scholarly journals MicroRNA Profiling During Mulberry (Morus atropurpurea Roxb) Fruit Development and Regulatory Pathway of miR477 for Anthocyanin Accumulation

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaonan Dong ◽  
Chaorui Liu ◽  
Yuqi Wang ◽  
Qing Dong ◽  
Yingping Gai ◽  
...  
Keyword(s):  
Fruit Development ◽  
Target Genes ◽  
Expression Patterns ◽  
Regulation Of Transcription ◽  
Anthocyanin Accumulation ◽  
Regulatory Pathway ◽  
Development Stages ◽  
Fruit Development And Ripening ◽  
Non Coding Rnas ◽  
Mulberry Fruits

To understand the mechanism of small non-coding RNAs (miRNA)-mediated development and ripening of mulberry fruits, three small RNA libraries from mulberry fruits at different development stages were constructed, and 159 conserved miRNAs as well as 86 novel miRNAs were successfully identified. Among the miRNAs identified, there were 90 miRNAs which showed differential expression patterns at different stages of fruit development and ripening. The target genes of these differential expressed (DE) miRNAs were involved in growth and development, transcription and regulation of transcription, metabolic processes, and etc. Interestingly, it was found that the expression level of mul-miR477 was increased with fruit ripening, and it can target the antisense lncRNA (Mul-ABCB19AS) of the ATP binding cassette (ABC) transporter B 19 gene (Mul-ABCB19). Our results showed that mul-miR477 can repress the expression of Mul-ABCB19AS and increase the expression of Mul-ABCB19, and it acted as a positive regulator participating anthocyanin accumulation through the regulatory network of mul-miR477—Mul-ABCB19AS—Mul-ABCB19.

Expression patterns of genes involved in sugar metabolism and accumulation during peach fruit development and ripening

2019 ◽  
Vol 257 ◽  
pp. 108633 ◽  
Author(s):  
Muhammad Muzammal Aslam ◽  
Li Deng ◽  
Xiaobei Wang ◽  
Yan Wang ◽  
Lei Pan ◽  
...  
Keyword(s):  
Fruit Development ◽  
Expression Patterns ◽  
Sugar Metabolism ◽  
Peach Fruit ◽  
Fruit Development And Ripening

scholarly journals Developmental Variation in Fruit Polyphenol Content and Related Gene Expression of a Red-Fruited versus a White-Fruited Fragaria vesca Genotype

Horticulturae ◽  
2018 ◽  
Vol 4 (4) ◽  
pp. 30
Author(s):  
Sutapa Roy ◽  
Sanjay Singh ◽  
Douglas Archbold
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Fruit Development ◽  
Biosynthetic Pathway ◽  
Receptor Gene ◽  
Expression Patterns ◽  
Related Gene ◽  
Pathway Gene ◽  
Fruit Development And Ripening ◽  
Flavonoid Biosynthetic Pathway

Two cultivars of F. vesca, red-fruited Baron Solemacher (BS) and white-fruited Pineapple Crush (PC), were studied to compare and contrast the quantitative accumulation of major polyphenols and related biosynthetic pathway gene expression patterns during fruit development and ripening. Developing PC fruit showed higher levels of hydroxycinnamic acids in green stages and a greater accumulation of ellagitannins in ripe fruit in comparison to BS. In addition to anthocyanin, red BS fruit had greater levels of flavan-3-ols when ripe than PC. Expression patterns of key structural genes and transcription factors of the phenylpropanoid/flavonoid biosynthetic pathway, an abscisic acid (ABA) biosynthetic gene, and a putative ABA receptor gene that may regulate the pathway, were also analyzed during fruit development and ripening to determine which genes exhibited differences in expression and when such differences were first evident. Expression of all pathway genes differed between the red BS and white PC at one or more times during development, most notably at ripening when phenylalanine ammonia lyase 1 (PAL1), chalcone synthase (CHS), flavanone-3′-hydroxylase (F3′H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), and UDP:flavonoid-O-glucosyltransferase 1 (UFGT1) were significantly upregulated in the red BS fruit. The transcription factors MYB1 and MYB10 did not differ substantially between red and white fruit except at ripening, when both the putative repressor MYB1 and promoter MYB10 were upregulated in red BS but not white PC fruit. The expression of ABA-related gene 9-cis-epoxycarotenoid dioxygenase 1 (NCED1) was higher in red BS fruit but only in the early green stages of development. Thus, a multigenic effect at several points in the phenylpropanoid/flavonoid biosynthetic pathway due to lack of MYB10 upregulation may have resulted in white PC fruit.

