Identification and Characterization of Rice Circular RNAs Responding to Xanthomonas Oryzae pv. Oryzae Invasion

2021 ◽  
Author(s):  
Peihong Wang ◽  
Sai Wang ◽  
Yan Wu ◽  
Wenhan Nie ◽  
Ayizekeranmu Yiming ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Circular Rnas ◽  
Pathogen Invasion ◽  
Rice Leaves ◽  
Transcriptional Gene Regulation ◽  
Identification And Characterization ◽  
Host Genes

Abstract BackgroundThe emerging role of circular RNAs (circRNAs) in various biological processes have advanced our knowledge of transcriptional and post-transcriptional gene regulation. The number and expression of plant circRNAs vary with species and treatments. However, the expression profile and the potential role of circRNAs during plant response to pathogen invasion are still elusive. ResultsIn this study, we identified 3517 circRNAs from PXO99A-infected rice leaves using the ribosomal RNA (rRNA) depleted RNA-Sequencing technique coupled with the CIRI2 and CIRCexplorer2 pipeline. Among them, 2994 (85.13%) circRNAs arised from the exons of their parent genes, 1214 circRNAs were previously unknown and 276 circRNAs exhibited differential expression profiles upon PXO99A infection over time. In addition, 31 differentially expressed circRNAs (DEcircRNAs) were predicted as the corresponding 121 miRNAs sponges. Functional analysis of both host genes and target mRNAs suggested that these identified circRNAs might play an important role in reprogramming rice responses to PXO99A invasion, mainly by mediating photorespiration, chloroplast, peroxisome and diterpenoid biosynthesis associated pathways.ConclusionThese results inferred a potential functional role of circRNAs in the regulation of rice immunity and provide novel clues for revealing the molecular mechanisms of rice-PXO99A interaction.

Identification and characterization of rice circular RNAs responding to Xanthomonas oryzae pv. oryzae invasion

2021 ◽  
Author(s):  
Peihong Wang ◽  
Sai Wang ◽  
Yan Wu ◽  
Wenhan Nie ◽  
Ayizekeranmu Yiming ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Enrichment Analysis ◽  
Xanthomonas Oryzae ◽  
Pcr Analysis ◽  
Circular Rnas ◽  
Transcriptional Gene Regulation ◽  
Identification And Characterization ◽  
Host Genes

Emerging role of circular RNAs (circRNAs) in various biological processes have advanced our knowledge of transcriptional and post-transcriptional gene regulation. To date, no research has been conducted to explore their roles in the rice- Xanthomonas oryzae pv. oryzae (Xoo) interaction. Therefore, we identified 3517 circRNAs from the highly virulent Xoo strain PXO99A-infected rice leaves using the ribosomal RNA (rRNA) depleted RNA-sequencing technique coupled with the CIRI2 and CIRCexplorer2 pipeline. Characterization analyses showed that these circRNAs were distributed across the whole genome of rice, and most circRNAs arised from exons (85.13 %), ranged from 200 bp to 1000 bp and were with a non-canonical GT/AG (including CT/AC equivalent) splicing signal. Functional annotation and enrichment analysis of the host genes that produced the DEcircRNAs suggested that these identified circRNAs might play an important role in reprogramming rice responses to PXO99A invasion, mainly by mediating photorespiration, chloroplast, peroxisome and diterpenoid biosynthesis. Moreover, 31 differentially expressed circRNAs (DEcircRNAs) were predicted to act as miRNA decoys in rice. The expression profile of 4 DEcircRNAs were validated by RT-qPCR with divergent primers, and the back-splicing sites of seven DEcircRNAs were verified by PCR analysis and Sanger sequencing. Collectively, these results inferred a potential functional role of circRNAs in the regulation of rice immunity and provide novel clues for revealing the molecular mechanisms of rice-PXO99A interaction.

scholarly journals Identification and characterization of circular RNAs in Qinchuan cattle testis

2018 ◽  
Vol 5 (7) ◽  
pp. 180413 ◽  
Author(s):  
Yuan Gao ◽  
Mingli Wu ◽  
Yingzhi Fan ◽  
Shipeng Li ◽  
Zhenyu Lai ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Length Distribution ◽  
Circular Rnas ◽  
Genomic Feature ◽  
Qinchuan Cattle ◽  
Adult Cattle ◽  
Testis Development ◽  
Identification And Characterization

