HepG2.2.15-derived exosomes facilitate the activation and fibrosis of hepatic stellate cells

BACKGROUND

The role of exosomes derived from HepG2.2.15 cells, which express hepatitis B virus (HBV)-related proteins, in triggering the activation of LX2 liver stellate cells and promoting liver fibrosis and cell proliferation remains elusive. The focus was on comprehending the relationship and influence of differentially expressed microRNAs (DE-miRNAs) within these exosomes.

AIM

To elucidate the effect of exosomes derived from HepG2.2.15 cells on the activation of hepatic stellate cell (HSC) LX2 and the progression of liver fibrosis.

METHODS

Exosomes from HepG2.2.15 cells, which express HBV-related proteins, were isolated from parental HepG2 and WRL68 cells. Western blotting was used to confirm the presence of the exosomal marker protein CD9. The activation of HSCs was assessed using oil red staining, whereas DiI staining facilitated the observation of exosomal uptake by LX2 cells. Additionally, we evaluated LX2 cell proliferation and fibrosis marker expression using 5-ethynyl-2′-deoxyuracil staining and western blotting, respectively. DE-miRNAs were analyzed using DESeq2. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were used to annotate the target genes of DE-miRNAs.

RESULTS

Exosomes from HepG2.2.15 cells were found to induced activation and enhanced proliferation and fibrosis in LX2 cells. A total of 27 miRNAs were differentially expressed in exosomes from HepG2.2.15 cells. GO analysis indicated that these DE-miRNA target genes were associated with cell differentiation, intracellular signal transduction, negative regulation of apoptosis, extracellular exosomes, and RNA binding. KEGG pathway analysis highlighted ubiquitin-mediated proteolysis, the MAPK signaling pathway, viral carcinogenesis, and the toll-like receptor signaling pathway, among others, as enriched in these targets.

CONCLUSION

These findings suggest that exosomes from HepG2.2.15 cells play a substantial role in the activation, proliferation, and fibrosis of LX2 cells and that DE-miRNAs within these exosomes contribute to the underlying mechanisms.

Testicular piRNA Analysis Identified Dysregulated piRNAs in Non-obstructive Azoospermia

Male infertility has remained idiopathic in a remarkable proportion of all cases. Gonadal expression of PIWI-interacting RNAs (piRNAs) has been shown to be vital to normal spermatogenesis, as they are expressed in almost all types of testicular germ cells. These molecules and their related Piwi proteins strictly regulate transposable elements' activity and gene expression. We aimed to identify dysregulated piRNAs in idiopathic non-obstructive azoospermic (NOA) testis by global expression analysis. Testis tissue samples from 18 azoospermic patients (ten NOA and eight OA) were studied by small RNA sequencing. To validate high-throughput sequencing data, quantitative real-time polymerase chain reactions for two differentially altered piRNAs were performed. Bioinformatics analyses were undertaken to identify pathways affected by piRNA dysregulation. In the NOA group, 1328 piRNAs were identified to be differentially expressed, of which 1322 were downregulated and 6 were upregulated. Bioinformatics analysis corroborated the involvement of dysregulated piRNA in spermatogenesis. We also identified 64 clusters of differentially expressed piRNAs, of which 42 clusters had a minimum of ten absolute piRNA hits. Our study suggests that piRNAs show significant dysregulation in infertility. Their target genes play a role in their self-biogenesis, probably by regulating their own production through a feedback mechanism. The downregulated piRNAs may find value as biomarkers for the presence of spermatozoa in the testis of azoospermic individuals, while the upregulated piRNAs are great candidates for further investigation of their precise functions in spermatogenesis.

Importance of core microRNA pathway genes and microRNAs associated with the defense of Odontotermes formosanus (Shiraki) against Serratia marcescens infection

MicroRNAs (miRNAs) are noncoding small regulatory RNAs involved in diverse biological processes. Odontotermes formosanus (Shiraki) is a polyphagous pest that causes economic damage to agroforestry. Serratia marcescens is a bacterium with great potential for controlling this insect. However, knowledge about the miRNA pathway and the role of miRNAs in O. formosanus defense against SM1 is limited. In this study, OfAgo1, OfDicer1 and OfDrosha were differentially expressed in different castes and tissues. SM1 infection affected the expression of all three genes in O. formosanus. Then, we used specific double-stranded RNAs to silence OfAgo1, OfDicer1 and OfDrosha. Knockdown of these genes enhanced the virulence of SM1 to O. formosanus, suggesting that miRNAs were critical in the defense of O. formosanus against SM1. Furthermore, we sequenced miRNAs from SM1-infected and uninfected O. formosanus. 33 differentially expressed (DE) miRNAs were identified, whereby 22 were upregulated and 11 were downregulated. Finally, the miRNA-mRNA networks were constructed, which further suggested the important role of miRNAs in the defense of O. formosanus against SM1. Totally, O. formosanus miRNA core genes defend against SM1 infection by regulating miRNA expression. This study elucidates the interactions between O. formosanus and SM1 and provides new theories for biological control.

Modulation of faecal miRNAs highlights the preventive effects of a Mediterranean low-inflammatory dietary intervention

BACKGROUND

Dietary interventions have been proposed as therapeutic approaches for several diseases, including cancer. A low-inflammatory Mediterranean dietary intervention, conducted as a pilot study in subjects with Familial Adenomatous Polyposis (FAP), reduced markers of local and systemic inflammation. We aim to determine whether this diet may modulate faecal microRNA (miRNA) and gene expression in the gut.

METHODS

Changes in the faecal miRNome were evaluated by small RNA sequencing at baseline (T0), after the three-month intervention (T1), and after an additional three months (T2). Changes in the transcriptome of healthy rectal mucosa and adenomas were evaluated by RNA sequencing at T0 and T2. The identification of validated miRNA-gene interactions and functional analysis of miRNA targets were performed using in silico approaches.

RESULTS

Twenty-seven subjects were included in this study. It was observed that the diet modulated 29 faecal miRNAs (p < 0.01; |log2 Fold Change|>1), and this modulation persisted for three months after the intervention. Levels of miR-3612-3p and miR-941 correlated with the adherence to the diet, miR-3670 and miR-4252-5p with faecal calprotectin, and miR-3670 and miR-6867 with serum calprotectin. Seventy genes were differentially expressed between adenoma and normal tissue, and most were different before the dietary intervention but reached similar levels after the diet. Functional enrichment analysis identified the proinflammatory ERK1/2, cell cycle regulation, and nutrient response pathways as commonly regulated by the modulated miRNAs and genes.

CONCLUSIONS

Faecal miRNAs modulated by the dietary intervention target genes that participate in inflammation. Changes in levels of miRNAs and genes with oncogenic and tumour suppressor functions further support the potential cancer-preventive effect of the low-inflammatory Mediterranean diet.

CLINICAL TRIAL NUMBER REGISTRATION

NCT04552405, Registered in ClinicalTrials.gov.

First Report of Sugarcane Mosaic Virus Infecting Goose Grass in Shandong Province, China

Sugarcane mosaic virus (SCMV genus Potyvirus, family Potyviridae) can infect maize, sugarcane, sorghum, other graminaceous crops, and some weed species (Alegria et al., 2003; Achon et al., 2007). In August 2023, the leaves of goose grass (Eleusine indica) plants surrounding maize fields in a village of Liaocheng City, Shandong Province, China showed mosaic and chlorotic symptoms (26%, 11 of 43 grasses; Figure S1). Three symptomatic goose grass samples were selected and pooled for total RNA isolation using TRIzol reagent (Tiangen, Beijing, China). A small RNA library was created using 2.0 μg of total RNA and the mirVana miRNA Isolation Kit, followed by size selection (18-28 nt), adapter ligation, purification, reverse transcription (RT), and polymerase chain reaction (PCR) enrichment. High-throughput sequencing (HTS) was then performed on a HiSeq 2500 platform (Illumina, San Diego, CA, USA). The adapter sequences were removed and the reads were assembled de novo into larger contigs using ABySS software v. 1.9.0 with a k-mer of 32. Fifty-one contigs were obtained after the reads were spliced and screened (alignment length > 30 bp; e-value ≤ 0.05). The contigs were compared with viral sequences in GenBank using local BLASTn. Thirty-four contigs (34-64 nt) had the highest identities (97.18-100%) with the SCMV genome sequence, covering approximately 12.8% of the SCMV genome (Table S1). The low coverage of small contigs mapping to the SCMV genome in the HTS results may be attributed to variations in sequencing depth and sample preparation quality, biological aspects of the virus affecting siRNA production and detection, as well as the variability in viral genome and its size (Golyaev et al., 2019; Valenzuela et al., 2022). The other 17 contigs did not align to any plant virus sequences, but aligned to plant sequences, including Phragmites australis and Panicum virgatum. Potyvirus-degenerated primers PotyF (5'-ATGGTHTGGTGYATHGARAAYGG-3') and PotyR (5'-TGCTGCKGCYTTCATYTG-3') (Marie-Jeanne et al. 2000) were used in RT-PCR to detect SCMV in symptomatic leaves, yielding a ~300 bp amplicon. Sanger sequencing and BLASTn analysis confirmed the 97.98% nucleotide identity with SCMV isolate BJ (GenBank accession No. AY042184.1). The sequence was deposited in GenBank under accession number OR777055. In addition, specific SCMV primers SCMV-F (5'- TCCGGAACTGTGGATGCA-3') and SCMV-R (5'- GTGGTGCTGCTGCACTCCC-3') (coat protein region, 939 bp) detected the virus in all 11 symptomatic goose grass leaves, with no detection in asymptomatic leaves. Inoculation tests using extracts from symptomatic goose grass on maize plants resulted in mosaic symptoms (7 of 15 plants) at 4-6 days post-inoculation (Figure S2 and 3). However, no symptoms were observed in maize plants following inoculation with leaf extracts from healthy goose grass. RT-PCR confirmed the presence of SCMV in the diseased maize plants. Sequencing analysis revealed that all amplified fragments shared 100% identity with the partial CP-encoding sequence of SCMV. Taken together these results support the presence of SCMV in symptomatic goose grass. To the best of our knowledge, this is the first report of SCMV in E. indica in China. In general, potyviruses can be easily transmitted in multiple ways including aphid vectors, grafting, and wounding. Therefore, investigating SCMV in goose grass is crucial for developing integrated strategies to prevent its transmission to economically important plants such as maize.

