Molecular mechanisms underlying roles of long non-coding RNA small nucleolar RNA host gene 16 in digestive system cancers

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.

Small nucleolar RNA host gene 3 functions as a novel biomarker in liver cancer and other tumour progression

Cancer has become the most life-threatening disease in the world.Mutations in and aberrant expression of genes encoding proteins and mutations in noncoding RNAs,especially long noncoding RNAs(lncRNAs),have significant effects in human cancers.LncRNAs have no protein-coding ability but function extensively in numerous physiological and pathological processes.Small nucleolar RNA host gene 3(SNHG3)is a novel lncRNA and has been reported to be differentially expressed in various tumors,such as liver cancer,gastric cancer,and glioma.However,the interaction mechanisms for the regulation between SNHG3 and tumor progression are poorly understood.In this review,we summarize the results of SNHG3 studies in humans,animal models,and cells to underline the expression and role of SNHG3 in cancer.SNHG3 expression is upregulated in most tumors and is detrimental to patient prognosis.SNHG3 expression in lung adenocarcinoma remains controversial.Concurrently,SNHG3 affects oncogenes and tumor suppressor genes through various mechanisms,including competing endogenous RNA effects.A deeper understanding of the contribution of SNHG3 in clinical applications and tumor development may provide a new target for cancer diagnosis and treatment.

Mechanism of lncRNA SNHG19 miR-299-5p MAPK6 signaling axis promoting metastasis of non-small cell lung cancer cells

Objective The aim of this study was to explore the mechanism behind lncRNA small nucleolar RNA host gene 19(lncRNA SNHG19)/microrNA-299-5P(miR-299-5p)/mitogen-activated protein kinase 6(MAPK6)signaling axis promoting metastasis of non-small cell lung cancer(NSCLC).Methods To analyze the abnormal expression of lncRNAs in NSCLC,50 surgically resected NSCLC and adjacent tissue samples were collected from August 2021 to August 2022.The mRNA expression levels of lncRNA SNHG19,Mir-299-5p,and MAPK6 were detected by qRT-PCR.The functions of lncRNA SNHG19,Mir-299-5p and MAPK6 were investigated by CCK-8,clone formation,EdU,scratch,Transwell western blotting(WB)and in vivo xenograft assay.RNA fluorescence in-situ hybridization(FISH),RNA pull-down,dual luciferase reporter,and RNA co-immunoprecipitation assays were used to explore the mechanism of action between lncRNA SNHG19,miR-299-5p,and MAPK6.Results High expression of lncRNA SNHG19 was correlated with poor prognosis,tumor size,lymph node metastasis,and TNM stage in NSCLC patients(P<0.05).Cell function experiments showed that lncRNA SNHG19 could improve the proliferation,clone formation,migration,and invasion ability of A549 cells both in vitro and in vivo(all P<0.05)and increased the relative expression levels of vimentin and MAPK6(P<0.05).The relative expression level of E-cadherin was decreased(P<0.05).lncRNA SNHG19 can interact with Mir-299-5p and regulate the expression level of MAPK6.Conclusion lncRNA SNHG19 is upregulated in NSCLC tissues and cells,and its high expression is associated with tumor progression and poor survival.Moreover,it can act as a molecular sponge for Mir-299-5p to regulate MAPK6 expression and promote the proliferation and metastasis of A549 cells.

Complete nuclear ribosomal DNA sequence amplification and molecular analyses of Bangia (Bangiales, Rhodophyta) from China

Filamentous Bangia,which are distributed extensively throughout the world,have simple and similar morphological characteristics.Scientists can classify these organisms using molecular markers in combination with morphology.We successfully sequenced the complete nuclear ribosomal DNA.approximately 13 kb in length,from a marine Bangia population.We further analyzed the small subunit ribosomal DNA gene(nrSSU) and the internal transcribed spacer(ITS) sequence regions along with nine other marine,and two freshwater Bangia samples from China.Pairwise distances of the nrSSU and 5.8S ribosomal DNA gene sequences show the marine samples grouping together with low divergences(0-0.003;0-0.006,respectively) from each other,but high divergences(0.123-0.126;0.198,respectively) from freshwater samples.An exception is the marine sample collected from Weihai,which shows high divergence from both other marine samples(0.063-0.065;0.129,respectively) and the freshwater samples(0.097;0.120,respectively).A maximum likelihood phylogenetic tree based on a combined SSU-ITS dataset with maximum likelihood method shows the samples divided into three clades,with the two marine sample clades containing Bangia spp.from North America,Europe,Asia,and Australia;and one freshwater clade,containing Bangia atropurpurea from North America and China.

