scholarly journals Transcriptome Profile Analysis Reveals an Estrogen Induced LncRNA Associated with Lipid Metabolism and Carcass Traits in Chickens (Gallus Gallus)

2018 ◽  
Vol 50 (5) ◽  
pp. 1638-1658 ◽  
Author(s):  
Hong Li ◽  
Zhenzhen Gu ◽  
Liyu Yang ◽  
Yadong Tian ◽  
Xiangtao Kang ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Target Genes ◽  
Laying Hens ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Chicken Carcass ◽  
Triglyceride Content

Background/Aims: Accumulating evidences have demonstrated that long noncoding RNAs (lncRNA) play important roles in hepatic lipid metabolism in mammals. However, no systematic screening of the potential lncRNAs in the livers of laying hens has been performed, and few studies have been reported concerning the effects of the lncRNAs on lipid metabolism in the livers of chickens during egg-laying period. The purpose of this study was to compare the difference in lncRNA expression in the livers of pre-laying and peak-laying hens at the age of 20 and 30 weeks old by transcriptome sequencing and to investigate the interaction networks among lncRNAs, mRNAs and miRNAs. Moreover, the regulatory mechanism and biological function of lncLTR, a significantly differentially expressed lncRNA in the liver between pre- and peak-laying hens, was explored in vitro and in vivo. Methods: Bioinformatics analyses were conducted to identify the differentially expressed (DE) lncRNAs between the two groups of hens. The target genes of the DE lncRNA were predicated for further functional enrichment. An integrated analysis was performed among the DE lncRNA datasets, DE mRNAs and DE miRNA datasets obtained from the same samples to predict the interaction relationship. In addition, in vivo and in vitro trials were carried out to determine the expression regulation of lncLTR, and polymorphism association analysis was conducted to detect the biological role of ncLTR. Results: A total of 124 DE lncRNAs with a P-value ≤ 0.05 were identified. Among them, 44 lncRNAs including 30 known and 14 novel lncRNAs were significant differentially expressed (SDE) with FDR ≤ 0.05. Thirty-two lncRNAs were upregulated and 12 were downregulated in peak-laying group compared with pre-laying group. The functional enrichment results revealed that target genes of some lncRNAs are involved in the lipid metabolism process. Integrated analysis suggested that some of the genes involved in lipid metabolism might be regulated by both the lncRNA and the miRNA. In addition, an upregulated lncRNA, designated lncLTR, was demonstrated to be induced by estrogen via ERβ signaling. The c242. G>A SNP in lncLTR was significantly associated with chicken carcass weight, evisceration weight, semi-evisceration weight, head weight, double-wing weight, claw weight traits, and blood biochemical index, especially for the blood triglyceride content. Conclusion: A series of lncRNAs associated with lipid metabolism in the livers of chickens were identified by transcriptome sequencing and functional analysis, providing a valuable data resource for further studies on chicken hepatic metabolism activities. LncLTR was regulated by estrogen via ERβ signaling and associated with chicken carcass trait and blood triglyceride content.

scholarly journals A combined microRNA and target protein-based panel for predicting the probability and severity of uraemic vascular calcification: a translational study

2020 ◽  
Author(s):  
Chia-Ter Chao ◽  
Hsiang-Yuan Yeh ◽  
You-Tien Tsai ◽  
Chih-Kang Chiang ◽  
Huei-Wen Chen
Keyword(s):  
Vascular Calcification ◽  
Target Genes ◽  
Ex Vivo ◽  
Target Protein ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Target Proteins ◽  
Differentially Expressed Mirnas

