Abstract:
BACKGROUND:Teleost intestine is crucial for seawater acclimation by sensing osmolality of imbibed seawater and regulating drinking and water/ion absorption. Regulatory genes for transforming intestinal function have not been identified. A transcriptomic approach was used to search for such genes in the intestine of euryhaline medaka. RESULTS:Quantitative RNA-seq by Illumina Hi-Seq Sequencing method was performed to analyze intestinal gene expression 0 h, 1 h, 3 h, 1 d, and 7 d after seawater transfer. Gene ontology (GO) enrichment results showed that cell adhesion, signal transduction, and protein phosphorylation gene categories were augmented soon after transfer, indicating a rapid reorganization of cellular components and functions. Among >50 transiently up-regulated transcription factors selected via co-expression correlation and GO selection, five transcription factors, including CEBPB and CEBPD, were confirmed by quantitative PCR to be specific to hyperosmotic stress, while others were also up-regulated after freshwater control transfer, including some well-known osmotic-stress transcription factors such as SGK1 and TSC22D3/Ostf1. Protein interaction networks suggest a high degree of overlapping among the signaling of transcription factors that respond to osmotic and general stresses, which sheds light on the interpretation of their roles during hyperosmotic stress and emergency. CONCLUSIONS:Since cortisol is an important hormone for seawater acclimation as well as for general stress in teleosts, emergency and osmotic challenges could have been evolved in parallel and resulted in the overlapped signaling networks. Our results revealed important interactions among transcription factors and offer a multifactorial perspective of genes involved in seawater acclimation.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Wong MK,Ozaki H,Suzuki Y,Iwasaki W,Takei Ydoi
10.1186/1471-2164-15-1134subject
Has Abstractpub_date
2014-12-18 00:00:00pages
1134issn
1471-2164pii
1471-2164-15-1134journal_volume
15pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The accurate determination of the genomic coordinates for a given gene - its gene model - is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currently-available methods of computational gene prediction, while on the whole successful, frequentl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4704-z
更新日期:2018-04-27 00:00:00
abstract:BACKGROUND:We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments. RESULTS:By using simulated and real datasets we showed that our tool, based on read count approac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4137-0
更新日期:2017-09-21 00:00:00
abstract:BACKGROUND:In biomedical research, gene expression profiling studies have been extensively conducted. The analysis of gene expression data has led to a deeper understanding of human genetics as well as practically useful models. Clustering analysis has been a critical component of gene expression data analysis and can ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3990-1
更新日期:2017-08-16 00:00:00
abstract:BACKGROUND:Medicago truncatula has been chosen as a model species for genomic studies. It is closely related to an important legume, alfalfa. Transporters are a large group of membrane-spanning proteins. They deliver essential nutrients, eject waste products, and assist the cell in sensing environmental conditions by f...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-60
更新日期:2012-02-06 00:00:00
abstract:BACKGROUND:The numerous classes of repeats often impede the assembly of genome sequences from the short reads provided by new sequencing technologies. We demonstrate a simple and rapid means to ascertain the repeat structure and total size of a bacterial or archaeal genome without the need for assembly by directly anal...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-537
更新日期:2013-08-08 00:00:00
abstract:BACKGROUND:Second-generation sequencing technologies have revolutionized our ability to recover genetic information from the past, allowing the characterization of the first complete genomes from past individuals and extinct species. Recently, third generation Helicos sequencing platforms, which perform true Single-Mol...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-177
更新日期:2012-05-10 00:00:00
abstract:BACKGROUND:Effector proteins are translocated into host cells by plant-pathogens to undermine pattern-triggered immunity (PTI), the plant response to microbe-associated molecular patterns that interferes with the infection process. Individual effectors are found in variable repertoires where some constituents target th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2534-4
更新日期:2016-03-14 00:00:00
abstract:BACKGROUND:Azadirachtin A is a triterpenoid from neem tree exhibiting excellent activities against over 600 insect species in agriculture. The production of azadirachtin A depends on extraction from neem tissues, which is not an eco-friendly and sustainable process. The low yield and discontinuous supply of azadirachti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07124-6
更新日期:2020-10-28 00:00:00
abstract:BACKGROUND:Although second generation sequencing (2GS) technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-247
更新日期:2011-05-19 00:00:00
abstract:BACKGROUND:The membrane protein CD46, a ubiquitous cell surface pathogen receptor, can bind Streptococcus to trigger cell autophagy, which is a critical step in the control of infection. RESULTS:In this study, we found a new splice variant designated CD46 transcript variant (CD46-TV). The splice variant is characteriz...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-630
更新日期:2014-07-28 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known to be associated with disease phenotypes and to display tissue-specific patterns of expression. ME...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3114-3
更新日期:2016-10-04 00:00:00
abstract:BACKGROUND:Aedes aegypti is the principle vector of many arboviruses, including dengue virus and Zika virus, which are transmitted when an infected female mosquito takes a blood meal in order to initiate vitellogenesis. During blood digestion, ~ 10 mM heme-iron is ingested into the midgut lumen. While heme acts as both...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06981-5
