scholarly journals Coordination of m6A mRNA methylation and gene transcriptome in rice response to cadmium stress

2021 ◽  
Author(s):  
Qin Cheng ◽  
Peng Wang ◽  
Guangliang Wu ◽  
Yanning Wang ◽  
Jingai Tan ◽  
...  
Keyword(s):  
Kegg Pathway ◽  
Stop Codon ◽  
Cadmium Stress ◽  
Protein Processing ◽  
Nucleotide Position ◽  
Tryptophan Biosynthesis ◽  
Kegg Pathway Analysis ◽  
Mrna Methylation ◽  
Higher Eukaryotes

Abstract N6-methyladenosine (m6A) is the most prevalent internal modification present in mRNAs of all higher eukaryotes. However, the role of the m6A methylomes in rice is still poorly understood. With the development of MeRIP-seq technique, in-depth identification of mRNAs with m6A modification becomes feasible. We investigated the m6A methylomes in roots of cadmium (Cd) group and compared that with the roots in the control (CK) group by m6A sequencing, in 9311 and Nipponbare (NIP), respectively. The results indicated that Cd leads to altered modification profile in 3,406 differential m6A peaks in 9311, and 2,065 differential m6A peaks in NIP. KEGG pathway analysis of genes with differentially modified m6A peaks indicates that the “phenylalanine”, “tyrosine and tryptophan biosynthesis”, “glycine”, “adherens junctions”, “glycerophospholipid metabolism” and “threonine metabolism” signaling pathways may be associated with abnormal roots development of rice due to exposure to cadmium in 9311. “Arginine”, “proline metabolism”, “glycerolipid”, “protein processing in endoplasmic reticulum”, metabolism pathways were significantly enriched in genes with differentially modified m6A peaks in NIP. Different from that in Arabidopsis, the m6A peak (m6A-modified nucleotide position on mRNAs) distribution exhibits preference toward both the stop codon and 3′UTRs region. These findings provide a resource for plant RNA epi-transcriptomics studies and further enlarge our knowledge on the function of RNA m6A modification in plants.

scholarly journals Coordination of m6A mRNA methylation and gene transcriptome in rice response to cadmium stress

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Qin Cheng ◽  
Peng Wang ◽  
Guangliang Wu ◽  
Yanning Wang ◽  
Jingai Tan ◽  
...  
Keyword(s):  
Posttranscriptional Regulation ◽  
Kegg Pathway ◽  
Stop Codon ◽  
Cadmium Stress ◽  
Treated Group ◽  
Untranslated Regions ◽  
Nucleotide Position ◽  
Kegg Pathway Analysis ◽  
Higher Eukaryotes

AbstractN6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNAs of all higher eukaryotes. However, the role of the m6A methylomes in rice is still poorly understood. With the development of the MeRIP-seq technique, the in-depth identification of mRNAs with m6A modification has become feasible. A study suggested that m6A modification is crucial for posttranscriptional regulation related to Cd2+-induced malignant transformation, but the association between m6A modification in plants and Cd tolerance has not been reported. We investigated the m6A methylomes in the roots of a cadmium (Cd)-treated group and compared them with the roots in the control (CK) group by m6A sequencing of cv. 9311 and cv. Nipponbare (NIP) plants. The results indicated that Cd leads to an altered modification profile in 3,406 differential m6A peaks in cv. 9311 and 2,065 differential m6A peaks in cv. NIP. KEGG pathway analysis of the genes with differentially modified m6A peaks indicated that the “phenylalanine”, “tyrosine and tryptophan biosynthesis”, “glycine”, “adherens junctions”, “glycerophospholipid metabolism” and “threonine metabolism” signalling pathways may be associated with the abnormal root development of cv. 9311 rice due to exposure to Cd. The “arginine”, “proline metabolism”, “glycerolipid”, and “protein processing in endoplasmic reticulum” metabolism pathways were significantly enriched in genes with differentially modified m6A peaks in cv. NIP. Unlike that in Arabidopsis, the m6A-modified nucleotide position on mRNAs (m6A peak) distribution in rice exhibited a preference towards both the stop codon and 3′ untranslated regions (3′ UTRs). These findings provide a resource for plant RNA epitranscriptomic studies and further increase our knowledge on the function of m6A modification in RNA in plants.

scholarly journals Comprehensive Analysis of Differentially Expressed Profiles of circRNAs in Diabetic Cardiomyopathy

