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He Y, Bao X, Chen T, Jiang Q, Zhang L, He LN, Zheng J, Zhao A, Ren J, Zuo Z. RPS 2.0: an updated database of RNAs involved in liquid-liquid phase separation. Nucleic Acids Res 2025; 53:D299-D309. [PMID: 39460625 PMCID: PMC11701738 DOI: 10.1093/nar/gkae951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Revised: 10/05/2024] [Accepted: 10/14/2024] [Indexed: 10/28/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) is a crucial process for the formation of biomolecular condensates such as coacervate droplets, P-bodies and stress granules, which play critical roles in many physiological and pathological processes. Increasing studies have shown that not only proteins but also RNAs play a critical role in LLPS. To host LLPS-associated RNAs, we previously developed a database named 'RPS' in 2021. In this study, we present an updated version RPS 2.0 (https://rps.renlab.cn/) to incorporate the newly generated data and to host new LLPS-associated RNAs driven by post-transcriptional regulatory mechanisms. Currently, RPS 2.0 hosts 171 301 entries of LLPS-associated RNAs in 24 different biomolecular condensates with four evidence types, including 'Reviewed', 'High-throughput (LLPS enrichment)', 'High-throughput (LLPS perturbation)' and 'Predicted', and five event types, including 'Expression', 'APA', 'AS', 'A-to-I' and 'Modification'. Additionally, extensive annotations of LLPS-associated RNAs are provided in RPS 2.0, including RNA sequence and structure features, RNA-protein/RNA-RNA interactions, RNA modifications, as well as diseases related annotations. We expect that RPS 2.0 will further promote research of LLPS-associated RNAs and deepen our understanding of the biological functions and regulatory mechanisms of LLPS.
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Affiliation(s)
- Yongxin He
- School of Life Sciences, State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Xiaoqiong Bao
- School of Life Sciences, State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Tianjian Chen
- School of Life Sciences, State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Qi Jiang
- School of Life Sciences, State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Luowanyue Zhang
- School of Life Sciences, State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Li-Na He
- School of Life Sciences, State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Jian Zheng
- School of Life Sciences, State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - An Zhao
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310000, China
| | - Jian Ren
- School of Life Sciences, State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhixiang Zuo
- School of Life Sciences, State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou 510060, China
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das Neves W, Alves CRR, Dos Santos G, Alves MJNN, Deik A, Pierce K, Dennis C, Buckley L, Clish CB, Swoboda KJ, Brum PC, de Castro Junior G. Physical performance and plasma metabolic profile as potential prognostic factors in metastatic lung cancer patients. Eur J Clin Invest 2024; 54:e14288. [PMID: 39058257 DOI: 10.1111/eci.14288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND Low physical performance is associated with higher mortality rate in multiple pathological conditions. Here, we aimed to determine whether body composition and physical performance could be prognostic factors in non-small cell lung cancer (NSCLC) patients. Moreover, we performed an exploratory approach to determine whether plasma samples from NSCLC patients could directly affect metabolic and structural phenotypes in primary muscle cells. METHODS This prospective cohort study included 55 metastatic NSCLC patients and seven age-matched control subjects. Assessments included physical performance, body composition, quality of life and overall survival rate. Plasma samples from a sub cohort of 18 patients were collected for exploratory studies in cell culture and metabolomic analysis. RESULTS We observed a higher survival rate in NSCLC patients with high performance in the timed up-and-go (+320%; p = .007), sit-to-stand (+256%; p = .01) and six-minute walking (+323%; p = .002) tests when compared to NSCLC patients with low physical performance. There was no significant association for similar analysis with body composition measurements (p > .05). Primary human myotubes incubated with plasma from NSCLC patients with low physical performance had impaired oxygen consumption rate (-54.2%; p < .0001) and cell proliferation (-44.9%; p = .007). An unbiased metabolomic analysis revealed a list of specific metabolites differentially expressed in the plasma of NSCLC patients with low physical performance. CONCLUSION These novel findings indicate that physical performance is a prognostic factor for overall survival in NSCLC patients and provide novel insights into circulating factors that could impair skeletal muscle metabolism.
