Flower development plays vital role in horticultural plants.Post-transcriptional regulation via small RNAs is important for plant flower development.To uncover post-transcriptional regulatory networks during the flowe...Flower development plays vital role in horticultural plants.Post-transcriptional regulation via small RNAs is important for plant flower development.To uncover post-transcriptional regulatory networks during the flower development in Dimocarpus longan Lour.‘Shixia’,an economically important fruit crop in subtropical regions,we collected and analyzed sRNA deep-sequencing datasets and degradome libraries Apart from identifying miRNAs and phased siRNA generating loci(PHAS loci),120 hairpin loci,producing abundant sRNAs,were identified by in-house protocols.Our results suggested that 56 miRNA-target pairs,2221-nt-PHAS loci,and 111 hairpin loci are involved in posttranscriptional gene silencing during longan reproductive development.Lineage-specific or species-specific post-transcriptional regulatory modules have been unveiled,including miR482-PHAS and miRN15.miR482-PHAS might be involved in longan flower development beyond their conserved roles in plant defense,and miRN15 is a novel miRNA likely associated with a hairpin locus(HPL-056)to regulate strigolactone receptor gene DWARF14(D14)and the biogenesis of phasiRNAs from D14.These small RNAs are enriched in flower buds,suggesting they are likely involved in post-transcriptional regulatory networks essential for longan flower development via the strigolactone signaling pathway.展开更多
Transfer RNA(t RNA)-derived small RNAs(ts RNAs) are a recently established family of regulatory small non-coding RNAs that modulate diverse biological processes. Growing evidence indicates that ts RNAs are involved in...Transfer RNA(t RNA)-derived small RNAs(ts RNAs) are a recently established family of regulatory small non-coding RNAs that modulate diverse biological processes. Growing evidence indicates that ts RNAs are involved in neurological disorders and play a role in the pathogenesis of neurodegenerative disease. However, whether ts RNAs are involved in traumatic brain injury-induced secondary injury remains poorly understood. In this study, a mouse controlled cortical impact model of traumatic brain injury was established, and integrated ts RNA and messenger RNA(m RNA) transcriptome sequencing were used. The results revealed that 103 ts RNAs were differentially expressed in the mouse model of traumatic brain injury at 72 hours, of which 56 ts RNAs were upregulated and 47 ts RNAs were downregulated. Based on micro RNA-like seed matching and Pearson correlation analysis, 57 differentially expressed ts RNA-m RNA interaction pairs were identified, including 29 ts RNAs and 26 m RNAs. Moreover, Gene Ontology annotation of target genes revealed that the significantly enriched terms were primarily associated with inflammation and synaptic function. Collectively, our findings suggest that ts RNAs may be associated with traumatic brain injury-induced secondary brain injury, and are thus a potential therapeutic target for traumatic brain injury. The study was approved by the Beijing Neurosurgical Institute Animal Care and Use Committee(approval No. 20190411) on April 11, 2019.展开更多
Small RNAs are non-coding RNA molecules with 20-30 nucleotides （nt） in length that mainly play regulatory roles in gene expression at the post-transcription level by directly cutting target mRNA or inhibiting its tr...Small RNAs are non-coding RNA molecules with 20-30 nucleotides （nt） in length that mainly play regulatory roles in gene expression at the post-transcription level by directly cutting target mRNA or inhibiting its translation. Small RNAs play regulatory roles in the growth and development process of plants at the core of gene regulatory networks, which has been widely studied and confirmed in sporophyte generation of plants. However, few researches have been conducted on small RNAs and gametophyte generation. It is reported that small RNAs play important roles in floral organ development, gametogenesis, fertilization, and early zygotic development of plants. In addition, various small RNAs also play roles in controlling genetic integrity, cell differentiation and functions during the sexual reproduction process of plants. However, most of the specific functions of small RNAs in the sexual reproduction process are unknown yet. This study mainly aimed to introduce small RNAs in plants, summarize the latest advances in researches of small RNAs and plant sexual reproduction, and make prospect on its future.展开更多
AIM： To investigate the positive rate and types of cells that express Epstein-Barr virus-encoded small RNAs （EBERs） and to determine the distribution of EBER-expressing cells in idiopathic orbital inflammatory pseu...AIM： To investigate the positive rate and types of cells that express Epstein-Barr virus-encoded small RNAs （EBERs） and to determine the distribution of EBER-expressing cells in idiopathic orbital inflammatory pseudotumor （IOIP） tissues. METHODS： We retrospectively examined 40 archived paraffin specimens from two teaching hospitals in Southern China between January 2007 and January 2015 that were pathologically determined to exhibit IOIP. Eleven concurrent paraffin specimens of thyroid-associated ophthalmopathy （TAO） composed the control group. In situ hybridization was performed to detect EBERs. Immunohistochemistry was employed to detect CD3, CD20, Vimentin, and smooth muscle actin （SMA）, and the positive rate, types of positive cells, and distribution and location of EBERs were evaluated. RESULTS： The positive expression rate of EBERs was 47.5% （19/40） in the IOIP group, which was significantly higher than that in the TAO group [0 （0/11）, P=-0.011]. in the IOIP group, the lymphocyte infiltrative subtype, fibrotic subtype, and mixed subtype exhibited EBER-positive rates of 57.1% （12121）, 12.5% （118）, and 54.5% （6/11）, respectively, and no significant differences were found between these subtypes （P=0.085）. Positive signals of EBERs were mainly present in medium-small lymphocytes between or around follicles and in the nuclei of activated immunoblasts （14/19）. CONCLUSION： The positive rate, types, and distribution of EBER-expressing cells in IOIP have been documented.These findings are conducive for a better understanding of the underlying mechanisms of Epstein-Barr virus infection in IOIP pathogenesis.展开更多