Abstract Aims  Vascular calcification (VC) increases the future risk of cardiovascular events in uraemic patients, but effective therapies are still unavailable. Accurate identification of those at risk of developing VC using pathogenesis-based biomarkers is of particular interest and may facilitate individualized risk stratification. We aimed to uncover microRNA (miRNA)-target protein-based biomarker panels for evaluating uraemic VC probability and severity. Methods and results  We created a three-tiered in vitro VC model and an in vivo uraemic rat model receiving high phosphate diet to mimic uraemic VC. RNAs from the three-tiered in vitro and in vivo uraemic VC models underwent miRNA and mRNA microarray, with results screened for differentially expressed miRNAs and their target genes as biomarkers. Findings were validated in original models and additionally in an ex vivo VC model and human cells, followed by functional assays of identified miRNAs and target proteins, and tests of sera from end-stage renal disease (ESRD) and non-dialysis-dependent chronic kidney disease (CKD) patients without and with VC. Totally 122 down-regulated and 119 up-regulated miRNAs during calcification progression were identified initially; further list narrowing based on miRNA–mRNA pairing, anti-correlation, and functional enrichment left 16 and 14 differentially expressed miRNAs and mRNAs. Levels of four miRNAs (miR-10b-5p, miR-195, miR-125b-2-3p, and miR-378a-3p) were shown to decrease throughout all models tested, while one mRNA (SULF1, a potential target of miR-378a-3p) exhibited the opposite trend concurrently. Among 96 ESRD (70.8% with VC) and 59 CKD patients (61% with VC), serum miR-125b2-3p and miR-378a-3p decreased with greater VC severity, while serum SULF1 levels increased. Adding serum miR-125b-2-3p, miR-378a-3p, and SULF1 into regression models for VC substantially improved performance compared to using clinical variables alone. Conclusion  Using a translational approach, we discovered a novel panel of biomarkers for gauging the probability/severity of uraemic VC based on miRNAs/target proteins, which improved the diagnostic accuracy.

scholarly journals Potential function and molecular mechanism of circRNAs involved in idiopathic pulmonary fibrosis

2020 ◽  
Author(s):  
Fangwei Li ◽  
Hong Wang ◽  
Hongyan Tao ◽  
Fanqi Wu ◽  
Dan Wang ◽  
...  
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Molecular Mechanism ◽  
Target Genes ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Circular Rnas

Abstract Background: Recent studies have found a regulatory role of circular RNAs (circRNAs) in the pathogenesis of idiopathic pulmonary fibrosis (IPF). However, the function and underlying molecular mechanism of circRNAs involved in IPF are uncertain and incomplete. This study aimed to further provide some critical information for the circRNA function in IPF using bioinformatic analysis. Methods: We searched in the NCBI (National Center for Biotechnology Information) Gene Expression Omnibus (GEO) database to find the circRNA expression profiles of human IPF. The microarray data GSE102660 was obtained and differentially expressed circRNAs were identified through R software. Results: 6 significantly up-regulated and 13 significantly down-regulated circRNAs were identified involved in the pathogenesis of IPF. The binding sites of miRNAs for each differentially expressed circRNA were also predicted and circRNA-miRNA-mRNA networks were constructed for the most up-regulated hsa_circ_0004099 and down-regulated hsa_circ_0029633. In addition, GO and KEGG enrichment analysis revealed the molecular function and enriched pathways of the target genes of circRNAs in IPF.Conclusion: These findings suggest that candidate circRNAs might serve an important role in the pathogenesis of IPF. Therefore, these circRNAs might be potential biomarkers for diagnosis and promising targets for treatment of IPF, which still need further verification in vivo and in vitro.

scholarly journals Screening, Identification and Interaction Analysis of Key MicroRNAs and Genes in Asthenozoospermia

2020 ◽  
Author(s):  
Li-Man Li ◽  
Song Chen
Keyword(s):  
Signaling Pathway ◽  
Target Genes ◽  
Interaction Analysis ◽  
Pathological Condition ◽  
Wnt Signaling Pathway ◽  
Notch Signaling Pathway ◽  
Differentially Expressed ◽  
Pathophysiological Mechanism

