MARS and RNAcmap3:The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search

sequences found in the huge,integrated database of protein sequences(Big Fantastic Database).In contrast,the existing nucleotide databases were not consolidated to facilitate wider and deeper homology search.Here,we built a comprehensive database by incorporating the non-coding RNA(ncRNA)sequences from RNAcentral,the transcriptome assembly and metagenome assembly from metagenomics RAST(MG-RAST),the genomic sequences from Genome Warehouse(GWH),and the genomic sequences from MGnify,in addition to the nucleotide(nt)database and its subsets in National Center of Biotechnology Information(NCBI).The resulting Master database of All possible RNA sequences(MARS)is 20-fold larger than NCBI’s nt database or 60-fold larger than RNAcentral.The new dataset along with a new split-search strategy allows a substantial improvement in homology search over existing state-of-the-art techniques.It also yields more accurate and more sensitive multiple sequence alignments(MSAs)than manually curated MSAs from Rfam for the majority of structured RNAs mapped to Rfam.The results indicate that MARS coupled with the fully automatic homology search tool RNAcmap will be useful for improved structural and functional inference of ncRNAs and RNA language models based on MSAs.MARS is accessible at https://ngdc.cncb.ac.cn/omix/release/OMIX003037,and RNAcmap3 is accessible at http://zhouyq-lab.szbl.ac.cn/download/.

Spatial transcriptomics combined with single-nucleus RNA sequencing reveals glial cell heterogeneity in the human spinal cord

Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis.

Genetic variation of circHIBADH enhances prostate cancer risk through regulating HNRNPA1-related RNA splicing

The current study aimed to investigate associations of circRNAs and related genetic variants with the risk of prostate cancer(PCa)as well as to elucidate biological mechanisms underlying the associations.We first compared expression levels of circRNAs between 25 paired PCa and adjacent normal tissues to identify riskassociated circRNAs by using the MiOncoCirc database.We then used logistic regression models to evaluate associations between genetic variants in candidate circRNAs and PCa risk among 4662 prostate cancer patients and 3114 healthy controls,and identified circHIBADH rs11973492 T>C as a significant risk-associated variant(odds ratio=1.20,95%confidence interval:1.08-1.34,P=7.06×10^(-4))in a dominant genetic model,which altered the secondary structure of the corresponding RNA chain.In the in silico analysis,we found that circHIBADH sponged and silenced 21 RNA-binding proteins(RBPs)enriched in the RNA splicing pathway,among which HNRNPA1 was identified and validated as a hub RBP using an external RNA-sequencing data as well as the in-house(four tissue samples)and publicly available single-cell transcriptomes.Additionally,we demonstrated that HNRNPA1 influenced hallmarks including MYC target,DNA repair,and E2F target signaling pathways,thereby promoting carcinogenesis.In conclusion,genetic variants in circHIBADH may act as sponges and inhibitors of RNA splicing-associated RBPs including HNRNPA1,playing an oncogenic role in PCa.

Identification and validation of a pyroptosis-related prognostic model for colorectal cancer based on bulk and single-cell RNA sequencing data

BACKGROUND Pyroptosis impacts the development of malignant tumors,yet its role in colorectal cancer(CRC)prognosis remains uncertain.AIM To assess the prognostic significance of pyroptosis-related genes and their association with CRC immune infiltration.METHODS Gene expression data were obtained from The Cancer Genome Atlas(TCGA)and single-cell RNA sequencing dataset GSE178341 from the Gene Expression Omnibus(GEO).Pyroptosis-related gene expression in cell clusters was analyzed,and enrichment analysis was conducted.A pyroptosis-related risk model was developed using the LASSO regression algorithm,with prediction accuracy assessed through K-M and receiver operating characteristic analyses.A nomo-gram predicting survival was created,and the correlation between the risk model and immune infiltration was analyzed using CIBERSORTx calculations.Finally,the differential expression of the 8 prognostic genes between CRC and normal samples was verified by analyzing TCGA-COADREAD data from the UCSC database.RESULTS An effective pyroptosis-related risk model was constructed using 8 genes-CHMP2B,SDHB,BST2,UBE2D2,GJA1,AIM2,PDCD6IP,and SEZ6L2(P<0.05).Seven of these genes exhibited differential expression between CRC and normal samples based on TCGA database analysis(P<0.05).Patients with higher risk scores demonstrated increased death risk and reduced overall survival(P<0.05).Significant differences in immune infiltration were observed between low-and high-risk groups,correlating with pyroptosis-related gene expression.CONCLUSION We developed a pyroptosis-related prognostic model for CRC,affirming its correlation with immune infiltration.This model may prove useful for CRC prognostic evaluation.