Fibulin 1, targeted by microRNA-24-3p, promotes cell proliferation and migration in vascular smooth muscle cells, contributing to the development of atherosclerosis in APOE-/- mice

Extracellular matrix (ECM) and vascular smooth muscle cells (VSMCs) are the main components of atherosclerosis (AS) plaque. VSMCs participate in plaque formation through phenotypic transformation. The complex interplay between ECM and VSMCs plays vital roles in the progression of AS throughout the disease. An in-depth investigation into the functions of ECM-related molecules in VSMC development might contribute to deciphering the complexity of AS pathogenesis. In this study, the roles and molecular mechanisms of the ECM-related molecule Fibulin-1 (FBLN1) in the development of AS and VSMCs were explored using RNA sequencing, bioinformatics analysis, and cell experiments. Furthermore, the expression of FBLN1, as determined by western blot analysis, immunohistochemistry, and real-time quantitative PCR, was significantly increased in AS vascular samples compared to normal vascular samples. Silencing the FBLN1 through AAV viral injection in mice revealed an improvement in AS. Functional analyses revealed that FBLN1 promoted VSMC proliferation, migration, and wound healing. Combined with RNA sequencing and TargetScan7.2 prediction data, 22 microRNAs (miRNAs) were found to have the potential for direct interaction with the FBLN1 3'UTR in VSMCs. Among these 22 miRNAs, it was demonstrated that microRNA-24-3p (miR-24-3p) could negatively regulate FBLN1 expression by directly binding to the FBLN1 3'UTR. Moreover, miR-24-3p inhibited cell proliferation, migration, and wound healing, and suppressed the expression of Ki67, matrix metalloproteinase-2 and -9 (MMP2/9) by targeting FBLN1 in VSMCs. Meanwhile, inhibition of FBLN1 expression could restrain VSMC phenotypic transformation. In conclusion, miR-24-3p inhibited VSMC proliferation and migration by targeting FBLN1. Additionally, multiple miRNAs with the potential to interact with the FBLN1 3'UTR were identified. These findings might deepen our understanding of ECM gene regulatory networks and the complex etiology of AS.

Milk exosomal microRNA profiling identified miR-375 and miR-199-5p for regulation of immune response during subclinical mastitis of crossbred cattle

BACKGROUND

The dairy industry has experienced significant economic losses as a result of mastitis, an inflammatory disease of cows, including both subclinical and clinical cases. Milk exosome microRNAs have gained attention due to their stable and selective wrapping nature, offering potential for the prognosis and diagnosis of bovine mastitis, the most common pathological condition of the mammary gland.

METHODS AND RESULTS

 In the present investigation, the microRNA profile of milk exosomes was explored using high-throughput small RNA sequencing data in sub-clinical mastitic and healthy crossbred Vrindavani cattle. In both groups, 349 microRNAs were identified, with 238 (68.19%) microRNAs co-expressed; however, 35 and 76 distinct microRNAs were found in subclinical mastitic and healthy cattle, respectively. Differential expression analysis revealed 11 microRNAs upregulated, and 18 microRNAs were downregulated in sub-clinical mastitic cattle. The functional annotation of the target genes of differentially expressed known and novel microRNAs including bta-miR-375, bta-miR-199-5p and bta-miR-12030 reveals their involvement in the regulation of immune response and inflammatory mechanisms and could be involved in development of mastitis.

CONCLUSIONS

The analysis of milk exosomal miRNAs cargos hold great promise as an approach to study the underlying molecular mechanisms associated with mastitis in high milk producing dairy cattle. Concurrently, the significantly downregulated miR-375 may upregulate key target genes, including CTLA4, IHH, IRF1, and IL7R. These genes are negative regulators of immune response pathways, which could be associated with impaired inflammatory mechanisms in mammary cells. According to the findings, bta-miR-375 could be a promising biomarker for the development of mastitis in dairy cattle.

Inhibition of ferroptosis alleviates chronic unpredictable mild stress-induced depression in mice via tsRNA-3029b

Depression is a common mental illness. Ferroptosis is a form of cell death that may be responsible for neurological disease, but the role of ferroptosis in depression remains unclear. tRNA-derived small RNA (tsRNA) is an emerging non-coding small RNA, making it an important medium for studying neurological diseases. Chronic unpredictable mild stress (CUMS) was used to construct the depression model in mice, which was treated with ferrostatin-1 (Fer-1). Classical behavioral test, immunofluorescence and small RNA sequencing were used to detect depression-like behaviors, neuronal proliferation and the expression profile of tsRNAs in mice, respectively. The primary neuronal cell damage model was constructed by corticosterone (CORT), and the function of key tsRNA was investigated by quantitative real-time PCR, western blot and CCK-8 assays. Here, Fer-1 reduced the depression-like behavior of CUMS-induced mice and promoted neuronal growth. In addition, CUMS caused the disorder of tsRNA expression profile in hippocampal tissues of mice, and Fer-1 alleviated the abnormal tsRNA expression, among which tsRNA-3029b was an effective target. In vitro experiments manifested that ROS accumulation and decreased expression of SLC7A11 and GPX4 were found in CORT-induced depression-like cell model, suggesting that ferroptosis was involved in neuronal injury. However, inhibition of tsRNA-3029b suppressed neuronal cell ferroptosis and facilitated neuronal regeneration. In conclusion, Fer-1 showed an antidepressant effect in CUMS-induced mice and alleviated the abnormal expression profile of tsRNA. tsRNA-3029b was a key target in depression, and silencing of tsRNA-3029b reduced the occurrence of ferroptosis and protected neurons from injury, which may provide novel target for the treatment of depression.

Profiling small RNAs in fecal immunochemical tests: is it possible?

Fecal microRNAs represent promising molecules with potential clinical interest as non-invasive diagnostic and prognostic biomarkers. Colorectal cancer (CRC) screening based on the fecal immunochemical test (FIT) is an effective tool for prevention of cancer development. However, due to the poor sensitivity of FIT especially for premalignant lesions, there is a need for implementation of complementary tests. Improving the identification of individuals who would benefit from further investigation with colonoscopy using molecular analysis, such as miRNA profiling of FIT samples, would be ideal due to their widespread use. In the present study, we assessed the feasibility of applying small RNA sequencing to measure human miRNAs in FIT leftover buffer in samples from two European screening populations. We showed robust detection of miRNAs with profiles similar to those obtained from specimens sampled using the established protocol of RNA stabilizing buffers, or in long-term archived samples. Detected miRNAs exhibited differential abundances for CRC, advanced adenoma, and control samples that were consistent for FIT and RNA-stabilizing buffers. Interestingly, the sequencing data also allowed for concomitant evaluation of small RNA-based microbial profiles. We demonstrated that it is possible to explore the human miRNome in FIT leftover samples across populations and envision that the analysis of small RNA biomarkers can complement the FIT in large scale screening settings.

Viral infections inhibit saponin biosynthesis and photosynthesis in Panax notoginseng

Virus-infected Panax notoginseng plants with chlorotic, mosaic, and pitted leaves are ubiquitous in the primary P. notoginseng-producing region in Wenshan autonomous prefecture, Yunnan province, China. However, the viruses that infect P. notoginseng and the effects of viral infections on the biosynthesis of secondary metabolites and photosynthesis remain unknown. This study identified a variety of viruses infecting P. notoginseng plants via deep-sequencing of small RNA (sRNA). Of the 10 identified viruses, seven had not previously been detected in P. notoginseng, including Cauliflower mosaic virus and Soybean chlorotic mottle virus. In addition, the simultaneous infection of P. notoginseng by Panax notoginseng virus A (PnVA), Panax cryptic virus 4 (PCV4), and Tomato yellow leaf curl China virus (TYLCCNV) was confirmed by PCR. Moreover, a quantitative PCR analysis showed that the expression levels of key genes related to saponin biosynthesis were generally down-regulated in the virus-infected P. notoginseng. Additionally, high-performance liquid chromatography results indicated the saponin content decreased in the roots of virus-infected P. notoginseng plants. The activities of photosynthesis-related enzymes, including ribulose-1,5-bisphosphate carboxylase/oxygenase, fructose 1,6-bisphosphatase, and fructose 1,6-biphosphate aldolase, decreased significantly in the virus-infected P. notoginseng plants. The viral infections also induced the expression of antioxidant genes and increased antioxidant enzyme activities. Furthermore, the expression levels of many resistance-related genes were up-regulated in P. notoginseng plants inoculated with a viral suspension. The study results provide the foundation for future research on P. notoginseng viral diseases, which may lead to the development of enhanced disease control measures.

