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

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.

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

10.21203/rs.3.rs-78772/v1 ◽

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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Pseudogene ACTBP2 increases blood–brain barrier permeability by promoting KHDRBS2 transcription through recruitment of KMT2D/WDR5 in Aβ1–42 microenvironment

Cell Death Discovery ◽

10.1038/s41420-021-00531-y ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Qianshuo Liu ◽

Xiaobai Liu ◽

Defeng Zhao ◽

Xuelei Ruan ◽

Rui Su ◽

...

Keyword(s):

Blood Brain Barrier ◽

Molecular Mechanisms ◽

Rna Binding ◽

Vital Role ◽

Brain Barrier ◽

Blood Brain ◽

Bbb Permeability ◽

Novel Target ◽

And Function

AbstractThe blood–brain barrier (BBB) has a vital role in maintaining the homeostasis of the central nervous system (CNS). Changes in the structure and function of BBB can accelerate Alzheimer’s disease (AD) development. β-Amyloid (Aβ) deposition is the major pathological event of AD. We elucidated the function and possible molecular mechanisms of the effect of pseudogene ACTBP2 on the permeability of BBB in Aβ1–42 microenvironment. BBB model treated with Aβ1–42 for 48 h were used to simulate Aβ-mediated BBB dysfunction in AD. We proved that pseudogene ACTBP2, RNA-binding protein KHDRBS2, and transcription factor HEY2 are highly expressed in ECs that were obtained in a BBB model in vitro in Aβ1–42 microenvironment. In Aβ1–42-incubated ECs, ACTBP2 recruits methyltransferases KMT2D and WDR5, binds to KHDRBS2 promoter, and promotes KHDRBS2 transcription. The interaction of KHDRBS2 with the 3′UTR of HEY2 mRNA increases the stability of HEY2 and promotes its expression. HEY2 increases BBB permeability in Aβ1–42 microenvironment by transcriptionally inhibiting the expression of ZO-1, occludin, and claudin-5. We confirmed that knocking down of Khdrbs2 or Hey2 increased the expression levels of ZO-1, occludin, and claudin-5 in APP/PS1 mice brain microvessels. ACTBP2/KHDRBS2/HEY2 axis has a crucial role in the regulation of BBB permeability in Aβ1–42 microenvironment, which may provide a novel target for the therapy of AD.

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Detoxification and Immune Transcriptomic Response of the Gill Tissue of Bay Scallop (Argopecten irradians) Following Exposure to the Algicide Palmitoleic Acid

Biomolecules ◽

10.3390/biom8040139 ◽

2018 ◽

Vol 8 (4) ◽

pp. 139 ◽

Cited By ~ 3

Author(s):

Cheng Chi ◽

Sib Giri ◽

Jin Jun ◽

Hyoun Kim ◽

Sang Kim ◽

...

Keyword(s):

Gene Expression ◽

Cytochrome P450 ◽

Palmitoleic Acid ◽

Molecular Mechanisms ◽

Functional Enrichment ◽

Alexandrium Tamarense ◽

Read Length ◽

Related Factor ◽

Transcriptomic Response ◽

Bay Scallop

Palmitoleic acid (PA) is an effective algicide against Alexandrium tamarense. However, the toxicological mechanism of PA exposure is unclear. The transcript abundance and differentially expressed genes (DEGs) in gills of bay scallop were investigated following 80 mg/L PA exposure up to 48 h using the Illumina HiSeq 4000 deep-sequencing platform with the recommended read length of 100 bp. De novo assembly of paired-end reads yielded 62,099 unigenes; 5414 genes were identified as being significantly increased, and 4452 were decreased. Based on gene ontology classification and enrichment analysis, the ‘cellular process’, ‘metabolic process’, ‘response to stimulus’, and ‘catalytic process’ with particularly high functional enrichment were revealed. The DEGs, which are related to detoxification and immune responses, revealed that acid phosphatase, fibrinogen C domain-containing protein, cyclic AMP-responsive element-binding protein, glutathione reductase, ATP-binding cassette, nuclear factor erythroid 2-related factor, NADPH2:quinone reductase, and cytochrome P450 4F22, 4B1, and 2C8-related gene expression decreased. In contrast, some genes related to glutathione S-transferase, C-type lectin, superoxide dismutase, toll-like receptors, and cytochrome P450 2C14, 2U1, 3A24 and 4A2 increased. The results of current research will be a valuable resource for the investigation of gene expression stimulated by PA, and will help understanding of the molecular mechanisms underlying the scallops’ response to PA exposure.

