Abstract:
:Amphioxus is the closest living proxy for exploring the evolutionary origin of the immune system in vertebrates. To understand the immune responses of amphioxus to lipopolysaccharide (LPS), 5 ribosomal RNA (rRNA)-depleted libraries of amphioxus were constructed, including one control (0 h) library and 4 treatment libraries at 6, 12, 24, and 48 h post-injection (hpi) with LPS. The transcriptome of Branchiostoma belcheri was analyzed using strand-specific RNA sequencing technology (RNA-seq). A total of 6161, 6665, 7969, and 6447 differentially expressed genes (DEGs) were detected at 6, 12, 24, and 48 hpi, respectively, compared with expression levels at 0 h. We identified amphioxus genes active during the acute-phase response to LPS at different time points after stimulation. Moreover, to better visualize the resolution phase of the immune process during immune response, we identified 6057 and 5235 DEGs at 48 hpi by comparing with 6 and 24 hpi, respectively. Through real-time quantitative PCR (qRT-PCR) analysis of 12 selected DEGs, we demonstrated the accuracy of the RNA-seq data in this study. Functional enrichment analysis of DEGs demonstrated that most terms were related to defense and immune responses, disease and infection, cell apoptosis, and metabolism and catalysis. Subsequently, we identified 1330, 485, 670, 911, and 1624 time-specific genes (TSGs) at 0, 6, 12, 24, and 48 hpi. Time-specific terms at each of 5 time points were primarily involved in development, immune signaling, signal transduction, DNA repair and stability, and metabolism and catalysis, respectively. As this is the first study to report the transcriptome of an organism with primitive immunity following LPS challenge at multiple time points, it provides gene expression information for further research into the evolution of immunity in vertebrates.
journal_name
RNA Bioljournal_title
RNA biologyauthors
Zhang QL,Zhu QH,Xie ZQ,Xu B,Wang XQ,Chen JYdoi
10.1080/15476286.2017.1367890subject
Has Abstractpub_date
2017-12-02 00:00:00pages
1799-1809issue
12eissn
1547-6286issn
1555-8584journal_volume
14pub_type
杂志文章相关文献
RNA Biology文献大全abstract::Alternative splicing (AS) plays a central role during cell-fate determination. However, how the core spliceosomal factors (CSFs) are involved in this process is poorly understood. Here, we report the down-regulation of the U2AF1 CSF during stem cell differentiation. To investigate its function in stemness and differen...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2020.1733800
更新日期:2020-06-01 00:00:00
abstract::The acquisition of antibiotic resistance by human pathogens poses a significant threat to public health. The mechanisms that control the proliferation and expression of antibiotic resistance genes are not yet completely understood. The aminoglycosides are a historically important class of antibiotics that were introdu...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.25757
更新日期:2013-08-01 00:00:00
abstract::RNA methylation, catalysed by a set of RNA methyltransferases (RNMTs), modulates RNA structures, properties, and biological functions. RNMTs are increasingly documented to be dysregulated in various human diseases, particularly developmental disorders and cancer. However, the genomic and transcriptomic alterations of ...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2019.1708549
更新日期:2020-04-01 00:00:00
abstract::microRNAs (miRNAs) play significant regulatory roles in gene expression at the post-transcriptional level. This includes modulating processes such as development, immunity, cancer, and host-pathogen interactions. It was recently shown that the phylogenetically deeply conserved miRNA, miR-8, plays a role in maintaining...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.25481
更新日期:2013-08-01 00:00:00
abstract::Epstein-Barr virus (EBV) was the first human cancer-causing virus to be discovered over fifty years ago. Given its relatively large genome size for a virus and hence the capacity to store more than mere protein-coding information, EBV also harbours genetic material for producing an array of distinct noncoding (nc)RNAs...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2021.1875184
更新日期:2021-01-30 00:00:00
abstract::Changing the abundance of transcripts by regulated RNA degradation is a critical step in the control of various biological pathways. Recently, genome-wide inhibitor-free technologies for determining RNA stabilities in mammalian cells have been developed. In these methods, endogenous RNAs are pulse labeled by uridine a...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.22036
更新日期:2012-10-01 00:00:00
abstract::Riboswitches are cis-encoded, cis-acting RNA elements that directly sense a physiological signal. Signal response results in a change in RNA structure that impacts gene expression. Elements of this type play an important role in bacteria, where they regulate a variety of fundamental cellular pathways. Riboswitch-media...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.7.1.10757