Bacterial quorum sensing （QS） has attracted much interests and it is an important process of cell communication. Recently, Bassler et al. studied the phenomena of QS regulated by small RNAs and the experimental data...Bacterial quorum sensing （QS） has attracted much interests and it is an important process of cell communication. Recently, Bassler et al. studied the phenomena of QS regulated by small RNAs and the experimental data showed that smafl RNAs played important role in the QS of Vibrio harveyi and it can permit the fine-tuning of gene regulation and mmntenance of homeostasis. According to Michaelis-Menten kinetics and mass action law in this paper, we construct a mathematical model to investigate the mechanism induced QS by coexist of small RNA and signal molecular （AI） and show that there are periodic oscillation when the time delay and Hill coefficient exceed a critical value and the periodic oscillation produces the change of concentration and induces QS. These results are fit to the experimental results. In the meanwhile, we also get some theoretical value of Hopf Bifurcation on time deday. In addition, we also find this network is robust against noise.展开更多
Small RNAs in Penicillium digitatum were identified and analyzed via transcriptome sequencing on the BGISEQ-500 platform. A total of 15 predicted miRNAs and 10718 novel siRNAs were found. Their length distribution, se...Small RNAs in Penicillium digitatum were identified and analyzed via transcriptome sequencing on the BGISEQ-500 platform. A total of 15 predicted miRNAs and 10718 novel siRNAs were found. Their length distribution, sequence, predicted construction, base bias, expression levels and potential targets were determined as well. Through pathway and KEGG enrichment analysis, the miRNA target genes were mostly involved in carbohydrate metabolism, transport and catabolism, translation and amino acid metabolism. The target genes involved in aflatoxin biosynthesis and proteasome had a higher rich factor value. The results will provide a theoretical foundation for understanding the developmental and pathogenic mechanisms of P. digitatum at the transcriptional level.展开更多
RNA silencing is a fundamental plant defence and gene control mechanism in plants that are directed by 20-24 nucleotide （nt） small interfering RNA （siRNA） and microRNA （miRNA）. Infection of plants with viral pat...RNA silencing is a fundamental plant defence and gene control mechanism in plants that are directed by 20-24 nucleotide （nt） small interfering RNA （siRNA） and microRNA （miRNA）. Infection of plants with viral pathogens or transformation of plants with RNA interference （RNAi） constructs is usually associated with high levels of exogenous siRNAs, but it is unclear if these siRNAs interfere with endogenous small RNA pathways and hence affect plant development. Here we provide evidence that viral satellite RNA （satRNA） infection does not affect siRNA and miRNA biogenesis or plant growth despite the extremely high level of satRNA-derived siRNAs. We generated transgenic Nicotiana benthamiana plants that no longer develop the specific yellowing symptoms generally associated with infection by Cucumber mosaic virus （CMV） Y-satellite RNA （Y-Sat）. We then used these plants to show that CMV Y-Sat infection did not cause any visible phenotypic changes in comparison to uninfected plants, despite the presence of high-level Y-Sat siRNAs. Furthermore, we showed that the accumulation of hairpin RNA （hpRNA）-derived siRNAs or miRNAs, and the level of siRNA-directed transgene silencing, are not significantly affected by CMV Y-Sat infection. Taken together, our results suggest that the high levels of exogenous siRNAs associated with viral infection or RNAi-inducing transgenes do not saturate the endogenous RNA silencing machineries and have no significant impact on normal plant development.展开更多
supported by the Specialized Research Fund for the Doctoral Program of Higher Education of China （20134320120013）;the Natural Science Foundation of Hunan Province, China （14JJ3095）
Noncoding small RNAs(sRNAs)packaged in bacterial outer membrane vesicles(OMVs)function as novel mediators of interspecies communication.While the role of bacterial sRNAs in enhancing virulence is well established,the ...Noncoding small RNAs(sRNAs)packaged in bacterial outer membrane vesicles(OMVs)function as novel mediators of interspecies communication.While the role of bacterial sRNAs in enhancing virulence is well established,the role of sRNAs in the interaction between OMVs from phytopathogenic bacteria and their host plants remains unclear.In this study,we employ RNA sequencing to characterize differentially pack-aged sRNAs in OMVs of the phytopathogen Xanthomonas oryzae pv.oryzicola(Xoc).Our candidate sRNA(Xosr001)was abundant in OMVs and involved in the regulation of OsJMT1 to impair host stomatal immu-nity.Xoc loads Xosr001 into OMVs,which are specifically ttransferred into the mechanical tissues of rice leaves.Xosr001 suppresses OsJMT1 transcript accumulation in vivo,leading to a reduction in MeJA accu-mulation in rice leaves.Furthermore,the application of synthesized Xosr001 sRNA to the leaves of OsJMT1-HA-OE transgenic line results in the suppression of OsJMT1 expression by Xosr001.Notably,the OsJMT1-HA-OE transgenic line exhibited attenuated stomatal immunity and disease susceptibility upon infection with DXosr001 compared to Xoc.These results suggest that Xosr001 packaged in Xoc OMVs functions to suppress stomatal immunity in rice.展开更多
Small non-coding RNAs are potential diagnostic biomarkers for lung cancer. Mitochondria-derived small RNA (mtRNA) is a novel regulatory small non-coding RNA that only recently has been identified and cataloged. Curren...Small non-coding RNAs are potential diagnostic biomarkers for lung cancer. Mitochondria-derived small RNA (mtRNA) is a novel regulatory small non-coding RNA that only recently has been identified and cataloged. Currently, there are no reports of studies of mtRNA in human lung cancer. Currently, normalization methods are unstable, and they often fail to identify differentially expressed small non-coding RNAs (sncRNAs). In order to identify reliable biomarkers for lung cancer screening, we used a ratio-based method using mtRNAs newly discovered in human peripheral blood mononuclear cells. In the discovery cohort (AUC = 0.981) and independent validation cohort (AUC = 0.916) the prediction model of eight mtRNA ratios distinguished lung cancer patients from controls. The prediction model will provide reliable biomarkers that will allow blood-based screening to become more feasible and will help make lung cancer diagnosis more accurate in clinical practice.展开更多
