Regulation of microRNAs(miRNAs)on various biological processes has been a surprising and exciting field.Identification of miRNAs is the first step to comprehensively understand their functions.However,attempts on glob...Regulation of microRNAs(miRNAs)on various biological processes has been a surprising and exciting field.Identification of miRNAs is the first step to comprehensively understand their functions.However,attempts on global identification and functional verification of miRNAs are very limited in penaeid shrimp Marsupenaeus japonicus,an economically important aquatic species.By performing an integrated analysis of transcriptomic profile from gastrula embryos of M.japonicus,21conserved miRNAs in M.japonicas(mja-miRNAs),belonging to 19 miRNA families,were identified and characterized.Of the 21 mja-miRNAs,15 miRNAs were successfully verified to be predominantly expressed in gastrula stage,where they displayed dynamic expression patterns compared with those in naupliuin stage.Based on perfect or near-perfect match to target region,120 target genes were predicted at transcriptome-wide level.Noteworthy,gene ontology(GO)classification and metabolic pathway annotation revealed eight targets that were actively involved in developmental processes.Of the predicted miRNA-mRNA pairs,six targets were then randomly selected and experimentally validated by dual luciferase reporter assay,where three pairs were proved with potential targeting activity.Overall,to search for conserved miRNAs potentially involved in early development of M.japonicus,we combined in silico and experimental methods,which can be applied in other organisms as well.Our data implied important roles of miRNAs in the early embryonic development and also suggested the presence of complex miRNA-mRNA functional networks in M.japonicus.展开更多
Inflammatory bowel disease(IBD)is a complex and multifactorial disease characterized by chronic inflammation of the gastrointestinal tract,mainly manifested by the accumulation of immune cells and pro-inflammatory cyt...Inflammatory bowel disease(IBD)is a complex and multifactorial disease characterized by chronic inflammation of the gastrointestinal tract,mainly manifested by the accumulation of immune cells and pro-inflammatory cytokines in the intestinal mucosa.It is a kind of immune digestive system disease with high incidence in humans and can be divided into ulcerative colitis(UC)and Crohn's disease(CD).The pathogenesis of IBD is complex,and numerous studies have shown that genetic,environmental,microbial,immune,autophagy and other factors may be involved in the pathogenesis of IBD.MicroRNAs(miRNAs)play an important role in the pathophysiology of IBD.Studies have confirmed that miRNA play an important role in the targeted regulation of intestinal barrier homeostasis,immune response,and intestinal epithelial autophagy.MiRNA have not only been confirmed as important diagnostic biomarkers for IBD.It also shows new prospects for treatment strategies for IBD.This article mainly describes the differences in miRNA expression between UC and CD,summarizes the relationship between miRNA and intestinal barrier,immune homeostasis and autophagy mechanism in the pathogenesis of IBD,and the research progress of miRNA involved in the diagnosis and treatment of IBD,so as to provide new insights for the development of IBD.展开更多
The coronavirus disease 2019(COVID-19)coronavirus is a new strain of coronavirus that had not been previously detected in humans.As its severe pathogenicity is concerned,it is important to study it thoroughly to aid i...The coronavirus disease 2019(COVID-19)coronavirus is a new strain of coronavirus that had not been previously detected in humans.As its severe pathogenicity is concerned,it is important to study it thoroughly to aid in the discovery of a cure.In this study,the microRNAs(miRNAs)of COVID-19 were annotated to provide a powerful tool for the study of this novel coronavirus.We obtained 16 novel coronavirus genome sequences and the mature sequences of all viruses in the microRNA database(miRbase),and then used the miRNA matures sequences of the virus to perform the Basic Local Alignment Search Tool(BLAST)analysis in the coronavirus genome,extending the matched regions of approximately 20 bp to two segments by 200 bp.Six sequences were obtained after deleting redundant sequences.Then,the hairpin structures of the mature miRNAs were determined using RNAfold.The mature sequence on one hairpin arm was selected into a total of 4 sequences,and finally the relevant miRNA precursor prediction tools were used to verify whether the selected sequences are miRNA precursor sequences of the novel coronavirus.The miRNAs of the novel coronavirus were annotated by our newly developed method,which will lay the foundation for further study of this virus.展开更多