Circular RNA (circRNA) is a new class of non-coding RNA that has recently attracted researchers' interest. Studies have demonstrated that circRNA can function as microRNA sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in cattle remains unknown. We performed ribo-depleted total RNA-Seq to detect circRNA expression profiles of neonatal (one week old) and adult (4 years old) Qinchuan cattle testes. We obtained 91 112 596 and 80 485 868 clean reads and detected 21 753 circRNAs. A total of 4248 circRNAs were significantly differentially expressed between neonatal and adult cattle testes. Among these circRNAs, 2225 were upregulated, and 2023 were downregulated in adult cattle testis. Genomic feature, length distribution and other characteristics of the circRNAs in cattle testis were studied. Moreover, Gene Ontology and KEGG pathway analyses were performed for source genes of circRNAs. These source genes were mainly involved in tight junction, adherens junction, TGFβ signalling pathway and reproduction, such as PIWIL1, DPY19L2, SLC26A8, IFT81, SMC1B, IQCG and TTLL5 . CircRNA expression patterns were validated by RT-qPCR. Our discoveries provide a solid foundation for the identification and characterization of key circRNAs involved in testis development or spermatogenesis.

scholarly journals Comprehensive mechanistic characterization of mQTLs in an Asian population

2021 ◽  
Author(s):  
Sijia Wang ◽  
Qianqian Peng ◽  
Xinxuan Liu ◽  
Han Jing ◽  
Wenran Li ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Disease Risk ◽  
Asian Population ◽  
Chromatin Accessibility ◽  
Ethnic Populations ◽  
Cell Type Specific ◽  
Nfkb Pathway ◽  
Identification And Characterization

Abstract Identification and characterization of methylation quantitative trait loci (mQTLs) can help elucidate the role of DNA methylation changes as a potential mediator of genetic risk loci. However, mQTLs remain poorly characterized: they have not yet been mapped in the largest ethnic populations, their cell-type specific nature has not been resolved, and the proportion of mQTLs attributed to different molecular mechanisms is unknown. Here we perform the first mQTL-mapping study in a large Han Chinese population, demonstrating that over 80% of mQTLs are shared with those identified in White Caucasians. We further estimate that over 90% of mQTLs are shared between different blood cell-lineages. mQTLs demonstrate a strong enrichment for variants influencing chromatin accessibility. We identify a number of GWAS-linked transcription factor trans-mQTL hotspots associated with eosinophilia, ulcerative colitis and body mass index, and a subset of trans-mQTLs within the NFKB-pathway that may mediate the risk of obesity. In summary, this study significantly expands our understanding of mQTLs and their potential role in mediating disease risk, whilst also contributing the first mQTL-database in an Asian population.

scholarly journals Circular RNA hsa_circ_0000277 sequesters miR-4766-5p to upregulate LAMA1 and promote esophageal carcinoma progression

2021 ◽  
Vol 12 (7) ◽  
Author(s):  
Peng Li Zhou ◽  
Zhengyang Wu ◽  
Wenguang Zhang ◽  
Miao Xu ◽  
Jianzhuang Ren ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Bioinformatics Analysis ◽  
Epithelial Mesenchymal Transition ◽  
Expression Profiles ◽  
Luciferase Reporter ◽  
Migration And Invasion ◽  
Circular Rnas ◽  
Mesenchymal Transition ◽  
Dismal Prognosis ◽  
Advanced Tumor

AbstractGrowing evidence has indicated that circular RNAs (circRNAs) play a pivotal role as functional RNAs in diverse cancers. However, most circRNAs involved in esophageal squamous cell carcinoma (ESCC) remain undefined, and the underlying molecular mechanisms mediated by circRNAs are largely unclear. Here, we screened human circRNA expression profiles in ESCC tissues and found significantly increased expression of hsa_circ_0000277 (termed circPDE3B) in ESCC tissues and cell lines compared to the normal controls. Moreover, higher circPDE3B expression in patients with ESCC was correlated with advanced tumor-node-metastasis (TNM) stage and dismal prognosis. Functional experiments demonstrated that circPDE3B promoted the tumorigenesis and metastasis of ESCC cells in vitro and in vivo. Mechanistically, bioinformatics analysis, a dual-luciferase reporter assay, and anti-AGO2 RNA immunoprecipitation showed that circPDE3B could act as a competing endogenous RNA (ceRNA) by harboring miR-4766-5p to eliminate the inhibitory effect on the target gene laminin α1 (LAMA1). In addition, LAMA1 was significantly upregulated in ESCC tissues and was positively associated with the aggressive oncogenic phenotype. More importantly, rescue experiments revealed that the oncogenic role of circPDE3B in ESCC is partly dependent on the miR-4766-5p/LAMA1 axis. Furthermore, bioinformatics analysis combined with validation experiments showed that epithelial-mesenchymal transition (EMT) activation was involved in the oncogenic functions of the circPDE3B–miR-4766-5p/LAMA1 axis in ESCC. Taken together, we demonstrate for the first time that the circPDE3B/miR-4766-5p/LAMA1 axis functions as an oncogenic factor in promoting ESCC cell proliferation, migration, and invasion by inducing EMT, implying its potential prognostic and therapeutic significance in ESCC.

