scholarly journals A 31-bp indel localised in the 5' untranslated region of OsSUT3 affects the gene expression and rice (Oryza sativa L.) pollen development

2021 ◽  
Author(s):  
Chunlong Zhang ◽  
Qiuping Li ◽  
Hong Yang ◽  
Tuo Wang ◽  
Juan Li ◽  
...  
Keyword(s):  
Pollen Development ◽  
Untranslated Region ◽  
Oryza Sativa L ◽  
Biological Processes ◽  
Seeding Rate ◽  
Qrt Pcr ◽  
Evolution Analysis ◽  
Close Relationship ◽  
Pollen Number ◽  
Panicle Traits

OsSUT genes have been demonstrated to be relevant for diverse biological processes in rice. In this study, we identified the close relationship between a 31-bp insertion in a 5' untranslated region (5' UTR) of the OsSUT3 gene and higher OsSUT3 expression in rice panicles by qRT-PCR and transgenic research. Statistically significant results (P < 0.01) were found for this 31-bp insertions/deletions (indels) in the rice pollen development and other panicle traits, such as the pollen number, pollen fertility, seeding rate, and grain length. An evolution analysis showed that the proportion of the 31-bp insertion significantly increases in rice domestication. Therefore, the 31-bp Indel could be considered as a convenient molecular marker to screen more pollen and better panicle traits in rice breeding.

scholarly journals Melatonin promotes bone marrow mesenchymal stem cell osteogenic differentiation and prevents osteoporosis development through modulating circ_0003865 that sponges miR-3653-3p

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Xudong Wang ◽  
Taiqiu Chen ◽  
Zhihuai Deng ◽  
Wenjie Gao ◽  
Tongzhou Liang ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Stem Cell ◽  
Mesenchymal Stem Cell ◽  
Osteogenic Differentiation ◽  
Luciferase Reporter ◽  
Specific Gene ◽  
Biological Processes ◽  
Alizarin Red ◽  
Qrt Pcr ◽  
Dual Luciferase Reporter Assay

Abstract Background Little is known about the implications of circRNAs in the effects of melatonin (MEL) on bone marrow mesenchymal stem cell (BMSC) osteogenic differentiation and osteoporosis (OP) progression. The aim of our study was to investigate circRNAs in MEL-regulated BMSC differentiation and OP progression. Methods BMSC osteogenic differentiation was measured by qRT-PCR, western blot (WB), Alizarin Red, and alkaline phosphatase (ALP) staining. Differential circRNA and mRNA profiles of BMSCs treated by MEL were characterized by deep sequencing, followed by validation using RT-PCR, Sanger sequencing, and qRT-PCR. Silencing and overexpression of circ_0003865 were conducted for functional investigations. The sponged microRNAs and targeted mRNAs were predicted by bioinformatics and validated by qRT-PCR, RNA pull-down, and dual-luciferase reporter assay. The function of miR-3653-3p and circ_0003865/miR-3653-3p/growth arrest-specific gene 1 (GAS1) cascade was validated for the osteogenic differentiation of BMSCs by CCK-8, qRT-PCR, WB, Alizarin Red, and ALP staining. The effects of circ_0003865 on OP development were tested in murine OP model. Results MEL promoted osteogenic differentiation of BMSCs. RNA sequencing revealed significant alterations in circRNA and mRNA profiles associated with multiple biological processes and signaling pathways. Circ_0003865 expression in BMSCs was significantly decreased by MEL treatment. Silencing of circ_0003865 had no effect on proliferation while promoted osteogenic differentiation of BMSCs. Overexpression of circ_0003865 abrogated the promotion of BMSC osteogenic differentiation induced by MEL, but proliferation of BMSCs induced by MEL had no change whether circ_0003865 was overexpression or not. Furthermore, circ_0003865 sponged miR-3653-3p to promote GAS1 expression in BMSCs. BMSC osteogenic differentiation was enhanced by miR-3653-3p overexpression while BMSC proliferation was not affected. By contrast, miR-3653-3p silencing mitigated the promoted BMSC osteogenic differentiation caused by circ_0003865 silencing, but had no effect on proliferation. Finally, circ_0003865 silencing repressed OP development in mouse model. Conclusion MEL promotes BMSC osteogenic differentiation and inhibits OP pathogenesis by suppressing the expression of circ_0003865, which regulates GAS1 gene expression via sponging miR-3653-3p.