Transcriptome Profiling of miRNA-mRNA Interactions and Associated Mechanisms in Chemotherapy-Induced Neuropathic Pain

Chemotherapy-induced neuropathic pain (CINP) is a dose-limiting adverse event affecting 40% of chemotherapy patients. MiRNA-mRNA interaction plays an important role in various processes. However, detailed profiling of miRNA-mRNA interactions in CINP remains unclear. Here, a rat-based CINP model was established using paclitaxel, followed by nociceptive behavioral tests related to mechanical allodynia, thermal hyperalgesia, and cold allodynia. The landscape of miRNA-mRNA interaction in the spinal dorsal horn was investigated through mRNA transcriptomics and small RNA sequencing. Under CINP condition, 86 differentially expressed mRNAs and 56 miRNAs were identified. Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated the activity of Odorant binding, postsynaptic specialization and synaptic density, extracellular matrix, mitochondrial matrix, retrograde endocannabinoid signaling, and GTPase activity. Protein-protein interaction (PPI), networks of circRNA-miRNA-mRNA, lncRNA-miRNA-mRNA, and TF-genes were demonstrated. We next explored the immune infiltration microenvironment and found a higher infiltration abundance of Th17 and a lower abundance of MDSC in CINP. RT-qPCR and dual-luciferase assays were used to verify the sequencing results, and single-cell analysis based on the SekSeeq database was conducted. Combined with bioinformatics analyses and experimental validations, Mpz, a protein-coding gene specifically expressed in Schwann cells, was found critical in maintaining CINP under miRNA regulation. Therefore, these data highlight the expression patterns of miRNA-mRNA, and the underlying mechanism in the spinal dorsal horn under CINP condition, and Mpz may serve as a promising therapeutic target for patients with CINP.

In silico analysis of serum miRNA profiles in seronegative and seropositive rheumatoid arthritis patients by small RNA sequencing

Rheumatoid arthritis (RA) is a refractory autoimmune disease, affecting about 1% of the world's population. RA is divided into seronegative RA and seropositive RA. However, biomarkers for discriminating between seronegative and seropositive RA have not been reported. In this study, we profiled serum miRNAs in seronegative RA patients (N-RA), seropositive RA patients (P-RA) and healthy controls (HC) by small RNA sequencing. Results indicated that compared with HC group, there were one up-regulated and four downregulated miRNAs in N-RA group (fold change ≥ 2 and P value < 0.05); compared with P-RA group, there were two up-regulated and four downregulated miRNAs in N-RA group; compared with HC group, there were three up-regulated and four downregulated miRNAs in P-RA group. Among them, the level of hsa-miR-362-5p in N-RA group was up-regulated compared with that in HC group and P-RA group, and the level of hsa-miR-6855-5p and hsa-miR-187-3p in P-RA group was upregulated compared with that in N-RA group and HC group. Validation by qPCR confirmed that serum hsa-miR-362-5p level was elevated in N-RA group. Subsequently, by analyzing the target genes using RNAhybrid, PITA, Miranda and TargetScan and functions of differential miRNAs utilizing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we found that the target genes and molecular pathways regulated by miRNAs in seronegative RA and seropositive RA were roughly the same, and miRNAs in these two diseases may participate in the occurrence and development of diseases by regulating the immune system. In conclusion, this study revealed the profiles of serum miRNAs in seronegative and seropositive RA patients for the first time, providing potential biomarkers and targets for the diagnosis and treatment of seronegative and seropositive RA.

Integrated analysis of smRNAome, transcriptome, and degradome data to decipher microRNAs regulating costunolide biosynthesis in Saussurea lappa

Saussurea lappa (S. lappa) has been known to synthesize medicinally important, costunolide. Due to its immense therapeutic importance, understanding of regulatory mechanism associated with its biosynthesis is crucial. The identification of genes and transcription factors (TFs) in S. lappa, created a clear picture of costunolide biosynthesis pathways. Further to understand the regulation of costunolide biosynthesis by miRNAs, an integrated study of transcriptome, miRNAs, and degradome was performed. Identified candidate miRNAs and associated feed-forward loops (FFLs) illustrates their regulatory role in secondary metabolite biosynthesis. Small RNA and degradome sequencing were performed for leaf and root tissues to determine miRNAs-targets pairs. A total of 711 and 525 such targets were obtained for novel and known miRNAs respectively. This data was used to generate costunolide-specific miRNA-TF-gene interactome to perform systematic analyses through graph theoretical approach. Interestingly, miR171c.1 and sla-miR121 were identified as key regulators to connect and co-regulate both mevalonate and sesquiterpenoid pathways to bio-synthesize costunolide. Tissue-specific FFLs were identified to be involved in costunolide biosynthesis which further suggests the evolutionary co-relation of root-specific networks in synthesis of secondary metabolites in addition to leaf-specific networks. This integrative approach allowed us to determine candidate miRNAs and associated tissue-specific motifs involved in the diversification of secondary metabolites. MiRNAs identified in present study can provide alternatives for bioengineering tool to enhance the synthesis of costunolide and other secondary metabolites in S. lappa.

MicroRNAs from Holarrhena pubescens stems: Identification by small RNA Sequencing and their Potential Contribution to Human Gene Targets

Holarrhena pubescens is an effective medicinal plant from the Apocynaceae family, widely distributed over the Indian subcontinent and extensively used by Ayurveda and ethno-medicine systems without apparent side effects. We postulated that miRNAs, endogenous non-coding small RNAs that regulate gene expression at the post-transcriptional level, may, after ingestion into the human body, contribute to the medicinal properties of plants of this species by inducing regulated human gene expression to modulate. However, knowledge is scarce about miRNA in Holarrhena. In addition, to test the hypothesis on the potential pharmacological properties of miRNA, we performed a high-throughput sequencing analysis using the Next Generation Sequencing Illumina platform; 42,755,236 raw reads have been generated from H. pubescens stems from a library of small RNA isolated, identifying 687 known and 50 new miRNAs led. The novel H. pubescens miRNAs were predicted to regulate specific human genes, and subsequent annotations of gene functions suggested a possible role in various biological processes and signaling pathways, such as Wnt, MAPK, PI3K-Akt, and AMPK signaling pathways and endocytosis. The association of these putative targets with many diseases, including cancer, congenital malformations, nervous system disorders, and cystic fibrosis, has been demonstrated. The top hub proteins STAT3, MDM2, GSK3B, NANOG, IGF1, PRKCA, SNAP25, SRSF1, HTT, and SNCA show their interaction with human diseases, including cancer and cystic fibrosis. To our knowledge, this is the first report of uncovering H. pubescens miRNAs based on high-throughput sequencing and bioinformatics analysis. This study has provided new insight into a potential cross-species control of human gene expression. The potential for miRNA transfer should be evaluated as one possible mechanism of action to account for the beneficial properties of this valuable species.

Investigating microRNAs in diabetic cardiomyopathy as tools for early detection and therapeutics

To profile microRNAs population of glucose-induced cardiomyoblast cell line and identify the differentially expressed microRNAs and their role under pre-diabetes and diabetes condition in vitro. Rat fetal ventricular cardiomyoblast cell line H9c2 was treated with D-glucose to mimic pre-diabetic, diabetic, and high-glucose conditions. Alteration in cellular, nuclear morphology, and change in ROS generation was analyzed through fluorescent staining. Small RNA sequencing was performed using Illumina NextSeq 550 sequencer and was validated using stem-loop qRT-PCR. A large number (~ 100) differential miRNAs were detected in each treated samples as compared to control; however, a similar expression pattern was observed between pre-diabetes and diabetes conditions with the exception for miR-429, miR-101b-5p, miR-503-3p, miR-384-5p, miR-412-5p, miR-672-5p, and miR-532-3p. Functional annotation of differential expressed target genes revealed their involvement in significantly enriched key pathways associated with diabetic cardiomyopathy. For the first time, we report the differential expression of miRNAs (miR-1249, miR-3596d, miR- 3586-3p, miR-7b-3p, miR-191, miR-330-3p, miR-328a, let7i-5p, miR-146-3p, miR-26a-3p) in diabetes-induced cardiac cells. Hyperglycemia threatens the cell homeostasis by dysregulation of miRNAs that begins at a glucose level 10 mM and remains undetected. Analysis of differential expressed miRNAs in pre-diabetes and diabetes conditions and their role in regulatory mechanisms of diabetic cardiomyopathy holds high potential in the direction of using miRNAs as minimally invasive diagnostic and therapeutic tools.

Genome-Wide Analysis of Planarian piRNAs

In planarian flatworms, the piRNA pathway is operated by three PIWI proteins, termed SMEDWI-1, SMEDWI-2, and SMEDWI-3 (SMEDWI = Schmidtea mediterranea PIWI). The interplay between these three PIWI proteins and their associated small noncoding RNAs, termed piRNAs, fuels the outstanding regenerative abilities of planarians, enables tissue homeostasis, and, ultimately, ensures animal survival. As the molecular targets of PIWI proteins are determined by the sequences of their co-bound piRNAs, it is imperative to identify these sequences by next-generation sequencing applications. Following sequencing, the genomic targets and the regulatory potential of the isolated piRNA populations need to be uncovered. To that end, here we present a bioinformatics analysis pipeline for processing and systematic characterization of planarian piRNAs. The pipeline includes steps for the removal of PCR duplicates based on unique molecular identifier (UMI) sequences, and it accounts for piRNA multimapping to different loci in the genome. Importantly, our protocol also includes a fully automated pipeline that is freely available at GitHub. Together with the piRNA isolation and library preparation protocol (see accompanying chapter), the presented computational pipeline enables researchers to explore the functional role of the piRNA pathway in flatworm biology.