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Mechanically Sensitive HSF1 is a Key Regulator of Left-Right Symmetry Breaking in Zebrafish Embryos

10.1101/2021.02.25.432863 ◽

2021 ◽

Author(s):

Jing Du ◽

Shu-Kai Li ◽

Liu-Yuan Guan ◽

Zheng Guo ◽

Jiang-Fan Yin ◽

...

Keyword(s):

Gene Expression ◽

Symmetry Breaking ◽

Molecular Mechanisms ◽

Fluid Shear Stress ◽

Gene Expression Regulation ◽

Early Stage ◽

Expression Regulation ◽

Zebrafish Embryos ◽

Mechanical Stimuli ◽

Nodal Flow

AbstractThe left-right symmetry breaking of vertebrate embryos requires fluid flow (called nodal flow in zebrafish). However, the molecular mechanisms that mediate the asymmetric gene expression regulation under nodal flow remain elusive. In this paper, we report that heat shock factor 1 (HSF1) is asymmetrically activated in the Kuppfer’s vesicle at the early stage of zebrafish embryos in the presence of nodal flow. Deficiency in HSF1 expression caused a significant situs inversus and disrupted gene expression asymmetry of nodal signaling proteins in zebrafish embryos. Further studies demonstrated that HSF1 could be immediately activated by fluid shear stress. The mechanical sensation ability of HSF1 is conserved in a variety of mechanical stimuli in different cell types. Moreover, cilia and the Ca2+-Akt signaling axis are essential for the activation of HSF1 under mechanical stress in vitro and in vivo. Considering the conserved expression of HSF1 in organisms, these findings unveil a fundamental mechanism of gene expression regulation triggered by mechanical clues during embryonic development and other physiological and pathological transformations.

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The essential activities of the bacterial sigma factor

Canadian Journal of Microbiology ◽

10.1139/cjm-2016-0576 ◽

2017 ◽

Vol 63 (2) ◽

pp. 89-99 ◽

Cited By ~ 16

Author(s):

Maria C. Davis ◽

Christopher A. Kesthely ◽

Emily A. Franklin ◽

Shawn R. MacLellan

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Rna Synthesis ◽

Gene Expression Regulation ◽

Structure And Function ◽

Structural Studies ◽

General Transcription Factors ◽

Transcription Process ◽

Promoter Dna ◽

And Function

Transcription is the first and most heavily regulated step in gene expression. Sigma (σ) factors are general transcription factors that reversibly bind RNA polymerase (RNAP) and mediate transcription of all genes in bacteria. σ Factors play 3 major roles in the RNA synthesis initiation process: they (i) target RNAP holoenzyme to specific promoters, (ii) melt a region of double-stranded promoter DNA and stabilize it as a single-stranded open complex, and (iii) interact with other DNA-binding transcription factors to contribute complexity to gene expression regulation schemes. Recent structural studies have demonstrated that when σ factors bind promoter DNA, they capture 1 or more nucleotides that are flipped out of the helical DNA stack and this stabilizes the promoter open-complex intermediate that is required for the initiation of RNA synthesis. This review describes the structure and function of the σ70 family of σ proteins and the essential roles they play in the transcription process.