Small nucleolar RNAs(snoRNAs)represent a class of non-coding RNAs that play pivotal roles in post-transcriptional RNA processing and modification,thereby contributing significantly to the maintenance of cellular funct...Small nucleolar RNAs(snoRNAs)represent a class of non-coding RNAs that play pivotal roles in post-transcriptional RNA processing and modification,thereby contributing significantly to the maintenance of cellular functions related to protein synthesis.SnoRNAs have been discovered to possess the ability to influence cell fate and alter disease progression,holding immense potential in controlling human diseases.It is suggested that the dysregulation of snoRNAs in cancer exhibits differential expression across various cancer types,stages,metastasis,treatment response and/or prognosis in patients.On the other hand,colorectal cancer(CRC),a prevalent malignancy of the digestive system,is characterized by high incidence and mortality rates,ranking as the third most common cancer type.Recent research indicates that snoRNA dysregulation is associated with CRC,as snoRNA expression significantly differs between normal and cancerous conditions.Consequently,assessing snoRNA expression level and function holds promise for the prognosis and diagnosis of CRC.Nevertheless,current comprehension of the potential roles of snoRNAs in CRC remains limited.This review offers a comprehensive survey of the aberrant regulation of snoRNAs in CRC,providing valuable insights into the discovery of novel biomarkers,therapeutic targets,and potential tools for the diagnosis and treatment of CRC and furnishing critical cues for advancing research into CRC and the judicious selection of therapeutic targets.展开更多
Objective:To give a brief overview of the field of epigenetics and the potential predictive power that small non-coding RNA(sncRNA)may hold in relation to improving the treatment and diagnosis of male infertility.Meth...Objective:To give a brief overview of the field of epigenetics and the potential predictive power that small non-coding RNA(sncRNA)may hold in relation to improving the treatment and diagnosis of male infertility.Methods:PRISMA-ScR was used as the scoping review guideline for this investigation.All article data here have been accessed from MEDLINE–PubMed,Science Direct,EBSCO,Scopus,Sage Journals,and Google Scholar.The terms"small non coding RNA,male,infertility,miRNA,sperm"were used in the search between 2015 and 2023.Results:The study comprised 35 publications in total.Several sncRNAs,miR-155,miR-16,miR-196,miR-525-3p,miR-891 were found to be effective in regulating the mechanism of spermatozoa processing in the infertility of men.sncRNA can be used as a biomarker of male infertility.Conclusions:sncRNAs can act as biomarkers for the diagnosis of reproductive diseases.Actually,by recognizing sncRNAs and their mechanisms,a new way to treat infertile men would be paved.The functional annotation of sncRNAs in spermatogenesis is still in its infancy but has enormous potential.This is despite the fact that many potential sncRNAs have been found to date with the use of cutting-edge technology and publicly accessible sncRNA annotation tools.展开更多
Small non-coding RNAs(sncRNAs),such as microRNAs(miRNAs),small interfering RNAs(siRNAs),PIWIinteracting RNAs(piRNAs),and transfer RNA(tRNA)-derived small RNAs(tsRNAs),play essential roles in regulating various cellula...Small non-coding RNAs(sncRNAs),such as microRNAs(miRNAs),small interfering RNAs(siRNAs),PIWIinteracting RNAs(piRNAs),and transfer RNA(tRNA)-derived small RNAs(tsRNAs),play essential roles in regulating various cellular and developmental processes.Over the past three decades,researchers have identified novel sncRNA species from various organisms.These molecules demonstrate dynamic expression and diverse functions,and they are subject to intricate regulation through RNA modifications in both healthy and diseased states.Notably,certain sncRNAs in gametes,particularly sperm,respond to environmental stimuli and facilitate epigenetic inheritance.Collectively,the in-depth understanding of sncRNA functions and mechanisms has accelerated the development of small RNA-based therapeutics.In this review,we present the recent advances in the field,including new sncRNA species and the regulatory influences of RNA modifications.We also discuss the current limitations and challenges associated with using small RNAs as either biomarkers or therapeutic drugs.展开更多
Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and hap...Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and haplotype.Methods:Thirty-nine blood samples infected with P.knowlesi were collected in Sabah,Malaysian Borneo and Peninsular Malaysia.The S-type SSU rRNA gene was amplified using polymerase chain reaction,cloned into a vector,and sequenced.The natural selection and haplotype of the S-type SSU rRNA gene sequences were determined using DnaSP v6 and illustrated using NETWORK v10.This study's 39 S-type SSU rRNA sequences and eight sequences from the Genbank database were subjected to phylogenetic analysis using MEGA 11.Results:Overall,the phylogenetic analysis showed no evidence of a geographical cluster of P.knowlesi isolates from different areas in Malaysia based on the S-type SSU rRNA gene sequences.The S-type SSU rRNA gene sequences were relatively conserved and with a purifying effect.Haplotype sharing of the S-type SSU rRNA gene was observed between the P.knowlesi isolates in Sabah,Malaysian Borneo,but not between Sabah,Malaysian Borneo and Peninsular Malaysia.Conclusions:This study suggests that the S-type SSU rRNA gene of P.knowlesi isolates in Sabah,Malaysian Borneo,and Peninsular Malaysia has fewer polymorphic sites,representing the conservation of the gene.These features make the S-type SSU rRNA gene suitable for comparative studies,such as determining the evolutionary relationships and common ancestry among P.knowlesi species.展开更多
