scholarly journals Precise Regulation and Site-specifically Covalent Labeling of NSUN2 Enable by Genetic Encoding Expansion

2020 ◽  
Author(s):  
Jizhong Zhao ◽  
Hongmei Hu ◽  
Sheng Wang ◽  
Li Wang ◽  
Rui Wang
Keyword(s):  
Gene Expression Regulation ◽  
Click Reaction ◽  
Critical Role ◽  
Living Organism ◽  
Fluorescent Labeling ◽  
Rna Modification ◽  
Genetic Encoding ◽  
Special Groups ◽  
Substitution System ◽  
Lysine Substitution

ABSTRACTRNA plays a critical role in gene expression regulation, cell migration, differentiation, cell death in living organism. 5-Methylcytosine is a post transcriptional RNA modification identified across wide ranges of RNA species including message RNAs. It is reported the addition of m5C to RNA cytosines is enabled by use of NSUN family enzyme, NSUN2 is identified as a critical RNA methyltransferase for adding m5C to mRNA. We demonstrated here that natural lysines modified with special groups were synthesized via chemical synthesis. Through two rounds of positive screening and one round of negative screening, MbPylRS-tRNAcua unnatural lysine substitution system which can specifically recognize lysine with defined group was evaluated and identified. Non-natural lysine substitution at C271 of NSUN2 active site and subsequently fluorescent labeling was realized via so-called click reaction. The function of NSUN2 mutant and its upregulated CDK1 gene and its effect on cell proliferation were also evaluated.

scholarly journals Regulation and Site-Specific Covalent Labeling of NSUN2 via Genetic Encoding Expansion

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1488
Author(s):  
Jizhong Zhao ◽  
Hongmei Hu ◽  
Sheng Wang ◽  
Li Wang ◽  
Rui Wang
Keyword(s):  
Click Reaction ◽  
Fluorescent Labeling ◽  
Rna Modification ◽  
Messenger Rnas ◽  
Special Groups ◽  
Wide Range ◽  
Substitution System ◽  
Living Organisms ◽  
Lysine Substitution ◽  
Upregulated Genes

In living organisms, RNA regulates gene expression, cell migration, differentiation, and cell death. 5-Methylcytosine is a post-transcriptional RNA modification in a wide range of RNA species, including messenger RNAs. The addition of m5C to RNA cytosines is enabled by the NSUN enzyme family, a critical RNA methyltransferase. In this study, natural lysines modified with special groups were synthesized. Through two rounds of positive screening and one round of negative screening, we evaluated and identified the MbPylRS-tRNACUA unnatural lysine substitution system, which specifically recognizes lysine with a defined group. Moreover, non-natural lysine substitution at C271 of NSUN2 active site and the subsequent fluorescent labeling was realized through the click reaction. Then, the function of the NSUN2 mutant and its upregulated CDK1 gene as well as its effect on cell proliferation were evaluated. Efficient labeling and regulation of NSUN2 was achieved, laying the basis for further studies on the function and regulatory mechanism of upregulated genes.

scholarly journals Identification of Expression Patterns and Potential Prognostic Significance of m5C-Related Regulators in Head and Neck Squamous Cell Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhenyuan Han ◽  
Biao Yang ◽  
Yu Wang ◽  
Xiuxia Zeng ◽  
Zhen Tian
Keyword(s):  
Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Head And Neck ◽  
Squamous Cell ◽  
Expression Patterns ◽  
Critical Role ◽  
Low Risk ◽  
Neck Squamous Cell Carcinoma ◽  
Differentially Expressed ◽  
Rna Modification

5-Methylcytosine (m5C) methylation is a major epigenetic technique of RNA modification and is dynamically mediated by m5C “writers,” “erasers,” and “readers.” m5C RNA modification and its regulators are implicated in the onset and development of many tumors, but their roles in head and neck squamous cell carcinoma (HNSCC) have not yet been completely elucidated. In this study, we examined expression patterns of core m5C regulators in the publicly available HNSCC cohort via bioinformatic methods. The differentially expressed m5C regulators could divide the HNSCC cohort into four subgroups with distinct prognostic characteristics. Furthermore, a three-gene expression signature model, comprised of NSUN5, DNMT1, and DNMT3A, was established to identify individuals with a high or low risk of HNSCC. To explore the underlying mechanism in the prognosis of HNSCC, screening of differentially expressed genes, followed by the analysis of functional and pathway enrichment, from individuals with high- or low-risk HNSCC was performed. The results revealed a critical role for m5C RNA modification in two aspects of HNSCC: (1) dynamic m5C modification contributes to the regulation of HNSCC progression and (2) expression patterns of NSUN5, DNMT1, and DNMT3A help to predict the prognosis of HNSCC.

scholarly journals Guide snoRNAs: Drivers or Passengers in Human Disease?