Abstract Background: Asthenozoospermia, one of the most common causes of male infertility, is a complicate multifactorial pathological condition that genetic factors are involved in. However, the epigenetic signature and mechanism of asthenozoospermia still remain limited. Our study aimed to confirm the key microRNAs (miRNAs) and genes in asthenozoospermia and demonstrate the underlying epigenetic regulatory mechanisms. Methods: We screened out and pooled previous studies to extracted potential differentially expressed miRNAs (DEMs). GSE22331 and a published profile dataset were integrated to identify differentially expressed genes (DEGs). Pathway and gene ontology analysis were performed using DAVID. A protein-protein network (PPI) was constructed using STRING. The target genes of DEMs were predicted using TargetScan and then built the miRNA-mRNA network.Results: We reported 3 DEMs and 423 DEGs by pooling included dataset and published studies. Pathway analysis showed that these DEGs might participate in signaling pathways regulating pluripotency of stem cells, wnt signaling pathway and notch signaling pathway. 25 hub genes were identified, and the most significant gene was BDNF. We screened out the overlapped DEGs between the predicted target genes of 3 DEMs and the 423 DEGs. Then we constructed miRNA-mRNA network. Conclusion: This study firstly pooled several published studies and a GEO dataset to determine the significance of potential miRNAs and genes, such as miR-374b, miR-193a, miR-34b, BDNF, NTRK2, HNRNPD and EFTUD2 in regulating asthenozoospermia and underscore their interactions in the pathophysiological mechanism. Our results provided theoretical basis and new clues for potential therapeutic treatment in asthenozoospermia. Validations in vivo and in vitro are required in future studies.

scholarly journals LncRNA MALAT1 Regulates iPSC-derived Β-cell Differentiation by Targeting the miR-15b-5p/Ihh Axis

2020 ◽  
Author(s):  
Yao Wang ◽  
Xinxing Lin ◽  
Jin Lv ◽  
Jiachen Zhu ◽  
Haowen Fan ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Cell Therapy ◽  
Target Genes ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Β Cells ◽  
Pancreatic Β Cells ◽  
Lncrna Malat1

Abstract Background: iPSCs-derived β-like cell differentiation provides a novel strategy for type 1 diabetes treatment. Clarifying the regulatory mechanisms of lncRNAs in β-like cells derived from induced pluripotent stem cells (iPSCs) is not only significant for understanding the development of pancreas or pancreatic β cells, but also helpful for improving the quality of β-like cells for stem cell therapy.Methods: β-like cells derived from iPSCs followed a three-step protocol. RNA-sequencing was carried out to screen the differentially expressed lncRNAs which was probably involved in the differentiation of pancreatic β cells. Bioinformatics was performed to analyze the putative target genes of significantly differentially expressed lncRNAs. LncRNA Malat1 was chosen for further research. Lentivirus victor, siRNA victor, antagomir victor and mimic victor were constructed for overexpression of lncRNA Malat1, knockdown of lncRNA Malat1, knockdown of miR-15b-5p and overexpression of miR-15b-5p respectively. Quantitative Real-Time PCR (qRT-PCR), Western Blot and Immunofluorescence (IF) staining were carried out to detect the functions of pancreatic β cells at mRNA and protein level separately. Cytoplasmic and nuclear RNA fractionation and Fluorescence in situ hybridization (FISH) were to ventilate the subcellar location of lncRNA Malat1 in β-like cells. Flow cytometry and ELISA were performed to examine differentiation efficiency and function of insulin secretion from β-like cells after being stimulated with different concentrations of glucose. Structural interactions between lncRNA Malat1 and miR-15b-5p and between miR-15b-5p and Ihh were detected by Dual luciferase reporter assay (LRA).Results: We found that expression of lncRNA Malat1 was on the decline during the differentiation and overexpression of this lncRNA obviously impaired the differentiation and maturation of β-like cells derived from iPSCs in vitro and in vivo. Localized to the cytoplasm, lncRNA Malat1 could function as a competing endogenous RNA (ceRNA) of miR-15b-5p to regulate the expression of Ihh according the bioinformatic prediction, mechanistic analysis and downstream experiments.Conclusion: This study built an unreported regulatory network of lncRNA Malat1 and miR-15b-5p/Ihh axis during differentiation of iPSCs into β-like cells. Except for acting as a proverbial oncogene promoting tumorigenesis, lncRNA Malat1 may provide effective and novel molecule for diabetes cell therapy in the future.

scholarly journals Downregulation of miR-142a Contributes to the Enhanced Anti-Apoptotic Ability of Murine Chronic Myelogenous Leukemia Cells

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhiwei Chen ◽  
Yinyin Xie ◽  
Dan Liu ◽  
Ping Liu ◽  
Fei Li ◽  
...  
Keyword(s):  
Transgenic Mice ◽  
Chronic Myelogenous Leukemia ◽  
Regulatory Networks ◽  
Target Genes ◽  
Expression Profiles ◽  
Myelogenous Leukemia ◽  
Integrated Analysis ◽  
Apoptotic Pathway