This editorial reviews the molecular mechanisms underlying the roles of the long non-coding RNA(lncRNA)small nucleolar RNA host gene 16(SNHG16)in digestive system cancers based on two recent studies on lncRNAs in dige...This editorial reviews the molecular mechanisms underlying the roles of the long non-coding RNA(lncRNA)small nucleolar RNA host gene 16(SNHG16)in digestive system cancers based on two recent studies on lncRNAs in digestive system tumors.The first study,by Zhao et al,explored how hBD-1 affects colon cancer,via the lncRNA TCONS_00014506,by inhibiting mTOR and promoting autophagy.The second one,by Li et al,identified the lncRNA prion protein testis specific(PRNT)as a factor in oxaliplatin resistance by sponging ZNF184 to regulate HIPK2 and influence colorectal cancer progression and chemoresistance,suggesting PRNT as a potential therapeutic target for colorectal cancer.Both of these two articles discuss the mechanisms by which lncRNAs contribute to the development and progression of digestive system cancers.As a recent research hotspot,SNHG16 is a typical lncRNA that has been extensively studied for its association with digestive system cancers.The prevailing hypothesis is that SNHG16 participates in the development and progression of digestive system tumors by acting as a competing endogenous RNA,interacting with other proteins,regulating various genes,and affecting downstream target molecules.This review systematically examines the recently reported biological functions,related molecular mechanisms,and potential clinical significance of SNHG16 in various digestive system cancers,and explores the relationship between SNHG16 and digestive system cancers.The findings suggest that SNHG16 may serve as a potential biomarker and therapeutic target for human digestive system cancers.展开更多
Due to global climate change, temperature stress has become one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms in plants, particularly ...Due to global climate change, temperature stress has become one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms in plants, particularly in the identification of temperature stress responsive protein-coding genes. Recently discovered micro RNAs(mi RNAs) and endogenous small-interfering RNAs(si RNAs) have also been demonstrated as simportant players in plant temperature stress response.Using high-throughput sequencing, many small RNAs,especially mi RNAs, have been identified to be triggered by cold or heat. Subsequently, several studies have shown an important functional role for these small RNAs in cold or heat tolerance. These findings greatly broaden our understanding of endogenous small RNAs in plant stress response control. Here, we highlight new findings regarding the roles of mi RNAs and si RNAs in plant temperature stress response and acclimation. We also review the current understanding of the regulatory mechanisms of small RNAs in temperature stress response, and explore the outlook for the use of these small RNAs in molecular breeding for improvement of temperature stress tolerance in plants.展开更多
The continuing discoveries of novel classes of RNA modifications in various organisms have raised the need for improving sensitive,convenient,and reliable methods for quantifying RNA modifications.In particular,a subs...The continuing discoveries of novel classes of RNA modifications in various organisms have raised the need for improving sensitive,convenient,and reliable methods for quantifying RNA modifications.In particular,a subset of small RNAs,including microRNAs(miRNAs)and Piwi-interacting RNAs(piRNAs),are modified at their 3'-terminal nucleotides via 2'-0-methylation.However,quantifying the levels of these small RNAs is difficult because 2'-0-methylation at the RNA 3'-terminus inhibits the activity of polyadenylate polymerase and T4 RNA ligase.These two enzymes are indispensable for RNA labeling or ligation in conventional miRNA quantification assays.In this study,we profiled 3'-terminal 2'-0-methyl plant miRNAs in the livers of rice-fed mice by oxidative deep sequencing and detected increasing amounts of plant miRNAs with prolonged oxidation treatment.We further compared the efficiency of stem-loop and poly(A)-tailed RT-qPCR in quantifying plant miRNAs in animal tissues and identified stem-loop RT-qPCR as the only suitable approach.Likewise,stem-loop RT-qPCR was superior to poly(A)-tailed RT-qPCR in quantifying 3'-terminal 2'-0-methyl piRNAs in human seminal plasma.In summary,this study established a standard procedure for quantifying the levels of 3'-terminal 2'-0-methyl miRNAs in plants and piRNAs.Accurate measurement of the 3'-terminal 2'-0-methylation of small RNAs has profound implications for understanding their pathophysiologic roles in biological systems.展开更多
DNA double-strand break （DSB） is the most deleterious form of DNA damage and poses great threat to genome stability. Eu- karyotes have evolved complex mechanisms to repair DSBs through coordinated actions of protein...DNA double-strand break （DSB） is the most deleterious form of DNA damage and poses great threat to genome stability. Eu- karyotes have evolved complex mechanisms to repair DSBs through coordinated actions of protein sensors, transducers, and effectors. DSB-induced small RNAs （diRNAs） or Dicer/Drosha-dependent RNAs （DDRNAs） have been recently discovered in plants and vertebrates, adding an unsuspected RNA component into the DSB repair pathway. DiRNAs/DDRNAs control DNA damage response （DDR） activation by affecting DDR loci formation and cell cycle checkpoint enforcement and are required for efficient DSB repair. Here, we summarize the findings of diRNAs/DDRNAs and discuss the possible mechanisms through which they act to facilitate DSB repair.展开更多
In plants, non-coding small RNAs play a vital role in plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate （JA） pathway, we compared the no...In plants, non-coding small RNAs play a vital role in plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate （JA） pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. Thirty new miRNAs and 27 new miRNA candidates were identified through bioinformatics approach. Forty-nine known miRNAs （belonging to 24 families）, 15 new miRNAs and new miRNA candidates （belonging to 11 families） and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs （belonging to 9 families） were repressed by JA.展开更多
基金funded by the National Key Research and Developmental Program of China(Grant No.2018YFD1000104)supported by awards from the National Natural Science Foundation of China(Grant Nos.32002009 and 32072547)The Special Support Program of Guangdong Province(Grant No.2019TX05N193).