The involvement of small RNAs in cotton fiber development is under explored.The objective of this work was to directly clone,annotate,and analyze small RNAs of developing ovules to reveal
Dunaliella salina is a classic halophilic alga.However,its molecular mechanisms in response to high salinity at the post transcriptional level remain unknown.A unique halophilic alga strain,DS-CN1,was screened from fo...Dunaliella salina is a classic halophilic alga.However,its molecular mechanisms in response to high salinity at the post transcriptional level remain unknown.A unique halophilic alga strain,DS-CN1,was screened from four D.salina strains via cell biological,physiological,and biochemical methods.High-throughput sequencing of small RNAs(sRNAs)of DS-CN1 in culture medium containing 3.42-mol/L NaCl(SS group)or 0.05-mol/L NaCl(CO group)was performed on the BGISEQ-500 platform.The annotation and sequences of D.salina sRNAs were profiled.Altogether,44 novel salt stress-responsive microRNAs(miRNAs)with a relatively high C content,with the majority of them being 24 nt in length,were identified and characterized in DS-CN1.Twenty-one differentially expressed miRNAs(DEMs)in SS and CO were screened via bioinformatic analysis.A total of 319 putative salt stress-related genes targeted(104 overlapping genes)by novel miRNAs in this alga were screened based on our previous transcriptome sequencing research.Furthermore,these target genes were classified and enriched by GO and KEGG pathway analysis.Moreover,5 novel DEMs(dsa-mir3,dsa-mir16,dsa-mir17,and dsa-mir26 were significantly upregulated,and dsa-mir40 was significantly downregulated)and their corresponding 10 target genes involved in the 6 significantly enriched metabolic pathways were verified by quantitative real-time PCR.Next,their regulatory relationships were comprehensively analyzed.Lastly,a unique salt stress response metabolic network was constructed based on the novel DEM-target gene pairs.Taken together,our results suggest that 44 novel salt stress-responsive microRNAs were identified,and 4 of them might play important roles in D.salina upon salinity stress and contribute to clarify its distinctive halophilic feature.Our study will shed light on the regulatory mechanisms of salt stress responses.展开更多
基金the National Natural Science Foundation of China(No.32273116)the Natural Science Foundation of Shandong Province(China)(No.ZR2020MC189)the National Key R&D Program of China(No.2018YFD0901301)。
文摘Regulation of microRNAs(miRNAs)on various biological processes has been a surprising and exciting field.Identification of miRNAs is the first step to comprehensively understand their functions.However,attempts on global identification and functional verification of miRNAs are very limited in penaeid shrimp Marsupenaeus japonicus,an economically important aquatic species.By performing an integrated analysis of transcriptomic profile from gastrula embryos of M.japonicus,21conserved miRNAs in M.japonicas(mja-miRNAs),belonging to 19 miRNA families,were identified and characterized.Of the 21 mja-miRNAs,15 miRNAs were successfully verified to be predominantly expressed in gastrula stage,where they displayed dynamic expression patterns compared with those in naupliuin stage.Based on perfect or near-perfect match to target region,120 target genes were predicted at transcriptome-wide level.Noteworthy,gene ontology(GO)classification and metabolic pathway annotation revealed eight targets that were actively involved in developmental processes.Of the predicted miRNA-mRNA pairs,six targets were then randomly selected and experimentally validated by dual luciferase reporter assay,where three pairs were proved with potential targeting activity.Overall,to search for conserved miRNAs potentially involved in early development of M.japonicus,we combined in silico and experimental methods,which can be applied in other organisms as well.Our data implied important roles of miRNAs in the early embryonic development and also suggested the presence of complex miRNA-mRNA functional networks in M.japonicus.
