scholarly journals Metabolome and Transcriptome Analysis of Hexaploid Solidago canadensis Roots Reveals its Invasive Capacity Related to Polyploidy

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 187 ◽  
Author(s):  
Miao Wu ◽  
Yimeng Ge ◽  
Chanchan Xu ◽  
Jianbo Wang
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Gene Expression Regulation ◽  
Mapk Signaling ◽  
Vital Role ◽  
Solidago Canadensis ◽  
Metabolome Analysis ◽  
Regulation Of Expression ◽  
Invasive Capacity ◽  
Metabolite Synthesis

Polyploid plants are more often invasive species than their diploid counterparts. As the invasiveness of a species is often linked to its production of allelopathic compounds, we hypothesize that differences in invasive ability between cytotypes may be due to their different ability to synthesize allelopathic metabolites. We test this using two cytotypes of Solidago canadensis as the model and use integrated metabolome and transcriptome data to resolve the question. Metabolome analysis identified 122 metabolites about flavonoids, phenylpropanoids and terpenoids, of which 57 were differentially accumulated between the two cytotypes. Transcriptome analysis showed that many differentially expressed genes (DEGs) were enriched in ‘biosynthesis of secondary metabolites’, ‘plant hormone signal transduction’, and ‘MAPK signaling’, covering most steps of plant allelopathic metabolite synthesis. Importantly, the differentially accumulated flavonoids, phenylpropanoids and terpenoids were closely correlated with related DEGs. Furthermore, 30 miRNAs were found to be negatively associated with putative targets, and they were thought to be involved in target gene expression regulation. These miRNAs probably play a vital role in the regulation of metabolite synthesis in hexaploid S. canadensis. The two cytotypes of S. canadensis differ in the allelopathic metabolite synthesis and this difference is associated with regulation of expression of a range of genes. These results suggest that changes in gene expression may underlying the increased invasive potential of the polyploidy.

scholarly journals Metabolic Alterations in Spheroid-Cultured Hepatic Stellate Cells

2020 ◽  
Vol 21 (10) ◽  
pp. 3451 ◽  
Author(s):  
Koichi Fujisawa ◽  
Taro Takami ◽  
Nanami Sasai ◽  
Toshihiko Matsumoto ◽  
Naoki Yamamoto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Hepatic Stellate Cells ◽  
Nuclear Translocation ◽  
Smooth Muscle Actin ◽  
Hippo Pathway ◽  
Lipid Synthesis ◽  
Stellate Cells ◽  
Vital Role ◽  
Metabolome Analysis ◽  
The Hippo Pathway

Hepatic stellate cells (HSCs) play a vital role in liver fibrosis, and a greater understanding of their regulation is required. Recent studies have focused on relationships between extracellular matrix (ECM) stiffness and gene expression or cellular metabolism, but none have provided a detailed metabolic analysis of HSC changes in spheroid cultures. Accordingly, in the present study, we created an HSC spheroid culture and analyzed changes in gene expression and metabolism. Expression of α-smooth muscle actin (α-SMA) decreased in the spheroids, suppressing proliferation. Gene expression analysis revealed the cell cycle, sirtuin signaling, mitochondrial dysfunction, and the Hippo pathway to be canonical pathways, believed to result from decreased proliferative ability or mitochondrial suppression. In the Hippo pathway, nuclear translocation of the yes-associated protein (YAP) was decreased in the spheroid, which was associated with the stiffness of the ECM. Metabolome analysis showed glucose metabolism changes in the spheroid, including glutathione pathway upregulation and increased lipid synthesis. Addition of the glycolytic product phosphoenolpyruvate (PEP) led to increased spheroid size, with increased expression of proteins such as α-SMA and S6 ribosomal protein (RPS6) phosphorylation, which was attributed to decreased suppression of translation. The results of our study contribute to the understanding of metabolic changes in HSCs and the progression of hepatic fibrosis.

scholarly journals Methods for the analysis of transcriptome dynamics

2019 ◽  
Vol 8 (5) ◽  
pp. 597-612 ◽  
Author(s):  
Daniela F. Rodrigues ◽  
Vera M. Costa ◽  
Ricardo Silvestre ◽  
Maria L. Bastos ◽  
Félix Carvalho
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Messenger Rna ◽  
Noncoding Rna ◽  
Gene Expression Regulation ◽  
System Level ◽  
Rna Transcription ◽  
Expression Control ◽  
Gene Expression Control ◽  
Gene Expression Alterations