scholarly journals MicroRNA-202 Induces Myoblast to Myocyte Differentiation through Targeting Rock-1

2021 ◽  
Author(s):  
Maryam Honardoost ◽  
Mahsa Bourbour ◽  
Ehsan Arefian
Keyword(s):  
Target Genes ◽  
Horse Serum ◽  
Expression Patterns ◽  
C2c12 Cell ◽  
Inhibitory Effect ◽  
Luciferase Assay ◽  
Differentiation Process ◽  
Myocyte Differentiation ◽  
Non Coding Rnas ◽  
The Impact

Abstract The expression patterns of microRNAs (small non-coding RNAs) are altered in many biological processes such as myogenesis. In this study, we aimed to investigate the impact of predicted miR-202, its target genes Akt2 and Rock-1 as a potential regulator of myoblast in the myocyte differentiation process using the C2C12 cell line. After confirmation of the differentiation process induced by 3% horse serum, the expression level of miRNA and its targets were evaluated. In the following, a luciferase assay was conducted to approve the effect of miRNA on its target. Our results indicated that miR-202 and Akt2 were significantly up-regulated during differentiation, while Rock-1 was downregulated. Co-transfection of miRNA with psiCHECK2-Rock-1 significantly presented that Rock-1 was directly targeted by miR-202. On the contrary, miR-202 has failed to enforce its inhibitory effect on Akt2 expression. In particular, miR-202 seems to be a regulator of muscle differentiation pathway thought targeting Rock-1.

scholarly journals Integrative Analyses of Widely Targeted Metabolic Profiling and Transcriptome Data Reveals Molecular Insight into Metabolomic Variations during Apple (Malus domestica) Fruit Development and Ripening

2020 ◽  
Vol 21 (13) ◽  
pp. 4797 ◽  
Author(s):  
Jidi Xu ◽  
Jinjiao Yan ◽  
Wenjie Li ◽  
Qianying Wang ◽  
Caixia Wang ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Fruit Quality ◽  
Fruit Development ◽  
Large Scale ◽  
Tricarboxylic Acid Cycle ◽  
Flavonoid Pathway ◽  
Primary And Secondary Metabolites ◽  
Development Stages ◽  
Fruit Development And Ripening ◽  
Fruit Stage

The apple is a favorite fruit for human diet and is one of the most important commercial fruit crops around the world. Investigating metabolic variations during fruit development can provide a better understanding on the formation of fruit quality. The present study applied a widely targeted LC-MS-based metabolomics approach with large-scale detection, identification and quantification to investigate the widespread metabolic changes during “Pinova” apple development and ripening. A total of 462 primary and secondary metabolites were simultaneously detected, and their changes along with the four fruit-development stages were further investigated. The results indicated that most of the sugars presented increasing accumulation levels while organic acid, including Tricarboxylic acid cycle (TCA) intermediates, showed a distinct decreasing trend across the four fruit-development stages. A total of 207 secondary metabolites consisted of 104 flavonoids and 103 other secondary metabolites. Many flavonoids maintained relatively high levels in the early fruit stage and then rapidly decreased their levels at the following developmental stages. Further correlation analyses of each metabolite–metabolite pair highlighted the cross talk between the primary and secondary metabolisms across fruit development and ripening, indicating the significant negative correlations between sugars and secondary metabolites. Moreover, transcriptome analysis provided the molecular basis for metabolic variations during fruit development. The results showed that most differentially expressed genes (DEGs) involved in the TCA cycle were upregulated from the early fruit stage to the preripening stage. The extensive downregulation of controlling genes involved in the flavonoid pathway is probably responsible for the rapid decrease of flavonoid content at the early fruit stage. These data provide a global view of the apple metabolome and a comprehensive analysis on metabolomic variations during fruit development, providing a broader and better understanding on the molecular and metabolic basis of important fruit quality traits in commercial apples.