基金Natural Science Foundation Project of Hainan Province(No.821QN390)。
文摘Inflammatory bowel disease(IBD)is a complex and multifactorial disease characterized by chronic inflammation of the gastrointestinal tract,mainly manifested by the accumulation of immune cells and pro-inflammatory cytokines in the intestinal mucosa.It is a kind of immune digestive system disease with high incidence in humans and can be divided into ulcerative colitis(UC)and Crohn's disease(CD).The pathogenesis of IBD is complex,and numerous studies have shown that genetic,environmental,microbial,immune,autophagy and other factors may be involved in the pathogenesis of IBD.MicroRNAs(miRNAs)play an important role in the pathophysiology of IBD.Studies have confirmed that miRNA play an important role in the targeted regulation of intestinal barrier homeostasis,immune response,and intestinal epithelial autophagy.MiRNA have not only been confirmed as important diagnostic biomarkers for IBD.It also shows new prospects for treatment strategies for IBD.This article mainly describes the differences in miRNA expression between UC and CD,summarizes the relationship between miRNA and intestinal barrier,immune homeostasis and autophagy mechanism in the pathogenesis of IBD,and the research progress of miRNA involved in the diagnosis and treatment of IBD,so as to provide new insights for the development of IBD.
基金the National Natural Science Foundation of China under Grants No.31572618 and No.31972791.
文摘The coronavirus disease 2019(COVID-19)coronavirus is a new strain of coronavirus that had not been previously detected in humans.As its severe pathogenicity is concerned,it is important to study it thoroughly to aid in the discovery of a cure.In this study,the microRNAs(miRNAs)of COVID-19 were annotated to provide a powerful tool for the study of this novel coronavirus.We obtained 16 novel coronavirus genome sequences and the mature sequences of all viruses in the microRNA database(miRbase),and then used the miRNA matures sequences of the virus to perform the Basic Local Alignment Search Tool(BLAST)analysis in the coronavirus genome,extending the matched regions of approximately 20 bp to two segments by 200 bp.Six sequences were obtained after deleting redundant sequences.Then,the hairpin structures of the mature miRNAs were determined using RNAfold.The mature sequence on one hairpin arm was selected into a total of 4 sequences,and finally the relevant miRNA precursor prediction tools were used to verify whether the selected sequences are miRNA precursor sequences of the novel coronavirus.The miRNAs of the novel coronavirus were annotated by our newly developed method,which will lay the foundation for further study of this virus.
文摘The involvement of small RNAs in cotton fiber development is under explored.The objective of this work was to directly clone,annotate,and analyze small RNAs of developing ovules to reveal
基金Supported by the National Natural Science Foundation of China(No.32170204)Science and Technology Strategy Research Special Project of Shanxi Province of China(No.202204031401051)+2 种基金the Basic Research Programs of Shanxi Province of China(No.202103021224009)the Teaching Reform and Innovation Project of Colleges and Universities in Shanxi of China(No.J20220046)the Shanxi“1331 Project”.
文摘Dunaliella salina is a classic halophilic alga.However,its molecular mechanisms in response to high salinity at the post transcriptional level remain unknown.A unique halophilic alga strain,DS-CN1,was screened from four D.salina strains via cell biological,physiological,and biochemical methods.High-throughput sequencing of small RNAs(sRNAs)of DS-CN1 in culture medium containing 3.42-mol/L NaCl(SS group)or 0.05-mol/L NaCl(CO group)was performed on the BGISEQ-500 platform.The annotation and sequences of D.salina sRNAs were profiled.Altogether,44 novel salt stress-responsive microRNAs(miRNAs)with a relatively high C content,with the majority of them being 24 nt in length,were identified and characterized in DS-CN1.Twenty-one differentially expressed miRNAs(DEMs)in SS and CO were screened via bioinformatic analysis.A total of 319 putative salt stress-related genes targeted(104 overlapping genes)by novel miRNAs in this alga were screened based on our previous transcriptome sequencing research.Furthermore,these target genes were classified and enriched by GO and KEGG pathway analysis.Moreover,5 novel DEMs(dsa-mir3,dsa-mir16,dsa-mir17,and dsa-mir26 were significantly upregulated,and dsa-mir40 was significantly downregulated)and their corresponding 10 target genes involved in the 6 significantly enriched metabolic pathways were verified by quantitative real-time PCR.Next,their regulatory relationships were comprehensively analyzed.Lastly,a unique salt stress response metabolic network was constructed based on the novel DEM-target gene pairs.Taken together,our results suggest that 44 novel salt stress-responsive microRNAs were identified,and 4 of them might play important roles in D.salina upon salinity stress and contribute to clarify its distinctive halophilic feature.Our study will shed light on the regulatory mechanisms of salt stress responses.