Selective extracellular secretion of small double-stranded RNA by Tetragenococcus halophilus

Small double-stranded RNAs (dsRNAs) abundantly produced by lactic acid bacteria demonstrate immunomodulatory activity and antiviral protective immunity. However, the extracellular secretion of dsRNA from lactic acid bacteria and their compositional and functional differences compared to the intracellular dsRNA is unknown. In this study, we compared the intracellular and secreted extracellular dsRNA of the lactic acid bacteria, Tetragenococcus halophilus, commonly present in fermented foods, by growing in RNA-free and RNase-free media. We used RNA deep sequencing and in-silico analysis to annotate potential regulatory functions for the comparison. A time series sampling of T. halophilus culture demonstrated growth phase-dependent dynamics in extracellular dsRNA secretion with no major change in the intracellular dsRNA profile. The RNA deep sequencing resulted in thousands of diverse dsRNA fragments with 14-21 nucleotides in size from T. halophilus culture. Over 70% of the secreted extracellular dsRNAs were unique in their sequences compared to the intracellular dsRNAs. Furthermore, the extracellular dsRNA abundantly contains sequences that are not T. halophilus genome encoded, not detected intracellularly and showed higher hits on human transcriptome during in-silico analysis, which suggests the presence of extrachromosomal mobile regulatory elements. Further analysis showed significant enrichment of dsRNA target genes of human transcriptome on cancer pathways and transcription process, indicating the extracellular dsRNA of T. halophilus is different not only at the sequence level but also in function. Studying the bacterial extracellular dsRNA is a promising area of future research, particularly for developing postbiotic fermented functional foods and understanding the impact of commensal gut bacteria on human health.

Characterization of plasma-derived exosomal miRNA changes following traffic-related air pollution exposure: A randomized, crossover trial based on small RNA sequencing

BACKGROUND

The underlying mechanisms for health effects of traffic-related air pollution (TRAP) are still unclear. Small RNA sequencing (RNA-seq) in exosomes represents as a powerful approach to elucidate biological pathways in response to environmental exposure. We therefore aimed to explore impact of TRAP exposure on exosomal miRNAs.

METHODS

We performed a randomized, crossover study among 35 healthy college students in Shanghai, China. Participants were randomly assigned to 4-hour exposure in a traffic-polluted Road and in a traffic-free Park, respectively, intermitted by a washout period (at least 2 weeks). RNA-seq was conducted to identify plasma-derived exosomal miRNAs and the differential miRNAs were explored using linear mixed-effect models. Pathway enrichment was conducted using ingenuity pathway analysis. Further, we validated several selected miRNAs by droplet digital PCR (ddPCR).

RESULTS

The average concentrations of air pollutants including ultrafine particles, black carbon, nitrogen dioxide, and carbon dioxide were 2-3 times higher in the Road compared to those in the Park. We identified 271 exosomal miRNAs (212 up-regulated and 59 down-regulated) that were significantly associated with TRAP. We found 5 miRNAs with 242 experimentally validated mRNA targets that were involved in cardiovascular pathway, cytokine signaling, and immune response. The ddPCR analysis suggested that miR-3612, miR-21-5p, and miR-195-5p were significantly changed following TRAP exposure.

CONCLUSIONS

For the first time this trial characterized the genome-wide changes of exosomal miRNA associated with TRAP exposure. The molecular profiling of exosomal miRNAs and "novel" associations of some miRNAs were useful for understanding on biological mechanisms for the adverse effects of TRAP.

The microRNAs in the antennae of Apolygus lucorum (Hemiptera: Miridae): Expression properties and targets prediction

MicroRNAs (miRNAs) regulate gene expression and contribute to numerous physiological processes. However, little is known about the functions of miRNAs in insect chemosensation. In this study, nine small RNA libraries were constructed and sequenced from the antennae of nymphs, adult males, and adult females of Apolygus lucorum. In total, 399 (275 known and 124 novel) miRNAs were identified. miR-7-5p_1 was the most abundant miRNA. Altogether, 69,708 target genes related to biogenesis, membrane, and binding activities were predicted. In particular, 15 miRNAs targeted 16 olfactory genes. Comparing the antennae of nymphs and adult males and females, 94 miRNAs were differentially expressed. Alternatively, a subset of differentially expressed miRNAs was verified by qPCR, supporting the reliability of the sequencing results. This study provides a global miRNA transcriptome for the antennae of A. lucorum and valuable information for further investigations of the functions of miRNAs in the regulation of chemosensation.

EV-miRome-wide profiling uncovers miR-320c for detecting metastatic colorectal cancer and monitoring the therapeutic response

PURPOSE

Molecular composition of circulating small extracellular vesicles (EVs) does not merely reflect the cells of origin, but also is enriched in specific biomolecules directly associated with the cellular transformation. However, while most of the currently identified EV-miRs are only geared towards one-dimensional disease detection, their application for long-term tracking and treatment response monitoring has been largely elusive.

METHODS

We established and optimized a rapid, sensitive and robust liquid biopsy sampling method, and further used small RNA sequencing to comprehensively catalogue EV-miRomes in association with the progression and outcome of metastatic colorectal cancer (mCRC).

RESULTS

By cross-comparison of EV-miRomes (n = 290) from multi-stage and longitudinal cohorts, we uncovered a 15-EV-miR signature with dual detection and long-term monitoring of tumor size progression for mCRC. From this panel, EV-miR-320c was uncovered as a strong clinical marker - aside from its diagnostic power and a therapeutic monitoring performance superior to carcinoembryonic antigen (CEA), its high expression has also been linked to lower overall survival and a greater likelihood of disease recurrence. Further, integrative analyses of tissue transcriptomic and liquid biopsy implicated this 15-EV-miR signature in programming the mesenchymal-epithelial transition (MET) for distant localization of the metastasized cells and also in creating a tumor-favoring metastatic niche.

CONCLUSION

Our clinically-oriented delineation of the mCRC-associated circulating EV-miRomes systematically revealed the functional significance of these liquid biopsy markers and further strengthen their translational potential in mCRC therapeutic monitoring.

Transcriptome-wide identification of microRNAs in response to 20-hydroxyecdysone in Galeruca daurica

Both 20-hydroxyecdysone (20E) and miRNAs have multiple functions in the regulation of various physiological processes in insects. However, little is known about the interaction between 20E and miRNAs. In this study, six small RNA libraries were constructed from the adult Galeruca daurica treated with 20E and dimethyl sulfoxide (DMSO), respectively. Using small RNA sequencing, a total of 183 miRNAs, including 140 known and 43 novel miRNAs, were identified. Compared with the control (DMSO), 52 miRNAs (21 up-regulated and 31 down-regulated) were significantly differentially expressed after 20E treatment. The KEGG and GO analysis of the predicted genes targeted by 20E-responsive miRNAs indicate that 20E may influence the metabolic change during reproductive diapause in G. daurica via regulating miRNAs.

Creating and maintaining a high-confidence microRNA repository for crop research: A brief review and re-examination of the current crop microRNA registries

miRBase was established as an authoritative microRNA (miRNA) database with a uniform nomenclature system and a searchable web interface. Recent popularization of the next-generation sequencing technology in small RNA cloning led to an explosive growth of the miRNA repository. Although a specific definition system has been proposed for the plant miRNAs, the quality of the plant miRNA registries deposited in miRBase is largely dependent on the submitters. With the growing concerns over the annotation quality, a set of criteria for identification of the high-confidence (HC) miRNAs was recently developed by miRBase. Since miRNAs could serve as a powerful tool for crop genetic improvement and breeding, we present a brief overview of the miRBase-registered crop miRNAs in this study. A total of 54 plants were identified from the 82 Viridiplantae species in the current version of miRBase, and were regarded as the crops. A total of 6316 precursors encoding 7422 mature miRNAs (miRBase release 22.1) were included in our survey. Based on the HC annotation criteria, we performed structure- and sequencing data-based analyses of the confidence of the crop miRNAs. According to the results, we propose suggestions for improvements of the HC annotation system and, moreover, discuss strategies for creating and maintaining an HC miRNA repository of crops. Finally, we hope that this study inspires more efforts devoted to HC miRNA discoveries for crop research.

Detecting MicroRNAs in Plant Genomes with miRkwood

We present miRkwood, a comprehensive software tool developed to identify microRNAs and their precursor in plant genomes, with or without small-RNA-seq sequencing data. We describe how to install the software, how to set up and run it, and how to explore and analyse the results: genomic annotations, secondary structure of the precursor, alignments, reads distribution.

Analysis of Small RNA Sequencing Data in Plants

Over the past decades, next-generation sequencing (NGS) has been employed extensively for investigating the regulatory mechanisms of small RNAs. Several bioinformatics tools are available for aiding biologists to extract meaningful information from enormous amounts of data generated by NGS platforms. This chapter describes a detailed methodology for analyzing small RNA sequencing data using different open source tools. We elaborate on various steps involved in analysis, from processing the raw sequencing reads to identifying miRNAs, their targets, and differential expression studies.

Isolation and Characterization of Urinary Extracellular Vesicles for MicroRNA Biomarker Signature Development with Reference to MISEV Compliance

Urine bears high potential for serving as biomarker repository for renal and urinary tract associated disorders. Besides various metabolites and salts, urine carries extracellular vesicles (EVs)-a heterogeneous group of cell-derived mediators comprising proteins, lipids, and nucleic acids such as microRNAs (miRNAs). Particularly, EV-derived miRNA biomarkers have already been identified for numerous disorders such as sepsis, various blood and solid cancer entities, respiratory and renal diseases. However, study results are often incomparable due to poorly reported EV separation and miRNA isolation protocols and emphasize the need for standardization and reproducibility. To ensure valid EV-derived miRNA biomarker findings from urine, a step-by-step protocol compliant with the "Minimal Information for Studies of Extracellular Vesicles" (MISEV) is outlined in the following paragraphs. Actually, an immunoaffinity-based EV separation method followed by EV characterization, quantification, and normalization, as well as consecutive miRNA isolation and miRNA profiling by small RNA sequencing, are described.