scholarly journals CRISP2, CATSPER1 and PATE1 Expression in Human Asthenozoospermic Semen

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1956
Author(s):  
Francesco Manfrevola ◽  
Bruno Ferraro ◽  
Carolina Sellitto ◽  
Domenico Rocco ◽  
Silvia Fasano ◽  
...  
Keyword(s):  
Sperm Motility ◽  
Molecular Mechanisms ◽  
Gradient Centrifugation ◽  
Circular Rnas ◽  
Amino Acid Supplementation ◽  
Differential Analysis ◽  
Mrna Targets ◽  
Motility Regulation ◽  
Quantitative Changes

The etiology of human asthenozoospermia is multifactorial. The need to unveil molecular mechanisms underlying this state of infertility is, thus, impelling. Circular RNAs (circRNAs) are involved in microRNA (miRNA) inhibition by a sponge activity to protect mRNA targets. All together they form the competitive endogenous RNA network (ceRNET). Recently, we have identified differentially expressed circRNAs (DE-circRNAs) in normozoospermic and asthenozoospermic patients, associated with high-quality (A-spermatozoa) and low-quality (B-spermatozoa) sperm. Here, we carried out a differential analysis of CRISP2, CATSPER1 and PATE1 mRNA expression in good quality (A-spermatozoa) and low quality (B-spermatozoa) sperm fractions collected from both normozoospermic volunteers and asthenozoospermic patients. These sperm fractions are usually separated on the basis of morphology and motility parameters by a density gradient centrifugation. B-spermatozoa showed low levels of mRNAs. Thus, we identified the possible ceRNET responsible for regulating their expression by focusing on circTRIM2, circEPS15 and circRERE. With the idea that motility perturbations could be rooted in quantitative changes of transcripts in sperm, we evaluated circRNA and mRNA modulation in A-spermatozoa and B-spermatozoa after an oral amino acid supplementation known to improve sperm motility. The profiles of CRISP2, CATSPER1 and PATE1 proteins in the same fractions of sperm well matched with the transcript levels. Our data may strengthen the role of circRNAs in asthenozoospermia and shed light on the molecular pathways linked to sperm motility regulation.

scholarly journals Transcriptome-based identification and characterization of genes responding to imidacloprid in Myzus persicae

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jianyu Meng ◽  
Xingjiang Chen ◽  
Changyu Zhang
Keyword(s):  
Genetic Basis ◽  
Expression Profiles ◽  
Control Measure ◽  
Effective Control ◽  
Agricultural Pest ◽  
Functional Classification ◽  
Quantitative Real Time Pcr ◽  
Underlying Mechanisms ◽  
Identification And Characterization

Abstract Myzus persicae is a serious and widespread agricultural pest, against which, imidacloprid remains an effective control measure. However, recent reports indicate that this aphid has evolved and developed resistance to imidacloprid. This study aimed to elucidate the underlying mechanisms and genetic basis of this resistance by conducting comparative transcriptomics studies on both imidacloprid-resistant (IR) and imidacloprid-susceptible (IS) M. persicae. The comparative analysis identified 252 differentially expressed genes (DEGs) among the IR and IS M. persicae transcriptomes. These candidate genes included 160 and 92 genes that were down- and up-regulated, respectively, in the imidacloprid-resistant strain. Using functional classification in the GO and KEGG databases, 187 DEGs were assigned to 303 functional subcategories and 100 DEGs were classified into 45 pathway groups. Moreover, several genes were associated with known insecticide targets, cuticle, metabolic processes, and oxidative phosphorylation. Quantitative real-time PCR of 10 DEGs confirmed the trends observed in the RNA sequencing expression profiles. These findings provide a valuable basis for further investigation into the complicated mechanisms of imidacloprid resistance in M. persicae.

scholarly journals Genome-wide miRNA profiling of villus and decidua of recurrent spontaneous abortion patients

Reproduction ◽  
2014 ◽  
Vol 148 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Fulu Dong ◽  
Yuan Zhang ◽  
Fei Xia ◽  
Yi Yang ◽  
Sidong Xiong ◽  
...  
Keyword(s):  
Spontaneous Abortion ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Normal Pregnancy ◽  
Recurrent Spontaneous Abortion ◽  
Future Research ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Transcriptional Gene Regulation