BackgroundLeukemic stem cell (LSC) is thought to be responsible for chronic myelogenous leukemia (CML) initiation and relapse. However, the inherent regulation of LSCs remains largely obscure. Herein, we integratedly analyzed miRNA and gene expression alterations in bone marrow (BM) Lin-Sca1+c-Kit+ cells (LSKs) of a tet-off inducible CML mouse model, Scl/tTA-BCR/ABL (BA).MethodsScl/tTA and TRE-BA transgenic mice were crossed in the presence of doxycycline to get double transgenic mice. Both miRNA and mRNA expression profiles were generated from BM LSKs at 0 and 3 weeks after doxycycline withdrawal. The target genes of differentially expressed miRNAs were predicted, followed by the miRNA-mRNA network construction. In vitro and in vivo experiments were further performed to elucidate their regulation and function in CML progression.ResultsAs a result of the integrated analysis and experimental validation, an anti-apoptotic pathway emerged from the fog. miR-142a was identified to be downregulated by enhanced ERK-phosphorylation in BA-harboring cells, thereby relieving its repression on Ciapin1, an apoptosis inhibitor. Moreover, miR-142a overexpression could partially rescue the abnormal anti-apoptotic phenotype and attenuate CML progression.ConclusionTaken together, this study explored the miRNA-mRNA regulatory networks in murine CML LSKs and demonstrated that ERK-miR-142a-Ciapin1 axis played an essential role in CML pathogenesis.

scholarly journals Differential mRNA and miRNA Profiles Reveal the Potential Roles of Genes and miRNAs Involved in LPS Infection in Chicken Macrophages

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 760
Author(s):  
Qi Zhang ◽  
Jie Wang ◽  
Jin Zhang ◽  
Jie Wen ◽  
Guiping Zhao ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Immune Response ◽  
Target Genes ◽  
Differentially Expressed ◽  
Gram Negative Bacteria ◽  
Potential Candidate ◽  
Gram Negative ◽  
Immune Related Genes

Lipopolysaccharide (LPS) is a component of the cell wall of Gram-negative bacteria, and triggers an inflammatory response both in vitro and in vivo. Here, we used LPS from Escherichia coli serotype enteritidis to stimulate chicken macrophages (HD11) and conducted the transcriptome analysis using a bioinformatics approach to explore the functions of immune-related genes and miRNAs. In total, 1759 differentially expressed genes (DEGs) and 18 differentially expressed (DE)-miRNAs were detected during LPS infection. At 6 h post infection, 1025 DEGs and 10 miRNAs were up-regulated, and 734 DEGs and 8 DE-miRNAs were down-regulated. Based on both RNA hybrid and miRanda systems, 55 DEGs could be targeted by 14 DE-miRNAs. The target genes were related to the immune response, such as IRF8, STAT3, TRAF7, and other potential candidate genes. The DE-miRNAs miR146a-3p, miR6583-5p, and miR30c-2-3p were investigated further. They were predicted to target 34 genes that may also be candidates for immune-related miRNAs and genes. Our results enhanced our understanding of the pathogenic mechanisms of Gram-negative bacteria in chickens.

scholarly journals A combined microRNA and transcriptome analysis illuminates the resistance response of rice against brown planthopper

2020 ◽  
Author(s):  
Jiaoyan Tan ◽  
Yan Wu ◽  
Jianping Guo ◽  
Huimin Li ◽  
Lili Zhu ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Brown Planthopper ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Resistance Response