2020 ◽  
Author(s):  
Yuanbin Wu ◽  
Nan Cheng ◽  
Yuhai Zhang ◽  
Libing Li ◽  
Lei Mao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Diabetic Cardiomyopathy ◽  
Trp Channels ◽  
Kegg Pathway ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Pathway Enrichment ◽  
Kegg Pathway Analysis ◽  
Pathway Regulation

Abstract Objective: To assess the circular RNAs (circRNA) expression profile and explore their potential functions in diabetic cardiomyopathy (DCM). Methods: Using an STZ induced DCM model, microarray analysis was adopted to assess the circRNAs profiles. Then 6 differentially expressed circRNAs were confirmed by quantitative Real-Time PCR. Furthermore, gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and TargetScan were used to reveal the underlying function of the differentially expressed circRNAs. Cytoscape was used to visualize the interaction networks as well. Results: We revealed a total of 171dyrgulated circRNAs, including 89 upregulated, and 82 downregulated circRNAs in DCM. And confirmed 5 circRNAs distinct expressions (rno_circRNA_000466, rno_circRNA_000964, rno_circRNA_003395, rno_circRNA_000173, rno_circRNA_013989) in DCM by qRT-PCR. GO, and KEGG pathway enrichment revealed the differentially expressed circRNAs might participate in the insulin signaling pathway, autophagy, HIF-1 signaling pathway, inflammatory mediator regulation of TRP channels. rno_circRNA_000466 function through competing endogenous RNA mechanism, and may involve in the TGF-β signaling pathway, regulation of glucose transmembrane transport, endocrine process and response to lipoprotein particle. Conclusions: This study opens new avenues for a better understanding of the involvement of circRNA leading to DCM. And unveiled the specific role of rno_circRNA_000466 in the pathogenesis of DCM. These results may provide important information and direction for the future development of novel targets for the treatment of DCM.

Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

2021 ◽  
pp. 1-14
Author(s):  
Peirong Li ◽  
Xinru Li ◽  
Wei Wang ◽  
Xiaoling Tan ◽  
Xiaoqi Wang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Developmental Stages ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Mythimna Separata ◽  
Kegg Pathway Analysis ◽  
Oriental Armyworm ◽  
Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

scholarly journals Lowering DNA binding affinity of SssI DNA methyltransferase does not enhance the specificity of targeted DNA methylation in E. coli

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Krystyna Ślaska-Kiss ◽  
Nikolett Zsibrita ◽  
Mihály Koncz ◽  
Pál Albert ◽  
Ákos Csábrádi ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Binding ◽  
Binding Affinity ◽  
Dna Methyltransferase ◽  
Restriction Enzymes ◽  
Dna Binding Protein ◽  
E Coli ◽  
Dna Binding Affinity ◽  
Higher Eukaryotes

AbstractTargeted DNA methylation is a technique that aims to methylate cytosines in selected genomic loci. In the most widely used approach a CG-specific DNA methyltransferase (MTase) is fused to a sequence specific DNA binding protein, which binds in the vicinity of the targeted CG site(s). Although the technique has high potential for studying the role of DNA methylation in higher eukaryotes, its usefulness is hampered by insufficient methylation specificity. One of the approaches proposed to suppress methylation at unwanted sites is to use MTase variants with reduced DNA binding affinity. In this work we investigated how methylation specificity of chimeric MTases containing variants of the CG-specific prokaryotic MTase M.SssI fused to zinc finger or dCas9 targeting domains is influenced by mutations affecting catalytic activity and/or DNA binding affinity of the MTase domain. Specificity of targeted DNA methylation was assayed in E. coli harboring a plasmid with the target site. Digestions of the isolated plasmids with methylation sensitive restriction enzymes revealed that specificity of targeted DNA methylation was dependent on the activity but not on the DNA binding affinity of the MTase. These results have implications for the design of strategies of targeted DNA methylation.

scholarly journals POS0399 TMT-BASED QUANTITATIVE PROTEOMICS ANALYSIS OF SYNOVIAL FLUID-DERIVED EXOSOMES IN RHEUMATOID ARTHRITIS, AXIAL SPONDYLOARTHRITIS, GOUT AND OSTEOARTHRITIS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 428.3-429
Author(s):  
Y. Liu ◽  
Y. Huang ◽  
Q. Huang ◽  
Z. Huang ◽  
Z. Li ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Cluster Analysis ◽  
Synovial Fluid ◽  
Pathway Analysis ◽  
Quantitative Proteomics ◽  
Axial Spondyloarthritis ◽  
Kegg Pathway ◽  
Hierarchical Cluster ◽  
Kegg Pathway Analysis ◽  
Differential Proteins