MicroRNAs (miRNAs) are non-coding RNA molecules of about 22 nucleotides that involved in post-transcriptional gene regulation. Evidence indicates that miRNAs play essential roles in endometriosis, pre-eclampsia, infertility and other reproductive system diseases. However, whether miRNAs are involved in recurrent spontaneous abortion (RSA) is unclear. In this work, we analysed the miRNA expression profiles in six pairs of villus or decidua from RSA patients and normal pregnancy (NP) women using a human miRNA microarray. Some of the chip results were confirmed by RT-qPCR. In the villi of RSA patients, expression of hsa-miR-184, hsa-miR-187 and hsa-miR-125b-2 was significantly higher, while expression of hsa-miR-520f, hsa-miR-3175 and hsa-miR-4672 was significantly lower, comparing with those of NP control. As well, a total of five miRNAs (hsa-miR-517c, hsa-miR-519a-1, hsa-miR-522, hsa-miR-520h and hsa-miR-184) were upregulated in the decidua of RSA patients. The target genes of these differentially expressed miRNAs were predicted by miRWalk, and we speculate a network of miRNA regulating RSA by target genes function on adhesion, apoptosis and angiogenesis. Our study may help clarify the molecular mechanisms which are involved in the progression of RSA, and provide a reference for future research.

scholarly journals EARLY BUD-BREAK 1 and EARLY BUD-BREAK 3 control resumption of poplar growth after winter dormancy

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Abdul Azeez ◽  
Yiru Chen Zhao ◽  
Rajesh Kumar Singh ◽  
Yordan S. Yordanov ◽  
Madhumita Dash ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Molecular Mechanisms ◽  
Negative Regulator ◽  
Bud Break ◽  
Positive Regulator ◽  
Regulatory Module ◽  
Trees And Shrubs ◽  
Poplar Growth ◽  
Identification And Characterization

AbstractBud-break is an economically and environmentally important process in trees and shrubs from boreal and temperate latitudes, but its molecular mechanisms are poorly understood. Here, we show that two previously reported transcription factors, EARLY BUD BREAK 1 (EBB1) and SHORT VEGETATIVE PHASE-Like (SVL) directly interact to control bud-break. EBB1 is a positive regulator of bud-break, whereas SVL is a negative regulator of bud-break. EBB1 directly and negatively regulates SVL expression. We further report the identification and characterization of the EBB3 gene. EBB3 is a temperature-responsive, epigenetically-regulated, positive regulator of bud-break that provides a direct link to activation of the cell cycle during bud-break. EBB3 is an AP2/ERF transcription factor that positively and directly regulates CYCLIND3.1 gene. Our results reveal the architecture of a putative regulatory module that links temperature-mediated control of bud-break with activation of cell cycle.

scholarly journals Comprehensive transcriptional profiling of aging porcine liver

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6949 ◽  
Author(s):  
Jianning Chen ◽  
Qin Zou ◽  
Daojun Lv ◽  
Muhammad Ali Raza ◽  
Xue Wang ◽  
...  
Keyword(s):  
Human Liver ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Genomic Structure ◽  
Circular Rnas ◽  
Transcriptional Level ◽  
Porcine Liver ◽  
Age Related ◽  
Micro Rnas ◽  
Model Animal

Background Aging is a major risk factor for the development of many diseases, and the liver, as the most important metabolic organ, is significantly affected by aging. It has been shown that the liver weight tends to increase in rodents and decrease in humans with age. Pigs have a genomic structure, with physiological as well as biochemical features that are similar to those of humans, and have therefore been used as a valuable model for studying human diseases. The molecular mechanisms of the liver aging of large mammals on a comprehensive transcriptional level remain poorly understood. The pig is an ideal model animal to clearly and fully understand the molecular mechanism underlying human liver aging. Methods In this study, four healthy female Yana pigs (an indigenous Chinese breed) were investigated: two young sows (180-days-old) and two old sows (8-years-old). High throughput RNA sequencing was performed to evaluate the expression profiles of messenger RNA, long non-coding RNAs, micro RNAs, and circular RNAs during the porcine liver aging process. Gene Ontology (GO) analysis was performed to investigate the biological functions of age-related genes. Results A number of age-related genes were identified in the porcine liver. GO annotation showed that up-regulated genes were mainly related to immune response, while the down-regulated genes were mainly related to metabolism. Moreover, several lncRNAs and their target genes were also found to be differentially expressed during liver aging. In addition, the multi-group cooperative control relationships and constructed circRNA-miRNA co-expression networks were assessed during liver aging. Conclusions Numerous age-related genes were identified and circRNA-miRNA co-expression networks that are active during porcine liver aging were constructed. These findings contribute to the understanding of the transcriptional foundations of liver aging and also provide further references that clarify human liver aging at the molecular level.

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