scholarly journals Genome-wide identification of microRNAs involved in the somatic embryogenesis of Eucalyptus

2021 ◽  
Author(s):  
Zihai Qin ◽  
Junji Li ◽  
Ye Zhang ◽  
Yufei Xiao ◽  
Xiaoning Zhang ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Target Prediction ◽  
Small Rna Sequencing ◽  
Eucalyptus Species ◽  
Mirna Regulation ◽  
Small Noncoding Rnas ◽  
First Time ◽  
Dedifferentiation Process

Abstract MicroRNAs (miRNAs) are small noncoding RNAs (18∼24 nt) and function in many biological processes in plants. Although Eucalyptus trees are widely planted across the world, our understanding of the miRNA regulation in the somatic embryogenesis (SE) of Eucalyptus is still poor. Here we reported, for the first time, the miRNA profiles of differentiated and dedifferentiated tissues of two Eucalyptus species and identified miRNAs involved in SE of Eucalyptus. Stem and tissue-culture induced callus were obtained from the subculture seedlings of E. camaldulensis and E. grandis x urophylla, and were used as differentiated and dedifferentiated samples, respectively. Small RNA sequencing generated 304.2 million clean reads for the Eucalyptus samples (n = 3) and identified 888 miRNA precursors (197 known and 691 novel) for Eucalyptus. These miRNAs were mainly distributed in chromosomes Chr03, Chr05 and Chr08, and can produce 46 miRNA clusters. Then, we identified 327 and 343 differentially expressed miRNAs (DEmiRs) in the dedifferentiation process of E. camaldulensis and E. grandis x urophylla, respectively. DEmiRs shared by the two Eucalyptus species might be involved in the development of embryonic callus, such as MIR156, MIR159, MIR160, MIR164, MIR166, MIR169, MIR171, MIR399 and MIR482. Notably, we identified 81 up-regulated and 67 down-regulated miRNAs specific to E. camaldulensis, which might be associated with the high embryogenic potential. Target prediction and functional analysis showed they might be involved in longevity regulating and plant hormone signal transduction pathways. Further, using the gene expression profiles we observed the negative regulation of miRNA∼target pairs, such as MIR160∼ARF18, MIR396∼GRF6, MIR166∼ATHB15/HD-ZIP and MIR156/MIR157∼SPL1. Interestingly, transcription factors such as WRKY, MYB, GAMYB, TCP4 and PIL1 were found to be regulated by the DEmiRs. The genes encoding PIL1 and RPS21C, regulated by up-regulated miRNAs (e.g., egd-N-miR63-5p, egd-N-miR63-5p and MIR169,) were down-regulated exclusively in the dedifferentiation of E. camaldulensis. This is the first time to study the miRNA regulation in the dedifferentiation process of Eucalyptus and it will provide a valuable resource for future studies. More importantly, it will improve our understanding of miRNA regulation during the somatic embryogenesis of Eucalyptus and benefit the Eucalyptus breeding program.

scholarly journals Genome-Wide Identification of MicroRNAs Associated With the Somatic Embryogenesis in Eucalyptus

2020 ◽  
Author(s):  
Zihai Qin ◽  
Junji Li ◽  
Ye Zhang ◽  
Yufei Xiao ◽  
Xiaoning Zhang ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Target Prediction ◽  
Mature Mirnas ◽  
Mirna Regulation ◽  
Small Noncoding Rnas ◽  
Mirna Clusters ◽  
First Time ◽  
Dedifferentiation Process