Background:The pathogeneses of the joint diseases rheumatoid arthritis (RA), axial spondyloarthritis (axSpA), gout, and osteoarthritis (OA) are still not fully elucidated. Exosomes in synovial fluid (SF) has a critical role in the pathogenesis of arthritis. None of study has compared the proteomics of SF-derived exosomes in RA, axSpA, gout and OA.Objectives:To compare the proteomics of SF-derived exosomes in RA, axSpA, gout and OA based on tandem mass tags (TMT) labeled quantitative proteomics technique.Methods:SF-derived exosomes was isolated from RA, axSpA, gout and OA patients by the Exoquick kit combined ultracentrifugation method. TMT labeled quantitative proteomics technique was used to compare the proteomics of SF-derived exosomes. Volcano plot, hierarchical cluster, Gene Ontologies (GO), Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted.Results:A total of 1678 credible proteins were detected. With the cut off criteria of |log2 (fold-change)| ≥1.2 and p-value <0.05, 267 (140 up-regulated and 127 down-regulated)differential proteins were found in OA vs gout, 291 (179 and 112) in axSpA vs OA, 515 (109 and 406) in RA vs axSpA, 298 (191 and 107) in axSpA vs gout, 462 (160 and 302) in RA vs gout, 536 (170 and 366) in RA vs OA. GO analysis showed that the biological progress of differential proteins were mainly enriched in the “immune response”. Regarding the molecular function, the differential proteins mainly mediated “antigen binding”. GO analysis of the cellular components indicated that most proteins were annotated as “extracellular exosomes”. KEGG pathway analysis demonstrated differential proteins were significantly enriched in “complement and coagulation cascades”. The hierarchical cluster analysis of the differential proteins in the four groups showed that Lysozyme C and Keratin were more abundant in gout, Hemoglobin and Actin-related protein 2/3 complex subunit 3 in OA, Sodium/potassium-transporting ATPase subunit alpha-1 and Immunoglobulin heavy constant delta in axSpA, Pregnancy zone protein and Stromelysin-1 in RA.Conclusion:The protein profiles of SF-derived exosomes in RA, axSpA, gout and OA patients were different. The differential proteins were the potential biomarkers of RA, axSpA, gout and OA.References:[1]Cretu D, Diamandis E P, Chandran V. Delineating the synovial fluid proteome: recent advancements and ongoing challenges in biomarker research.[J]. Critical reviews in clinical laboratory sciences, 2013,50(2):51-63.[2]McArdle A J, Menikou S. What is proteomics?[J]. Archives of disease in childhood. Education and practice edition, 2020.Figure 1.The hierarchical cluster analysis of differential proteins in axSpA, OA, Gout and RA.Disclosure of Interests:None declared

scholarly journals Identification of Pathways and Key Genes in Venous Remodeling After Arteriovenous Fistula by Bioinformatics Analysis

2020 ◽  
Vol 11 ◽  
Author(s):  
Kong Jie ◽  
Wang Feng ◽  
Zhao Boxiang ◽  
Gong Maofeng ◽  
Zhang Jianbin ◽  
...  
Keyword(s):  
Arteriovenous Fistula ◽  
Pathway Analysis ◽  
Kegg Pathway ◽  
Function Analysis ◽  
Gene Set Enrichment Analysis ◽  
Control Group ◽  
Hub Genes ◽  
Molting Cycle ◽  
Kegg Pathway Analysis ◽  
First Choice

The arteriovenous fistula (AVF) is the first choice for vascular access for hemodialysis of renal failure patients. Venous remodeling after exposure to high fistula flow is important for AVF to mature but the mechanism underlying remodeling is still unknown. The objective of this study is to identify the molecular mechanisms that contribute to venous remodeling after AVF. To screen and identify the differentially expressed genes (DEGs) that may involve venous remodeling after AVF, we used bioinformatics to download the public microarray data (GSE39488) from the Gene Expression Omnibus (GEO) and screen for DEGs. We then performed gene ontology (GO) function analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and gene set enrichment analysis (GSEA) for the functional annotation of DEGs. The protein-protein interaction (PPI) network was constructed and the hub genes were carried out. Finally, we harvested 12 normal vein samples and 12 AVF vein samples which were used to confirm the expressions of the hub genes by immunohistochemistry. A total of 45 DEGs were detected, including 32 upregulated and 13 downregulated DEGs. The biological process (BP) of the GO analysis were enriched in the extrinsic apoptotic signaling pathway, cGMP-mediated pathway signaling, and molting cycle. The KEGG pathway analysis showed that the upregulated DEGs were enriched in glycosaminoglycan biosynthesis and purine metabolism, while the downregulated DEGs were mainly enriched in pathways of glycosaminoglycan biosynthesis, antifolate resistance, and ABC transporters. The GSEA analysis result showed that the top three involved pathways were oxidative phosphorylation, TNFA signaling via NF-K B, and the inflammatory response. The PPI was constructed and the hub genes found through the method of DMNC showed that INHBA and NR4A2 might play an important role in venous remodeling after AVF. The integrated optical density (DOI) examined by immunohistochemistry staining showed that the expression of both INHBA and NR4A2 increased in AVF compared to the control group. Our research contributes to the understanding of the molecular mechanism of venous remodeling after exposure to high fistula flow, which may be useful in treating AVF failure.