Single‑cell RNA sequencing opens a new era for cotton genomic research and gene functional analysis

Single-cell RNA sequencing(scRNA-seq)is one of the most advanced sequencing technologies for studying transcriptome landscape at the single-cell revolution.It provides numerous advantages over traditional RNA-seq.Since it was first used to profile single-cell transcriptome in plants in 2019,it has been extensively employed to perform different research in plants.Recently,scRNA-seq was also quickly adopted by the cotton research community to solve lots of scientific questions which have been never solved.In this comment,we highlighted the significant progress in employing scRNA-seq to cotton genetic and genomic study and its future potential applications.

Global Annotation of Small RNA and MicroRNA Mature Sequences from Developing Ovules of Gossypium hirsutum L.

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

Single-cell RNA sequencing analysis of the retina under acute high intraocular pressure

High intraocular pressure causes retinal ganglion cell injury in primary and secondary glaucoma diseases,yet the molecular landscape characteristics of retinal cells under high intraocular pressure remain unknown.Rat models of acute hypertension ocular pressure were established by injection of cross-linked hyaluronic acid hydrogel(Healaflow■).Single-cell RNA sequencing was then used to describe the cellular composition and molecular profile of the retina following high intraocular pressure.Our results identified a total of 12 cell types,namely retinal pigment epithelial cells,rod-photoreceptor cells,bipolar cells,Müller cells,microglia,cone-photoreceptor cells,retinal ganglion cells,endothelial cells,retinal progenitor cells,oligodendrocytes,pericytes,and fibroblasts.The single-cell RNA sequencing analysis of the retina under acute high intraocular pressure revealed obvious changes in the proportions of various retinal cells,with ganglion cells decreased by 23%.Hematoxylin and eosin staining and TUNEL staining confirmed the damage to retinal ganglion cells under high intraocular pressure.We extracted data from retinal ganglion cells and analyzed the retinal ganglion cell cluster with the most distinct expression.We found upregulation of the B3gat2 gene,which is associated with neuronal migration and adhesion,and downregulation of the Tsc22d gene,which participates in inhibition of inflammation.This study is the first to reveal molecular changes and intercellular interactions in the retina under high intraocular pressure.These data contribute to understanding of the molecular mechanism of retinal injury induced by high intraocular pressure and will benefit the development of novel therapies.

Dissection of triple-negative breast cancer microenvironment and identification of potential therapeutic drugs using single-cell RNA sequencing analysis

Breast cancer remains a leading cause of mortality in women worldwide.Triple-negative breast cancer(TNBC)is a particularly aggressive subtype characterized by rapid progression,poor prognosis,and lack of clear therapeutic targets.In the clinic,delineation of tumor heterogeneity and development of effective drugs continue to pose considerable challenges.Within the scope of our study,high heterogeneity inherent to breast cancer was uncovered based on the landscape constructed from both tumor and healthy breast tissue samples.Notably,TNBC exhibited significant specificity regarding cell proliferation,differentiation,and disease progression.Significant associations between tumor grade,prognosis,and TNBC oncogenes were established via pseudotime trajectory analysis.Consequently,we further performed comprehensive characterization of the TNBC microenvironment.A crucial epithelial subcluster,E8,was identified as highly malignant and strongly associated with tumor cell proliferation in TNBC.Additionally,epithelial-mesenchymal transition(EMT)-associated fibroblast and M2 macrophage subclusters exerted an influence on E8 through cellular interactions,contributing to tumor growth.Characteristic genes in these three cluster cells could therefore serve as potential therapeutic targets for TNBC.The collective findings provided valuable insights that assisted in the screening of a series of therapeutic drugs,such as pelitinib.We further confirmed the anti-cancer effect of pelitinib in an orthotopic 4T1 tumor-bearing mouse model.Overall,our study sheds light on the unique characteristics of TNBC at single-cell resolution and the crucial cell types associated with tumor cell proliferation that may serve as potent tools in the development of effective anti-cancer drugs.

