Abstract:
BACKGROUND:MicroRNAs (miRNAs) exist pervasively across viruses, plants and animals and play important roles in the post-transcriptional regulation of genes. In the common carp, miRNA targets have not been investigated. In model species, single-nucleotide polymorphisms (SNPs) have been reported to impair or enhance miRNA regulation as well as to alter miRNA biogenesis. SNPs are often associated with diseases or traits. To date, no studies into the effects of SNPs on miRNA biogenesis and regulation in the common carp have been reported. RESULTS:Using homology-based prediction combined with small RNA sequencing, we have identified 113 common carp mature miRNAs, including 92 conserved miRNAs and 21 common carp specific miRNAs. The conserved miRNAs had significantly higher expression levels than the specific miRNAs. The miRNAs were clustered into three phylogenetic groups. Totally 394 potential miRNA binding sites in 206 target mRNAs were predicted for 83 miRNAs. We identified 13 SNPs in the miRNA precursors. Among them, nine SNPs had the potential to either increase or decrease the energy of the predicted secondary structures of the precursors. Further, two SNPs in the 3' untranslated regions of target genes were predicted to either disturb or create miRNA-target interactions. CONCLUSIONS:The common carp miRNAs and their target genes reported here will help further our understanding of the role of miRNAs in gene regulation. The analysis of the miRNA-related SNPs and their effects provided insights into the effects of SNPs on miRNA biogenesis and function. The resource data generated in this study will help advance the study of miRNA function and phenotype-associated miRNA identification.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Zhu YP,Xue W,Wang JT,Wan YM,Wang SL,Xu P,Zhang Y,Li JT,Sun XWdoi
10.1186/1471-2164-13-413subject
Has Abstractpub_date
2012-08-21 00:00:00pages
413issn
1471-2164pii
1471-2164-13-413journal_volume
13pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Membrane proteins constitute up to 30% of the human proteome. These proteins have special properties because the transmembrane segments are embedded into lipid bilayer while extramembranous parts are in different environments. Membrane proteins have several functions and are involved in numerous diseases. A ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5865-0
更新日期:2019-07-16 00:00:00
abstract:BACKGROUND:Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for pro...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2209-6
更新日期:2015-12-01 00:00:00
abstract:BACKGROUND:One challenge of systems biology is the integration of new data into the preexisting, and then re-interpretation of the integrated data. Here we use readily available metaanalysis computational methods to integrate new data on the transcriptomic effects of EGF in primary human epidermal keratinocytes with pr...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/1471-2164-14-85
更新日期:2013-02-08 00:00:00
abstract:BACKGROUND:Palmitoylation is a reversible post-translational protein modification which involves the addition of palmitate to cysteine residues. Palmitoylation is catalysed by the DHHC family of palmitoyl-acyl transferases (PATs) and reversibility is conferred by palmitoyl-protein thioesterases (PPTs). Mutations in gen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-841
更新日期:2014-10-02 00:00:00
abstract:BACKGROUND:The t(12;21)(p13;q22) translocation is found in 20 to 25% of cases of childhood B-lineage acute lymphoblastic leukemia (B-ALL). This rearrangement results in the fusion of ETV6 (TEL) and RUNX1 (AML1) genes and defines a relatively uniform category, although only some patients suffer very late relapse. TEL/AM...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-385
更新日期:2007-10-23 00:00:00
abstract:BACKGROUND:The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, in order to favor the use of a wider variety of feedstuffs. T...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5344-z
更新日期:2018-12-13 00:00:00
abstract:BACKGROUND:RNA sequencing (RNA-seq) and microarrays are two transcriptomics techniques aimed at the quantification of transcribed genes and their isoforms. Here we compare the latest Affymetrix HTA 2.0 microarray with Illumina 2000 RNA-seq for the analysis of patient samples - normal lung epithelium tissue and squamous...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3819-y
更新日期:2017-06-06 00:00:00
abstract:BACKGROUND:Thousands of intragenic long interspersed element 1 sequences (LINE-1 elements or L1s) reside within genes. These intragenic L1 sequences are conserved and regulate the expression of their host genes. When L1 methylation is decreased, either through chemical induction or in cancer, the intragenic L1 transcri...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-205
更新日期:2013-03-27 00:00:00
abstract:BACKGROUND:The sRNAs of bacterial pathogens are known to be involved in various cellular roles including environmental adaptation as well as regulation of virulence and pathogenicity. It is expected that sRNAs may also have similar functions for Burkholderia pseudomallei, a soil bacterium that can adapt to diverse envi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S7-S13
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that biomarkers are often low abundance proteins. However, LC/MS systems are subject to considerable noise...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-S3-S8
更新日期:2010-12-01 00:00:00
abstract:BACKGROUND:Cold tolerance is a key determinant of the geographical distribution range of a plant species and crop production. Cold acclimation can enhance freezing-tolerance of plant species through a period of exposure to low nonfreezing temperatures. As a subtropical evergreen broadleaf plant, oil-tea camellia demons...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3570-4
更新日期:2017-02-28 00:00:00
abstract:BACKGROUND:Acquisition of external phosphorus (P) and optimisation of internal P are essential for plant growth and development, and insufficient availability of P in soils is a major challenge in agriculture. Members of the purple acid phosphatase (PAP) family of enzymes are candidates for increasing P use efficiency....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5022-1
更新日期:2018-08-31 00:00:00