Abstract The transcriptome is the complete set of transcripts in a cell or tissue and includes ribosomal RNA (rRNA), messenger RNA (mRNA), transfer RNA (tRNA), and regulatory noncoding RNA. At steady-state, the transcriptome results from a compensatory variation of the transcription and decay rate to maintain the RNA concentration constant. RNA transcription constitutes the first stage in gene expression, and thus is a major and primary mode of gene expression control. Nevertheless, regulation of RNA decay is also a key factor in gene expression control, involving either selective RNA stabilization or enhanced degradation. Transcriptome analysis allows the identification of gene expression alterations, providing new insights regarding the pathways and mechanisms involved in physiological and pathological processes. Upon perturbation of cell homeostasis, rapid changes in gene expression are required to adapt to new conditions. Thus, to better understand the regulatory mechanisms associated with gene expression alterations, it is vital to acknowledge the relative contribution of RNA synthesis and decay to the transcriptome. To the toxicology field, the study of gene expression regulation mechanisms can help identify the early and mechanistic relevant cellular events associated with a particular response. This review aims to provide a critical comparison of the available methods used to analyze the contribution of RNA transcription and decay to gene expression dynamics. Notwithstanding, an integration of the data obtained is necessary to understand the entire repercussions of gene transcription changes at a system-level. Thus, a brief overview of the methods available for the integration and analysis of the data obtained from transcriptome analysis will also be provided.

scholarly journals Integrated Study of Transcriptome-wide m6A Methylome Reveals Novel Insights Into the Character and Function of m6A Methylation During Yak Adipocyte Differentiation

2021 ◽  
Vol 9 ◽  
Author(s):  
Yongfeng Zhang ◽  
Chunnian Liang ◽  
Xiaoyun Wu ◽  
Jie Pei ◽  
Xian Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Adipocyte Differentiation ◽  
Gene Expression Regulation ◽  
Positive Association ◽  
Cold Season ◽  
Vital Role ◽  
Functional Enrichment ◽  
Differentially Methylated Genes ◽  
And Function

Yak (Bos grunniens) is considered an iconic symbol of Tibet and high altitude, but they suffer from malnutrition during the cold season that challenges the metabolism of energy. Adipocytes perform a crucial role in maintaining the energy balance, and adipocyte differentiation is a complex process involving multiple changes in the expression of genes. N6-methyladenosine (m6A) plays a dynamic role in post-transcription gene expression regulation as the most widespread mRNA modification of the higher eukaryotes. However, currently there is no research existing on the m6A transcriptome-wide map of bovine animals and their potential biological functions in adipocyte differentiation. Therefore, we performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to determine the distinctions in m6A methylation and gene expression during yak adipocyte differentiation. In yak adipocyte and preadipocyte the content of m6A and m6A-associated enzymes was substantially different. In the two groups, a total of 14,710 m6A peaks and 13,388 m6A peaks were identified. For the most part, m6A peaks were enriched in stop codons, 3′-untranslated regions, and coding regions with consensus motifs of GGACU. The functional enrichment exploration displayed that differentially methylated genes participated in some of the pathways associated with adipogenic metabolism, and several candidate genes (KLF9, FOXO1, ZNF395, and UHRF1) were involved in these pathways. In addition to that, there was a positive association between m6A abundance and levels of gene expression, which displayed that m6A may play a vital role in modulating gene expression during yak adipocyte differentiation. Further, in the adipocyte group, several methylation gene protein expression levels were significantly higher than in preadipocytes. In short, it can be concluded that the current study provides a comprehensive explanation of the m6A features in the yak transcriptome, offering in-depth insights into m6A topology and associated molecular mechanisms underlying bovine adipocyte differentiation, which might be helpful for further understanding its mechanisms.

scholarly journals Integrated Study of Transcriptome-wide m6A Methylome Confirms a Potential Mechanism for Transcriptional Regulation During Yak Adipocytes Differentiation

2020 ◽  
Author(s):  
Yongfeng Zhang ◽  
Chunnian Liang ◽  
Xiaoyun Wu ◽  
Jie Pei ◽  
Xian Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Adipocyte Differentiation ◽  
Gene Expression Regulation ◽  
Positive Association ◽  
Cold Season ◽  
Vital Role ◽  
Functional Enrichment ◽  
Expression Of Genes ◽  
Differentially Methylated Genes

Abstract Background: Yak (Bos grunniens) is considered as an iconic symbol of Tibet and high altitude, but they suffer from malnutrition during the cold season that challenges the metabolism of energy. Adipocytes perform crucial role in maintaining the energy balance and adipocyte differentiation is a complex process involving multiple changes in expression of genes. N6-methyladenosine (m6A) plays an dynamic role in post-transcription gene expression regulation as the most widespread mRNA modification of the higher eukaryotes. However, currently there is no research existing on the m6A transcriptome-wide map of bovine animals and their potential biological functions in adipocyte differentiation. Results: We performed methylated RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq) to determine the distinctions in m6A methylation and gene expression during yak adipocyte differentiation. In yak adipocyte and preadipocyte the content of m6A and m6A associated enzymes were substantially different. In the two groups, a total of 14,710 m6A peaks and 13,388 m6A peaks were identified. In the most part, m6A peaks were enriched in stop codons, 3’-untranslated regions and coding regions. The functional enrichment exploration displayed that differentially methylated genes participated in some of the pathways associated with adipogenic metabolism. In addition to that there was a positive association between m6A abundance and levels of gene expression, which displayed that m6A plays vital role in modulating gene expression during yak adipocyte differentiation.Conclusions: In short, it could be concluded that the current study provides a comprehensive explanation of the m6A features in the yak transcriptome, offering in-depth insights into m6A topology and associated molecular mechanisms underlying bovine adipocyte differentiation which might be helpful for further understanding its mechanisms.

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