Biology ◽  
2018 ◽  
Vol 8 (1) ◽  
pp. 1 ◽  
Author(s):  
Manisha Deogharia ◽  
Mrinmoyee Majumder
Keyword(s):  
Protein Interactions ◽  
Human Disease ◽  
Critical Role ◽  
Mrna Translation ◽  
Causal Link ◽  
Rna Modification ◽  
Disease Manifestation ◽  
The Stability ◽  
Nucleoside Modification ◽  
Host Genes

In every domain of life, RNA-protein interactions play a significant role in co- and post-transcriptional modifications and mRNA translation. RNA performs diverse roles inside the cell, and therefore any aberrancy in their function can cause various diseases. During maturation from its primary transcript, RNA undergoes several functionally important post-transcriptional modifications including pseudouridylation and ribose 2′-O-methylation. These modifications play a critical role in the stability of the RNA. In the last few decades, small nucleolar RNAs (snoRNAs) were revealed to be one of the main components to guide these modifications. Due to their active links to the nucleoside modification, deregulation in the snoRNA expressions can cause multiple disorders in humans. Additionally, host genes carrying snoRNA-encoding sequences in their introns also show differential expression in disease. Although few reports support a causal link between snoRNA expression and disease manifestation, this emerging field will have an impact on the way we think about biomarkers or identify novel targets for therapy. This review focuses on the intriguing aspect of snoRNAs that function as a guide in post-transcriptional RNA modification, and regulation of their host genes in human disease.

scholarly journals Molecular Characterization and Clinical Relevance of m6A RNA Methylation Regulators in Cervical Cancer

2020 ◽  
Author(s):  
Jin Chen ◽  
Ji He ◽  
Xiaolei Ma ◽  
Xia Guo
Keyword(s):  
Cervical Cancer ◽  
Clinical Relevance ◽  
Cox Regression ◽  
Critical Role ◽  
The Cancer Genome Atlas ◽  
Rna Modification ◽  
Lasso Regression ◽  
Cox Regression Analysis ◽  
Rna Methylation ◽  
M6a Rna Methylation

Abstract Background: RNA modification, such as methylation of N6 adenosine (m6A), plays a critical role in many biological processes. However, the role of m6A RNA modification in cervical cancer (CC) remains largely unknown. Methods: The present study systematically investigated the molecular signatures and clinical relevance of 20 m6A RNA methylation regulators (writers, erasers, readers) in CC. The mRNA expression and clinical significance of m6A-related genes were investigated using data from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) cervical cancer cohort. Mutations, copy number variation (CNV), differential expression, gene ontology analysis and the construction of a mRNA-microRNA regulatory network were performed to investigate the underlying mechanisms involved in the abnormal expression of m6A-related genes. Results: We found inclusive genetic information alterations among the m6A regulators and that their transcript expression levels were significantly associated with cancer hallmark-related pathways activity, such as the PI3K-AKT signaling pathway, microRNAs in cancer and the focal adhesion pathway, which were significantly enriched. Moreover, m6A regulators were found to be potentially useful for prognostic stratification and we identified FMR1 and ZC3H13 as potential prognostic risk oncogenes by LASSO regression. The ROC curves of 3, 5 and 10 years were 0.685, 0.726 and 0.741, respectively. The specificity for 3, 5 and 10 years were 0.598, 0.631 and 0.833, the sensitivity were 0.707, 0.752 and 0.811, respectively. Conclusions: Multivariable Cox regression analysis revealed that the risk score is an independent prognostic marker and can be used to predict the clinical and pathological features of CC.

scholarly journals Mutation in the Jak kinase JH2 domain hyperactivates Drosophila and mammalian Jak-Stat pathways.

