scholarly journals Characterization of miRNAs in Embryonic, Larval, and Adult Lumpfish Provides a Reference miRNAome for Cyclopterus lumpus

Biology ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 130
Author(s):  
Setu Chakraborty ◽  
Nardos T. Woldemariam ◽  
Tina Visnovska ◽  
Matthew L. Rise ◽  
Danny Boyce ◽  
...  
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
Developmental Stages ◽  
Head Kidney ◽  
Mature Mirnas ◽  
Mirna Precursor ◽  
Specific Expression ◽  
Cyclopterus Lumpus ◽  
Novel Mirna

MicroRNAs (miRNAs) are endogenous small RNA molecules involved in the post-transcriptional regulation of protein expression by binding to the mRNA of target genes. They are key regulators in teleost development, maintenance of tissue-specific functions, and immune responses. Lumpfish (Cyclopterus lumpus) is becoming an emergent aquaculture species as it has been utilized as a cleaner fish to biocontrol sea lice (e.g., Lepeophtheirus salmonis) infestation in the Atlantic Salmon (Salmo salar) aquaculture. The lumpfish miRNAs repertoire is unknown. This study identified and characterized miRNA encoding genes in lumpfish from three developmental stages (adult, embryos, and larvae). A total of 16 samples from six different adult lumpfish organs (spleen, liver, head kidney, brain, muscle, and gill), embryos, and larvae were individually small RNA sequenced. Altogether, 391 conserved miRNA precursor sequences (discovered in the majority of teleost fish species reported in miRbase), eight novel miRNA precursor sequences (so far only discovered in lumpfish), and 443 unique mature miRNAs were identified. Transcriptomics analysis suggested organ-specific and age-specific expression of miRNAs (e.g., miR-122-1-5p specific of the liver). Most of the miRNAs found in lumpfish are conserved in teleost and higher vertebrates, suggesting an essential and common role across teleost and higher vertebrates. This study is the first miRNA characterization of lumpfish that provides the reference miRNAome for future functional studies.

scholarly journals Analysis of miRNAs Targeted Storage Regulatory Genes during Soybean Seed Development Based on Transcriptome Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 408 ◽  
Author(s):  
Jing-Yao Yu ◽  
Zhan-Guo Zhang ◽  
Shi-Yu Huang ◽  
Xue Han ◽  
Xin-Yu Wang ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Seed Development ◽  
Small Rna ◽  
Target Genes ◽  
Soybean Seed ◽  
Regulatory Genes ◽  
Small Rna Sequencing ◽  
Grain Development ◽  
Regulatory Relationship ◽  
Novel Mirna

Soybeans are an important cash crop and are widely used as a source of vegetable protein and edible oil. MicroRNAs (miRNA) are endogenous small RNA that play an important regulatory role in the evolutionarily conserved system of gene expression. In this study, we selected four lines with extreme phenotypes, as well as high or low protein and oil content, from the chromosome segment substitution line (CSSL) constructed from suinong (SN14) and ZYD00006, and planted and sampled at three stages of grain development for small RNA sequencing and expression analysis. The sequencing results revealed the expression pattern of miRNA in the materials, and predicted miRNA-targeted regulatory genes, including 1967 pairs of corresponding relationships between known-miRNA and their target genes, as well as 597 pairs of corresponding relationships between novel-miRNA and their target genes. After screening and annotating genes that were targeted for regulation, five specific genes were identified to be differentially expressed during seed development and subsequently analyzed for their regulatory relationship with miRNAs. The expression pattern of the targeted gene was verified by Real-time Quantitative PCR (RT-qPCR). Our research provides more information about the miRNA regulatory network in soybeans and further identifies useful genes that regulate storage during soy grain development, providing a theoretical basis for the regulation of soybean quality traits.

scholarly journals Genome-wide identification and expression profiling of glutathione S-transferase family under multiple abiotic and biotic stresses in Medicago truncatula L.