scholarly journals Transcriptome analysis for the restrained stem development of the wheat mutant dms

2017 ◽  
Vol 47 (12) ◽  
Author(s):  
Ruishi He ◽  
Xinxin Zhu ◽  
Qiaoyun Li ◽  
Yumei Jiang ◽  
Dongyan Yu ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Expression Profiles ◽  
Triticum Aestivum L ◽  
Sequencing Analysis ◽  
Biological Processes ◽  
Causal Factors ◽  
Qrt Pcr ◽  
Stem Development ◽  
Wheat Mutant ◽  
Phytohormone Signaling

ABSTRACT: Wheat (Triticum aestivum L.) stem development significantly affects grain yield. The dwarf plants (D) of wheat mutant dms was less than 30cm. Here, we were to explore the molecular basis for the restrained stem development of the dwarf plants. The results were reached by compare the young spikes and stems transcriptomes of the tall (T) and D plants of mutant dms. We identified 663 genes highly expressed in stem tips. We identified 997 differentially expressed genes (DEGs) in stem tips between T and D, 403 DEGs were significantly related with stem development. Most biological processes in stem tips on dwarf plants were significantly suppressed, such as phytohormone signaling etc. The sequencing analysis results were confirmed by quantitatively analysis the expression profiles of fourteen key DEGs via real-time QRT-PCR. We identified a group genes related to wheat stem development, identified a group DEGs related to the restrained stem development of D plants of dms. The suppressed phytohormone signaling, carbohydrate transport and metabolism were the major causal factors leading to dwarf plants of D. Our dataset provides a useful resource for investigating wheat stem development.

scholarly journals Circular RNA circ_0014717 Suppresses Hepatocellular Carcinoma Tumorigenesis Through Regulating miR-668-3p/BTG2 Axis

2021 ◽  
Vol 10 ◽  
Author(s):  
Hongxi Ma ◽  
Chunchun Huang ◽  
Qiuhuan Huang ◽  
Guangzhi Li ◽  
Jun Li ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Binding Sites ◽  
Close Association ◽  
Circular Rna ◽  
Migration And Invasion ◽  
Biological Processes ◽  
Tissue Samples ◽  
Qrt Pcr ◽  
Direct Binding ◽  
Hep3b Cells

Recent studies have reported a close association between circRNAs and cancer development. CircRNAs have been recognized to be involved in various biological processes. Up to now, the function of circRNAs in hepatocellular carcinoma (HCC) is still poorly known. qRT-PCR was used to test circ_0014717 expression in HCC tissue samples and cells was determined. It was shown that circ_0014717 was significantly decreased in HCC. Then, we observed overexpression of circ_0014717 obviously repressed HCC cell growth, migration and invasion. Next, we predicted circ_0014717 acted as a sponge of miR-668-3p. miR-668-3p has been reported to participate in several diseases. In our work, it was shown miR-668-3p was greatly increased in HCC and the direct binding sites between circ_0014717 and miR-668-3p were validated. In addition, B-cell translocation gene 2 (BTG2) is closely involved in cellular carcinogenic processes. BTG2 was predicted as a target for miR-668-3p. By performing rescue assays, we demonstrated that circ_0014717 repressed HCC progression via inhibiting BTG2 expression and sponging miR-668-3p. It was manifested loss of circ_0014717 induced HCC progression, which was reversed by BTG2 in Hep3B cells. In conclusion, our findings illustrated a novel circ_0014717/miR-668-3p/BTG2 regulatory signaling pathway in HCC.

scholarly journals Whole Genome Characterization and Genetic Evolution Analysis of a New Ostrich Parvovirus