Abstract Background: MicroRNAs (miRNAs) are a class of small noncoding RNAs with 18-24 nucleotides in length and function in many biological processes in plant. Although Eucalyptus trees are widely planted across the world, our understanding of the miRNA regulation in the somatic embryogenesis of Eucalyptus is still poor. Here we reported for the first time the miRNA profiles of differentiated and dedifferentiated tissues of two Eucalyptus cultivars and identified miRNAs involved in the somatic embryogenesis of Eucalyptus.Results: Stem and tissue-culture induced callus were obtained from the subculture seedlings of E. camaldulensis and E. grandis x urophylla, and were used as differentiated and dedifferentiated samples, respectively. We generated 346.4 million reads for 12 samples (n=3) and identified 888 miRNA precursors (197 known and 691 novel) which can produce 1,067 mature miRNAs. These miRNAs were mainly distributed in chromosomes Chr03, Chr05 and Chr08, and can produce 46 miRNA clusters. In these samples we detected 998 miRNAs with TPM (transcripts per million reads) > 5 and found that highly expressed miRNAs varied across samples. We identified 327 and 343 differentially expressed miRNAs in the dedifferentiation process of E. camaldulensis and E. grandis x urophylla, respectively. Dysregulated miRNAs shared by the two cultivars might be involved in the development of embryonic callus of Eucalyptus, such as MIR156, MIR159, MIR160, MIR164, MIR166, MIR169, MIR171, MIR399 and MIR482. We also identified 81 up-regulated (e.g., miR159c-3p, miR167a-5p, miR397a-3p, miR397c-5p, miR397d-3p, miR397d-5p, N-miR1-5p and N-miR5-5p) and 67 down-regulated (e.g., miR482b-3p, N-miR3-3p, miR156a-3p, N-miR40-3p and N-miR18-5p) miRNAs specific to E. camaldulensis. Target prediction and functional analysis showed they might be involved in longevity regulating and plant hormone signal transduction pathways. Then, the expression patterns of these miRNAs were confirmed by qRT-PCR. Conclusions: This is the first time to study the miRNAs profiles in the dedifferentiation process of Eucalyptus and it will provide a valuable resource for future studies. More importantly, our findings will improve our understanding of miRNA regulation and molecular mechanisms during the somatic embryogenesis of Eucalyptus, and the output of this study will benefit the Eucalyptus breeding program.

scholarly journals Genome-wide identification of microRNAs associated with the somatic embryogenesis in Eucalyptus

2020 ◽  
Author(s):  
Zihai Qin ◽  
Junji Li ◽  
Ye Zhang ◽  
Yufei Xiao ◽  
Xiaoning Zhang ◽  
...  
Keyword(s):  
Somatic Embryogenesis ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Target Prediction ◽  
Mature Mirnas ◽  
Mirna Regulation ◽  
Small Noncoding Rnas ◽  
Mirna Clusters ◽  
First Time ◽  
Dedifferentiation Process

Abstract Background: MicroRNAs (miRNAs) are a class of small noncoding RNAs with 18-24 nucleotides in length and function in many biological processes in plant. Although Eucalyptus trees are widely planted across the world, our understanding of the miRNA regulation in the somatic embryogenesis of Eucalyptus is still poor. Here we reported for the first time the miRNA profiles of differentiated and dedifferentiated tissues of two Eucalyptus cultivars and identified miRNAs involved in the somatic embryogenesis of Eucalyptus.Results: Stem and tissue-culture induced callus were obtained from the subculture seedlings of E. camaldulensis and E. grandis x urophylla, and were used as differentiated and dedifferentiated samples, respectively. We generated 346.4 million reads for 12 samples (n=3) and identified 888 miRNA precursors (197 known and 691 novel) which can produce 1,067 mature miRNAs. These miRNAs were mainly distributed in chromosomes Chr03, Chr05 and Chr08, and can produce 46 miRNA clusters. In these samples we detected 998 miRNAs with TPM (transcripts per million reads) > 5 and found that highly expressed miRNAs varied across samples. We identified 327 and 343 differentially expressed miRNAs in the dedifferentiation process of E. camaldulensis and E. grandis x urophylla, respectively. Dysregulated miRNAs shared by the two cultivars might be involved in the development of embryonic callus of Eucalyptus, such as MIR156, MIR159, MIR160, MIR164, MIR166, MIR169, MIR171, MIR399 and MIR482. We also identified 81 up-regulated (e.g., miR159c-3p, miR167a-5p, miR397a-3p, miR397c-5p, miR397d-3p, miR397d-5p, N-miR1-5p and N-miR5-5p) and 67 down-regulated (e.g., miR482b-3p, N-miR3-3p, miR156a-3p, N-miR40-3p and N-miR18-5p) miRNAs specific to E. camaldulensis. Target prediction and functional analysis showed they might be involved in longevity regulating and plant hormone signal transduction pathways. Then, the expression patterns of these miRNAs were confirmed by qRT-PCR. Conclusions: This is the first time to study the miRNAs profiles in the dedifferentiation process of Eucalyptus and it will provide a valuable resource for future studies. More importantly, our findings will improve our understanding of miRNA regulation and molecular mechanisms during the somatic embryogenesis of Eucalyptus, and the output of this study will benefit the Eucalyptus breeding program.

scholarly journals Time Dependent Gene Expression Changes in the Liver of Mice Treated with Benzene

2008 ◽  
Vol 3 ◽  
pp. BMI.S590 ◽  
Author(s):  
Han-Jin Park ◽  
Jung Hwa Oh ◽  
Seokjoo Yoon ◽  
S.V.S. Rana
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
General Purpose ◽  
Time Dependent ◽  
Expression Data ◽  
Benzene Exposure ◽  
Microarray Analyses ◽  
First Time ◽  
Affymetrix Gene Chip