更新日期:2010-01-01 00:00:00
abstract::YchF is one of two universally conserved GTPases with unknown cellular function. As a first step toward elucidating YchF's cellular role, we performed a detailed biochemical characterization of the protein from Escherichia coli. Our data from fluorescence titrations not only confirmed the surprising finding that YchFE...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.22131
更新日期:2012-10-01 00:00:00
abstract::Seryl-tRNA synthetase (SerRS) catalyzes the ligation of serine to the 3'-end of serine tRNA (tRNA(Ser)), which is typical of the type-2 tRNAs characterized by a long extra arm. The SerRSs are divided into two types, the archaeal/eukaryal and bacterial types. In this study, we solved the crystal structures of the SerRS...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.5.3.6876
更新日期:2008-07-01 00:00:00
abstract::MicroRNAs are essential for spermatogenesis. However, the stage-specific requirements for particular miRNAs in the male mammalian germ line remain largely uncharacterized. The miR-34 family is, to date, the only miRNA proven to be necessary for the production of sperm in mammals, though its germline roles are poorly u...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2016.1270002
更新日期:2017-02-01 00:00:00
abstract::Myocyte enhancer factor 2c (MEF2C) is the MADS-box type transcription factor involved in the differentiation of cardiac and skeletal muscle and synaptic formation. Alternatively spliced transcripts of the MEF2C gene were proven to encode isoforms which exert distinct functions in transcriptional regulation. During the...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2015.1017213
更新日期:2015-01-01 00:00:00
abstract::5-fluorouracil (5-FU) was isolated as an inhibitor of thymidylate synthase, which is important for DNA synthesis. The drug was later found to also affect the conserved 3'-5' exoribonuclease EXOSC10/Rrp6, a catalytic subunit of the RNA exosome that degrades and processes protein-coding and non-coding transcripts. Work ...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2019.1581596
更新日期:2019-06-01 00:00:00
abstract::tRNA-dependent addition of amino acids to lipids on the outer surface of the bacterial membrane results in decreased effectiveness of antimicrobials such as cationic antimicrobial peptides (CAMPs) that target the membrane, and increased virulence of several pathogenic species. After a brief introduction to CAMPs and t...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.1080/15476286.2017.1356980
更新日期:2018-01-01 00:00:00
abstract::Alternative splicing (AS) of pre-messenger RNAs is a major process contributing to both transcriptome and proteome diversity in various physiological and pathological situations. There is also accumulating evidence that various stresses impact on AS. In particular, recent analyses of the transcriptome reveal large num...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.8.5.16016
更新日期:2011-09-01 00:00:00
abstract::Differential mRNA stability is an important mechanism for regulation of virulence factors in Streptococcus pyogenes (group A streptococcus, GAS), a serious and prevalent human pathogen. We have described 2 Classes of mRNA in GAS that are distinguishable by 1) stability in the stationary phase of growth, 2) kinetics of...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.7.5.13097
更新日期:2010-09-01 00:00:00
abstract::Circular RNAs (circRNAs) have been identified in diverse eukaryotic species and are characterized by RNA backsplicing events. Current available methods for circRNA identification are able to determine the start and end locations of circRNAs in the genome but not their full-length sequences. In this study, we developed...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2016.1245268
更新日期:2017-08-03 00:00:00
abstract::The muscle specific miRNA, miR-206, is important for the process of myogenesis; however, studying the function of miR-206 in muscle development and differentiation still proves challenging because the complement of mRNA targets it regulates remains undefined. In addition, miR-206 shares close sequence similarity to mi...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2020.1737443
更新日期:2020-07-01 00:00:00
abstract::The human genome contains some thousands of long non coding RNAs (lncRNAs). Many of these transcripts are presently considered crucial regulators of gene expression and functionally implicated in developmental processes in Eukaryotes. Notably, despite a huge number of lncRNAs are expressed in the Central Nervous Syste...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2015.1096488
更新日期:2015-01-01 00:00:00