1997 ◽  
Vol 17 (3) ◽  
pp. 1562-1571 ◽  
Author(s):  
H Luo ◽  
P Rose ◽  
D Barber ◽  
W P Hanratty ◽  
S Lee ◽  
...  
Keyword(s):  
Tyrosine Kinases ◽  
Critical Role ◽  
Developmental Defects ◽  
Type D ◽  
Jak Kinase ◽  
Lysine Substitution ◽  
Nonreceptor Tyrosine Kinases ◽  
Drosophila Cells ◽  
Stat Pathway

The Jak (Janus) family of nonreceptor tyrosine kinases plays a critical role in cytokine signal transduction pathways. In Drosophila melanogaster, the dominant hop(Tum-l) mutation in the Hop Jak kinase causes leukemia-like and other developmental defects. Previous studies have suggested that the Hop(Tum-l) protein might be a hyperactive kinase. Here, we report on the new dominant mutation hop(T42), which causes abnormalities that are similar to but more extreme than those caused by hop(Tum-l). We determined that Hop(T42) contains a glutamic acid-to-lysine substitution at amino acid residue 695 (E695K). This residue occurs in the JH2 (kinase-like) domain and is conserved among all Jak family members. We determined that Hop(Tum-1) and Hop(T42) both hyperphosphorylated and hyperactivated D-Stat when overexpressed in Drosophila cells. Moreover, we found that the hop(T42) phenotype was partially rescued by a reduction of wild-type D-stat activity. Finally, generation of the corresponding E695K mutation in murine Jak2 resulted in increased autophosphorylation and increased activation of Stat5 in COS cells. These results demonstrate that the mutant Hop proteins do indeed have increased tyrosine kinase activity, that the mutations hyperactivate the Hop-D-Stat pathway, and that Drosophila is a relevant system for the functional dissection of mammalian Jak-Stat pathways. Finally, we propose a model for the role of the Hop-D-Stat pathway in Drosophila hematopoiesis.

scholarly journals Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications

2016 ◽  
Vol 213 (1) ◽  
pp. 15-22 ◽  
Author(s):  
Konstantin Licht ◽  
Michael F. Jantsch
Keyword(s):  
Gene Expression ◽  
Mass Spectrometry ◽  
Rna Editing ◽  
Messenger Rna ◽  
Gene Expression Regulation ◽  
Rna Modification ◽  
Rna Modifications ◽  
Transcriptome Regulation ◽  
Affect Gene Expression ◽  
Generation Sequencing

Advances in next-generation sequencing and mass spectrometry have revealed widespread messenger RNA modifications and RNA editing, with dramatic effects on mammalian transcriptomes. Factors introducing, deleting, or interpreting specific modifications have been identified, and analogous with epigenetic terminology, have been designated “writers,” “erasers,” and “readers.” Such modifications in the transcriptome are referred to as epitranscriptomic changes and represent a fascinating new layer of gene expression regulation that has only recently been appreciated. Here, we outline how RNA editing and RNA modification can rapidly affect gene expression, making both processes as well suited to respond to cellular stress and to regulate the transcriptome during development or circadian periods.

scholarly journals tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

2019 ◽  
Vol 201 (9) ◽  
Author(s):  
Ningxi Yu ◽  
Manasses Jora ◽  
Beulah Solivio ◽  
Priti Thakur ◽  
Carlos G. Acevedo-Rocha ◽  
...  
Keyword(s):  
Critical Role ◽  
Rna Modification ◽  
Trna Modification ◽  
High Quality ◽  
Methanocaldococcus Jannaschii ◽  
Content Type ◽  
Trna Modifications ◽  
Posttranscriptional Modifications ◽  
Eukaryotic Organisms ◽  
Decoding Efficiency

ABSTRACT tRNAs play a critical role in mRNA decoding, and posttranscriptional modifications within tRNAs drive decoding efficiency and accuracy. The types and positions of tRNA modifications in model bacteria have been extensively studied, and tRNA modifications in a few eukaryotic organisms have also been characterized and localized to particular tRNA sequences. However, far less is known regarding tRNA modifications in archaea. While the identities of modifications have been determined for multiple archaeal organisms, Haloferax volcanii is the only organism for which modifications have been extensively localized to specific tRNA sequences. To improve our understanding of archaeal tRNA modification patterns and codon-decoding strategies, we have used liquid chromatography and tandem mass spectrometry to characterize and then map posttranscriptional modifications on 34 of the 35 unique tRNA sequences of Methanocaldococcus jannaschii. A new posttranscriptionally modified nucleoside, 5-cyanomethyl-2-thiouridine (cnm5s2U), was discovered and localized to position 34. Moreover, data consistent with wyosine pathway modifications were obtained beyond the canonical tRNAPhe as is typical for eukaryotes. The high-quality mapping of tRNA anticodon loops enriches our understanding of archaeal tRNA modification profiles and decoding strategies. IMPORTANCE While many posttranscriptional modifications in M. jannaschii tRNAs are also found in bacteria and eukaryotes, several that are unique to archaea were identified. By RNA modification mapping, the modification profiles of M. jannaschii tRNA anticodon loops were characterized, allowing a comparative analysis with H. volcanii modification profiles as well as a general comparison with bacterial and eukaryotic decoding strategies. This general comparison reveals that M. jannaschii, like H. volcanii, follows codon-decoding strategies similar to those used by bacteria, although position 37 appears to be modified to a greater extent than seen in H. volcanii.