Abstract Background : The brown planthopper (BPH, Nilaparvata lugens Stål) is a kind of phloem-feeding pest that adversely affects rice yield. Recently, the BPH-resistance gene, BPH6 , was cloned and applied in rice breeding to effectively control BPH. However, the molecular mechanisms underlying BPH6 are poorly understood. Results: Here, an integrated miRNA and mRNA expression profiling analysis was performed on BPH6 -transgenic (BPH6G) and Nipponbare (wild type, WT) plants after BPH infestation, and a total of 217 differentially expressed miRNAs (DEMs) and 7,874 differentially expressed mRNAs (DEGs) were identified. 29 miRNAs, including members of miR160, miR166 and miR169 family were opposite expressed during early or late feeding stages between the two varieties, whilst 9 miRNAs were specifically expressed in BPH6G plants, suggesting involvement of these miRNAs in BPH6 -mediated resistance to BPH. In the transcriptome analysis, 949 DEGs were opposite expressed during early or late feeding stages of the two genotypes, which were enriched in metabolic processes, cellular development, cell wall organization, cellular component movement and hormone transport, and certain primary and secondary metabolite synthesis. 24 genes were further selected as candidates for BPH resistance. Integrated analysis of the DEMs and DEGs showed that 34 miRNAs corresponding to 42 target genes were candidate miRNA-mRNA pairs for BPH resistance, 18 pairs were verified by qRT-PCR, and two pairs were confirmed by in vivo analysis. Conclusions: For the first time, we reported integrated small RNA and transcriptome sequencing to illustrate resistance mechanisms against BPH in rice. Our results provide a valuable resource to ascertain changes in BPH-induced miRNA and mRNA expression profiles and enable to comprehend plant-insect interactions and find a way for efficient insect control.

scholarly journals Hypothalamic Transcriptome Analysis Reveals the Crucial MicroRNAs and mRNAs Affecting Litter Size in Goats

2021 ◽  
Vol 8 ◽  
Author(s):  
Chen Liang ◽  
Miaoceng Han ◽  
Zuyang Zhou ◽  
Yufang Liu ◽  
Xiaoyun He ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Litter Size ◽  
Transcriptome Analysis ◽  
Target Genes ◽  
Hormone Secretion ◽  
Follicular Phase ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Integrated Analysis

The hypothalamus was the coordination center of the endocrine system, which played an important role in goat reproduction. However, the molecular mechanism of hypothalamus regulating litter size in goats was still poorly understood. This study aims to investigate the key functional genes associated with prolificacy by hypothalamus transcriptome analysis of goats. In this research, an integrated analysis of microRNAs (miRNAs)-mRNA was conducted using the hypothalamic tissue of Yunshang black goats in the follicular stage. A total of 72,220 transcripts were detected in RNA-seq. Besides, 1,836 differentially expressed genes (DEGs) were identified between high fecundity goats at the follicular phase (FP-HY) and low fecundity goats at the follicular phase (FP-LY). DEGs were significantly enriched in 71 Gene Ontology (GO) terms and 8 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The transcriptome data suggested that DEGs such as BMPR1B, FGFR1, IGF1 and CREB1 are directly or indirectly involved in many processes like hypothalamic gonadal hormone secretion. The miRNA-seq identified 1,837 miRNAs, of which 28 differentially expressed miRNAs (DEMs). These DEMs may affect the nerve cells survival of goat hypothalamic regulating the function of target genes and further affect the hormone secretion activities related to reproduction. They were enriched in prolactin signaling pathway, Jak-STAT signaling pathway and GnRH signaling pathway, as well as various metabolic pathways. Integrated analysis of DEMs and DEGs showed that 87 DEGs were potential target genes of 28 DEMs. After constructing a miRNA-mRNA pathway network, we identified several mRNA-miRNAs pairs by functional enrichment analysis, which was involved in hypothalamic nerve apoptosis. For example, NTRK3 was co-regulated by Novel-1187 and Novel-566, as well as another target PPP1R13L regulated by Novel-566. These results indicated that these key genes and miRNAs may play an important role in the development of goat hypothalamus and represent candidate targets for further research. This study provides a basis for further explanation of the basic molecular mechanism of hypothalamus, but also provides a new idea for a comprehensive understanding of prolificacy characteristics in Yunshang black goats.