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 334
Author(s):  
Kunpeng Yuan ◽  
Dongdong Wang ◽  
Qingdong Luan ◽  
Ju Sun ◽  
Qianwen Gao ◽  
...  
Keyword(s):  
Comprehensive Analysis ◽  
Open Reading Frames ◽  
Genome Characterization ◽  
Distance Analysis ◽  
Evolution Analysis ◽  
New Information ◽  
Close Relationship ◽  
Goose Parvovirus ◽  
Genetic Distance Analysis ◽  
Reading Frames

Ostrich diseases characterized by paralysis have been breaking out in broad areas of China since 2015, causing major damage to the ostrich breeding industry in China. This report describes a parvovirus detected in ostriches from four different regions. The entire genomes of four parvovirus strains were sequenced following amplification by PCR, and we conducted comprehensive analysis of the ostrich parvovirus genome. Results showed that the length genomes of the parvovirus contained two open reading frames. Ostrich parvovirus (OsPV) is a branch of goose parvovirus (GPV). Genetic distance analysis revealed a close relationship between the parvovirus and goose parvovirus strains from China, with the closest being the 2016 goose parvovirus RC16 strain from Chongqing. This is the first report of a parvovirus in ostriches. However, whether OsPV is the pathogen of ostrich paralysis remains uncertain. This study contributes new information about the evolution and epidemiology of parvovirus in China, which provides a new way for the study of paralysis in ostriches.

scholarly journals Comprehensive genomic analysis and expression profiling of the BTB and TAZ (BT) genes in cucumber (Cucumis sativus L.)

2019 ◽  
Vol 56 (No. 1) ◽  
pp. 15-23 ◽  
Author(s):  
Yong Zhou ◽  
Guanghua Li ◽  
Lin Zhang ◽  
Jie Xu ◽  
Lifang Hu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Expression Patterns ◽  
Genomic Analysis ◽  
Biological Processes ◽  
Quantitative Real Time Pcr ◽  
Cucumis Sativus L ◽  
Btb Domain ◽  
Qrt Pcr ◽  
Cucumber Genome ◽  
Bt Genes

BTB-TAZ (BT) proteins are plant-specific transcription factors containing a BTB domain and a TAZ domain. They play vital roles in various biological processes and stress responses. In this study, a total of three BT genes (CsBT1–3) were identified from cucumber genome, and they were unevenly distributed in two of the seven chromosomes. Phylogenetic analysis of the BT proteins from cucumber, Arabidopsis, apple, tomato, and rice revealed that these proteins could be distinctly divided into two groups in accordance with their motif distributions. We also determined the structures of BT genes from cucumber, Arabidopsis, and rice to demonstrate their differences. The quantitative real-time PCR (qRT-PCR) results showed that the CsBT genes displayed differential expression patterns in cucumber tissues, and their expression was regulated by cold, salt, and drought stresses. These findings suggest that CsBT genes may participate in cucumber development and responses to various abiotic stresses.

scholarly journals Genome-wide characterization and expression analysis of the Dof gene family related to abiotic stress in watermelon

2019 ◽  
Author(s):  
Yong Zhou ◽  
Yuan Cheng ◽  
Chunpeng Wan ◽  
Youxin Yang ◽  
Jinyin Chen
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Family ◽  
Expression Patterns ◽  
Future Research ◽  
Biological Processes ◽  
Biological Functions ◽  
Specific Expression ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Intron Structure

The plant DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors that play vital roles in many biological processes and response to stresses. In the present study, a total of 36 ClDof genes were identified in the watermelon genome, which were unevenly distributed on 10 chromosomes. Phylogenetic analysis showed that the ClDof proteins could be divided into nine groups, and the members in a particular group had similar motif arrangement and exon-intron structure. We then analyzed the expression patterns of nine selected ClDof genes in eight specific tissues by qRT-PCR, and the results showed that they have tissue-specific expression patterns. We also evaluated the expression levels of the nine selected ClDof genes under salt stress and ABA treatments using qRT-PCR, and they showed differential expression under these treatments, suggesting their important roles in stress response. Taken together, our results provide a basis for future research on the biological functions of Dof genes in watermelon.