scholarly journals Functions of RNA N6-methyladenosine modification in acute myeloid leukemia

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Xue Zheng ◽  
Yuping Gong
Keyword(s):  
Acute Myeloid Leukemia ◽  
Nuclear Export ◽  
Myeloid Leukemia ◽  
Molecular Mechanisms ◽  
Gene Expression Regulation ◽  
Epigenetic Modification ◽  
Hematologic Malignancy ◽  
Critical Role ◽  
Leukemia Cell ◽  
Acute Myeloid

AbstractAcute myeloid leukemia (AML) is a hematologic malignancy with an unfavorable prognosis. A better understanding of AML pathogenesis and chemotherapy resistance at the molecular level is essential for the development of new therapeutic strategies. Apart from DNA methylation and histone modification, RNA epigenetic modification, another layer of epigenetic modification, also plays a critical role in gene expression regulation. Among the more than 150 kinds of RNA epigenetic modifications, N6-methyladenosine (m6A) is the most prevalent internal mRNA modification in eukaryotes and is involved in various biological processes, such as circadian rhythms, adipogenesis, T cell homeostasis, spermatogenesis, and the heat shock response. As a reversible and dynamic modification, m6A is deposited on specific target RNA molecules by methyltransferases and is removed by demethylases. Moreover, m6A binding proteins recognize m6A modifications, influencing RNA splicing, stability, translation, nuclear export, and localization at the posttranscriptional level. Emerging evidence suggests that dysregulation of m6A modification is involved in tumorigenesis, including that of AML. In this review, we summarize the most recent advances regarding the biological functions and molecular mechanisms of m6A RNA methylation in normal hematopoiesis, leukemia cell proliferation, apoptosis, differentiation, therapeutic resistance, and leukemia stem cell/leukemia initiating cell (LSC/LIC) self-renewal. In addition, we discuss how m6A regulators are closely correlated with the clinical features of AML patients and may serve as new biomarkers and therapeutic targets for AML.

scholarly journals Potential causes of high performance of pure-oxygen aerobic granules in SBR under high organic loading condition

2017 ◽  
Vol 19 (4) ◽  
pp. 687-696
Keyword(s):  
High Performance ◽  
Loading Condition ◽  
Critical Role ◽  
Living Organism ◽  
Pure Oxygen ◽  
Aerobic Granules ◽  
Organic Loading ◽  
Dense Structure ◽  
Average Value ◽  
N Removal

Aerobic granules were cultivated using pure oxygen aeration (POAG) in SBR for wastewater treatment under high organic loading condition (HOLC) to reveal its performance and potential causes. Compared to conventional granules and activated sludge, mature POAG with more compact and dense structure were formed in a shorter term using pure-oxygen aeration in SBR. The system shows high and stable COD and NH4+-N removal efficiencies with an average value of 91% and 84%, respectively, under HOLC. Adequate dissolved oxygen (DO) supplied by pure-oxygen aeration is the prerequisite explaining the elevated performance. POAG have more stable compact granular structure and elevated biomass than that of conventional biogranules and bioflocs under HOLC. High EPS content facilitate the formation of POAG and maintain its integrity and stability of spatial structure, which is in favor of biomass growth. Abundant catalase synthesized by its biomass ensure the ability to hydrolyze and mineralize organic substance under HOLC. A great deal of dehydrogenase secreted by POAG play a critical role in maintaining its metabolism under HOLC, which in turn enhance multiplication capacity of living organism in POAG and elevate removal performance of organic pollutants from wastewater.

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