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The expanding world of metabolic enzymes moonlighting as RNA binding proteins

Biochemical Society Transactions ◽

10.1042/bst20200664 ◽

2021 ◽

Author(s):

Nicole J. Curtis ◽

Constance J. Jeffery

Keyword(s):

Gene Expression ◽

Regulatory Networks ◽

Binding Proteins ◽

Molecular Mechanisms ◽

Rna Binding ◽

Rna Binding Proteins ◽

Molecular Structures ◽

Intermediary Metabolism ◽

The Many ◽

And Function

RNA binding proteins play key roles in many aspects of RNA metabolism and function, including splicing, transport, translation, localization, stability and degradation. Within the past few years, proteomics studies have identified dozens of enzymes in intermediary metabolism that bind to RNA. The wide occurrence and conservation of RNA binding ability across distant branches of the evolutionary tree suggest that these moonlighting enzymes are involved in connections between intermediary metabolism and gene expression that comprise far more extensive regulatory networks than previously thought. There are many outstanding questions about the molecular structures and mechanisms involved, the effects of these interactions on enzyme and RNA functions, and the factors that regulate the interactions. The effects on RNA function are likely to be wider than regulation of translation, and some enzyme–RNA interactions have been found to regulate the enzyme's catalytic activity. Several enzyme–RNA interactions have been shown to be affected by cellular factors that change under different intracellular and environmental conditions, including concentrations of substrates and cofactors. Understanding the molecular mechanisms involved in the interactions between the enzymes and RNA, the factors involved in regulation, and the effects of the enzyme–RNA interactions on both the enzyme and RNA functions will lead to a better understanding of the role of the many newly identified enzyme–RNA interactions in connecting intermediary metabolism and gene expression.

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Identification of Four Key Biomarkers and Small Molecule Drugs Innasopharyngeal Carcinoma by Weighted Gene Co-expression Network Analysis

10.21203/rs.3.rs-49643/v1 ◽

2020 ◽

Author(s):

Xi Pan ◽

Jian-Hao Liu

Keyword(s):

Gene Expression ◽

Network Analysis ◽

Small Molecule ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Tumor Stage ◽

Functional Enrichment ◽

Hub Genes ◽

Therapeutic Goals ◽

Small Molecule Drugs

Abstract Background Nasopharyngeal carcinoma (NPC) is a heterogeneous carcinoma that the underlying molecular mechanisms involved in the tumor initiation, progression, and migration are largely unclear. The purpose of the present study was to identify key biomarkers and small-molecule drugs for NPC screening, diagnosis, and therapy via gene expression profile analysis. Methods Raw microarray data of NPC were retrieved from the Gene Expression Omnibus (GEO) database and analyzed to screen out the potential differentially expressed genes (DEGs). The key modules associated with histology grade and tumor stage was identified by using weighted correlation network analysis (WGCNA). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of genes in the key module were performed to identify potential mechanisms. Candidate hub genes were obtained, which based on the criteria of module membership (MM) and high connectivity. Then we used receiver operating characteristic (ROC) curve to evaluate the diagnostic value of hub genes. The Connectivity map database was further used to screen out small-molecule drugs of hub genes. Results A total of 430 DEGs were identified based on two GEO datasets. The green gene module was considered as key module for the tumor stage of NPC via WGCNA analysis. The results of functional enrichment analysis revealed that genes in the green module were enriched in regulation of cell cycle, p53 signaling pathway, cell part morphogenesis. Furthermore, four DEGs-related hub genes in the green module were considered as the final hub genes. Then ROC revealed that the final four hub genes presented with high areas under the curve, suggesting these hub genes may be diagnostic biomarkers for NPC. Meanwhile, we screened out several small-molecule drugs that have provided potentially therapeutic goals for NPC. Conclusions Our research identified four potential prognostic biomarkers and several candidate small-molecule drugs for NPC, which may contribute to the new insights for NPC therapy.

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

Genes ◽

10.3390/genes11020187 ◽

2020 ◽

Vol 11 (2) ◽

pp. 187 ◽

Cited By ~ 1

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.