文摘Flower development plays vital role in horticultural plants.Post-transcriptional regulation via small RNAs is important for plant flower development.To uncover post-transcriptional regulatory networks during the flower development in Dimocarpus longan Lour.‘Shixia’,an economically important fruit crop in subtropical regions,we collected and analyzed sRNA deep-sequencing datasets and degradome libraries Apart from identifying miRNAs and phased siRNA generating loci(PHAS loci),120 hairpin loci,producing abundant sRNAs,were identified by in-house protocols.Our results suggested that 56 miRNA-target pairs,2221-nt-PHAS loci,and 111 hairpin loci are involved in posttranscriptional gene silencing during longan reproductive development.Lineage-specific or species-specific post-transcriptional regulatory modules have been unveiled,including miR482-PHAS and miRN15.miR482-PHAS might be involved in longan flower development beyond their conserved roles in plant defense,and miRN15 is a novel miRNA likely associated with a hairpin locus(HPL-056)to regulate strigolactone receptor gene DWARF14(D14)and the biogenesis of phasiRNAs from D14.These small RNAs are enriched in flower buds,suggesting they are likely involved in post-transcriptional regulatory networks essential for longan flower development via the strigolactone signaling pathway.
基金supported by grants from the National Natural Science Foundation of China,Nos.81471238,81771327Construction of Central Nervous System Injury Basic Science and Clinical Translational Research Platform,Budget of Beijing Municipal Health Commission 2020,No.PXM2020_026280_000002(all to BYL)。
文摘Transfer RNA(t RNA)-derived small RNAs(ts RNAs) are a recently established family of regulatory small non-coding RNAs that modulate diverse biological processes. Growing evidence indicates that ts RNAs are involved in neurological disorders and play a role in the pathogenesis of neurodegenerative disease. However, whether ts RNAs are involved in traumatic brain injury-induced secondary injury remains poorly understood. In this study, a mouse controlled cortical impact model of traumatic brain injury was established, and integrated ts RNA and messenger RNA(m RNA) transcriptome sequencing were used. The results revealed that 103 ts RNAs were differentially expressed in the mouse model of traumatic brain injury at 72 hours, of which 56 ts RNAs were upregulated and 47 ts RNAs were downregulated. Based on micro RNA-like seed matching and Pearson correlation analysis, 57 differentially expressed ts RNA-m RNA interaction pairs were identified, including 29 ts RNAs and 26 m RNAs. Moreover, Gene Ontology annotation of target genes revealed that the significantly enriched terms were primarily associated with inflammation and synaptic function. Collectively, our findings suggest that ts RNAs may be associated with traumatic brain injury-induced secondary brain injury, and are thus a potential therapeutic target for traumatic brain injury. The study was approved by the Beijing Neurosurgical Institute Animal Care and Use Committee(approval No. 20190411) on April 11, 2019.
基金Supported by National Natural Science Foundation of China(30971986)Specialized Research Fund for the Doctoral Program of Higher Education of China(20110182110013)Doctoral Fund of Southwestern University(SWU111016)~~
文摘Small RNAs are non-coding RNA molecules with 20-30 nucleotides （nt） in length that mainly play regulatory roles in gene expression at the post-transcription level by directly cutting target mRNA or inhibiting its translation. Small RNAs play regulatory roles in the growth and development process of plants at the core of gene regulatory networks, which has been widely studied and confirmed in sporophyte generation of plants. However, few researches have been conducted on small RNAs and gametophyte generation. It is reported that small RNAs play important roles in floral organ development, gametogenesis, fertilization, and early zygotic development of plants. In addition, various small RNAs also play roles in controlling genetic integrity, cell differentiation and functions during the sexual reproduction process of plants. However, most of the specific functions of small RNAs in the sexual reproduction process are unknown yet. This study mainly aimed to introduce small RNAs in plants, summarize the latest advances in researches of small RNAs and plant sexual reproduction, and make prospect on its future.
基金Supported by the National Natural Science Foundation of China(No.81260149No.81360152+2 种基金No.81560162)Guangxi Natural Science Foundation(No.2016GXNSFAA380301)Youth Science Foundation of Guangxi Medical University(No.GXMUYSF2014040)
文摘AIM： To investigate the positive rate and types of cells that express Epstein-Barr virus-encoded small RNAs （EBERs） and to determine the distribution of EBER-expressing cells in idiopathic orbital inflammatory pseudotumor （IOIP） tissues. METHODS： We retrospectively examined 40 archived paraffin specimens from two teaching hospitals in Southern China between January 2007 and January 2015 that were pathologically determined to exhibit IOIP. Eleven concurrent paraffin specimens of thyroid-associated ophthalmopathy （TAO） composed the control group. In situ hybridization was performed to detect EBERs. Immunohistochemistry was employed to detect CD3, CD20, Vimentin, and smooth muscle actin （SMA）, and the positive rate, types of positive cells, and distribution and location of EBERs were evaluated. RESULTS： The positive expression rate of EBERs was 47.5% （19/40） in the IOIP group, which was significantly higher than that in the TAO group [0 （0/11）, P=-0.011]. in the IOIP group, the lymphocyte infiltrative subtype, fibrotic subtype, and mixed subtype exhibited EBER-positive rates of 57.1% （12121）, 12.5% （118）, and 54.5% （6/11）, respectively, and no significant differences were found between these subtypes （P=0.085）. Positive signals of EBERs were mainly present in medium-small lymphocytes between or around follicles and in the nuclei of activated immunoblasts （14/19）. CONCLUSION： The positive rate, types, and distribution of EBER-expressing cells in IOIP have been documented.These findings are conducive for a better understanding of the underlying mechanisms of Epstein-Barr virus infection in IOIP pathogenesis.