scholarly journals miRNA Clusters with Up-Regulated Expression in Colorectal Cancer

Cancers ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2979
Author(s):  
Paulína Pidíková ◽  
Iveta Herichová
Keyword(s):  
Colorectal Cancer ◽  
Target Genes ◽  
Expression Patterns ◽  
Clinicopathological Characteristics ◽  
Cancer Tissue ◽  
Poor Patient ◽  
Regulated Expression ◽  
Mirna Clusters ◽  
Non Coding Rnas ◽  
Poor Patient Survival

Colorectal cancer (CRC) is one of the most common malignancies in Europe and North America. Early diagnosis is a key feature of efficient CRC treatment. As miRNAs can be used as CRC biomarkers, the aim of the present study was to analyse experimentally validated data on frequently up-regulated miRNA clusters in CRC tissue and investigate their members with respect to clinicopathological characteristics of patients. Based on available data, 15 up-regulated clusters, miR-106a/363, miR-106b/93/25, miR-17/92a-1, miR-181a-1/181b-1, miR-181a-2/181b-2, miR-181c/181d, miR-183/96/182, miR-191/425, miR-200c/141, miR-203a/203b, miR-222/221, mir-23a/27a/24-2, mir-29b-1/29a, mir-301b/130b and mir-452/224, were selected. The positions of such clusters in the genome can be intronic or intergenic. Most clusters are regulated by several transcription factors, and miRNAs are also sponged by specific long non-coding RNAs. In some cases, co-expression of miRNA with other cluster members or host gene has been proven. miRNA expression patterns in cancer tissue, blood and faeces were compared. Based on experimental evidence, 181 target genes of selected clusters were identified. Panther analysis was used to reveal the functions of the target genes and their corresponding pathways. Clusters miR-17/92a-1, miR-106a/363, miR-106b/93/25 and miR-183/96/182 showed the strongest association with metastasis occurrence and poor patient survival, implicating them as the most promising targets of translational research.

scholarly journals Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wenjuan Zhao ◽  
Zijing Li ◽  
Quan Liu ◽  
Su Xie ◽  
Mengxun Li ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Signaling Pathway ◽  
Muscle Development ◽  
Target Genes ◽  
Muscle Growth ◽  
Skeletal Muscle Development ◽  
Protein Coding ◽  
Development Stages ◽  
Non Coding Rnas ◽  
Embryonic Muscle

AbstractSkeletal muscle growth plays a critical role during porcine muscle development stages. Genome-wide transcriptome analysis reveals that long intergenic non-coding RNAs (lincRNAs) are implicated as crucial regulator involving in epigenetic regulation. However, comprehensive analysis of lincRNAs in embryonic muscle development stages remain still elusive. Here, we investigated the transcriptome profiles of Duroc embryonic muscle tissues from days 33, 65, and 90 of gestation using RNA-seq, and 228 putative lincRNAs were identified. Moreover, these lincRNAs exhibit the characteristics of shorter transcripts length, longer exons, less exon numbers and lower expression level compared with protein-coding transcripts. Expression profile analysis showed that a total of 120 lincRNAs and 2638 mRNAs were differentially expressed. In addition, we also performed quantitative trait locus (QTL) mapping analysis for differentially expressed lincRNAs (DE lincRNAs), 113 of 120 DE lincRNAs were localized on 2200 QTLs, we observed many QTLs involved in growth and meat quality traits. Furthermore, we predicted potential target genes of DE lincRNAs in cis or trans regulation. Gene ontology and pathway analysis reveals that potential targets of DE lincRNAs mostly were enriched in the processes and pathways related to tissue development, MAPK signaling pathway, Wnt signaling pathway, TGF-beta signaling pathway and insulin signaling pathway, which involved in skeletal muscle physiological functions. Based on cluster analysis, co-expression network analysis of DE lincRNAs and their potential target genes indicated that DE lincRNAs highly regulated protein-coding genes associated with skeletal muscle development. In this study, many of the DE lincRNAs may play essential roles in pig muscle growth and muscle mass. Our study provides crucial information for further exploring the molecular mechanisms of lincRNAs during skeletal muscle development.