Applications of single-cell RNA sequencing in spermatogenesis and molecular evolution

Spermatogenic cell heterogeneity is determined by the complex process of spermatogenesis differentiation.However,effectively revealing the regulatory mechanisms underlying mammalian spermatogenic cell development and differentiation via traditional methods is difficult.Advances in technology have led to the emergence of many single-cell transcriptome sequencing protocols,which have partially addressed these challenges.In this review,we detail the principles of 10x Genomics technology and summarize the methods for downstream analysis of single-cell transcriptome sequencing data.Furthermore,we explore the role of single-cell transcriptome sequencing in revealing the heterogeneity of testicular ecological niche cells,delineating the establishment and disruption of testicular immune homeostasis during human spermatogenesis,investigating abnormal spermatogenesis in humans,and,ultimately,elucidating the molecular evolution of mammalian spermatogenesis.

Learning Sequential and Structural Dependencies Between Nucleotides for RNA N6-Methyladenosine Site Identification

N6-methyladenosine(m6A)is an important RNA methylation modification involved in regulating diverse biological processes across multiple species.Hence,the identification of m6A modification sites provides valuable insight into the biological mechanisms of complex diseases at the post-transcriptional level.Although a variety of identification algorithms have been proposed recently,most of them capture the features of m6A modification sites by focusing on the sequential dependencies of nucleotides at different positions in RNA sequences,while ignoring the structural dependencies of nucleotides in their threedimensional structures.To overcome this issue,we propose a cross-species end-to-end deep learning model,namely CR-NSSD,which conduct a cross-domain representation learning process integrating nucleotide structural and sequential dependencies for RNA m6A site identification.Specifically,CR-NSSD first obtains the pre-coded representations of RNA sequences by incorporating the position information into single-nucleotide states with chaos game representation theory.It then constructs a crossdomain reconstruction encoder to learn the sequential and structural dependencies between nucleotides.By minimizing the reconstruction and binary cross-entropy losses,CR-NSSD is trained to complete the task of m6A site identification.Extensive experiments have demonstrated the promising performance of CR-NSSD by comparing it with several state-of-the-art m6A identification algorithms.Moreover,the results of cross-species prediction indicate that the integration of sequential and structural dependencies allows CR-NSSD to capture general features of m6A modification sites among different species,thus improving the accuracy of cross-species identification.

Expression changes of mi RNA-regulated genes associated with the formation of the leafy head in cabbage

The vegetative development of cabbage(Brassica oleracea var.capitata)passes through seedling,rosette,folding and heading stages.Leaves that form the rosette are large and mostly flat.In the following developmental stages,the plants produce leaves that curve inward to produce the leafy head.Many microRNAs and their target genes have been described participating in leaf development and leaf curvature.The aim of this study is to investigate the role of miRNA-regulated genes in the transition from the rosette to the heading stage.We compared the mi RNA and gene abundances between emerging rosette and heading leaves.To remove transcripts(miRNAs and genes)whose regulation was most likely associated with plant age rather than the change from rosette to heading stage,we utilized a non-heading collard green(B.oleracea var.acephala)morphotype as control.This resulted in 33 DEMs and 1998 DEGs with likely roles in the transition from rosette to heading stage in cabbage.Among these 1998 DEGs,we found enriched GO terms related to DNA-binding transcription factor activity,transcription regulator activity,iron ion binding,and photosynthesis.We predicted the target genes of these 33 DEMs and focused on the subset that was differentially expressed(1998DEGs)between rosette and heading stage leaves to construct mi RNA-target gene interaction networks.Our main finding is a role for miR396b-5p targeting two Arabidopsis thaliana orthologues of GROWTH REGULATING FACTORs 3(GRF3)and 4(GRF4)in pointed cabbage head formation.