Identification and bioinformatics analysis of differentially expressed milk exosomal microRNAs in milk exosomes of heat-stressed Holstein cows

In summer, heat stress is one of the primary reasons for the compromised health and low milk productivity of dairy cows. Hyperthermia affects milk synthesis and secretion in the mammary glands of dairy cows. As molecules for intercellular communication, milk-derived exosomes carry genetic material, proteins, and lipids, playing a crucial role in mammary tissue growth and milk synthesis in dairy cows. The aim of this study was to explore the milk exosomal miRNA profile of heat-stressed and normal Holstein cows. We isolated and identified milk exosomes to screening for differentially expressed miRNAs using small RNA sequencing. Then, TargetScan and miRanda algorithms were used to predict the putative targets of the differentially expressed miRNAs, whereas GO and KEGG pathway enrichment analyses were performed for the differentially expressed miRNA-target genes. Our results showed that 215 miRNAs were significantly differentially expressed in heat-stressed milk exosomes, of which one was upregulated and 214 were significantly downregulated. GO and KEGG enrichment analyses indicated that differentially expressed miRNAs might play a role in apoptosis, autophagy, and the p38 MAPK pathway. qRT-PCR assay verified that the expression of miRNAs was consistent with the sequencing results, warranting further verification of their specific targets of action. In conclusion, changes in the miRNA expression profile of milk exosomes indicated the role of exosomal miRNAs in regulating heat stress resistance and apoptosis in dairy cows. Our results suggested that milk-derived exosomal miRNAs could increase mammary gland resistance to heat stress, thereby enhancing milk synthesis in dairy cows.

Liver injury changes the biological characters of serum small extracellular vesicles and reprograms hepatic macrophages in mice

BACKGROUND

Serum small extracellular vesicles (sEVs) and their small RNA (sRNA) cargoes could be promising biomarkers for the diagnosis of liver injury. However, the dynamic changes in serum sEVs and their sRNA components during liver injury have not been well characterized. Given that hepatic macrophages can quickly clear intravenously injected sEVs, the effect of liver injury-related serum sEVs on hepatic macrophages deserves to be explored.

AIM

To identify the characteristics of serum sEVs and the sRNAs during liver injury and explore their effects on hepatic macrophages.

METHODS

To identify serum sEV biomarkers for liver injury, we established a CCL₄-induced mouse liver injury model in C57BL/6 mice to simulate acute liver injury (ALI), chronic liver injury (CLI) and recovery. Serum sEVs were obtained and characterized by transmission electron microscopy and nanoparticle tracking analysis. Serum sEV sRNAs were profiled by sRNA sequencing. Differentially expressed microRNAs (miRNAs) were compared to mouse liver-enriched miRNAs and previously reported circulating miRNAs related to human liver diseases. The biological significance was evaluated by Ingenuity Pathway Analysis of altered sEV miRNAs and conditioned cultures of ALI serum sEVs with primary hepatic macrophages.

RESULTS

We found that both ALI and CLI changed the concentration and morphology of serum sEVs. The proportion of serum sEV miRNAs increased upon liver injury, with the liver as the primary contributor. The altered serum sEV miRNAs based on mouse studies were consistent with human liver disease-related circulating miRNAs. We established serum sEV miRNA signatures for ALI and CLI and a panel of miRNAs (miR-122-5p, miR-192-5p, and miR-22-3p) as a common marker for liver injury. The differential serum sEV miRNAs in ALI contributed mainly to liver steatosis and inflammation, while those in CLI contributed primarily to hepatocellular carcinoma and hyperplasia. ALI serum sEVs decreased both CD86 and CD206 expression in monocyte-derived macrophages but increased CD206 expression in resident macrophages in vitro.

CONCLUSION

Serum sEVs acquired different concentrations, sizes, morphologies and sRNA contents upon liver injury and could change the phenotype of liver macrophages. Serum sEVs therefore have good diagnostic and therapeutic potential for liver injury.

MicroRNA expression profiling during the suckling-to-weaning transition in pigs

Weaning induces physiological changes in intestinal development that affect pigs’ growth performance and susceptibility to disease. As a posttranscriptional regulator, microRNAs (miRNAs) regulate cellular homeostasis during intestinal development. We performed small RNA expression profiling in the small intestine of piglets before weaning (BW), 1 week after weaning (1W), and 2 weeks after weaning (2W) to identify weaning-associated differentially expressed miRNAs. We identified 38 differentially expressed miRNAs with varying expression levels among BW, 1W, and 2W. Then, we classified expression patterns of the identified miRNAs into four types. ssc-miR-196a and ssc-miR-451 represent pattern 1, which had an increased expression at 1W and a decreased expression at 2W. ssc-miR-499-5p represents pattern 2, which had an increased expression at 1W and a stable expression at 2W. ssc-miR-7135-3p and ssc-miR-144 represent pattern 3, which had a stable expression at 1W and a decreased expression at 2W. Eleven miRNAs (ssc-miR-542-3p, ssc-miR-214, ssc-miR-758, ssc-miR-4331, ssc-miR-105-1, ssc-miR-1285, ssc-miR-10a-5p, ssc-miR-4332, ssc-miR-503, ssc-miR-6782-3p, and ssc-miR-424-5p) represent pattern 4, which had a decreased expression at 1W and a stable expression at 2W. Moreover, we identified 133 candidate targets for miR-196a using a target prediction database. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the target genes were associated with 19 biological processes, 4 cellular components, 8 molecular functions, and 7 KEGG pathways, including anterior/posterior pattern specification as well as the cancer, PI3K–Akt, MAPK, GnRH, and neurotrophin signaling pathways. These findings suggest that miRNAs regulate the development of the small intestine during the weaning process in piglets by anterior/posterior pattern specification as well as the cancer, PI3K–Akt, MAPK, GnRH, and neurotrophin signaling pathways.

Identification of microRNAs and their target genes related to needle discoloration of evergreen tree Chinese cedar (Cryptomeria fortunei) in cold winters

Comparative analysis of miRNAs and their gene targets between the evergreen and yellowish-brown Cryptomeria fortunei phenotypes in cold winters suggests a possible role of miRNA-regulated pathways in needle color. Cryptomeria fortunei (Chinese cedar) is a conifer tree of considerable economic, ornamental and ecological importance. Despite the evergreen nature of C. fortunei, most needles turn yellowish- or reddish-brown in winter. The roles of microRNAs (miRNAs) in regulating pigment biosynthesis in color-leafed plants have been widely investigated. However, whether or not an miRNA-mediated staged discoloration mechanism exists in evergreen C. fortunei is currently unknown. In this study, we deciphered the microRNAs landscape in overwintering C. fortunei needles using high-throughput sequencing. A total of 517 known and 212 novel miRNA mature/star sequences, including 233 differentially expressed miRNAs, were identified. Based on integrated transcriptome and miRNA analysis, 2702 target unigenes of the miRNAs were predicted and these targets were significantly enriched in pigment-related biosynthesis pathways. A miRNA-target pigment biosynthesis regulatory network was then constructed, and its module miRNA (ath-miR858b, aly-miR858-3p, cme-miR828 and novel33_mature)-MYBs (v-myb avian myeloblastosis viral oncogene homolog) appeared to be a key factor regulating needle discoloration in C. fortunei. These miRNA-MYBs were further confirmed by degradome sequencing. Overall, these findings provide new insight into the posttranscriptional regulatory mechanism of leaf/needle discoloration in gymnosperms and may contribute to the miRNA-mediated genetic improvement of evergreen C. fortunei needles.

Comparative profile of exosomal microRNAs in postmenopausal women with various bone mineral densities by small RNA sequencing

To explore the role of plasma miRNAs in exosomes in early postmenopausal women. Small RNA sequencing was implemented to clarify the expression of miRNA in plasma exosomes obtained from 15 postmenopausal women, divided into groups of osteoporosis, osteopenia, and normal bone mass based on bone mineral density. Differentially expressed miRNAs (DEMs) were identified by comparing miRNA expression profiles. Five putative miRNAs, miR-224-3p, miR-25-5p, miR-302a-3p, miR-642a-3p, and miR-766-5p were confirmed by real-time PCR; miRNA target genes were obtained from 4 databases: miRWalk, miRDB, RNA22, and TargetScan. The miRNA-mRNA- Kyoto Encyclopedia of Genes and Genomes (KEGG) networks were analyzed, and the DEMs' potential role was investigated by gene ontology terms and KEGG pathway annotation. The results suggest that characterizing plasma exosomal miRNA profiles of early postmenopausal women by small RNA sequencing could identify novel exo-miRNAs involved in bone remodeling, and miR-642a-3p maybe contribute to the prediction and diagnosis of early postmenopausal osteoporosis.