基金Supported by National Natural Science Foundation of China under Grant Nos. 10802043 and 10832006, Program for Science ＆ Technology Innovation Talents in Universities of Henan under Grant No. 2009HASTIT033 and Key Disciplines of Shanghai municipality （$30104）
文摘Bacterial quorum sensing （QS） has attracted much interests and it is an important process of cell communication. Recently, Bassler et al. studied the phenomena of QS regulated by small RNAs and the experimental data showed that smafl RNAs played important role in the QS of Vibrio harveyi and it can permit the fine-tuning of gene regulation and mmntenance of homeostasis. According to Michaelis-Menten kinetics and mass action law in this paper, we construct a mathematical model to investigate the mechanism induced QS by coexist of small RNA and signal molecular （AI） and show that there are periodic oscillation when the time delay and Hill coefficient exceed a critical value and the periodic oscillation produces the change of concentration and induces QS. These results are fit to the experimental results. In the meanwhile, we also get some theoretical value of Hopf Bifurcation on time deday. In addition, we also find this network is robust against noise.
文摘Small RNAs in Penicillium digitatum were identified and analyzed via transcriptome sequencing on the BGISEQ-500 platform. A total of 15 predicted miRNAs and 10718 novel siRNAs were found. Their length distribution, sequence, predicted construction, base bias, expression levels and potential targets were determined as well. Through pathway and KEGG enrichment analysis, the miRNA target genes were mostly involved in carbohydrate metabolism, transport and catabolism, translation and amino acid metabolism. The target genes involved in aflatoxin biosynthesis and proteasome had a higher rich factor value. The results will provide a theoretical foundation for understanding the developmental and pathogenic mechanisms of P. digitatum at the transcriptional level.
基金funded by MOA’s Public Benefi t Research Foundation of China (201203076)the grants from the National Key Technology R&D Program (2007BAD47B03)the project from Prof. Wang Mingbo was supported by an Australian Research Council Future Fellowship (FT0991956)
文摘RNA silencing is a fundamental plant defence and gene control mechanism in plants that are directed by 20-24 nucleotide （nt） small interfering RNA （siRNA） and microRNA （miRNA）. Infection of plants with viral pathogens or transformation of plants with RNA interference （RNAi） constructs is usually associated with high levels of exogenous siRNAs, but it is unclear if these siRNAs interfere with endogenous small RNA pathways and hence affect plant development. Here we provide evidence that viral satellite RNA （satRNA） infection does not affect siRNA and miRNA biogenesis or plant growth despite the extremely high level of satRNA-derived siRNAs. We generated transgenic Nicotiana benthamiana plants that no longer develop the specific yellowing symptoms generally associated with infection by Cucumber mosaic virus （CMV） Y-satellite RNA （Y-Sat）. We then used these plants to show that CMV Y-Sat infection did not cause any visible phenotypic changes in comparison to uninfected plants, despite the presence of high-level Y-Sat siRNAs. Furthermore, we showed that the accumulation of hairpin RNA （hpRNA）-derived siRNAs or miRNAs, and the level of siRNA-directed transgene silencing, are not significantly affected by CMV Y-Sat infection. Taken together, our results suggest that the high levels of exogenous siRNAs associated with viral infection or RNAi-inducing transgenes do not saturate the endogenous RNA silencing machineries and have no significant impact on normal plant development.
基金supported by the Specialized Research Fund for the Doctoral Program of Higher Education of China (20134320120013)the Natural Science Foundation of Hunan Province, China (14JJ3095)
文摘supported by the Specialized Research Fund for the Doctoral Program of Higher Education of China （20134320120013）;the Natural Science Foundation of Hunan Province, China （14JJ3095）
基金supported by the National Natural Science Foundation of China (32272479,32200142)Open Project Program of State Key Laboratory of Rice Biology (20190109)+3 种基金Open Project Program of State Key Laboratory for Biology of Plant Diseases and Insect Pests (SKLOF202201)Zhejiang Province Ecological Environment Research and Promotion Project (2020HT0009)Shanghai Committee of Science and Technology (19390743300 and 21ZR1435500)Chongqing Natural Science Foundation (CSTB2022NSCQ-MSX0524).
文摘Noncoding small RNAs(sRNAs)packaged in bacterial outer membrane vesicles(OMVs)function as novel mediators of interspecies communication.While the role of bacterial sRNAs in enhancing virulence is well established,the role of sRNAs in the interaction between OMVs from phytopathogenic bacteria and their host plants remains unclear.In this study,we employ RNA sequencing to characterize differentially pack-aged sRNAs in OMVs of the phytopathogen Xanthomonas oryzae pv.oryzicola(Xoc).Our candidate sRNA(Xosr001)was abundant in OMVs and involved in the regulation of OsJMT1 to impair host stomatal immu-nity.Xoc loads Xosr001 into OMVs,which are specifically ttransferred into the mechanical tissues of rice leaves.Xosr001 suppresses OsJMT1 transcript accumulation in vivo,leading to a reduction in MeJA accu-mulation in rice leaves.Furthermore,the application of synthesized Xosr001 sRNA to the leaves of OsJMT1-HA-OE transgenic line results in the suppression of OsJMT1 expression by Xosr001.Notably,the OsJMT1-HA-OE transgenic line exhibited attenuated stomatal immunity and disease susceptibility upon infection with DXosr001 compared to Xoc.These results suggest that Xosr001 packaged in Xoc OMVs functions to suppress stomatal immunity in rice.
基金supported by the National Institutes of Health(NIH)grants 1R01CA223490,5P30GM114737,5P20GM103466,5U54MD007601,5P30CA071789,1R01CA230514,U54CA143727 and P20GM139753.
文摘Small non-coding RNAs are potential diagnostic biomarkers for lung cancer. Mitochondria-derived small RNA (mtRNA) is a novel regulatory small non-coding RNA that only recently has been identified and cataloged. Currently, there are no reports of studies of mtRNA in human lung cancer. Currently, normalization methods are unstable, and they often fail to identify differentially expressed small non-coding RNAs (sncRNAs). In order to identify reliable biomarkers for lung cancer screening, we used a ratio-based method using mtRNAs newly discovered in human peripheral blood mononuclear cells. In the discovery cohort (AUC = 0.981) and independent validation cohort (AUC = 0.916) the prediction model of eight mtRNA ratios distinguished lung cancer patients from controls. The prediction model will provide reliable biomarkers that will allow blood-based screening to become more feasible and will help make lung cancer diagnosis more accurate in clinical practice.