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0247170
Author(s):  
Md. Soyib Hasan ◽  
Vishal Singh ◽  
Shiful Islam ◽  
Md. Sifatul Islam ◽  
Raju Ahsan ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expression Profiling ◽  
Developmental Stages ◽  
Functional Characterization ◽  
Drought Treatment ◽  
Specific Expression ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Genome Wide

Glutathione transferases (GSTs) constitute an ancient, ubiquitous, multi-functional antioxidant enzyme superfamily that has great importance on cellular detoxification against abiotic and biotic stresses as well as plant development and growth. The present study aimed to a comprehensive genome-wide identification and functional characterization of GST family in one of the economically important legume plants—Medicago truncatula. Here, we have identified a total of ninety-two putative MtGST genes that code for 120 proteins. All these members were classified into twelve classes based on their phylogenetic relationship and the presence of structural conserved domain/motif. Among them, 7 MtGST gene pairs were identified to have segmental duplication. Expression profiling of MtGST transcripts revealed their high level of organ/tissue-specific expression in most of the developmental stages and anatomical tissues. The transcripts of MtGSTU5, MtGSTU8, MtGSTU17, MtGSTU46, and MtGSTU47 showed significant up-regulation in response to various abiotic and biotic stresses. Moreover, transcripts of MtGSTU8, MtGSTU14, MtGSTU28, MtGSTU30, MtGSTU34, MtGSTU46 and MtGSTF8 were found to be highly upregulated in response to drought treatment for 24h and 48h. Among the highly stress-responsive MtGST members, MtGSTU17 showed strong affinity towards its conventional substrates reduced glutathione (GSH) and 1‐chloro‐2,4‐dinitrobenzene (CDNB) with the lowest binding energy of—5.7 kcal/mol and -6.5 kcal/mol, respectively. Furthermore, the substrate-binding site residues of MtGSTU17 were found to be highly conserved. These findings will facilitate the further functional and evolutionary characterization of GST genes in Medicago.

A dual‐luciferase reporter system for characterization of small RNA target genes in both mammalian and insect cells

2021 ◽  
Author(s):  
Zhongyuan Deng ◽  
Yuting Zhang ◽  
Leyao Li ◽  
Xingcheng Xie ◽  
Jinyong Huang ◽  
...  
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
Insect Cells ◽  
Luciferase Reporter ◽  
Reporter System ◽  
Luciferase Reporter System

Sequencing and characterization of lncRNAs in the breast muscle of Gushi and Arbor Acres chickens

Genome ◽  
2018 ◽  
Vol 61 (5) ◽  
pp. 337-347 ◽  
Author(s):  
Tuanhui Ren ◽  
Zhuanjian Li ◽  
Yu Zhou ◽  
Xuelian Liu ◽  
Ruili Han ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Muscle Development ◽  
Target Genes ◽  
Expression Profiles ◽  
Economic Value ◽  
Muscle Quality ◽  
Specific Expression ◽  
Chicken Muscle ◽  
Molecular Regulatory Mechanisms

Chicken muscle quality is one of the most important factors determining the economic value of poultry, and muscle development and growth are affected by genetics, environment, and nutrition. However, little is known about the molecular regulatory mechanisms of long non-coding RNAs (lncRNAs) in chicken skeletal muscle development. Our study aimed to better understand muscle development in chickens and thereby improve meat quality. In this study, Ribo-Zero RNA-Seq was used to investigate differences in the expression profiles of muscle development related genes and associated pathways between Gushi (GS) and Arbor Acres (AA) chickens. We identified two muscle tissue specific expression lncRNAs. In addition, the target genes of these lncRNAs were significantly enriched in certain biological processes and molecular functions, as demonstrated by Gene Ontology (GO) analysis, and these target genes participate in five signaling pathway, as revealed by an analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Taken together, these data suggest that different lncRNAs might be involved in regulating chicken muscle development and growth and provide new insight into the molecular mechanisms of lncRNAs.

scholarly journals Characterization of Putative Effectors from the Cereal Cyst Nematode Heterodera avenae

2018 ◽  
Vol 108 (2) ◽  
pp. 264-274 ◽  
Author(s):  
Jiang-Kuan Cui ◽  
Huan Peng ◽  
Fen Qiao ◽  
Gao-Feng Wang ◽  
Wen-Kun Huang ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Target Genes ◽  
Developmental Stages ◽  
Heterodera Avenae ◽  
Parasitic Nematodes ◽  
Sequencing Analysis ◽  
Rnai Technology