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SUN-587 IDH1-Dependent Alpha-KG Regulates Brown Fat Differentiation and Function by Modulating Histone Methylation

Journal of the Endocrine Society ◽

10.1210/jendso/bvaa046.1484 ◽

2020 ◽

Vol 4 (Supplement_1) ◽

Author(s):

Won Kon Kim ◽

Baek-Soo Han

Keyword(s):

Histone Methylation ◽

Molecular Mechanisms ◽

Adipocyte Differentiation ◽

Uncoupling Protein ◽

Ectopic Expression ◽

Brown Adipocyte ◽

Brown Adipocytes ◽

Brown Adipose ◽

And Function ◽

Brown Adipogenesis

Abstract Brown adipocytes play important roles in the regulation of energy homeostasis by uncoupling protein 1-mediated non-shivering thermogenesis. Recent studies suggest that brown adipocytes as novel therapeutic targets for combating obesity and associated diseases, such as type II diabetes. However, the molecular mechanisms underlying brown adipocyte differentiation and function are not fully understood. We employed previous findings obtained through proteomic studies performed to assess proteins displaying altered levels during brown adipocyte differentiation. Here, we performed assays to determine the functional significance of their altered levels during brown adipogenesis and development. We identified isocitrate dehydrogenase 1 (IDH1) as upregulated during brown adipocyte differentiation, with subsequent investigations revealing that ectopic expression of IDH1 inhibited brown adipogenesis, whereas suppression of IDH1 levels promoted differentiation of brown adipocytes. Additionally, Idh1 overexpression resulted in increased levels of intracellular α-ketoglutarate (α-KG) and inhibited the expression of genes involved in brown adipogenesis. Exogenous treatment with α-KG reduced brown adipogenesis during the early phase of differentiation, and ChIP analysis revealed that IDH1-mediated α-KG reduced trimethylation of histone H3 lysine 4 in the promoters of genes associated with brown adipogenesis. Furthermore, administration of α-KG decreased adipogenic gene expression by modulating histone methylation in brown adipose tissues of mice. These results suggested that the IDH1–α-KG axis plays an important role in regulating brown adipocyte differentiation and might represent a therapeutic target for treating metabolic diseases.

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Intrauterine calorie restriction affects placental DNA methylation and gene expression

Physiological Genomics ◽

10.1152/physiolgenomics.00034.2013 ◽

2013 ◽

Vol 45 (14) ◽

pp. 565-576 ◽

Cited By ~ 57

Author(s):

Pao-Yang Chen ◽

Amit Ganguly ◽

Liudmilla Rubbi ◽

Luz D. Orozco ◽

Marco Morselli ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Chronic Diseases ◽

Calorie Restriction ◽

Molecular Mechanisms ◽

Target Genes ◽

Specific Effects ◽

Differentially Methylated Genes ◽

Critical Organ ◽

Successive Generations

Maternal nutrient restriction causes the development of adult onset chronic diseases in the intrauterine growth restricted (IUGR) fetus. Investigations in mice have shown that either protein or calorie restriction during pregnancy leads to glucose intolerance, increased fat mass, and hypercholesterolemia in adult male offspring. Some of these phenotypes are shown to persist in successive generations. The molecular mechanisms underlying IUGR remain unclear. The placenta is a critical organ for mediating changes in the environment and the development of embryos. To shed light on molecular mechanisms that might affect placental responses to differing environments we examined placentas from mice that had been exposed to different diets. We measured gene expression and whole genome DNA methylation in both male and female placentas of mice exposed to either caloric restriction or ad libitum diets. We observed several differentially expressed pathways associated with IUGR phenotypes and, most importantly, a significant decrease in the overall methylation between these groups as well as sex-specific effects that are more pronounced in males. In addition, a set of significantly differentially methylated genes that are enriched for known imprinted genes were identified, suggesting that imprinted loci may be particularly susceptible to diet effects. Lastly, we identified several differentially methylated microRNAs that target genes associated with immunological, metabolic, gastrointestinal, cardiovascular, and neurological chronic diseases, as well as genes responsible for transplacental nutrient transfer and fetal development.

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