Single-Nucleus RNA Sequencing Reveals Cardiac Macrophage Landscape in Hypoplastic Left Heart Syndrome

Background:Hypoplastic left heart syndrome(HLHS)is one of the most challenging congenital heart diseases in clinical treatment.In cardiac tissues,resident macrophages fulfill critical functions in maintaining a stable cardiac state and have strong regenerative capacity and organ specificity.However,the molecular mechanisms of macro-phages in HLHS remained unclear.Methods:Single-nucleus RNA sequencing(snRNA-seq)data of HLHS and healthy control(donors)samples obtained from the Gene Expression Omnibus(GEO)database were normalized and clustered using the Seurat package.The“FindMarkers”function was used to screen differentially expressed genes(DEGs)between the HLHS and donor groups and to analyze the functional enrichment of the set of genes of interest.Finally,cell-cell communication,pseudotime,and single-cell regulatory network inference and cluster-ing(SCENIC)analyses were used to study the mechanisms of macrophages in HLHS.Results:Based on the snRNA-seq data of HLHS and donors,we identified a total of 9 cell clusters,among which the proportion of macrophages was significantly less in the HLHS group than in the control group.Subdivision of macrophage subpopulations(Macrophages 1,2,and 3)showed that Macrophages 1 was mainly involved in nervous system development,angiogenesis,and apoptotic processes.In addition,analysis of communication between Macro-phages 1 and cardiomyocytes revealed that ligand-acceptor pairs such as GAS6/AXL,IL6,IGF1,THY1,and L1CAM were present only in the donor group.Finally,pesudotime and SCENIC analyses demonstrated that FOXO3 and ELF2 played a critical role for Macrophages 1 to maintain cardiac function in patients with HLHS.Conclusion:Our study improved the current understanding of the molecular mechanisms of macrophage devel-opment in HLHS,showing that manipulating the regulatory role of macrophages in the heart can be a novel treat-ment for HLHS.

Perilipin-2 mediates ferroptosis in oligodendrocyte progenitor cells and myelin injury after ischemic stroke

Differentiation of oligodendrocyte progenitor cells into mature myelin-forming oligodendrocytes contributes to remyelination.Failure of remyelination due to oligodendrocyte progenitor cell death can result in severe nerve damage.Ferroptosis is an iron-dependent form of regulated cell death caused by membrane rupture induced by lipid peroxidation,and plays an important role in the pathological process of ischemic stroke.However,there are few studies on oligodendrocyte progenitor cell ferroptosis.We analyzed transcriptome sequencing data from GEO databases and identified a role of ferroptosis in oligodendrocyte progenitor cell death and myelin injury after cerebral ischemia.Bioinformatics analysis suggested that perilipin-2(PLIN2)was involved in oligodendrocyte progenitor cell ferroptosis.PLIN2 is a lipid storage protein and a marker of hypoxia-sensitive lipid droplet accumulation.For further investigation,we established a mouse model of cerebral ischemia/reperfusion.We found significant myelin damage after cerebral ischemia,as well as oligodendrocyte progenitor cell death and increased lipid peroxidation levels around the infarct area.The ferroptosis inhibitor,ferrostatin-1,rescued oligodendrocyte progenitor cell death and subsequent myelin injury.We also found increased PLIN2 levels in the peri-infarct area that co-localized with oligodendrocyte progenitor cells.Plin2 knockdown rescued demyelination and improved neurological deficits.Our findings suggest that targeting PLIN2 to regulate oligodendrocyte progenitor cell ferroptosis may be a potential therapeutic strategy for rescuing myelin damage after cerebral ischemia.