scholarly journals RNA Sequencing Reveals Novel LncRNAs/mRNAs Network Associated with Puerarin-mediated Inhibition of Cardiac Hypertrophy in Mice

2021 ◽  
Author(s):  
Shan Ye ◽  
Wei-Yang Chen ◽  
Caiwen Ou ◽  
Min-Sheng Chen
Keyword(s):  
Mouse Model ◽  
Cardiac Hypertrophy ◽  
Protective Effect ◽  
Rna Sequencing ◽  
Expression Patterns ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Biological Processes ◽  
Rna Seq ◽  
Qrt Pcr

Abstract Background: Evidence has demonstrated that puerarin is a potential drug for the treatment of cardiac hypertrophy. However, the precise underlying molecular mechanisms of the protective effect of puerarin are still unclear. Here, we aimed to explore the regulatory mechanisms of lncRNAs/mRNAs in a cardiac hypertrophy mouse model after puerarin treatment.Methods: A mouse model of cardiac hypertrophy was established by transverse aortic constriction (TAC). The echocardiography, tissue staining and western blot were used to examine the protective effect of puerarin. Then RNA sequencing (RNA-seq) was carried out to systematically analyze global gene expression. The target lncRNAs were confirmed using qRT-PCR. Moreover, a coding/non-coding gene co-expression (CNC) network was established to find the interaction of lncRNAs and mRNAs. The molecular functions, biological processes, molecular components and pathways of different expression mRNAs targeted by lncRNA were explored using Gene Ontology (GO) analysis and Kyto Encyclopedia of Genes and Genomes (KEGG) pathways analysis.Results: Puerarin exhibited obvious inhibitory effect in cardiac hypertrophy in TAC model. RNA-seq analysis was performed to investigate the lncRNAs and mRNAs expression patterns of cardiomyocytes in sham and TAC groups treated with or without puerarin. RNA-seq identified that TAC upregulated 19 lncRNAs and downregulated 18 lncRNAs, which could be revised by puerarin treatment (Fold change ≥ 3 and P< 0.05). Expression alterations of selected lncRNAs ENSMUST00000125726, ENSMUST00000143044 and ENSMUST00000212795 were confirmed by qRT-PCR. Pearson’s correlation coefficients of co-expression levels suggested that there was interactive relationship between those 3 validated altered lncRNAs and 5,500 mRNAs (r > 0.95 or r < −0.95). Those co-expressed mRNAs were enriched in some important biological processes such as vesicle-mediated transport, sin 3 complex, and translation initiation factor activity. KEGG analyses suggested that those lncRNA-interacted mRNAs were enriched in RNA transport, ribosome biogenesis in eukaryotes and proteasome signaling pathway. Conclusion: Puerarin may exert beneficial effects on cardiac hypertrophy through regulating the ENSMUST00000125726 /ENSMUST00000143044 / ENSMUST00000212795 -mRNAs network.

scholarly journals MiR-181a Reduces Platelet Activation via the Inhibition of Endogenous RAP1B

MicroRNA ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 240-246 ◽  
Author(s):  
Neetu Dahiya ◽  
Chintamani D. Atreya
Keyword(s):  
Platelet Activation ◽  
Binding Sites ◽  
Untranslated Region ◽  
Ex Vivo ◽  
Ectopic Expression ◽  
Surface Expression ◽  
Factors Affecting ◽  
Protein Levels ◽  
Qrt Pcr ◽  
Platelet Functions