scholarly journals Dynamic Changes of Ascorbic Acid Occurring During Fruit Development and Ripening of Actinida Latifolia and Their Associated Molecular Mechanisms Deciphered by Weighted Gene Co-Expression Network Analysis

2020 ◽  
Author(s):  
Hui Xia ◽  
Honghong Deng ◽  
Rongping Hu ◽  
Lijin Lin ◽  
Jin Wang ◽  
...  
Keyword(s):  
Ascorbic Acid ◽  
Network Analysis ◽  
Fruit Development ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Network Module ◽  
Dynamic Changes ◽  
Fruit Development And Ripening ◽  
Expansion Stage ◽  
Highly Correlated

Abstract Background: Actinidia latifolia is an exceptional source with extremely high ascorbic acid (AsA) content. However, its transcriptome atlas is lacking and how AsA accumulates during fruit development and ripening of this special kiwifruit and its associated molecular mechanisms are still poorly understood.Results: Herein, the dynamic changes of AsA content of six stages of A. latifolia fruit development and ripening determined by HPLC demonstrated a rapid increasing profile during the initial expansion stage with a peak around 60 days after flowering (1194.21±69.25 mg 100g-1 FW), followed by a progressive, albeit not significant decrease tendency and reached the minimum levels (1028.76±31.19 mg 100g-1 FW) at maturity. A high-quality full-length (FL) transcriptome of A. latifolia was successfully constructed by third-generation sequencing for the first time, comprising 326,926 FL non-chimeric reads, 15,505 coding sequences, 2882 transcription factors, 18,797 simple sequence repeats, 3328 long noncoding RNAs, and 231 alternative splicing events. Illumina RNA-seq in combination with weighted gene co-expression network analysis revealed a network module highly correlated (r=0.5, p=0.03) with AsA content. Gene co-expression in this network module was explained by its roles in protein processing in endoplasmic reticulum (ko04141), glycolysis/gluconeogenesis (ko00010), and carbon metabolism (ko01200). Moreover, the expression patterns of genes involved in AsA biosynthesis and metabolism validated by qRT-PCR exhibited a similar trend with AsA accumulation.Conclusions: Overall, the dynamic changes of AsA content and associated key genes and enriched metabolic pathways were deciphered, which paves the way for genetic improvement that aims for development of kiwifruit with super-high AsA content.

scholarly journals Analysis of Long Intergenic Non-Coding RNAs Transcriptomic Profiling in Skeletal Muscle Growth During Porcine Embryonic Development

2021 ◽  
Author(s):  
Wenjuan Zhao ◽  
Zijing Li ◽  
Quan Liu ◽  
Su Xie ◽  
Mengxun Li ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Signaling Pathway ◽  
Muscle Development ◽  
Target Genes ◽  
Muscle Growth ◽  
Skeletal Muscle Development ◽  
Protein Coding ◽  
Development Stages ◽  
Non Coding Rnas ◽  
Embryonic Muscle

Abstract Skeletal muscle growth plays a critical role during porcine muscle development stages. Genome-wide transcriptome analysis reveals that thousands of long intergenic non-coding RNAs (lincRNAs) have been identified in various species and implicated as crucial regulator involving in epigenetic regulation. However, comprehensive analysis of lincRNAs in embryonic muscle development stages remain still elusive. Here, we investigated the transcriptome profiles of duroc embryonic muscle tissues from days 33, 65, and 90 of gestation using RNA-seq, there were 228 putative lincRNAs identified. Moreover, these lincRNAs exhibit the characteristics of shorter transcripts length, longer exons, less exon numbers and lower expression level compared with protein-coding transcripts. Differential expression analysis showed that a total of 91 lincRNAs and 2638 mRNAs were differentially expressed. In addition, we also performed quantitative trait locus (QTL) mapping analysis for DE lincRNAs, 113 of 120 DE lincRNAs were localized on 2200 QTLs, we observed many QTLs involved in growth and meat quality traits. Furthermore, we predicted potential target genes of DE lincRNAs in cis or trans regulation. Gene ontology and pathway analysis reveals that potential targets of DE lincRNAs mostly were enriched in the processes and pathways related to tissue development, MAPK signaling pathway, Wnt signaling pathway, TGF-beta signaling pathway and insulin signaling pathway, which involved in skeletal muscle physiological functions. Based on cluster analysis, a co-expression network analysis of DE lincRNAs and their potential target genes indicated that DE lincRNAs highly regulated protein-coding genes associated with skeletal muscle development. In this study, many of the DE lincRNAs identified may play essential roles in pig muscle growth and muscle mass. Our study provides crucial information for exploring further the molecular mechanisms of lincRNAs during skeletal muscle development.