Benzene is used as a general purpose solvent. Benzene metabolism starts from phenol and ends with p-benzoquinone and o-benzoquinone. Liver injury inducted by benzene still remains a toxicologic problem. Tumor related genes and immune responsive genes have been studied in patients suffering from benzene exposure. However, gene expression profiles and pathways related to its hepatotoxicity are not known. This study reports the results obtained in the liver of BALB/C mice (SLC, Inc., Japan) administered 0.05 ml/100 g body weight of 2% benzene for six days. Serum, ALT, AST and ALP were determined using automated analyzer (Fuji., Japan). Histopathological observations were made to support gene expression data. c-DNA microarray analyses were performed using Affymetrix Gene-chip system. After six days of benzene exposure, twenty five genes were down regulated whereas nineteen genes were up-regulated. These gene expression changes were found to be related to pathways of biotransformation, detoxification, apoptosis, oxidative stress and cell cycle. It has been shown for the first time that genes corresponding to circadian rhythms are affected by benzene. Results suggest that gene expression profile might serve as potential biomarkers of hepatotoxicity during benzene exposure.

scholarly journals Genotype and transcriptome effects on somatic embryogenesis in Cryptomeria japonica

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0244634
Author(s):  
Ayako Izuno ◽  
Tsuyoshi E. Maruyama ◽  
Saneyoshi Ueno ◽  
Tokuko Ujino-Ihara ◽  
Yoshinari Moriguchi
Keyword(s):  
Gene Expression ◽  
Somatic Embryogenesis ◽  
Tree Species ◽  
Somatic Embryos ◽  
Cryptomeria Japonica ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Normal Embryo ◽  
Conifer Species ◽  
Embryogenic Potential

Somatic embryogenesis (SE), which is in vitro regeneration of plant bodies from somatic cells, represents a useful means of clonal propagation and genetic engineering of forest trees. While protocols to obtain calluses and induce regeneration in somatic embryos have been reported for many tree species, the knowledge of molecular mechanisms of SE development is still insufficient to achieve an efficient supply of somatic embryos required for the industrial application. Cryptomeria japonica, a conifer species widely used for plantation forestry in Japan, is one of the tree species waiting for a secure SE protocol; the probability of normal embryo development appears to depend on genotype. To discriminate the embryogenic potential of embryonal masses (EMs) and efficiently obtain normal somatic embryos of C. japonica, we investigated the effects of genotype and transcriptome on the variation in embryogenic potential. Using an induction experiment with 12 EMs each from six genotypes, we showed that embryogenic potential differs between/within genotypes. Comparisons of gene expression profiles among EMs with different embryogenic potentials revealed that 742 differently expressed genes were mainly associated with pattern forming and metabolism. Thus, we suggest that not only genotype but also gene expression profiles can determine success in SE development. Consistent with previous findings for other conifer species, genes encoding leafy cotyledon, wuschel, germin-like proteins, and glutathione-S-transferases are likely to be involved in SE development in C. japonica and indeed highly expressed in EMs with high-embryogenic potential; therefore, these proteins represent candidate markers for distinguishing embryogenic potential.

MiRACLe: an individual-specific approach to improve microRNA-target prediction based on a random contact model

2020 ◽  
Author(s):  
Pan Wang ◽  
Qi Li ◽  
Nan Sun ◽  
Yibo Gao ◽  
Jun S Liu ◽  
...  
Keyword(s):  
Predictive Power ◽  
Expression Profiles ◽  
Target Prediction ◽  
Contact Model ◽  
Prediction Algorithm ◽  
Large Sample Size ◽  
Messenger Rnas ◽  
Expression Data ◽  
Mirna Regulation ◽  
Microrna Target

Abstract Deciphering microRNA (miRNA) targets is important for understanding the function of miRNAs as well as miRNA-based diagnostics and therapeutics. Given the highly cell-specific nature of miRNA regulation, recent computational approaches typically exploit expression data to identify the most physiologically relevant target messenger RNAs (mRNAs). Although effective, those methods usually require a large sample size to infer miRNA–mRNA interactions, thus limiting their applications in personalized medicine. In this study, we developed a novel miRNA target prediction algorithm called miRACLe (miRNA Analysis by a Contact modeL). It integrates sequence characteristics and RNA expression profiles into a random contact model, and determines the target preferences by relative probability of effective contacts in an individual-specific manner. Evaluation by a variety of measures shows that fitting TargetScan, a frequently used prediction tool, into the framework of miRACLe can improve its predictive power with a significant margin and consistently outperform other state-of-the-art methods in prediction accuracy, regulatory potential and biological relevance. Notably, the superiority of miRACLe is robust to various biological contexts, types of expression data and validation datasets, and the computation process is fast and efficient. Additionally, we show that the model can be readily applied to other sequence-based algorithms to improve their predictive power, such as DIANA-microT-CDS, miRanda-mirSVR and MirTarget4. MiRACLe is publicly available at https://github.com/PANWANG2014/miRACLe.