abstract::Contributions of dietary miRNAs to circulating small RNA profiles would have profound implications for interpretation of miRNA biomarker studies: presumptive disease-specific markers might instead indicate responses to disease-associated quantitative or qualitative dietary alteration. This examination weighs the evide...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.21619
更新日期:2012-09-01 00:00:00
abstract::Prokaryotes immunize themselves against transmissible genetic elements by the integration (acquisition) in clustered regularly interspaced short palindromic repeats (CRISPR) loci of spacers homologous to invader nucleic acids, defined as protospacers. Following acquisition, mono-spacer CRISPR RNAs (termed crRNAs) guid...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.24023
更新日期:2013-05-01 00:00:00
abstract::The non-coding roX1 and roX2 RNAs are components of the MSL dosage compensation complex in Drosophila. We found that multiple species of roX2 RNA are produced by alternative splicing, with one major and at least 20 different minor forms associated with MSL proteins. The alternative forms are generated by variable usag...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.2.4.2473
更新日期:2005-10-01 00:00:00
abstract::The chromatoid body is a large perinuclear ribonucleoprotein particle of germ cells. The chromatoid body is also present in stem cells from planarians. This particle shares markers specific to protein aggresomes and P-bodies, and concentrate several RNA pathways. The assembly mechanism of chromatoid bodies is unknown,...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.6.2.8049
更新日期:2009-04-01 00:00:00
abstract::Ribonuclease P (RNase P) is a ribonucleoprotein comprised of a catalytic RNA subunit and one or several protein subunits. RNase P is best known for its role in 5'-processing of tRNA precursors. RNase P enzymes from almost all forms of life, including protein-synthesizing organelles, contain an RNase P with a conserved...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.6.4.9241
更新日期:2009-09-01 00:00:00
abstract::microRNAs (miRNAs) are critical regulators of gene expression. For elucidating functional roles of miRNAs, it is critical to identify their direct targets. There are debates about whether pulldown of biotinylated miRNA mimics can be used to identify miRNA targets or not. Here we show that biotin-labelled miR-34a can b...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2017.1391441
更新日期:2018-01-02 00:00:00
abstract::Circular RNAs (circRNAs) are closely associated with the development of non-small cell lung cancer (NSCLC); however, it is still unclear whether circular RNA circ-LDLRAD3 participated in the regulation of NSCLC progression. In this study, we found that circ-LDLRAD3 was high-expressed and miR-137 was low-expressed in N...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2020.1789819
更新日期:2020-12-01 00:00:00
abstract::Transcriptional regulation of microRNA (miRNA) expression is one of the least understood aspects of miRNA biogenesis. In C. elegans the list of miRNAs whose transcriptional control has been described in some detail is currently limited to four: let-7, lin-4, lsy-6, and mir-61. Each of these genes has been shown experi...
journal_title:RNA biology
pub_type: 杂志文章,评审
doi:10.4161/rna.6.1.7574
更新日期:2009-01-01 00:00:00
abstract::Single-stranded oligonucleotides (ssOligos) are efficiently taken up by living cells without the use of transfection reagents. This phenomenon called 'gymnosis' enables the sequence-specific silencing of target genes in various types of cells. Several antisense ssOligos are used for the treatment of human diseases. Ho...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2017.1302641
更新日期:2017-11-02 00:00:00
abstract::In an earlier report two P-transposon insertion alleles of the noncoding hsromega gene, hsromega(05241) and P292 were shown to enhance neurodegeneration caused by expression of ataxin-1 protein with expanded poly-Q in a Drosophila model. In present study, we examined the possible relation between hsromega gene express...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.3.1.2559
更新日期:2006-01-01 00:00:00
abstract::RNase J is a prokaryotic 5'-3' exo/endoribonuclease that functions in mRNA decay and rRNA maturation. Here, we report a novel duplex unwinding activity of mpy-RNase J, an archaeal RNase J from Methanolobus psychrophilus, which enables it to degrade duplex RNAs with hairpins up to 40 bp when linking a 5' single-strande...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.1080/15476286.2020.1777379
更新日期:2020-10-01 00:00:00
abstract::Two different isolates of the myxomycete Didymium iridis harbour homing endonuclease genes that are expressed from group I introns inserted into identical sites within the small subunit ribosomal DNA. The homing endonuclease proteins are related in sequence, and their gene structures share similar features such as the...
journal_title:RNA biology
pub_type: 杂志文章
doi:10.4161/rna.3.4.3958
更新日期:2006-10-01 00:00:00