DNA methylation balance is involved in anthocyanin accumulation during Vaccinium corymbosum fruit ripening

2020 ◽  
Vol 10 (4) ◽  
pp. 651-663
Author(s):  
Lei Yu ◽  
Ya Zhou ◽  
Yihui Zhang ◽  
Wei Liu ◽  
Yongqiang Li ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Fruit Ripening ◽  
Fruit Development ◽  
Expression Patterns ◽  
Vaccinium Corymbosum ◽  
Anthocyanin Accumulation ◽  
Flower Bud ◽  
Biosynthetic Genes ◽  
Relative Expression ◽  
Anthocyanin Biosynthetic Genes

BACKGROUND: DNA methylation balance is an important regulatory mechanism for mammalian and plant development. The fruit ripening and anthocyanin accumulation of Vaccinium corymbosum are complex developmental processes that involve numerous physiological, biochemical, and structural alterations. OBJECTIVE: This study aimed to investigate the correlation of DNA methylation balance, DNA methylation and demethylation-related gene expression models and anthocyanin accumulation during blueberry fruit ripening. METHODS: The anthocyanin contents during V. corymbosum ‘O’Neal’ fruit development were evaluated. The V. corymbosum DNA methylation- and anthocyanin accumulation-related genes were isolated, and their relative expression patterns were detected during flower bud enlargement and fruit development. Moreover, the relative expression patterns of anthocyanin biosynthetic genes and the dynamic changes in the DNA methylation of the promoter sequences of key anthocyanin biosynthetic genes were evaluated. RESULTS: The results showed that the DNA methylation level of V. corymbosum fruit was consistent with anthocyanin accumulation during ripening, and the expression levels of anthocyanin biosynthetic and DNA methylation-related genes. CONCLUSIONS: During V. corymbosum fruit ripening, anthocyanin accumulation is regulated partially by DNA methylation balance of VcCHS and VcANS promoters.

scholarly journals Genome-Wide Analysis of the MADS-Box Transcription Factor Family in Solanum lycopersicum

2019 ◽  
Vol 20 (12) ◽  
pp. 2961 ◽  
Author(s):  
Yunshu Wang ◽  
Jianling Zhang ◽  
Zongli Hu ◽  
Xuhu Guo ◽  
Shibing Tian ◽  
...  
Keyword(s):  
Gene Family ◽  
Fruit Development ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Constitutive Expression ◽  
Floral Organ ◽  
Mads Box ◽  
Mads Box Genes ◽  
Fruit Development And Ripening ◽  
Mads Box Gene

MADS-box family genes encode transcription factors that are involved in multiple developmental processes in plants, especially in floral organ specification, fruit development, and ripening. However, a comprehensive analysis of tomato MADS-box family genes, which is an important model plant to study flower fruit development and ripening, remains obscure. To gain insight into the MADS-box genes in tomato, 131 tomato MADS-box genes were identified. These genes could be divided into five groups (Mα, Mβ, Mγ, Mδ, and MIKC) and were found to be located on all 12 chromosomes. We further analyzed the phylogenetic relationships among Arabidopsis and tomato, as well as the protein motif structure and exon–intron organization, to better understand the tomato MADS-box gene family. Additionally, owing to the role of MADS-box genes in floral organ identification and fruit development, the constitutive expression patterns of MADS-box genes at different stages in tomato development were identified. We analyzed 15 tomato MADS-box genes involved in floral organ identification and five tomato MADS-box genes related to fruit development by qRT-PCR. Collectively, our study provides a comprehensive and systematic analysis of the tomato MADS-box genes and would be valuable for the further functional characterization of some important members of the MADS-box gene family.

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