scholarly journals Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways

2020 ◽  
Vol 21 (3) ◽  
pp. 861 ◽  
Author(s):  
Yingdan Yuan ◽  
Bo Zhang ◽  
Xinggang Tang ◽  
Jinchi Zhang ◽  
Jie Lin
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Active Ingredients ◽  
Hub Genes ◽  
Transcriptome Database ◽  
Gene Modules ◽  
Functional Investigation ◽  
First Time

Dendrobium is widely used in traditional Chinese medicine, which contains many kinds of active ingredients. In recent years, many Dendrobium transcriptomes have been sequenced. Hence, weighted gene co-expression network analysis (WGCNA) was used with the gene expression profiles of active ingredients to identify the modules and genes that may associate with particular species and tissues. Three kinds of Dendrobium species and three tissues were sampled for RNA-seq to generate a high-quality, full-length transcriptome database. Based on significant changes in gene expression, we constructed co-expression networks and revealed 19 gene modules. Among them, four modules with properties correlating to active ingredients regulation and biosynthesis, and several hub genes were selected for further functional investigation. This is the first time the WGCNA method has been used to analyze Dendrobium transcriptome data. Further excavation of the gene module information will help us to further study the role and significance of key genes, key signaling pathways, and regulatory mechanisms between genes on the occurrence and development of medicinal components of Dendrobium.

scholarly journals The origin, fate and function of macrophages in the peripheral nervous system—an update

2020 ◽  
Vol 32 (11) ◽  
pp. 709-717 ◽  
Author(s):  
Lukas Amann ◽  
Marco Prinz
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Rna Sequencing ◽  
Peripheral Nervous System ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
New Techniques ◽  
Macrophage Populations ◽  
And Function ◽  
First Time

Abstract The field of macrophage biology has made enormous progress over recent years. This was triggered by the advent of several new techniques such as the establishment of Cre/loxP-based transgenic mouse models that allowed for the first time delineation of the ontogeny and function of specific macrophage populations across many tissues. In addition, the introduction of new high-throughput technologies like bulk RNA sequencing and later single-cell RNA sequencing as well as advances in epigenetic analysis have helped to establish gene expression profiles, enhancer landscapes and local signaling cues that define and shape the identity of diverse macrophage populations. Nonetheless, some macrophage populations, like the ones residing in the peripheral nervous system (PNS), have not been studied in such detail yet. Here, we discuss recent studies that shed new light on the ontogeny, heterogeneity and gene expression profiles of resident macrophages in peripheral nerves and described differential activation of macrophage subsets during and after acute sciatic nerve injury.

scholarly journals Transcriptome profiling of ulcerative colitis mouse model suggests biomarkers and therapeutic targets for human colitis

2020 ◽  
Author(s):  
Reza Yarani ◽  
Oana Palasca ◽  
Nadezhda T. Doncheva ◽  
Christian Anthon ◽  
Bartosz Pilecki ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ulcerative Colitis ◽  
Mouse Model ◽  
High Throughput ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Unknown Etiology ◽  
Small Rna Sequencing ◽  
Complex Nature

1.AbstractBACKGROUND & AIMSUlcerative colitis (UC) is an inflammatory bowel disorder with unknown etiology. Given its complex nature, in vivo studies to investigate its pathophysiology is vital. Animal models play an important role in molecular profiling necessary to pinpoint mechanisms that contribute to human disease. Thus, we aim to identify common conserved gene expression signatures and differentially regulated pathways between human UC and a mouse model hereof, which can be used to identify UC patients from healthy individuals and to suggest novel treatment targets and biomarker candidates.METHODSTherefore, we performed high-throughput total and small RNA sequencing to comprehensively characterize the transcriptome landscape of the most widely used UC mouse model, the dextran sodium sulfate (DSS) model. We used this data in conjunction with publicly available human UC transcriptome data to compare gene expression profiles and pathways.RESULTSWe identified differentially regulated protein-coding genes, long non-coding RNAs and microRNAs from colon and blood of UC mice and further characterized the involved pathways and biological processes through which these genes may contribute to disease development and progression. By integrating human and mouse UC datasets, we suggest a set of 51 differentially regulated genes in UC colon and blood that may improve molecular phenotyping, aid in treatment decisions, drug discovery and the design of clinical trials.CONCLUSIONGlobal transcriptome analysis of the DSS-UC mouse model supports its use as an efficient high-throughput tool to discover new targets for therapeutic and diagnostic applications in human UC through identifying relationships between gene expression and disease phenotype.

