Recent advances in functional annotation and prediction of the epitranscriptome

Zhang, Song-Yao; Zhang, Shaowu; Zhang, Teng; Fan, Xiao-Nan; Meng, Jia

doi:10.1016/j.csbj.2021.05.030

Cited by 16 publications

(7 citation statements)

References 191 publications

(241 reference statements)

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“…M7G modification is one of the most common base modification methods in gene regulation and plays an important role in maintaining the structural stability of RNA, affecting RNA processing and metabolism, and regulating protein translation. [7,8] Studies have shown that N7-methylguanosine modification-related lncRNAs (m7G-lncRNAs) participate in the regulation of the molecular biological processes of tumor cells in vivo and affect the occurrence and development of tumors. [9] However, to the best of our knowledge, no studies of m7G-lncRNAs in THCA have been reported.…”

Section: The Authors Have No Funding and Conflicts Of Interest To Dis...mentioning

confidence: 99%

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Construction and validation of a novel prognostic model for thyroid cancer based on N7-methylguanosine modification-related lncRNAs

et al. 2022

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Background: To construct and verify a novel prognostic model for thyroid cancer (THCA) based on N7-methylguanosine modification-related lncRNAs (m7G-lncRNAs) and their association with immune cell infiltration. Methods: In this study, we identified m7G-lncRNAs using co-expression analysis and performed differential expression analysis of m7G-lncRNAs between groups. We then constructed a THCA prognostic model, performed survival analysis and risk assessment for the THCA prognostic model, and performed independent prognostic analysis and receiver operating characteristic curve analyses to evaluate and validate the prognostic value of the model. Furthermore, analysis of the regulatory relationship between prognostic differentially expressed m7G-related lncRNAs (PDEm7G-lncRNAs) and mRNAs and correlation analysis of immune cells and risk scores in THCA patients were carried out. Results: We identified 29 N7-methylguanosine modification-related mRNAs and 116 differentially expressed m7G-related lncRNAs, including 87 downregulated and 29 upregulated lncRNAs. Next, we obtained 8 PDEm7G-lncRNAs. A final optimized model was constructed consisting of 5 PDEm7G-lncRNAs (DOCK9−DT, DPP4–DT, TMEM105, SMG7–AS1 and HMGA2–AS1). Six PDEm7G-lncRNAs (DOCK9–DT, DPP4–DT, HMGA2–AS1, LINC01976, MID1IP1–AS1, and SMG7–AS1) had positive regulatory relationships with 10 PDEm7G-mRNAs, while 2 PDEm7G-lncRNAs (LINC02026 and TMEM105) had negative regulatory relationships with 2 PDEm7G-mRNAs. Survival curves and risk assessment predicted the prognostic risk in both groups of patients with THCA. Forest maps and receiver operating characteristic curves were used to evaluate and validate the prognostic value of the model. Finally, we demonstrated a correlation between different immune cells and risk scores. Conclusion: Our results will help identify high-risk or low-risk patients with THCA and facilitate early prediction and clinical intervention in patients with high risk and poor prognosis.

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Section: The Authors Have No Funding and Conflicts Of Interest To Dis...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Construction and validation of a novel prognostic model for thyroid cancer based on N7-methylguanosine modification-related lncRNAs

et al. 2022

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“…Then, DNA fragments assembled with adapters were amplified to prepare DNA clusters, and the clusters were sequenced (Gao et al, 2020;Zhang et al, 2021). The sequences obtained using fastq software (Version 0.20.0) were filtered by removing reads that contained adapters and poly-N as well as those with a lower sequencing quality (<Q 20).…”

Section: Comparative Genomic Analysismentioning

confidence: 99%

Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis

Guo

Fang

et al. 2021

Front. Microbiol.