Exosomal miRNA profiling from H5N1 avian influenza virus-infected chickens

Exosomes are membrane vesicles containing proteins, lipids, DNA, mRNA, and micro RNA (miRNA). Exosomal miRNA from donor cells can regulate the gene expression of recipient cells. Here, Ri chickens were divided into resistant (Mx/A; BF2/B21) and susceptible (Mx/G; BF2/B13) trait by genotyping of Mx and BF2 genes. Then, Ri chickens were infected with H5N1, a highly pathogenic avian influenza virus (HPAIV). Exosomes were purified from blood serum of resistant chickens for small RNA sequencing. Sequencing data were analysed using FastQCv0.11.7, Cutadapt 1.16, miRBase v21, non-coding RNA database, RNAcentral 10.0, and miRDeep2. Differentially expressed miRNAs were determined using statistical methods, including fold-change, exactTest using edgeR, and hierarchical clustering. Target genes were predicted using miRDB. Gene ontology analysis was performed using gProfiler. Twenty miRNAs showed significantly different expression patterns between resistant control and infected chickens. Nine miRNAs were up-regulated and 11 miRNAs were down-regulated in the infected chickens compared with that in the control chickens. In target gene analysis, various immune-related genes, such as cytokines, chemokines, and signalling molecules, were detected. In particular, mitogen-activated protein kinase (MAPK) pathway molecules were highly controlled by differentially expressed miRNAs. The result of qRT-PCR for miRNAs was identical with sequencing data and miRNA expression level was higher in resistant than susceptible chickens. This study will help to better understand the host immune response, particularly exosomal miRNA expression against HPAIV H5N1 and could help to determine biomarkers for disease resistance.

Identification and functional analysis of microRNAs in the regulation of summer diapause in Galeruca daurica

MicroRNAs (miRNAs) regulate gene expression at the post-transcriptional level. Although the regulatory roles of miRNAs in various physiological processes throughout insect development have been investigated, it is almost unknown about the roles of miRNAs involved in regulation of diapause in insects. We constructed nine small RNA libraries from Galeruca daurica adults at different diapause stages: pre-diapause (PD), diapause (D), and post-diapause (TD). Using Illumina sequencing, a total of 95.06 million valid reads was obtained, and 222 miRNAs, including 135 conserved and 87 novel miRNAs, were identified from G. daurica. The expression profiles of these miRNAs were analyzed across different diapause stages. The 30 and 13 miRNAs were differentially expressed in the D/PD and TD/D comparisons, respectively. The KEGG and GO analysis of the predicted target genes suggested the essential roles of miRNAs in the regulation of summer diapause in G. daurica, especially via the juvenile hormone, ribosome, MAPK signaling, and Ca²⁺ signaling pathways. Our research results indicate that miRNAs may be involved in the regulation of summer diapause in G. daurica, and these results also provide an important new small RNA genomics resource for further studies on insect diapause.

Identification of microRNA-like RNAs in Cordyceps guangdongensis and their expression profile under differential developmental stages

Cordyceps guangdongensis is a well-known fungus with high nutritional and medicinal value. The metabolite profile of C. guangdongensis is similar to that of Ophiocordyceps sinensis. In plants and animals, microRNAs play important roles in regulating gene expression at the post-transcriptional level. MicroRNA-like RNAs (milRNAs) have been documented in several macro-fungi. To comprehensively investigate the milRNAs in C. guangdongensis, three small RNA libraries from the differentially developmental stages were constructed. Twenty-six conserved milRNAs were identified, and 19 novel milRNA candidates were predicted. Among them, 20 milRNAs were differentially expressed across the developmental processes, and 12 milRNAs were verified using stem-loop quantitative real-time reverse transcription polymerase chain reaction. In addition, the potential target genes of milRNA were predicted to be involved in the development of fruiting bodies and metabolite biosynthesis. This study is the first to report the milRNAs of C. guangdongensis, and provides important insights into studies of milRNA regulation pathways in ascomycete fungi.

Identification of oligo-adenylated small RNAs in the parasite Entamoeba and a potential role for small RNA control

Background

The RNA interference (RNAi) pathway is a gene regulation mechanism that utilizes small RNA (sRNA) and Argonaute (Ago) proteins to silence target genes. Our previous work identified a functional RNAi pathway in the protozoan parasite Entamoeba histolytica, including abundant 27 nt antisense sRNA populations which associate with EhAgo2–2 protein. However, there is lack of understanding about the sRNAs that are bound to two other EhAgos (EhAgo2–1 and 2–3), and the mechanism of sRNA regulation itself is unclear in this parasite. Therefore, identification of the entire pool of sRNA species and their sub-populations that associate with each individual EhAgo protein would be a major step forward.

Results

In the present study, we sequenced sRNA libraries from both total RNAs and EhAgo bound RNAs. We identified a new population of 31 nt sRNAs that results from the addition of a non-templated 3–4 adenosine nucleotides at the 3′-end of the 27 nt sRNAs, indicating a non-templated RNA-tailing event in the parasite. The relative abundance of these two sRNA populations is linked to the efficacy of gene silencing for the target gene when parasites are transfected with an RNAi-trigger construct, indicating that non-templated sRNA-tailing likely play a role in sRNA regulation in this parasite. We found that both sRNA populations (27 nt and 31 nt) are present in the related parasite Entamoeba invadens, and are unchanged during the development. In sequencing the sRNAs associating with the three EhAgo proteins, we observed that despite distinct cellular localization, all three EhAgo sRNA libraries contain 27 nt sRNAs with 5′-polyphosphate (5′-polyP) structure and share a largely overlapping sRNA repertoire. In addition, our data showed that a fraction of 31 nt sRNAs associate with EhAgo2–2 but not with its mutant protein (C-terminal deletion), nor other two EhAgos, indicating a specific EhAgo site may be required for sRNA modification process in the parasite.

Conclusion

We identified a new population of sRNA with non-templated oligo-adenylation modification, which is the first such observation amongst single celled protozoan parasites. Our sRNA sequencing libraries provide the first comprehensive sRNA dataset for all three Entamoeba Ago proteins, which can serve as a useful database for the amoeba community.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07275-6.

Identification of genuine and novel miRNAs in Amaranthus hypochondriacus from high-throughput sequencing data

Amaranth has been proposed as an exceptional alternative for food security and climate change mitigation. Information about the distribution, abundance, or specificity of miRNAs in amaranth species is scare. Here, small RNAs from seedlings under control, drought, heat, and cold stress conditions of the Amaranthus hypocondriacus variety "Gabriela" were sequenced and miRNA loci identified in the amaranth genome using the ShortStack software. Fifty-three genuine miRNA clustersthirty-nine belonging to conserved families, and fourteen novel, were identified. Identification of their target genes suggests that conserved amaranth miRNAs are involved in growth and developmental processes, as well as stress responses. MiR0005, an amaranth-specific miRNA, exhibited an unusual high level of expression, akin to that of conserved miRNAs. Overall, our results broaden our knowledge regarding the distribution, abundance and expression of miRNAs in amaranth, providing the basis for future research on miRNAs and their functions in this important species.

The first report on circulating microRNAs at Pre- and Post-metamorphic stages of axolotls

MicroRNAs (miRNAs) are endogenously coded small RNAs, implicated in post-transcriptional gene regulation by targeting messenger RNAs (mRNAs). Circulating miRNAs are cell-free molecules, found in body fluids, such as blood and saliva, and emerged recently as potential diagnostic biomarkers. Functions of circulating miRNAs and their roles in target tissues have been extensively investigated in mammals, and the reports on circulating miRNAs in non-mammalian clades are largely missing. Salamanders display remarkable regenerative potential, and the Mexican axolotl (Ambystoma mexicanum), a critically endangered aquatic salamander, has emerged as a powerful model organism in regeneration and developmental studies. This study aimed to explore the circulating miRNA signature in axolotl blood plasma. Small RNA sequencing on plasma samples revealed 16 differentially expressed (DE) circulating miRNAs between neotenic and metamorphic stages out of identified 164 conserved miRNAs. Bioinformatics predictions provided functional annotation of detected miRNAs for both stages and enrichment of DE miRNAs in cancer-related and developmental pathways was notable. Comparison with previous reports on axolotl miRNAs unraveled common and unique members of the axolotl circulating miRNome. Overall, this work provides novel insights into non-mammalian aspects of circulating miRNA biology and expands the multi-omics toolkit for this versatile model organism.

Serum exosomal miRNA as biomarkers for Retinoblastoma

Retinoblastoma (RB) is a childhood eye tumor, caused by RB1 mutation. Though diagnosing RB is easier, prognosticating RB is limited to examining the patient under anesthesia and imaging technique. The aim of the study is to find exosomal miRNA biomarkers to prognosticate RB. Exosomes were isolated from one control - MIO-M1 and two RB cell lines - WERI-Rb-1 and NCC-RbC-51. Small RNA sequencing was performed on exosomal miRNA isolated from the three cell lines. miRNAs specific to each cell line were shortlisted. A total of 243, 606 and 400 miRNAs were identified in MIO-M1, WERI-Rb-1 and NCC-RbC-51 cell lines respectively. Nine miRNAs were shortlisted based on adjusted p value and literature, MIO-M1 specific (n = 1), WERI-RB-1 specific (n = 2), NCC-RbC-51 specific (n = 2) and miRNAs common to both RB cell lines (n = 4) were chosen. Validation was done using specific Taqman miRNA assays.miRNA validation was carried out on cell lines, cell line derived exosomes, primary RB tissues and exosomes isolated from serum of the RB patients. Validation of the miRNAs in cell lines and exosomes derived from the cell lines, confirmed the sequencing data. However, only 2 miRNAs - hsa-miR-301b-3p and hsa-miR-216b-5p were upregulated in the primary RB tissues. None of the miRNAs had significant expression in the serum exosomes of RB patients. Therefore, serum exosomal miRNA may not be ideal for prognosticating RB.Further research on other body fluids like CSF and vitreous could serve as potential source for biomarkers for prognosticating RB.