LncRNA Airsci increases the inflammatory response after spinal cord injury in rats through the nuclear factor kappa B signaling pathway

Spinal cord injury(SCI)is a serious traumatic event to the central nervous system.Studies show that long non-coding RNAs(lncRNAs)play an important role in regulating the inflammatory response in the acute stage of SCI.Here,we investigated a new lncRNA related to spinal cord injury and acute inflammation.We analyzed the expression profile of lncRNAs after SCI,and explored the role of lncRNA Airsci(acute inflammatory response in SCI)on recovery following acute SCI.The rats were divided into the control group,SCI group,and SCI+lncRNA Airsci-siRNA group.The expression of inflammatory factors,including nuclear factor kappa B[NF-κB(p65)],NF-κB inhibitor IκBαand phosphorylated IκBα(p-IκBα),and the p-IκBα/IκBαratio were examined 1–28 days after SCI in rats by western blot assay.The differential lncRNA expression profile after SCI was assessed by RNA sequencing.The differentially expressed lncRNAs were analyzed by bioinformatics technology.The differentially expressed lncRNA Airsci,which is involved in NF-κB signaling and associated with the acute inflammatory response,was verified by quantitative real-time PCR.Interleukin(IL-1β),IL-6 and tumor necrosis factor(TNF-α)at 3 days after SCI were measured by western blot assay and quantitative real-time PCR.The histopathology of the spinal cord was evaluated by hematoxylin-eosin and Nissl staining.Motor function was assessed with the Basso,Beattie and Bresnahan Locomotor Rating Scale.Numerous differentially expressed lncRNAs were detected after SCI,including 151 that were upregulated and 186 that were downregulated in the SCI 3 d group compared with the control group.LncRNA Airsci was the most significantly expressed among the five lncRNAs involved in the NF-κB signaling pathway.LncRNA Airsci-siRNA reduced the inflammatory response by inhibiting the NF-κB signaling pathway,alleviated spinal cord tissue injury,and promoted the recovery of motor function in SCI rats.These findings show that numerous lncRNAs are differentially expressed following SCI,and that inhibiting lncRNA Airsci reduces the inflammatory response through the NF-κB signaling pathway,thereby promoting functional recovery.All experimental procedures and protocols were approved by the approved by the Animal Ethics Committee of Jining Medical University(approval No.JNMC-2020-DW-RM-003)on January 18,2020.

Down-regulating Circular RNA Prkcsh suppresses the inflammatory response after spinal cord injury

Circular RNAs(circRNAs)are a class of conserved,endogenous non-coding RNAs that are involved in transcriptional and post-transcriptional gene regulation and are highly enriched in the nervous system.They participate in the survival and differentiation of multiple nerve cells,and may even promote the recovery of neurological function after stroke.However,their role in the inflammatory response after spinal cord injury remains unclear.In the present study,we established a mouse model of T9 spinal cord injury using the modified Allen’s impact method,and identified 16,013 circRNAs and 960 miRNAs that were differentially expressed after spinal cord injury.Of these,the expression levels of circPrkcsh were significantly different between injured and sham-treated mice.We then treated astrocytes with tumor necrosis factor-αin vitro to simulate the inflammatory response after spinal cord injury.Our results revealed an elevated expression of circPrkcsh with a concurrent decrease in miR-488 expression in injured cells.We also found that circPrkcsh regulated the expression of the inflammationrelated gene Ccl2.Furthermore,in tumor necrosis factor-α-treated astrocytes,circPrkcsh knockdown decreased the expression of Ccl2 by upregulating miR-488 expression,and reduced the secretion of inflammatory cytokines in vitro.These findings suggest that differentially expressed circRNAs participate in the inflammatory response after spinal cord injury and act as the regulators of certain microRNAs.Furthermore,circPrkcsh may be used as an miR-488 sponge to regulate Ccl2 expression,which might provide a new potential therapy for SCI.The study was approved by the Animal Ethics Committee of Shandong University of China(approval No.KYLL-20170303)on March 3,2017.

