search for additional homologs has been facilitated by the availability of the entire genomic sequence for each of these organisms. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2000-1-3-reviews0003
更新日期:2000-01-01 00:00:00
abstract::Reliable orthology prediction is central to comparative genomics. Although orthology is defined by phylogenetic criteria, most automated prediction methods are based on pairwise sequence comparisons. Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies....
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2008-9-10-235
更新日期:2008-10-30 00:00:00
abstract:BACKGROUND:Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which de...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-3-preprint0002
更新日期:2002-01-01 00:00:00