abstract:BACKGROUND:The microsporidian Encephalitozoon cuniculi is an obligate intracellular eukaryotic pathogen with a small nuclear genome (2.9 Mbp) consisting of 11 chromosomes. Although each chromosome end is known to contain a single rDNA unit, the incomplete assembly of subtelomeric regions following sequencing of the gen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1920-7
更新日期:2016-01-07 00:00:00
abstract:BACKGROUND:Spinal cord injury leads to neurological dysfunctions affecting the motor, sensory as well as the autonomic systems. Increased excitability of motor neurons has been implicated in injury-induced spasticity, where the reappearance of self-sustained plateau potentials in the absence of modulatory inputs from t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-365
更新日期:2010-06-09 00:00:00
abstract:BACKGROUND:Modifications of RNA bases have been found in some mRNAs and non-coding RNAs including rRNAs, tRNAs, and snRNAs, where modified bases are important for RNA function. Little is known about RNA base modifications in Arabidopsis thaliana. RESULTS:In the current work, we carried out a bioinformatics analysis of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-155
更新日期:2009-04-09 00:00:00
abstract:BACKGROUND:Pfam is a general-purpose database of protein domain alignments and profile Hidden Markov Models (HMMs), which is very popular for the annotation of sequence data produced by genome sequencing projects. Pfam provides models that are often very general in terms of the taxa that they cover and it has previousl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-97
更新日期:2007-04-10 00:00:00
abstract:BACKGROUND:Parasites employ proteases to evade host immune systems, feed and replicate and are often the target of anti-parasite strategies to disrupt these interactions. Myxozoans are obligate cnidarian parasites, alternating between invertebrate and fish hosts. Their genes are highly divergent from other metazoans, a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6705-y
更新日期:2020-06-16 00:00:00
abstract:BACKGROUND:Interactions between fish and pathogens, that may be harmless under natural conditions, often result in serious diseases in aquaculture systems. This is especially important due to the fact that the strains used in aquaculture are derived from wild strains that may not have had enough time to adapt to new di...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-541
更新日期:2011-11-02 00:00:00
abstract:BACKGROUND:Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into therapeutic response and resistance. In complex cases involving multiple timepoints, standard visuali...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3195-z
更新日期:2016-11-07 00:00:00
abstract:BACKGROUND:Oxidative stress caused by ground level ozone is a contributor to yield loss in a number of important crop plants. Soybean (Glycine max) is considered to be ozone sensitive, and current research into its response to oxidative stress is limited. To better understand the genetic response in soybean to oxidativ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1637-7
更新日期:2015-06-04 00:00:00
abstract:BACKGROUND:To understand gene expression networks leading to functional properties of the soybean seed, we have undertaken a detailed examination of soybean seed development during the stages of major accumulation of oils, proteins, and starches, as well as the desiccating and mature stages, using microarrays consistin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-136
更新日期:2010-02-24 00:00:00
abstract:BACKGROUND:Phlebotomine sand flies (Diptera, Nematocera) are important vectors of several pathogens, including Leishmania parasites, causing serious diseases of humans and dogs. Despite their importance as disease vectors, most aspects of sand fly biology remain unknown including the molecular basis of their reproducti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5898-4
更新日期:2019-06-25 00:00:00
abstract:BACKGROUND:Crocodilians (Order Crocodylia) are an ancient vertebrate group of tremendous ecological, social, and evolutionary importance. They are the only extant reptilian members of Archosauria, a monophyletic group that also includes birds, dinosaurs, and pterosaurs. Consequently, crocodilian genomes represent a gat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-S2-S9
更新日期:2009-07-14 00:00:00
abstract:BACKGROUND:The unfolded protein response (UPR) is a network of intracellular signaling pathways that supports the ability of the secretory pathway to maintain a balance between the load of proteins entering the endoplasmic reticulum (ER) and the protein folding capacity of the ER lumen. Current evidence indicates that ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-159
更新日期:2014-02-25 00:00:00
abstract:BACKGROUND:Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range of environments, including soil. RESULTS:Here we describe the genome sequencing and assessment o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5130-y
更新日期:2018-10-16 00:00:00
abstract:BACKGROUND:Foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2628-z
更新日期:2016-05-04 00:00:00
abstract:BACKGROUND:Intergenic splicing resulting in the combination of mRNAs sequences from distinct genes is a newly identified mechanism likely to contribute to protein diversity. Few cases have been described, most of them involving neighboring genes and thus suggesting a cotranscription event presumably due to transcriptio...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-71
更新日期:2006-04-04 00:00:00
abstract:BACKGROUND:The ability to rapidly map millions of oligonucleotide fragments to a reference genome is crucial to many high throughput genomic technologies. RESULTS:We propose an intuitive and efficient algorithm, titled extreme MApping of OligoNucleotide (xMAN), to rapidly map millions of oligonucleotide fragments to a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S1-S20
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Mango fruits contain a broad spectrum of phenolic compounds which impart potential health benefits; their biosynthesis is catalysed by enzymes in the phenylpropanoid-flavonoid (PF) pathway. The aim of this study was to reveal the variability in genes involved in the PF pathway in three different mango variet...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1784-x
更新日期:2015-07-30 00:00:00
abstract:BACKGROUND:Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the n...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-546
更新日期:2013-08-12 00:00:00