EPCO-05. GENOME-WIDE ANALYSIS OF TEAD1 OCCUPANCY IN BIOLOGICALLY DISTINCT GLIOBLASTOMA SAMPLES

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi2-vi2
Author(s):  
Tanvi Joshi ◽  
German Nudelman ◽  
Elena Zaslavsky ◽  
Nadejda Tsankova
Keyword(s):  
Cell Biology ◽  
Target Genes ◽  
Specific Binding ◽  
Treatment Options ◽  
Critical Role ◽  
Negative Control ◽  
Functional Enrichment ◽  
Rapid Progression

Abstract The diffusely infiltrative nature of glioblastoma (GBM) cells is a major contributor to the disease’s aggressive behavior, including its rapid progression and therapeutic resistance. Moreover, current treatment options do not target the invasive nature of GBM. Recent chromatin accessibility studies prioritized enrichment of the TEAD1 transcription factor motif in glioblastoma stem cell biology and subsequent knockout and overexpression studies confirmed a critical role for TEAD1 in GBM migration, in vitro and in vivo. However, the downstream mechanisms through which TEAD1 regulates GBM cell migration remain poorly understood. In this study, we performed chromatin immunoprecipitation (ChIP-seq) using TEAD1-specific antibody and IgG as non-specific binding control, to characterize TEAD1 occupancy across GBM samples with unique genomic alterations. ChIP-seq peaks were called using MACS2, filtered for duplicates and blacklisted regions, and normalized per sample to their respective genomic input. Initial functional enrichment analyses were performed on three GBM samples with the highest number of TEAD1 occupancy peaks using CistromeGO, which ranked genes based on their TEAD1-specific regulatory potential (RP) score, as a function of peak number and distance from the transcription start site. Analyses of the top 1000 genes with highest TEAD1 RP scores identified 132 common targets across all samples, including known TEAD target genes ETV1 and Cyr61, which related to angiogenesis, cadherin and integrin signaling, cell adhesion, and chromatin regulation gene ontology terms, among others. Interestingly, KEGG pathway analysis also revealed Hippo pathway enrichment across all GBM samples, suggesting a possible TEAD1 regulatory feedback loop in GBM. Analysis of TEAD1 ChIP-seq peaks in non-GBM negative control tissue did not show functional enrichment for any of the terms seen in the GBM samples. Ongoing analyses are focused on characterizing TEAD1 occupancy at active cis-regulatory regions using parallel H3K27ac ChIP-seq data, in order to prioritize the most salient TEAD1-regulatory targets in GBM.

scholarly journals A combined microRNA and transcriptome analysis illuminates the resistance response of rice against brown planthopper

2019 ◽  
Author(s):  
Jiaoyan Tan ◽  
Yan Wu ◽  
Jianping Guo ◽  
Huimin Li ◽  
Lili Zhu ◽  
...  
Keyword(s):  
Mrna Expression ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Brown Planthopper ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Resistance Response

Abstract Background: The brown planthopper (BPH, Nilaparvata lugens Stål) is a kind of phloem-feeding pest that adversely affects rice yield. Recently, the BPH-resistance gene, BPH6, was cloned and applied in rice breeding to effectively control BPH. However, the molecular mechanisms underlying BPH6 are poorly understood. Results: Here, an integrated miRNA and mRNA expression profiling analysis was performed on BPH6-transgenic (BPH6G) and Nipponbare (wild type, WT) plants after BPH infestation, and a total of 217 differentially expressed miRNAs (DEMs) and 7,874 differentially expressed mRNAs (DEGs) were identified. 29 miRNAs, including members of miR160, miR166 and miR169 family were opposite expressed during early or late feeding stages between the two varieties, whilst 9 miRNAs were specifically expressed in BPH6G plants, suggesting involvement of these miRNAs in BPH6-mediated resistance to BPH. In the transcriptome analysis, 949 DEGs were opposite expressed during early or late feeding stages of the two genotypes, which were enriched in metabolic processes, cellular development, cell wall organization, cellular component movement and hormone transport, and certain primary and secondary metabolite synthesis. 24 genes were further selected as candidates for BPH resistance. Integrated analysis of the DEMs and DEGs showed that 34 miRNAs corresponding to 42 target genes were candidate miRNA-mRNA pairs for BPH resistance, 18 pairs were verified by qRT-PCR, and two pairs were confirmed by in vivo analysis. Conclusions: For the first time, we reported integrated small RNA and transcriptome sequencing to illustrate resistance mechanisms against BPH in rice. Our results provide a valuable resource to ascertain changes in BPH-induced miRNA and mRNA expression profiles and enables the analysis of the comprehensive plant-insect interactions required for efficient insect control.

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