基金the National Natural Science Foundation of China,No.82273457Guangdong Basic and Applied Basic Research Foundation,No.2021A1515012180 and No.2023A1515012762+1 种基金Special Grant for Key Area Programs of Guangdong Department of Education,No.2021ZDZX2040and Science and Technology Special Project of Guangdong Province,No.210715216902829.
文摘Small nucleolar RNAs(snoRNAs)represent a class of non-coding RNAs that play pivotal roles in post-transcriptional RNA processing and modification,thereby contributing significantly to the maintenance of cellular functions related to protein synthesis.SnoRNAs have been discovered to possess the ability to influence cell fate and alter disease progression,holding immense potential in controlling human diseases.It is suggested that the dysregulation of snoRNAs in cancer exhibits differential expression across various cancer types,stages,metastasis,treatment response and/or prognosis in patients.On the other hand,colorectal cancer(CRC),a prevalent malignancy of the digestive system,is characterized by high incidence and mortality rates,ranking as the third most common cancer type.Recent research indicates that snoRNA dysregulation is associated with CRC,as snoRNA expression significantly differs between normal and cancerous conditions.Consequently,assessing snoRNA expression level and function holds promise for the prognosis and diagnosis of CRC.Nevertheless,current comprehension of the potential roles of snoRNAs in CRC remains limited.This review offers a comprehensive survey of the aberrant regulation of snoRNAs in CRC,providing valuable insights into the discovery of novel biomarkers,therapeutic targets,and potential tools for the diagnosis and treatment of CRC and furnishing critical cues for advancing research into CRC and the judicious selection of therapeutic targets.
文摘Objective:To give a brief overview of the field of epigenetics and the potential predictive power that small non-coding RNA(sncRNA)may hold in relation to improving the treatment and diagnosis of male infertility.Methods:PRISMA-ScR was used as the scoping review guideline for this investigation.All article data here have been accessed from MEDLINE–PubMed,Science Direct,EBSCO,Scopus,Sage Journals,and Google Scholar.The terms"small non coding RNA,male,infertility,miRNA,sperm"were used in the search between 2015 and 2023.Results:The study comprised 35 publications in total.Several sncRNAs,miR-155,miR-16,miR-196,miR-525-3p,miR-891 were found to be effective in regulating the mechanism of spermatozoa processing in the infertility of men.sncRNA can be used as a biomarker of male infertility.Conclusions:sncRNAs can act as biomarkers for the diagnosis of reproductive diseases.Actually,by recognizing sncRNAs and their mechanisms,a new way to treat infertile men would be paved.The functional annotation of sncRNAs in spermatogenesis is still in its infancy but has enormous potential.This is despite the fact that many potential sncRNAs have been found to date with the use of cutting-edge technology and publicly accessible sncRNA annotation tools.
基金National Natural Science Foundation of China(32170815,91940305,91640201 and 32300459)the National Key Research&Developmental Program of China(2021YFC2700200 and 2022YFC2702602)China Postdoctoral Science Foundation(2021M703212).
文摘Small non-coding RNAs(sncRNAs),such as microRNAs(miRNAs),small interfering RNAs(siRNAs),PIWIinteracting RNAs(piRNAs),and transfer RNA(tRNA)-derived small RNAs(tsRNAs),play essential roles in regulating various cellular and developmental processes.Over the past three decades,researchers have identified novel sncRNA species from various organisms.These molecules demonstrate dynamic expression and diverse functions,and they are subject to intricate regulation through RNA modifications in both healthy and diseased states.Notably,certain sncRNAs in gametes,particularly sperm,respond to environmental stimuli and facilitate epigenetic inheritance.Collectively,the in-depth understanding of sncRNA functions and mechanisms has accelerated the development of small RNA-based therapeutics.In this review,we present the recent advances in the field,including new sncRNA species and the regulatory influences of RNA modifications.We also discuss the current limitations and challenges associated with using small RNAs as either biomarkers or therapeutic drugs.
基金This study was supported by the Ministry of Higher Education,Malaysia(FRGS0322-SG-1/2013)Universiti Malaysia Sabah(GUG0521-2/2020).
文摘Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and haplotype.Methods:Thirty-nine blood samples infected with P.knowlesi were collected in Sabah,Malaysian Borneo and Peninsular Malaysia.The S-type SSU rRNA gene was amplified using polymerase chain reaction,cloned into a vector,and sequenced.The natural selection and haplotype of the S-type SSU rRNA gene sequences were determined using DnaSP v6 and illustrated using NETWORK v10.This study's 39 S-type SSU rRNA sequences and eight sequences from the Genbank database were subjected to phylogenetic analysis using MEGA 11.Results:Overall,the phylogenetic analysis showed no evidence of a geographical cluster of P.knowlesi isolates from different areas in Malaysia based on the S-type SSU rRNA gene sequences.The S-type SSU rRNA gene sequences were relatively conserved and with a purifying effect.Haplotype sharing of the S-type SSU rRNA gene was observed between the P.knowlesi isolates in Sabah,Malaysian Borneo,but not between Sabah,Malaysian Borneo and Peninsular Malaysia.Conclusions:This study suggests that the S-type SSU rRNA gene of P.knowlesi isolates in Sabah,Malaysian Borneo,and Peninsular Malaysia has fewer polymorphic sites,representing the conservation of the gene.These features make the S-type SSU rRNA gene suitable for comparative studies,such as determining the evolutionary relationships and common ancestry among P.knowlesi species.