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Many studies have shown that the space environment plays a pivotal role in changing the characteristics of conditional pathogens, especially their pathogenicity and virulence. However, Stenotrophomonas maltophilia, a type of conditional pathogen that has shown to a gradual increase in clinical morbidity in recent years, has rarely been reported for its impact in space. In this study, S. maltophilia was exposed to a simulated microgravity (SMG) environment in high-aspect ratio rotating-wall vessel bioreactors for 14days, while the control group was exposed to the same bioreactors in a normal gravity (NG) environment. Then, combined phenotypic, genomic, transcriptomic, and proteomic analyses were conducted to compare the influence of the SMG and NG on S. maltophilia. The results showed that S. maltophilia in simulated microgravity displayed an increased growth rate, enhanced biofilm formation ability, increased swimming motility, and metabolic alterations compared with those of S. maltophilia in normal gravity and the original strain of S. maltophilia. Clusters of Orthologous Groups (COG) annotation analysis indicated that the increased growth rate might be related to the upregulation of differentially expressed genes (DEGs) involved in energy metabolism and conversion, secondary metabolite biosynthesis, transport and catabolism, intracellular trafficking, secretion, and vesicular transport. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the increased motility might be associated the upregulation of differentially expressed proteins (DEPs) involved in locomotion, localization, biological adhesion, and binding, in accordance with the upregulated DEGs in cell motility according to COG classification, including pilP, pilM, flgE, flgG, and ronN. Additionally, the increased biofilm formation ability might be associated with the upregulation of DEPs involved in biofilm formation, the bacterial secretion system, biological adhesion, and cell adhesion, which were shown to be regulated by the differentially expressed genes (chpB, chpC, rpoN, pilA, pilG, pilH, and pilJ) through the integration of transcriptomic and proteomic analyses. These results suggested that simulated microgravity might increase the level of corresponding functional proteins by upregulating related genes to alter physiological characteristics and modulate growth rate, motility, biofilm formation, and metabolism. In conclusion, this study is the first general analysis of the phenotypic, genomic, transcriptomic, and proteomic changes in S. maltophilia under simulated microgravity and provides some suggestions for future studies of space microbiology.

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“…According to extant literature findings ( 10 ), tRNA guanine N7 methyltransferase, which belongs to the S-adenosylmethionine (SAM)-dependent RNA methyltransferase family, catalyzes m7G modification. In addition, m7G is also involved in many RNA metabolic processes in the human body, including transcription, mRNA splicing, and translation ( 11 ).…”

Section: Introductionmentioning

confidence: 99%

A novel m7G-related lncRNA risk model for predicting prognosis and evaluating the tumor immune microenvironment in colon carcinoma

et al. 2022

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N7-Methylguanosine (m7G) modifications are a common type of posttranscriptional RNA modifications. Its function in the tumor microenvironment (TME) has garnered widespread focus in the past few years. Long non-coding RNAs (lncRNAs) played an essential part in tumor development and are closely associated with the tumor immune microenvironment. In this study, we employed a comprehensive bioinformatics approach to develop an m7G-associated lncRNA prognostic model based on the colon adenocarcinoma (COAD) database from The Cancer Genome Atlas (TCGA) database. Pearson’s correlation analysis was performed to identify m7G-related lncRNAs. Differential gene expression analysis was used to screen lncRNAs. Then, we gained 88 differentially expressed m7G-related lncRNAs. Univariate Cox analysis and Lasso regression analysis were performed to build an eight-m7G-related-lncRNA (ELFN1-AS1, GABPB1-AS1, SNHG7, GS1-124K5.4, ZEB1-AS1, PCAT6, C1RL-AS1, MCM3AP-AS1) risk model. Consensus clustering analysis was applied to identify the m7G-related lncRNA subtypes. We also verified the risk prediction effect of a gene signature in the GSE17536 test set (177 patients). A nomogram was constructed to predict overall survival rates. Furthermore, we analyzed differentially expressed genes (DEGs) between high-risk and low-risk groups. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted with the analyzed DEGs. At last, single-sample gene set enrichment analysis (ssGSEA), CIBERSORT, MCP-COUNTER, and Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithms were utilized to discover the relationship between the risk model and the TME. Consequently, the m7G-related lncRNA risk model for COAD patients could be a viable prognostic tool and treatment target.

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Recent advances in functional annotation and prediction of the epitranscriptome

Abstract: Graphical abstract

Cited by 16 publications

References 191 publications

Construction and validation of a novel prognostic model for thyroid cancer based on N7-methylguanosine modification-related lncRNAs

Construction and validation of a novel prognostic model for thyroid cancer based on N7-methylguanosine modification-related lncRNAs

Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis

A novel m7G-related lncRNA risk model for predicting prognosis and evaluating the tumor immune microenvironment in colon carcinoma

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