Pauciramus yunnanensis,gen.et sp.nov.,a novel freshwater red alga from China with proposal of the Ottiales ord.nov.(Nemaliophycidae,Rhodophyta)

Species of the red algal order Acrochaetiales mostly inhabit marine environments,with only two freshwater taxa Audouinella and Ottia.A new genus and species are described for freshwater red alga Pauciramus yunnanensis from Ailao Mountain,Yunnan,China.It is closely related to Ottia and a new order Ottiales was proposed for these genera.Pauciramus has unique combination of morphological characteristics including the following:plants caespitose and densely pulvinate,slender uniseriate filaments with well-developed rhizoids,rarely branched,cylindrical vegetative cell with a single,ribbon-shaped and parietal chloroplast,reproduction by tetrasporangia,and dense sporangial branchlet only at the upper portion of filaments.Phylogenetic analysis of sequence data from the plastid ribulose-1,5-bisphosphate carboxylase-oxygenase large-subunit(rbc L),small subunit gene of the ribosomal cistron(SSU)and barcode region near the 5′end of the mitochondrial cytochrome oxidase subunit I(COI-5P)indicated that:the new taxon,P.yunnanensis,was in a well-supported clade with Ottia meiospora,and this clade was sister to order Palmariales and Acrochaetiales.To adhere to the principle of monophyly,a new freshwater order Ottiales including Ottia and Pauciramus is proposed.Despite the high sequence interspecific divergences and obvious morphological differences between genera Ottia and Pauciramus,seems impractical to establish a new family for a monospecific genus.Therefore,we temporarily classified Pauciramus into the family Ottiaceae,and made necessary revisions to the description to accommodate this genus.

Mutation in a novel gene SMALL AND CORDATELEAF 1 affects leaf morphology in cucumber

Plant species exhibit substantial variation in leaf morphology.VWe isolated a recessive mutant gene termed small and cordate leaf 1（sclh）that causes alteration in both leaf size and shape of cucumber.Compared to wild type leaves,the sclh mutant had fewer numbers of epidermal pavement cells.A single nucleotide polymorphism was associated with this leaf phenotype,which occurred in a putative nucleoside bisphosphate phosphatase.RNA-seq analysis of the wild type and sclh mutant leaves suggested that SCL;regulation may not involve known hormonal pathways.Our work identified a candidate gene for SCL;that may play a role in leaf development.

Expression and Regulatory Network Analysis of Function of Small Nucleolar RNA Host Gene 4 in Hepatocellular Carcinoma

Background and Aims:Long non-coding RNA small nucleolar RNA host genes(SNHGs)play a critical role in the occurrence and development of tumors.In this study,we aimed to investigate the role of SNHG4 in hepatocellular carcinoma(HCC)and its underlining mechanism.Methods:Datasets were acquired from The Cancer Genome Atlas(TCGA)database.lncLocator 2.0 was used to identify the distribution of SNHG4 in HCC cells.Gene expression,Kaplan-Meier survival,microRNA and transcription factor target analyses were performed with the University of Alabama Cancer(UALCAN)Database,Kaplan-Meier Plotter,LinkedOmics,WebGestalt and gene set enrichment analysis,respectively.Gene Ontology and pathway enrichment analyses and assessment of RNA binding proteins were performed by R software,circlncRNAnet and Encyclopedia of RNA Interactomes(EN-CORI).In addition,CirclncRNAnet and ENCORI were used to find the correlation between SNHG4 and important proteins,while the prognostic value was assessed with the Human Protein Atlas database and Kaplan-Meier Plotter.Results:Expression of SNHG4 in HCC is higher in HCC tissue than in normal healthy liver tissues and is mainly distributed in the nucleus.SNHG4 positively correlated with poor prognosis(p<0.01 for overall survival and recurrence-free survival).Functional enrichment analysis revealed SNHG4 involve-ment with regulation of ribosomal RNA synthesis and the RNA processing and surveillance pathway.SNHG4 is closely associated with miR-154 and miR-206,transcription factor target E2F family and the signaling pathway for MAPK/ERK and mTOR.U2 auxiliary factor 2(U2AF2)showed strong correlation with SNHG4,while low-expression of U2AF2 showed good prognosis.Conclusions:Based on our find-ings,we infer SNHG4 may play a role in the formation of HCC via regulation of tumor-related pathways.