scholarly journals Genome-Wide Expression Difference of MicroRNAs in Basal Cell Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Hai-Peng Wei ◽  
Song Zhan ◽  
Qing-An Zhu ◽  
Zhen-Juan Chen ◽  
Xian Feng ◽  
...  
Keyword(s):  
Basal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Basal Cell ◽  
Target Genes ◽  
Expression Profiles ◽  
Taqman Probe ◽  
Control Group ◽  
Small Rna Sequencing ◽  
Mirna Regulation ◽  
Genome Wide

Distinct expression of the miRNAs has rarely been explored in basal cell carcinoma (BCC) of skin, and the regulatory role of miRNAs in BCC development remains quite opaque. Here, we collected control tissues from adjacent noncancerous skin ( n = 15 ; control group) and tissues at tumor centers from patients with cheek BCC ( n = 15 ; BCC group) using punch biopsies. After six small RNA sequencing- (sRNA-seq-) based miRNA expression profiles were generated for both BCC and controls, including three biological replicates, we conducted comparative analysis on the sRNA-seq dataset, discovering 181 differentially expressed miRNAs (DEMs) out of the 1,873 miRNAs in BCCs. In order to validate the sRNA-seq data, expression of 15 randomly selected DEMs was measured using the TaqMan probe-based quantitative real-time PCR. Functional analysis of predicted target genes of DEMs in BCCs shows that these miRNAs are primarily involved in various types of cancers, immune response, epithelial growth, and morphogenesis, as well as energy production and metabolism, indicating that BCC development is caused, at least in part, by changes in miRNA regulation for biological and disease processes. In particular, the “basal cell carcinoma pathways” were found to be enriched by predicted DEM targets, and regulatory relationships between DEMs and their targeted genes in this pathway were further uncovered. These results revealed the association between BCCs and abundant miRNA molecules that regulate target genes, functional modules, and signaling pathways in carcinogenesis.

scholarly journals Integrated mRNA and small RNA sequencing reveals microRNA regulatory network associated with internode elongation in sugarcane (Saccharum officinarum L.)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Lihang Qiu ◽  
Rongfa Chen ◽  
Yegeng Fan ◽  
Xing Huang ◽  
Hanmin Luo ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Nitrogen Metabolism ◽  
Differentially Expressed Genes ◽  
Small Rna ◽  
Plant Hormone ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Internode Elongation ◽  
Mirna Regulation

Abstract Background Internode elongation is one of the most important traits in sugarcane because of its relation to crop productivity. Understanding the microRNA (miRNA) and mRNA expression profiles related to sugarcane internode elongation would help develop molecular improvement strategies but they are not yet well-investigated. To identify genes and miRNAs involved in internode elongation, the cDNA and small RNA libraries from the pre-elongation stage (EI), early elongation stage (EII) and rapid elongation stage (EIII) were sequenced and their expression were studied. Results Based on the sequencing results, 499,495,518 reads and 80,745 unigenes were identified from stem internodes of sugarcane. The comparisons of EI vs. EII, EI vs. EIII, and EII vs. EIII identified 493, 5035 and 3041 differentially expressed genes, respectively. Further analysis revealed that the differentially expressed genes were enriched in the GO terms oxidoreductase activity and tetrapyrrole binding. KEGG pathway annotation showed significant enrichment in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction”, which might be participating in internode elongation. miRNA identification showed 241 known miRNAs and 245 novel candidate miRNAs. By pairwise comparison, 11, 42 and 26 differentially expressed miRNAs were identified from EI and EII, EI and EIII, and EII and EIII comparisons, respectively. The target prediction revealed that the genes involved in “zeatin biosynthesis”, “nitrogen metabolism” and “plant hormone signal transduction” pathways are targets of the miRNAs. We found that the known miRNAs miR2592-y, miR1520-x, miR390-x, miR5658-x, miR6169-x and miR8154-x were likely regulators of genes with internode elongation in sugarcane. Conclusions The results of this study provided a global view of mRNA and miRNA regulation during sugarcane internode elongation. A genetic network of miRNA-mRNA was identified with miRNA-mediated gene expression as a mechanism in sugarcane internode elongation. Such evidence will be valuable for further investigations of the molecular regulatory mechanisms underpinning sugarcane growth and development.

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