Transcriptomic analysis reveals essential microRNAs after peripheral nerve injury

Studies have shown that microRNAs(miRNAs) mediate posttranscriptional regulation of target genes and participate in various physiological and pathological processes, including peripheral nerve injury. However, it is hard to select key miRNAs with essential biological functions among a large number of differentially expressed miRNAs. Previously, we collected injured sciatic nerve stumps at multiple time points after nerve crush injury, examined gene changes at different stages(acute, sub-acute, and post-acute), and obtained mRNA expression profiles. Here, we jointly analyzed mRNAs and miRNAs, and investigated upstream miRNAs of differentially expressed mRNAs using Ingenuity Pathway Analysis bioinformatic software. A total of 31, 42, 30, and 23 upstream miRNAs were identified at 1, 4, 7, and 14 days after rat sciatic nerve injury, respectively. Temporal expression patterns and biological involvement of commonly involved upstream miRNAs(miR-21, let-7, miR-223, miR-10 b, miR-132, miR-15 b, miR-127, miR-29 a, miR-29 b, and miR-9) were then determined at multiple time points. Expression levels of miR-21, miR-132, miR-29 a, and miR-29 b were robustly increased after sciatic nerve injury. Biological processes involving these miRNAs include multicellular organismal response to stress, positive regulation of the epidermal growth factor receptor signaling pathway, negative regulation of epithelial cell differentiation, and regulation of myocardial tissue growth. Moreover, we constructed mechanistic networks of let-7, miR-21, and miR-223, the most significantly involved upstream miRNAs. Our findings reveal that multiple upstream miRNAs(i.e., let-7, miR-21, and miR-223) were associated with gene expression changes in rat sciatic nerve stumps after nerve injury, and these miRNAs play an important role in peripheral nerve regeneration. This study was approved by the Experimental Animal Ethics Committee of Jiangsu Province of China(approval No. 20190303-18) on March 3, 2019.

Comprehensive circRNA-microRNA-mRNA network analysis revealed the novel regulatory mechanism of Trichosporon asahii infection

Background:Invasive Trichosporon asahii(T.asahii)infection frequently occurs with a high mortality in immunodeficient hosts,but the pathogenesis of T.asahii infection remains elusive.Circular RNAs(circRNAs)are a type of endogenous noncoding RNA that participate in various disease processes.However,the mechanism of circRNAs in T.asahii infection remains completely unknown.Methods:RNA sequencing(RNA-seq)was performed to analyze the expression profiles of circRNAs,microRNAs(miRNAs),and mRNAs in THP-1 cells infected with T.asahii or uninfected samples.Some of the RNA-seq results were verified by RT-qPCR.Gene Ontology(GO)enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway analyses were used to analyze the differentially expressed mRNAs.A circRNA-miRNA-mRNA network was constructed and verified by dual-luciferase reporter assay and overexpression experiments.Results:A total of 46 circRNAs,412 mRNAs and 47 miRNAs were differentially expressed at 12 h after T.asahii infection.GO and KEGG analyses showed that the differentially expressed mRNAs were primarily linked to the leukocyte migration involved in the inflammatory response,the Toll-like receptor signaling pathway,and the TNF signaling pathway.A competing endogenous RNA(ceRNA)network was constructed with 5 differentially expressed circRNAs,5 differentially expressed miRNAs and 42 differentially expressed mRNAs.Among them,hsa_circ_0065336 was found to indirectly regulate PTPN11 expression by sponging miR-505-3p.Conclusions:These data revealed a comprehensive circRNA-associated ceRNA network during T.asahii infection,thus providing new insights into the pathogenesis of the T.asahii-host interactions.

Genome-wide identification and comparative analysis of drought related genes in roots of two maize inbred lines with contrasting drought tolerance by RNA sequencing