A tRNA-derived fragment (tRF-3001b) aggravates the development of nonalcoholic fatty liver disease by inhibiting autophagy

AIM

Nonalcoholic fatty liver disease (NAFLD) is a growing health problem worldwide. Impaired autophagy has been linked to NAFLD pathogenesis. Whether transfer RNA (tRNA)-derived fragments (tRFs) regulate the progression of NAFLD via autophagy is not clear. Here, we aimed to identify autophagy- or adipogenesis-related tRFs and investigate their roles in NAFLD.

METHODS

Small RNA sequencing was performed on NAFLD and control mice, and candidate tRFs were validated using quantitative reverse transcription PCR (qRT-PCR). The role of a key tRF was investigated using Oil red O staining, western blotting, qRT-PCR and a luciferase reporter assay.

KEY FINDINGS

In NAFLD mice, the expression of p62 was increased and the ratio of LC3B-II/LC3-I was decreased compared to control mice. We identified nine differentially expressed tRFs, among which tRF-3001b was found to be significantly upregulated in NAFLD mice compared to the control liver tissues. Autophagy was decreased in FA （fatty acids)-induced LO2 cells, while silencing of tRF-3001b significantly abrogated the decrease in autophagy and increase in lipid formation. Moreover, chloroquine (CQ) dramatically abrogated the effect of tRF-3001b inhibition on lipid formation. Mechanistically, tRF-3001b targeted and inhibited the expression of the autophagy-related gene Prkaa1. In vivo, tRF-3001b silencing significantly improved pathology and decreased the levels of triglycerides and cholesterol in NAFLD mice, while CQ dramatically abrogated the effect of tRF-3001b deficiency.

SIGNIFICANCE

tRF-3001b may aggravate the development of NAFLD by inhibiting autophagy via targeting Prkaa1.

sRIS: A Small RNA Illustration System for Plant Next-Generation Sequencing Data Analysis

Small RNA (sRNA), such as microRNA (miRNA) and short interfering RNA, are well-known to control gene expression based on degradation of target mRNA in plants. A considerable amount of research has applied next-generation sequencing (NGS) to reveal the regulatory pathways of plant sRNAs. Consequently, numerous bioinformatics tools have been developed for the purpose of analyzing sRNA NGS data. However, most methods focus on the study of sRNA expression profiles or novel miRNAs predictions. The analysis of sRNA target genes is usually not integrated into their pipelines. As a result, there is still no means available for identifying the interaction mechanisms between host and virus or the synergistic effects between two viruses. For the present study, a comprehensive system, called the Small RNA Illustration System (sRIS), has been developed. This system contains two main components. The first is for sRNA overview analysis and can be used not only to identify miRNA but also to investigate virus-derived small interfering RNA. The second component is for sRNA target prediction, and it employs both bioinformatics calculations and degradome sequencing data to enhance the accuracy of target prediction. In addition, this system has been designed so that figures and tables for the outputs of each analysis can be easily retrieved and accessed, making it easier for users to quickly identify and quantify their results. sRIS is available at http://sris.itps.ncku.edu.tw/.

Differential expression of microRNA in exosomes derived from endometrial stromal cells of women with endometriosis-associated infertility

RESEARCH QUESTION

What is the expression pattern of microRNA (miRNA) in exosomes isolated from eutopic endometrial stromal cells (EuESC) of women with endometriosis-associated infertility?

DESIGN

Small RNA sequencing was conducted in exosomes isolated from EuESC of women with endometriosis-associated infertility (n = 3) and normal endometrial stromal cells (NESC) of fertile women without endometriosis (n = 3). The differentially expressed miRNA in exosomes derived from EuESC and NESC were identified. The functions of the differentially expressed miRNA were analysed by gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.

RESULTS

Small RNA sequencing showed that the percentages of exosomal miRNA in the total small RNA isolated from EuESC and NESC were not significantly different (P = 0.7804). A total of 49 differentially expressed miRNA (fold change >1.5 and P < 0.05) were identified, including 26 up-regulated and 23 down-regulated in EuESC exosomes as compared with NESC exosomes. Functional analysis revealed that 12 miRNA were predicted to target homeobox A10 (HOXA10) and/or the leukaemia inhibitory factor (LIF) 3' untranslated region (UTR). Both HOXA10 and LIF mRNA expression levels were significantly decreased in EuESC compared with NESC (P = 0.0222 and 0.0395, respectively). In addition, the predicated target genes of these differentially expressed exosomal miRNA were significantly (P < 0.05) enriched in 76 pathways, including the MAPK and Wnt signalling pathways.

CONCLUSIONS

The differential expression patterns of exosomal miRNA were identified. Many exosomal miRNA may be involved in regulating the endometrial receptivity of women with endometriosis-associated infertility.

Novel miRNA identification and comparative profiling of miRNA regulations revealed important pathways in Jinding duck ovaries by small RNA sequencing

Functional studies have revealed miRNAs play pivotal roles in ovulation and ovary development in mammalians, whereas little is known about the miRNA function in ducks. In this study, miRNA deep sequencing in the ovary tissues was carried out to obtain the miRNA profile from ovaries before oviposition (BO) and after oviposition (AO) in Jinding duck. Overall, an average of 23,128,075 and 26,020,523 reads were identified in the BO and AO samples, respectively, and 6739 miRNAs were identified from them through further mapping and analysis. Besides, 1570 miRNAs were identified as differentially expressed miRNAs compared with BO, including 493 miRNAs up-regulated and 1077 down-regulated in AO. Moreover, 2291 target genes were predicted from 443 significantly differentially expressed miRNAs. In addition, GO and KEGG pathway analysis indicated that target genes were enriched in some basic cell metabolism pathways as well as the productive pathways such as MAPK signaling pathway, gonadotropin-releasing hormone signaling pathway, TGF-beta signaling pathway which had been significantly changed. Our results helped to replenish the duck miRNA database and illustrate the potential mechanism of miRNA function in duck ovary development and reproduction process.

Rice Female Meiosis: Genome-Wide mRNA, Small RNA, and DNA Methylation Analysis During Ovule Development

Meiosis is an essential process in sexual life cycle, not only for the genomic stability maintenance but also for the genetic diversity creation through recombination. In rice ovule, megaspore mother cells undergo meiosis to form megaspores; then the functional megaspore performs three rounds of mitoses to form female gametophyte. However, the mechanism of gene expression and regulation in female meiosis process is still poorly understood. As important gene regulatory factors, miRNAs and DNA methylation are widely involved in plant meiosis and ovule development. In order to systematically study the potential mechanism of gene expression and regulation in female meiosis, ovules at megaspore mother cell meiosis stage, functional megaspore mitosis stage, and mature female gametophytes are collected to perform genome-wide RNA sequencing, small RNA sequencing, and bisulfite sequencing. Through bioinformatics analysis, we obtained many differentially expressed genes, miRNAs, and differentially methylated genes related to female meiosis. These data may provide important clues for further revealing the mechanism of female meiosis in rice.

MIQE-Compliant Validation of MicroRNA Biomarker Signatures Established by Small RNA Sequencing

MicroRNAs (miRNAs), a class of small non-coding RNAs that modulate gene expression at the post-transcriptional level, are attractive targets in many academic and diagnostic applications. Among them, assessing miRNA biomarkers in minimally invasive liquid biopsies was shown to be a promising tool for managing diseases, particularly cancer. The initial screening of disease-relevant transcripts is often performed by high-throughput next-generation sequencing (NGS), in here RNA sequencing (RNA-Seq). After complex processing of small RNA-Seq data, differential gene expression analysis is performed to evaluate miRNA biomarker signatures. To ensure experimental validity, biomarker candidates are commonly validated by an orthogonal technology such as reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). This chapter outlines in detail the material and methods one can apply to reproducibly identify miRNA biomarker signatures from blood total RNA. After screening miRNA profiles by small RNA-Seq, resulting data is validated in compliance with the "Minimum Information for Publication of Quantitative Real-Time PCR Experiments" (MIQE) guidelines.

MicroRNA expression profile of Lacrimal Glands in rabbit autoimmune dacryoadenitis model

Purpose: To identify the differential expression of microRNAs (miRs) and the related gene networks and signal pathways in lacrimal glands (LGs) of rabbit autoimmune dacryoadenitis. Methods: Autoimmune dacryoadenitis in rabbits was induced by transferring activated peripheral blood lymphocytes (PBLs). The LGs of normal and model group rabbits were collected for small RNA sequencing. The most differentially expressed miRs were validated by quantitative real time-polymerase chain reaction (qRT-PCR). Further, bioinformatics analysis including target gene prediction, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Results: A total of 15 miRs were differentially expressed in the LGs of rabbit autoimmune dacryoadenitis relative to normal controls. GO and KEGG analysis revealed that most target genes of these dysregulated miRs were implicated in MAPK signaling pathway. Conclusion: Our results showed for the first time the differentially expressed miRs and the related pathways involved in the pathogenesis of rabbit autoimmune dacryoadenitis. These results may contribute to elucidating molecular pathogenesis of Sjögren's syndrome (SS) dry eye.

Identification and characterization of microRNAs in phloem and xylem from ramie (Boehmeria nivea)

Ramie (Boehmeria nivea) is a widely cropped species in southern China due to its high economic value of natural fiber for industry. Development of phloem and xylem is key evidence for generating fiber. However, the MicroRNA (miRNA) profiles of phloem and xylem in ramie have not been reported yet. miRNA belong to a small RNA family which has been recognized as an important regulator for various biological processes. In the present study, we aimed to identify differently expressed miRNAs between phloem and xylem in adult ramie. The results showed that 137 and 122 unique conserved miRNAs were identified from phloem and xylem libraries, respectively. Meanwhile, 4 novel miRNAs were identified from ramie by miRDeep2. Of these miRNAs, 77 conserved miRNAs in ramie were differentially expressed. Among the differentially expressed miRNAs, 44 miRNAs and 33 miRNAs were up-regulated and down-regulated in phloem compared to that in xylem, respectively. The functions of differentially expressed miRNAs were associated with regulating the development and differentiation of phloem and xylem. The present study provides a glance of miRNA profiles for further understanding of miRNA role in ramie development.