文摘This editorial reviews the molecular mechanisms underlying the roles of the long non-coding RNA(lncRNA)small nucleolar RNA host gene 16(SNHG16)in digestive system cancers based on two recent studies on lncRNAs in digestive system tumors.The first study,by Zhao et al,explored how hBD-1 affects colon cancer,via the lncRNA TCONS_00014506,by inhibiting mTOR and promoting autophagy.The second one,by Li et al,identified the lncRNA prion protein testis specific(PRNT)as a factor in oxaliplatin resistance by sponging ZNF184 to regulate HIPK2 and influence colorectal cancer progression and chemoresistance,suggesting PRNT as a potential therapeutic target for colorectal cancer.Both of these two articles discuss the mechanisms by which lncRNAs contribute to the development and progression of digestive system cancers.As a recent research hotspot,SNHG16 is a typical lncRNA that has been extensively studied for its association with digestive system cancers.The prevailing hypothesis is that SNHG16 participates in the development and progression of digestive system tumors by acting as a competing endogenous RNA,interacting with other proteins,regulating various genes,and affecting downstream target molecules.This review systematically examines the recently reported biological functions,related molecular mechanisms,and potential clinical significance of SNHG16 in various digestive system cancers,and explores the relationship between SNHG16 and digestive system cancers.The findings suggest that SNHG16 may serve as a potential biomarker and therapeutic target for human digestive system cancers.
基金supported by the National Youth Science Foundation of China(31201198)the Key Project of Guangdong Scientific and Technological Plan(2015B020231002)the Guangdong Modern Agricultural Creation Team Project(2016LM2148)
文摘Due to global climate change, temperature stress has become one of the primary causes of crop losses worldwide. Much progress has been made in unraveling the complex stress response mechanisms in plants, particularly in the identification of temperature stress responsive protein-coding genes. Recently discovered micro RNAs(mi RNAs) and endogenous small-interfering RNAs(si RNAs) have also been demonstrated as simportant players in plant temperature stress response.Using high-throughput sequencing, many small RNAs,especially mi RNAs, have been identified to be triggered by cold or heat. Subsequently, several studies have shown an important functional role for these small RNAs in cold or heat tolerance. These findings greatly broaden our understanding of endogenous small RNAs in plant stress response control. Here, we highlight new findings regarding the roles of mi RNAs and si RNAs in plant temperature stress response and acclimation. We also review the current understanding of the regulatory mechanisms of small RNAs in temperature stress response, and explore the outlook for the use of these small RNAs in molecular breeding for improvement of temperature stress tolerance in plants.
基金This work was supported by the Fundamental Research Funds for the Central Universities(No.020814380146)National Basic Research Program of China(973 Program)(No.2014CB542300)+1 种基金National Natural Science Foundation of China(Nos.32022015,32001077,31871295,21877060,81250044,81602697,and 81772727)Research Unit of Extracellular Non-Coding RNA,Chinese Academy of Medical Sciences(No.2021RU015).
文摘The continuing discoveries of novel classes of RNA modifications in various organisms have raised the need for improving sensitive,convenient,and reliable methods for quantifying RNA modifications.In particular,a subset of small RNAs,including microRNAs(miRNAs)and Piwi-interacting RNAs(piRNAs),are modified at their 3'-terminal nucleotides via 2'-0-methylation.However,quantifying the levels of these small RNAs is difficult because 2'-0-methylation at the RNA 3'-terminus inhibits the activity of polyadenylate polymerase and T4 RNA ligase.These two enzymes are indispensable for RNA labeling or ligation in conventional miRNA quantification assays.In this study,we profiled 3'-terminal 2'-0-methyl plant miRNAs in the livers of rice-fed mice by oxidative deep sequencing and detected increasing amounts of plant miRNAs with prolonged oxidation treatment.We further compared the efficiency of stem-loop and poly(A)-tailed RT-qPCR in quantifying plant miRNAs in animal tissues and identified stem-loop RT-qPCR as the only suitable approach.Likewise,stem-loop RT-qPCR was superior to poly(A)-tailed RT-qPCR in quantifying 3'-terminal 2'-0-methyl piRNAs in human seminal plasma.In summary,this study established a standard procedure for quantifying the levels of 3'-terminal 2'-0-methyl miRNAs in plants and piRNAs.Accurate measurement of the 3'-terminal 2'-0-methylation of small RNAs has profound implications for understanding their pathophysiologic roles in biological systems.
基金supported in part by China National Funds for Distinguished Young Scientists(31225015)National Key Scientific Research Program of China(2012CB910900)to Qi YiJun
文摘DNA double-strand break （DSB） is the most deleterious form of DNA damage and poses great threat to genome stability. Eu- karyotes have evolved complex mechanisms to repair DSBs through coordinated actions of protein sensors, transducers, and effectors. DSB-induced small RNAs （diRNAs） or Dicer/Drosha-dependent RNAs （DDRNAs） have been recently discovered in plants and vertebrates, adding an unsuspected RNA component into the DSB repair pathway. DiRNAs/DDRNAs control DNA damage response （DDR） activation by affecting DDR loci formation and cell cycle checkpoint enforcement and are required for efficient DSB repair. Here, we summarize the findings of diRNAs/DDRNAs and discuss the possible mechanisms through which they act to facilitate DSB repair.
基金supported by grants from the National Basic Research 973 Program (2011CB915404)the National Natural Science Foundation of China (91017012)the National Program of Transgenic Variety Development of China (2011ZX08009-004)
文摘In plants, non-coding small RNAs play a vital role in plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate （JA） pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. Thirty new miRNAs and 27 new miRNA candidates were identified through bioinformatics approach. Forty-nine known miRNAs （belonging to 24 families）, 15 new miRNAs and new miRNA candidates （belonging to 11 families） and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs （belonging to 9 families） were repressed by JA.