A Novel Approach to Functional Analysis of the Ribulose Bisphosphate Carboxylase Small Subunit Gene by Agrobacterium-Mediated Gene Silencing

A novel approach to virus-induced post-transcriptional gene silencing for studying the function of the ribulose bisphosphate carboxylase small subunit （rbcS） gene was established and optimized using potato virus X vector and Nicotiana benthamiana as experimental material. The analysis of silencing phenomena, transcriptional level, protein expression, and pigment measurement showed that the expression of the rbcS endogenous gene was inactivated by the expression of a 500-bp homologous cDNA fragment carried in the virus vector.

Identifying the ‘unidentified’ fungi: a global-scale long-read third-generation sequencing approach

Molecular identification methods,in particular high-throughput sequencing tools,have greatly improved our knowledge about fungal diversity and biogeography,but many of the recovered taxa from natural environments cannot be identified to species or even higher taxonomic levels.This study addresses the phylogenetic placement of previously unrecognized fungal groups by using two complementary approaches:(i)third-generation amplicon sequencing analysis of DNA from global soil samples,screening out ITS reads of<90%similarity to other available Sanger sequences,and(ii)analysis of common fungal taxa that were previously indicated to be enigmatic in terms of taxonomic placement based on the ITS sequences alone(so-called top50 sequences).For the global soil samples,we chose to amplify the full rRNA gene operon using four partly overlapping amplicons and multiple newly developed primers or primer combinations that cover nearly all fungi and a vast majority of non-fungal eukaryotes.We extracted the rRNA 18S(SSU)and 28S(LSU)genes and performed phylogenetic analyses against carefully selected reference material.Both SSU and LSU analyses placed most soil sequences and top50 sequences to known orders and classes,but tens of monophyletic groups and single sequences remained outside described taxa.Furthermore,the LSU analyses recovered a few small groups of sequences that may potentially represent novel phyla.We conclude that rRNA genes-based phylogenetic analyses are efficient tools for determining phylogenetic relationships of fungal taxa that cannot be placed to any order or class using ITS sequences alone.However,in many instances,longer rRNA gene sequences and availability of both SSU and LSU reads are needed to improve taxonomic resolution.By leveraging third-generation sequencing from global soil samples,we successfully provided phylogenetic placement for many previously unidentified sequences and broadened our view on the fungal tree of life,with 10-20%new order-level taxa.In addition,the PacBio sequence data greatly extends fungal class-level information in reference databases.

ADRA2B gene insertion/deletion polymorphism and artery compliance

Background The ADRA2B gene insertion/deletion （I/D） polymorphism is associated with various cardiovascular and metabolic phenotypes. Large （C1） and small （C2） artery compliance, assessed by pulse wave analysis, is considered as sensitive markers or risk factors for cardiovascular disease. Therefore whether the ADRA2B I/D polymorphism is associated with CI and C2 need to be investigated. Methods A total of 227 men and 243 women were enrolled in a Chinese family-based study. C1 and C2 were measured by pulse wave analysis. ADRA2B genotypes were determined by polymerase chain reaction. Statistical methods included generalized estimation equations and quantitative transmission disequilibrium test. Results The II （31.9%）, ID （46.8%） and DD （21.3%） genotype frequencies were in Hardy-Weinberg equilibrium （P = 0. 73 ）. The covariates selected by stepwise regression for C1 and C2 were age, systolic pressure and gender. The population based association analysis showed that C1 and C2 were not associated with ADRA2B genotype both before （C1 ： P =0. 28; C2： P =0. 27） and after （C1 ： P =0. 58; C2： P =0. 18） the adjustment. The family-based analyses of 128 informative offspring showed that transmission of the D-allele was not associated with C1 orC2, both before （CI： P=0.42; C2： P=0.85） and after （CI： P=0.31; C2： P= 0. 82） the adjustment. Conclusion The study do not support that the ADRA2B gene I/D polymorphism has a major gene effect on C1 or C2 in the Chinese population of current sample size.