Drought is one of the most important abiotic stresses affecting maize growth and development and therefore resulting in yield loss.Thus it is essential to understand molecular mechanisms of drought stress responses in maize for drought tolerance improvement.The root plays a critical role in plants sensing water deficit.In the present study,two maize inbred lines,H082183,a drought-tolerant line,and Lv28,a drought-sensitive line,were grown in the field and treated with different water conditions(moderate drought,severe drought,and well-watered conditions)during vegetative stage.The transcriptomes of their roots were investigated by RNA sequencing.There were 1428 and 512 drought-responsive genes(DRGs)in Lv28,688 and 3363 DRGs in H082183 under moderate drought and severe drought,respectively.A total of 31 Gene Ontology(GO)terms were significantly over-represented in the two lines,13 of which were enriched only in the DRGs of H082183.Based on results of Kyoto encyclopedia of genes and genomes(KEGG)enrichment analysis,"plant hormone signal transduction"and"starch and sucrose metabolism"were enriched in both of the two lines,while"phenylpropanoid biosynthesis"was only enriched in H082183.Further analysis revealed the different expression patterns of genes related to abscisic acid(ABA)signal pathway,trehalose biosynthesis,reactive oxygen scavenging,and transcription factors might contribute to drought tolerance in maize.Our results contribute to illustrating drought-responsive molecular mechanisms and providing gene resources for maize drought improvement.

Differential mRNA expression profiling of oral squamous cell carcinoma by high-throughput RNA sequencing

Differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas （OSCC）. The purpose of this study was to screen differentially expressed mRNAs in OSCC and matched paraneoplastic normal tissues, and to explore the intrinsic mechanism of OSCC development and progres- sion. We obtained the differentially expressed mRNA expression profiles in 10 pairs of fresh-frozen OSCC tissue specimens and matched paraneoplastic normal tissue specimens by high-throughput RNA sequencing. By using Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analyses, the functional significance of the differentially expressed genes were analyzed. We identified 1,120 sig- nificantly up-regulated mRNAs and 178 significantly down-regulated mRNAs in OSCC, compared to normal tissue. The differentially expressed mRNAs were involved in 20 biological processes and 68 signal pathways. Compared to adjacent normal tissue, the expression of MAGEAll was up-regulated; TCHH was down-regulated. These find- ings were verified by real-time PCR. These differentially expressed mRNAs may function as oncogenes or tumor suppressors in the development and progression of OSCC. This study provides novel insights into OSCC. However, further work is needed to determine if these differentially expressed mRNAs have potential roles as diagnostic bio- markers and candidate therapeutic targets for OSCC.

Neuroprotective effects of long noncoding RNAs involved in ischemic postconditioning after ischemic stroke

During acute reperfusion,the expression profiles of long noncoding RNAs in adult rats with focal cerebral ischemia undergo broad changes.However,whether long noncoding RNAs are involved in neuroprotective effects following focal ischemic stroke in rats remains unclear.In this study,RNA isolation and library preparation was performed for long noncoding RNA sequencing,followed by determining the coding potential of identified long noncoding RNAs and target gene prediction.Differential expression analysis,long noncoding RNA functional enrichment analysis,and co-expression network analysis were performed comparing ischemic rats with and without ischemic postconditioning rats.Rats were subjected to ischemic postconditioning via the brief and repeated occlusion of the middle cerebral artery or femoral artery.Quantitative real-time reverse transcription-polymerase chain reaction was used to detect the expression levels of differentially expressed long noncoding RNAs after ischemic postconditioning in a rat model of ischemic stroke.The results showed that ischemic postconditioning greatly affected the expression profile of long noncoding RNAs and mRNAs in the brains of rats that underwent ischemic stroke.The predicted target genes of some of the identified long noncoding RNAs(cis targets)were related to the cellular response to ischemia and stress,cytokine signal transduction,inflammation,and apoptosis signal transduction pathways.In addition,15 significantly differentially expressed long noncoding RNAs were identified in the brains of rats subjected to ischemic postconditioning.Nine candidate long noncoding RNAs that may be related to ischemic postconditioning were identified by a long noncoding RNA expression profile and long noncoding RNA-mRNA co-expression network analysis.Expression levels were verified by quantitative real-time reverse transcription-polymerase chain reaction.These results suggested that the identified long noncoding RNAs may be involved in the neuroprotective effects associated with ischemic postconditioning following ischemic stroke.The experimental animal procedures were approved by the Animal Experiment Ethics Committee of Kunming Medical University(approval No.KMMU2018018)in January 2018.