Aim: Since RAP1B is critical for platelet functions, including hemostasis, this study was conducted to identify RAP1B regulating microRNAs (miRNAs) in ex vivo stored platelets. Background: Previous studies with platelets identified factors affecting RAP1B activity but regulatory miRNAs that affect RAP1B protein expression have not been reported. Objective : To understand the functional significance of miRNA mediated regulation of RAP1B in stored platelets, using microRNA, miR-181a as an example. Methods: A Tagged RNA Affinity approach (MS2-TRAP) was employed to identify miRNAs that bound to the 3` untranslated region (3`UTR) of the RAP1B mRNA in HeLa cells as an assay system. And subsequently, the mRNA 3’UTR:miRNA interactions were verified in platelets through the ectopic expression of miR-181a mimic and appropriate controls. The interaction of such miRNAs with RAP1B mRNA was also validated by qRT-PCR and Western analysis. Results: Sixty-two miRNAs from MS2 assay were then compared with already known 171 platelet abundant miRNAs to identify a common set of miRNAs. This analysis yielded six miRNAs (miR- 30e, miR-155, miR-181a, miR-206, miR-208a and miR-454), which are also predicted to target RAP1B mRNA. From this pool, miR-181a was selected for further study since RAP1B harbors two binding sites for miR-181a in its 3′UTR. Ectopic expression of miR-181a mimic in platelets resulted in lowering the endogenous RAP1B at both mRNA and protein levels. Further, miR-181a ectopic expression reduced the surface expression of the platelet activation marker, P-selectin. Conclusion: MicroRNA-181a can target RAP1B and this interaction has the potential to regulate platelet activation during storage.

Cause and Effect Relations of Panicle Traits in Rice (Oryza sativa L.)

2002 ◽  
Vol 1 (2) ◽  
pp. 123-125
Author(s):  
Muhammad Saif-ur-Ra ◽  
Hafeez Ahmad Sadaqat . ◽  
Muhammad Babar .
Keyword(s):  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Cause And Effect ◽  
Panicle Traits

La exposición de plantas de arroz (Oryza sativa L.) a nanopartículas de plata afecta la expresión de genes multifuncionales NAC

2019 ◽  
Vol 12 (4) ◽  
Author(s):  
Fernando Carlos Gómez-Merino ◽  
Robert Vilchis-Zimuta ◽  
Jericó Jabín Bello-Bello ◽  
Gabriel Alcántar-González ◽  
Libia Iris Trejo-Téllez
Keyword(s):  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Qrt Pcr ◽  
Expresión Génica

Objetivo: El objetivo de este estudio fue evaluar el efecto de las nanopartículas de plata (AgNPs) en la expresión de 17 genes NAC en plantas de arroz (Oryza sativa L.) en invernadero. Plántulas de arroz de 12 d de edad se trasfirieron a un sistema hidropónico. Catorce días después del trasplante se aplicaron los siguientes tratamientos a través de la solución nutritiva: 0, 20, 40 y 80 mg L-1 AgNPs. Cada tratamiento tuvo seis repeticiones en un diseño experimental completamente al azar. De las plantas tratadas y del testigo se extrajo RNA total de vástago, a partir del cual se sintetizó cDNA y se realizó una medición de la expresión génica por la técnica de qRT-PCR. Como gen de referencia se tomó el Factor de elongación 1?, que mostró mayor estabilidad. La expresión relativa de los genes se determinó utilizando el método 2-??Ct, con un valor de expresión diferencial de 2. Resultados: Se encontró que las AgNPs indujeron la expresión de cuatro genes NAC (Os02g56600, Os07g04560, Os12g43530 y Os06g5107) por al menos una dosis de AgNPs probada, y un gen (0s08g10080) mostró represión de la expresión por la presencia de estas nanopartículas en la solución nutritiva. En el gen Os07g04560, la expresión fue dependiente de la concentración de AgNPs, esto es, a mayor concentración de AgNPs en el medio, mayor expresión del gen. Limitaciones: En este estudio no fue posible analizar la expresión de genes NAC en respuesta a AgNPs en otros tejidos y en otras etapas fenológica. Conslusiones: Las nanopartículas de plata afectan diferencialmente la expresión de genes NAC en arroz, lo que corrobora la multifuncionalidad de estos genes en plantas.

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