Few molecular details of effectors of Heterodera avenae parasitism are known. We performed a high-throughput sequencing analysis of the H. avenae transcriptome at five developmental stages. A total of 82,549 unigenes were ultimately obtained, and 747 transcripts showed best hits to genes putatively encoding carbohydrate-active enzymes in plant-parasitic nematodes that play an important role in the invasion process. A total of 1,480 unigenes were homologous to known phytonematode effectors, and 63 putative novel effectors were identified in the H. avenae transcriptomes. Twenty-three unigenes were analyzed by qRT-PCR and confirmed to be highly expressed during at least one developmental stage. For in situ hybridization, 17 of the 22 tested putative effectors were specifically expressed and located in the subventral gland cells, and five putative novel effectors were specifically expressed in the dorsal gland. Furthermore, 115 transcripts were found to have putative lethal RNA interference (RNAi) phenotypes. Three target genes with lethal RNAi phenotypes and two of the four tested putative effectors were associated with a decrease in the number of cysts through in vitro RNAi technology. These transcriptomic data lay a foundation for further studies of interactions of H. avenae with cereal and H. avenae parasitic control.

scholarly journals Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Deding Su ◽  
Wei Xiang ◽  
Ling Wen ◽  
Wang Lu ◽  
Yuan Shi ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Transcriptional Repressors ◽  
Promoter Regions ◽  
Specific Expression ◽  
Genome Wide ◽  
Development Processes ◽  
Genomic Characterization ◽  
Functional Features

Abstract Background As the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family. Results Here, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses. Conclusions In this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.

scholarly journals Characterization of miRNAs in Cultured Atlantic Salmon Head Kidney Monocyte-Like and Macrophage-Like Cells

2020 ◽  
Vol 21 (11) ◽  
pp. 3989 ◽  
Author(s):  
Nicole C. Smith ◽  
Sherri L. Christian ◽  
Nardos T. Woldemariam ◽  
Kathy A. Clow ◽  
Matthew L. Rise ◽  
...  
Keyword(s):  
Atlantic Salmon ◽  
Morphological Analysis ◽  
Target Genes ◽  
Head Kidney ◽  
Small Rna Sequencing ◽  
Phagocytic Cells ◽  
Macrophage Differentiation ◽  
Functional Studies

Macrophages are among the first cells to respond to infection and disease. While microRNAs (miRNAs) are involved in the process of monocyte-to-macrophage differentiation in mammals, less is known in teleost fish. Here, Atlantic salmon head kidney leukocytes (HKLs) were used to study the expression of miRNAs in response to in vitro culture. The morphological analysis of cultures showed predominantly monocyte-like cells on Day 1 and macrophage-like cells on Day 5, suggesting that the HKLs had differentiated from monocytes to macrophages. Day 5 HKLs also contained a higher percentage of phagocytic cells. Small RNA sequencing and qPCR analysis were applied to examine the miRNA diversity and expression. There were 370 known mature Atlantic salmon miRNAs in HKLs. Twenty-two miRNAs (15 families) were downregulated while 44 miRNAs (25 families) were upregulated on Day 5 vs. Day 1. Mammalian orthologs of many of the differentially expressed (DE) miRNAs are known to regulate macrophage activation and differentiation, while the teleost-specific miR-2188, miR-462 and miR-731 were also DE and are associated with immune responses in fish. In silico predictions identified several putative target genes of qPCR-validated miRNAs associated with vertebrate macrophage differentiation. This study identified Atlantic salmon miRNAs likely to influence macrophage differentiation, providing important knowledge for future functional studies.

scholarly journals Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (Benincasa hispida) Based on High-Throughput Sequencing

2021 ◽  
Vol 11 (21) ◽  
pp. 10068
Author(s):  
Jinqiang Yan ◽  
Min Wang ◽  
Wenrui Liu ◽  
Dasen Xie ◽  
Xiaoming He ◽  
...  
Keyword(s):  
High Throughput ◽  
Small Rna ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Small Rna Sequencing ◽  
Specific Expression ◽  
Nac Transcription Factors ◽  
Benincasa Hispida ◽  
Wax Gourd

MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs of 20-24 nucleotides and play important roles in many plant biological and metabolic processes. Wax gourd is an important vegetable of Cucurbitacea family, with great economic and medicinal value. Although miRNAs have been extensively studied in model plant species, less is known in wax gourd (Benincasa hispida). In this study, in order to identify miRNAs in wax groud, five independent small RNA libraries were constructed using leaf, root, stem, flower, and fruit of B227. Based on high-throughput Illumina deep sequencing. In total, 422 known and 409 novel miRNAs were identified from five libraries. Comparative analysis revealed that many miRNAs were differentially expressed among different tissues, indicating tissue-specific expression of some miRNAs. qRT-PCR verified the reliability of small RNA sequencing results. Furthermore, miRNAs with similar expression patterns among five tissues were clustered into the same profile, among which many miRNAs were found with relatively high expression in the fruit of wax gourd. MiR164-x had the highest expression in fruit than in other tissues and many NAC transcription factors were predicted as its target genes. We propose that miR164 might regulate fruit development by forming miR164-NAC module in wax gourd. Taken together, this study provides the first global miRNAs profiling of wax gourd, and lays the foundation for understanding the regulatory roles of miRNAs in the growth and development processes of wax gourd.

Genome-wide identification, characterization and expression analysis of BES1 gene family in tomato

2021 ◽  
Author(s):  
Deding Su ◽  
Wei Xiang ◽  
Ling Wen ◽  
Wang Lu ◽  
Yuan Shi ◽  
...  
Keyword(s):  
Target Genes ◽  
Expression Patterns ◽  
Transcriptional Repressors ◽  
Promoter Regions ◽  
Specific Expression ◽  
Genome Wide ◽  
Development Processes ◽  
Genomic Characterization ◽  
Functional Features

Abstract Background: As the key regulators in BR signaling, BES1 family genes regulate thousands of target genes involved in various development processes. So far, the functions of BES1 family are poorly understood in tomato, and a comprehensive genomic and expressional analysis is worth to conduct for this family.Results: Here, nine SlBES1 family members were identified in tomato and classified into five groups based on the conserved motif, gene structure and phylogenetic analysis. Synteny among tomato, Arabidopsis, pepper and rice were further analyzed to obtain insights into evolutionary characteristics. Several cis-elements related to hormone, stress and plant development were exhibited in the promoter regions of SlBES1 family genes. Subcellular localization showed seven members localized both in the nucleus and cytoplasm, implying the presence of dephosphorylated and phosphorylated form of these seven proteins, furthermore, five of them possessed transcription activation activity whereas the left two functioned as transcriptional repressors. Another two members, however, neither localized in the nucleus nor had transactivation activity. Besides, SlBES1.8 showed flower-specific expression while other members expressed ubiquitously in all organs. Moreover, SlBES1 genes exhibited variational expression in response to nine principal plant hormones. Notably, the expression levels of SlBES1 genes presented a dominant downregulated trend in response to stresses.Conclusions: In this study, we systematically analyzed the genomic characterization of SlBES1 family, together with the analyses of protein functional features and expression patterns, our results lay a foundation for the functional research of SlBES1 family.

scholarly journals Identification and Characterization of a Promoter Cassette Conferring Adipocyte-Specific Gene Expression

Endocrinology ◽  
2010 ◽  
Vol 151 (6) ◽  
pp. 2933-2939 ◽  
Author(s):  
Zhao V. Wang ◽  
Yingfeng Deng ◽  
Qiong A. Wang ◽  
Kai Sun ◽  
Philipp E. Scherer
Keyword(s):  
Target Genes ◽  
Transgenic Animals ◽  
Cell Types ◽  
Specific Gene ◽  
Metabolic Dysfunction ◽  
Genomic Locus ◽  
Specific Expression ◽  
Promoter Sequences

The adipocyte-specific secretory molecule adiponectin has found widespread acceptance as a systemic marker that effectively integrates a number of signals associated with metabolic dysfunction at the level of adipose tissue. The widely used aP2 promoter cassette, which is frequently chosen to achieve adipocyte-specific expression of transgenes, conveys transcription in cell types other than adipocytes, such as macrophages and cardiomyocytes. To improve our ability to drive transgene expression in a more adipocyte-specific way, we aimed to define the minimal promoter segment from the adiponectin genomic locus. We generated a series of transgenic animals in which the expression of reporter genes and Cre recombinase was driven by 2, 4.9, and 5.4 kb of adiponectin promoter sequences. We found that the 5.4-kb adiponectin promoter fragment is the most effective cassette conveying adipocyte-specific expression of target genes. We therefore define a novel promoter cassette that ensures adipocyte-specific expression of passenger genes and may be used in the generation of transgenic mouse models to study gene function in vivo.

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