scholarly journals CRISPR/Cas9-mediated mutation revealed cytoplasmic tail is dispensable for IZUMO1 function and male fertility

Reproduction ◽  
2016 ◽  
Vol 152 (6) ◽  
pp. 665-672 ◽  
Author(s):  
Samantha A M Young ◽  
Haruhiko Miyata ◽  
Yuhkoh Satouh ◽  
Masanaga Muto ◽  
Martin R Larsen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Point Mutation ◽  
Male Fertility ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Cytoplasmic Tail ◽  
Binding Partner ◽  
C Terminus ◽  
Manipulation System

IZUMO1 is a protein found in the head of spermatozoa that has been identified as essential for sperm–egg fusion. Its binding partner in the egg has been discovered (JUNO); however, the roles of several domains within IZUMO1 remain unexplored. One such domain is the C-terminus, which undergoes major phosphorylation changes in the cytoplasmic portion of the protein during rat epididymal transit. However, the cytoplasmic tail of IZUMO1 in many species is highly variable, ranging from 55 to one amino acid. Therefore, to understand the role of the cytoplasmic tail of IZUMO1 in mouse, we utilised the gene manipulation system of CRISPR/Cas9 to generate a point mutation resulting in a premature stop codon, producing mice with truncated IZUMO1. Mice without the cytoplasmic tail of IZUMO1 showed normal fertility but decreased the amount of protein, indicating that whilst this region is important for the expression level of IZUMO1, it is dispensable for fertilisation in the mouse.

Abstract 391: The Pathophysiological Role of MYBPHL in Dilated Cardiomyopathy

2016 ◽  
Vol 119 (suppl_1) ◽  
Author(s):  
David Y Barefield ◽  
Megan J Puckelwartz ◽  
Lisa Dellefave-Castillo ◽  
Elizabeth M McNally
Keyword(s):  
Cardiac Function ◽  
Protein C ◽  
Stop Codon ◽  
Binding Protein ◽  
Premature Stop Codon ◽  
Myosin Binding Protein ◽  
Myosin Binding Protein C ◽  
Pathophysiological Role ◽  
Myosin Binding

Background: Cardiomyopathy is a leading cause of heart failure and is highly heritable. One common form of cardiomyopathy is dilated cardiomyopathy (DCM), which currently has over 70 identified genes that have been described as causative for the disease. Genetic testing for DCM employs gene panels and has a sensitivity of mutation detection less than 50%, indicating that additional genes contribute to DCM. Here, we employed whole genome sequencing (WGS) in a family with DCM and heart block who had previously undergone unrevealing genetic testing. We identified a premature stop codon in the MYBPHL gene, a gene that has not previously been linked to DCM as a likely cause of DCM in this family. Myosin binding protein H Like (MyBP-HL) is a muscle-expressed protein bearing structural similarity to myosin binding protein C (MyBP-C), which is commonly mutated gene in cardiomyopathies. Objective: Determine the physiological and pathophysiological role of Mybphl . Results: RNA-seq and qPCR from mouse hearts revealed that Mybphl is highly expressed in the right and left atria with lower expression in the ventricle and virtually no expression in skeletal muscle. As MyBP-HL shares a high homology with the myofilament proteins cardiac myosin binding protein-C and H, we investigated if MyBP-HL is also myofilament-associated. We determined that MyBP-HL protein is myofilament-associated in the atria although not clearly so in ventricle. To assess the requirement of MyBP-HL in cardiac function, we used a mouse model with an insertional disruption of the Mybphl gene. These mice have deficits in in vivo cardiac function, with reduced fractional shortening. In addition, ECG recordings from the Mybphl null mice show conduction system abnormalities affecting atrioventricular conduction. Conclusions: WGS identified a premature stop codon in MYBPHL in human DCM. A mouse model with a disrupted Mybphl gene showed similar pathophysiological features as the humans with reduced ventricular function and cardiac conduction system abnormalities. MyBP-HL is an important protein for normal cardiac function.

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