Detection of disease in Cucurbita maxima Duch. ex Lam. caused by a mixed infection of Zucchini yellow mosaic virus, Watermelon mosaic virus, and Cucumber mosaic virus in Southeast China using a novel small RNA sequencing method

The genus Cucurbita comprises many popular vegetable and ornamental plants, including pumpkins, squashes, and gourds, that are highly valued in China as well as in many other countries. During a survey conducted in Zhejiang province, Southeast China in 2016, severe symptoms of viral infection were observed on Cucurbita maxima Duch. ex Lam. Diseased plants showed symptoms such as stunting, mosaicking, Shoe string, blistering, yellowing, leaf deformation, and fruit distortion. Approximately, 50% of Cucurbita crops produced in Jinhua were diseased, causing an estimated yield loss of 35%. In this study, we developed a method using all known virus genomes from the NCBI database as a reference to map small RNAs to develop a diagnostic tool that could be used to diagnose virus diseases of C. maxima. 25 leaf samples from different symptomatic plants and 25 leaf samples from non-symptomatic plants were collected from the experimental field of Jihua National Agricultural Technology Garden for pathogen identification. Small RNAs from each set of three symptomatic and non-symptomatic samples were extracted and sequenced by Illumina sequencing. Twenty-four different viruses were detected in total. However, the majority of the small RNAs were from Zucchini yellow mosaic virus (ZYMV), Watermelon mosaic virus (WMV), and Cucumber mosaic virus (CMV). Mixed infections of these three viruses were diagnosed in leaf samples from diseased plants and confirmed by reverse transcription PCR (RT-PCR) using primers specific to these three viruses. Crude sap extract from symptomatic leaf samples was mechanically inoculated back into healthy C. maxima plants growing under greenhouse conditions. Inoculated plants developed the same disease symptoms as those observed in the diseased plants and a mixed infection of ZYMV, WMV, and CMV was detected again by RT-PCR, thus fulfilling Koch's postulates. The diagnostic method developed in this study involves fewer bioinformatics processes than other diagnostic methods, does not require complex settings for bioinformatics parameters, provides a high level of sensitivity to rapidly diagnose plant samples with symptoms of virus diseases and can be performed cheaply. This method therefore has the potential to be widely applied as a diagnostic tool for viruses that have genome information in the NCBI database.

Comparative profiling of roots small RNA expression and corresponding gene ontology and pathway analyses for low- and high-cadmium-accumulating genotypes of wheat in response to cadmium stress

MicroRNAs (miRNAs) participate in multiple biological processes in plant. Cd accumulation ability differs among varieties in wheat, but little is known about miRNAs and their function in Cd accumulation of wheat under Cd stress. Therefore, the present study detected small RNAs responsible for differential Cd accumulation between two contrasting wheat genotypes (low-Cd accumulation one L17 and high-Cd accumulation one H17) to identify novel targets to further study Cd stress in wheat. Under normal conditions, 139 miRNAs were differentially expressed between L17 and H17, while this value reached 142 after Cd exposure. For Cd-induced DEMs, total 25 miRNAs were differentially expressed in L17 after Cd treatment, while, 70 Cd-induced DEMs were found in H17. Moreover, GO analysis revealed that target genes of DEMs related to lipid biosynthetic process and chlorophyll binding are uniquely enriched in L17, target genes of DEMs related to ribosome biogenesis and sucrose alpha-glucosidase activity are uniquely enriched in H17. By pathway analysis, target genes of DEMs related to PI3K-Akt signaling pathway was specifically enriched in L17, target genes of DEMs related to carbohydrate digestion and absorption pathway was uniquely enriched in H17. In addition, miRNA-gene co-expression showed that tae-miR9774 was uniquely expressed between L17Cd and L17CK, while tae-miR398 was specially expressed between H17Cd and H17CK. Our results suggested that Cd-accumulating ability of L17 and H17 varied from the expression of induced unique miRNA, such as expression of tae-miR-9774 and tae-miR-398. Our study not only provide the foundation for further exploring the miRNAs-induced molecular mechanisms of Cd accumulation in wheat but also supply novel strategies for improving phytoremediation ability of food plants through genetic engineering.

Enumeration of deregulated miRNAs in liquid and tissue biopsies of cervical cancer

OBJECTIVE

The altered miRNAs expression in cervical cancer tissue can be a critical player during tumorigenesis, may contribute to tumor cell heterogeneity and may determine distinct phenotypes within the tumor. Recent studies have highlighted the role of circulating miRNAs as a minimally-invasive biomarker and its potential as biosignature to complement routine tissue-based procedures.

METHODS

In order to determine whether miRNAs in serum can indicate changes in cervical tissue specimens, we performed small RNA sequencing and selected miRNAs were validated using qRT-PCR in serum and tissue specimens (n = 115). Further, luciferase assay were performed to investigate the interactions between hsa-miR-409-3p and hsa-miR-454-3p binding sites on 3'UTR region of MTF2 and ST18 respectively.

RESULTS

We have identified a total of 14 differentially expressed miRNAs common in serum and tissue specimens. Among them, hsa-miR-17-5p, hsa-miR-32-5p and hsa-miR-454-3p were upregulated while, hsa-miR-409-3p was downregulated in serum and tissue of cervical cancer subjects. Our in-silico small RNA sequencing data analysis identified isomiRs and classified miRNA into clusters and subtypes (exonic, intronic and intergenic) with respect to the expression status in serum and tissue specimens. Expression level of hsa-miR-409-3p and hsa-miR-454-3p were inversely correlated with their target genes MTF2 and ST18 levels respectively in human cervical cancer specimens. Luciferase assay demonstrated that hsa-miR-409-3p and hsa-miR-454-3p functionally interacts with 3'-UTR of MTF2 and ST18 respectively to decrease their activity.

CONCLUSION

Our results support the significant role of circulating miRNAs in disease dissemination and their potential utility as biosignatures of clinical relevance.

Characterization and expression profiles of miRNAs in the triploid hybrids of Brassica napus and Brassica rapa

BACKGROUND

Polyploidy provides a means of interspecific genome transfer to incorporate preferable traits from progenitor to progeny. However, few studies on miRNA expression profiles of interspecific hybrids of B. napus (AnAnCnCn) and B. rapa (ArAr) have been reported.

RESULTS

Here, we apply small RNA sequencing to explore miRNA expression patterns between B. napus, B. rapa and their F1 hybrid. Bioinformatics analysis identified 376, 378, 383 conserved miRNAs and 82, 76, 82 novel miRNAs in B. napus, B. rapa and the F1 hybrid, respectively. Moreover, 213 miRNAs were found to be differentially expressed between B. napus, B. rapa and the F1 hybrid. The present study also shows 211 miRNAs, including 77 upregulated and 134 downregulated miRNAs, to be nonadditively expressed in the F1 hybrid. Furthermore, miRNA synteny analysis revealed high genomic conservation between the genomes of B. napus, B. rapa and their F1 hybrid, with some miRNA loss and gain events in the F1 hybrid.

CONCLUSIONS

This study not only provides useful resources for exploring global miRNA expression patterns and genome structure but also facilitates genetic research on the roles of miRNAs in genomic interactions of Brassica allopolyploids.

Physiological responses and small RNAs changes in maize under nitrogen deficiency and resupply

BACKGROUND

Maize is an important crop in the world, nitrogen stress severely reduces maize yield. Although a large number of studies have identified the expression changes of microRNAs (miRNAs) under N stress in several species, the miRNAs expression patterns of N-deficient plants under N resupply remain unclear.

OBJECTIVE

The primary objective of this study was to identify miRNAs in response to nitrogen stress and understand relevant physiological changes in nitrogen-deficient maize after nitrogen resupply.

METHODS

Physiological parameters were measured to study relevant physiological changes under different nitrogen conditions. Small RNA sequencing and qRT-PCR analysis were performed to understand the response of miRNAs under different nitrogen conditions.

RESULTS

The content of chlorophyll, soluble protein and nitrate nitrogen decreased than CK by 0.52, 0.49 and 0.82 times after N deficiency treatment and increased than ND by 0.52, 1.36 and 0.65 times after N resupply, respectively. Conversely, the activity of superoxide dismutase (SOD) and peroxidase (POD) increased by 0.67 and 1.64 times than CK after N deficiency, respectively, and decreased by 0.09 and 0.35 times than ND after N resupply. A total of 226 known miRNAs were identified by sRNA sequencing; 106 miRNAs were differentially expressed between the control and N-deficient groups, and 103 were differentially expressed between the N-deficient and N-resupply groups (P < 0.05). Real-time quantitative PCR (qPCR) was used to further validate and analyze the expression of the identified miRNAs. A total of 1609 target genes were identified by target prediction, and some differentially expressed miRNAs were predicted to target transcription factors and functional proteins. Gene Ontology (GO) analysis was used to determine the biological function of these targets and revealed that some miRNAs, such as miR169, miR1214, miR2199, miR398, miR408 and miR827 might be involved in nitrogen metabolism regulation.

CONCLUSION

Our study comprehensively provides important information on miRNA functions and molecular mechanisms in response to N stress. These findings may assist to improve nitrogen availability in plants.