更新日期:2020-08-31 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:Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4282-5
更新日期:2017-11-13 00:00:00
abstract:BACKGROUND:Aligning protein-protein interaction (PPI) networks is very important to discover the functionally conserved sub-structures between different species. In recent years, the global PPI network alignment problem has been extensively studied aiming at finding the one-to-one alignment with the maximum matching sc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5027-9
更新日期:2018-09-24 00:00:00
abstract:BACKGROUND:Protein phosphorylation by kinases plays crucial roles in various biological processes including signal transduction and tumorigenesis, thus a better understanding of protein phosphorylation events in cells is fundamental for studying protein functions and designing drugs to treat diseases caused by the malf...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06895-2
更新日期:2020-08-04 00:00:00
abstract:BACKGROUND:Litchi (Litchi chinensis Sonn.) is one of the most important fruit trees cultivated in tropical and subtropical areas. However, a lack of transcriptomic and genomic information hinders our understanding of the molecular mechanisms underlying fruit set and fruit development in litchi. Shading during early fru...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-552
更新日期:2013-08-14 00:00:00
abstract:BACKGROUND:Alternative synonymous codons are not used with equal frequencies. In addition, the contexts of codons - neighboring nucleotides and neighboring codons - can have certain patterns. The codon context can influence both translational accuracy and elongation rates. However, it is not known how strong or conserv...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-463
更新日期:2008-10-08 00:00:00
abstract:BACKGROUND:Obesity and phenotypic traits associated with this condition exhibit significant heritability in natural populations of most organisms. While a number of genes and genetic pathways have been implicated to play a role in obesity associated traits, the genetic architecture that underlies the natural variation ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-297
更新日期:2010-05-11 00:00:00
abstract:BACKGROUND:Tumor genomes are often highly heterogeneous, consisting of genomes from multiple subclonal types. Complete characterization of all subclonal types is a fundamental need in tumor genome analysis. With the advancement of next-generation sequencing, computational methods have recently been developed to infer t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S2-S1
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Citrus blight is a very important progressive decline disease of commercial citrus. The etiology is unknown, although the disease can be transmitted by root grafts, suggesting a viral etiology. Diagnosis is made by demonstrating physical blockage of xylem cells that prevents the movement of water. This test ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6339-0
更新日期:2019-12-11 00:00:00
abstract:BACKGROUND:The domestic cat (Felis catus) is an important companion animal and is used as a large animal model for human disease. However, the comprehensive study of adaptive immunity in this species is hampered by the lack of data on lymphocyte antigen receptor genes and usage. The objectives of this study were to ann...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6431-5
更新日期:2020-01-06 00:00:00
abstract:BACKGROUND:The understanding of the biological function, regulation, and cellular interactions of the yeast genome and proteome, along with the high conservation in gene function found between yeast genes and their human homologues, has allowed for Saccharomyces cerevisiae to be used as a model organism to deduce biolo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-524
更新日期:2009-11-15 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNAs that play important roles by regulating other genes. Rosa rugosa Thunb. is an important ornamental and edible plant, yet there are only a few studies on the miRNAs and their functions in R. rugosa. RESULTS:We sequenced 10 samll RNA profiles from the roots, petals...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5325-2
更新日期:2019-04-18 00:00:00
abstract:BACKGROUND:Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3782-7
更新日期:2017-05-22 00:00:00
abstract:BACKGROUND:Insect mitochondrial genomes (mitogenomes) are the most extensively used genetic marker for evolutionary and population genetics studies of insects. The Pentatomoidea superfamily is economically important and the largest superfamily within Pentatomomorpha with over 7,000 species. To better understand the div...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1679-x
更新日期:2015-06-16 00:00:00
abstract:BACKGROUND:Existing functional description of genes are categorical, discrete, and mostly through manual process. In this work, we explore the idea of gene embedding, distributed representation of genes, in the spirit of word embedding. RESULTS:From a pure data-driven fashion, we trained a 200-dimension vector represe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5370-x
更新日期:2019-02-04 00:00:00
abstract:BACKGROUND:Changes in gene regulation are thought to be crucial for the adaptation of organisms to their environment. Transcriptome analyses can be used to identify candidate genes for ecological adaptation, but can be complicated by variation in gene expression between tissues, sexes, or individuals. Here we use high-...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-654
更新日期:2012-11-21 00:00:00
abstract:BACKGROUND:Second generation sequencing has permitted detailed sequence characterisation at the whole genome level of a growing number of non-model organisms, but the data produced have short read-lengths and biased genome coverage leading to fragmented genome assemblies. The PacBio RS long-read sequencing platform off...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-670
更新日期:2013-10-01 00:00:00
abstract:BACKGROUND:Ser/Thr/Tyr kinases (STYKs) commonly found in eukaryotes have been recently reported in many bacterial species. Recent studies elucidating their cellular functions have established their roles in bacterial growth and development. However functions of a large number of bacterial STYKs still remain elusive. Th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-129
更新日期:2005-09-19 00:00:00