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Affiliation(s)
- Willian das Neves
- Faculdade de Medicina, Instituto do Cancer do Estado de Sao Paulo ICESP, Hospital das Clínicas HCFMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Christiano R R Alves
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
- School of Physical Education and Sport, University of São Paulo, São Paulo, Brazil
| | - Gabriela Dos Santos
- Faculdade de Medicina, Instituto do Cancer do Estado de Sao Paulo ICESP, Hospital das Clínicas HCFMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | - Amy Deik
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kerry Pierce
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Courtney Dennis
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lily Buckley
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Clary B Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kathryn J Swoboda
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Neurology, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Patricia C Brum
- School of Physical Education and Sport, University of São Paulo, São Paulo, Brazil
| | - Gilberto de Castro Junior
- Faculdade de Medicina, Instituto do Cancer do Estado de Sao Paulo ICESP, Hospital das Clínicas HCFMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
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Palos K, Nelson Dittrich AC, Lyons EH, Gregory BD, Nelson ADL. Comparative analyses suggest a link between mRNA splicing, stability, and RNA covalent modifications in flowering plants. BMC PLANT BIOLOGY 2024; 24:768. [PMID: 39134938 PMCID: PMC11318313 DOI: 10.1186/s12870-024-05486-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024]
Abstract
BACKGROUND In recent years, covalent modifications on RNA nucleotides have emerged as pivotal moieties influencing the structure, function, and regulatory processes of RNA Polymerase II transcripts such as mRNAs and lncRNAs. However, our understanding of their biological roles and whether these roles are conserved across eukaryotes remains limited. RESULTS In this study, we leveraged standard polyadenylation-enriched RNA-sequencing data to identify and characterize RNA modifications that introduce base-pairing errors into cDNA reads. Our investigation incorporated data from three Poaceae (Zea mays, Sorghum bicolor, and Setaria italica), as well as publicly available data from a range of stress and genetic contexts in Sorghum and Arabidopsis thaliana. We uncovered a strong enrichment of RNA covalent modifications (RCMs) deposited on a conserved core set of nuclear mRNAs involved in photosynthesis and translation across these species. However, the cohort of modified transcripts changed based on environmental context and developmental program, a pattern that was also conserved across flowering plants. We determined that RCMs can partly explain accession-level differences in drought tolerance in Sorghum, with stress-associated genes receiving a higher level of RCMs in a drought tolerant accession. To address function, we determined that RCMs are significantly enriched near exon junctions within coding regions, suggesting an association with splicing. Intriguingly, we found that these base-pair disrupting RCMs are associated with stable mRNAs, are highly correlated with protein abundance, and thus likely associated with facilitating translation. CONCLUSIONS Our data point to a conserved role for RCMs in mRNA stability and translation across the flowering plant lineage.
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Affiliation(s)
- Kyle Palos
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY, 14853, USA
| | | | - Eric H Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew D L Nelson
- Boyce Thompson Institute, Cornell University, 533 Tower Road, Ithaca, NY, 14853, USA.
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Araujo Tavares RDC, Mahadeshwar G, Wan H, Pyle AM. MRT-ModSeq - Rapid Detection of RNA Modifications with MarathonRT. J Mol Biol 2023; 435:168299. [PMID: 37802215 DOI: 10.1016/j.jmb.2023.168299] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/25/2023] [Accepted: 09/30/2023] [Indexed: 10/08/2023]
Abstract
Chemical modifications are essential regulatory elements that modulate the behavior and function of cellular RNAs. Despite recent advances in sequencing-based RNA modification mapping, methods combining accuracy and speed are still lacking. Here, we introduce MRT-ModSeq for rapid, simultaneous detection of multiple RNA modifications using MarathonRT. MRT-ModSeq employs distinct divalent cofactors to generate 2-D mutational profiles that are highly dependent on nucleotide identity and modification type. As a proof of concept, we use the MRT fingerprints of well-studied rRNAs to implement a general workflow for detecting RNA modifications. MRT-ModSeq rapidly detects positions of diverse modifications across a RNA transcript, enabling assignment of m1acp3Y, m1A, m3U, m7G and 2'-OMe locations through mutation-rate filtering and machine learning. m1A sites in sparsely modified targets, such as MALAT1 and PRUNE1 could also be detected. MRT-ModSeq can be trained on natural and synthetic transcripts to expedite detection of diverse RNA modification subtypes across targets of interest.
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Affiliation(s)
| | - Gandhar Mahadeshwar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA. https://twitter.com/gandzmakerdance
| | - Han Wan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA. https://twitter.com/HanWan19744358
| | - Anna Marie Pyle
- Department of Chemistry, Yale University, New Haven, CT 06511, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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5
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Liu J, Huang T, Yao J, Zhao T, Zhang Y, Zhang R. Epitranscriptomic subtyping, visualization, and denoising by global motif visualization. Nat Commun 2023; 14:5944. [PMID: 37741827 PMCID: PMC10517956 DOI: 10.1038/s41467-023-41653-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023] Open
Abstract
Advances in sequencing technologies have empowered epitranscriptomic profiling at the single-base resolution. Putative RNA modification sites identified from a single high-throughput experiment may contain one type of modification deposited by different writers or different types of modifications, along with false positive results because of the challenge of distinguishing signals from noise. However, current tools are insufficient for subtyping, visualization, and denoising these signals. Here, we present iMVP, which is an interactive framework for epitranscriptomic analysis with a nonlinear dimension reduction technique and density-based partition. As exemplified by the analysis of mRNA m5C and ModTect variant data, we show that iMVP allows the identification of previously unknown RNA modification motifs and writers and the discovery of false positives that are undetectable by traditional methods. Using putative m6A/m6Am sites called from 8 profiling approaches, we illustrate that iMVP enables comprehensive comparison of different approaches and advances our understanding of the difference and pattern of true positives and artifacts in these methods. Finally, we demonstrate the ability of iMVP to analyze an extremely large human A-to-I editing dataset that was previously unmanageable. Our work provides a general framework for the visualization and interpretation of epitranscriptomic data.
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Affiliation(s)
- Jianheng Liu
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA.
| | - Tao Huang
- Department of Pathology and Pathophysiology, Shantou University Medical College, Shantou, 515041, P. R. China
| | - Jing Yao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Tianxuan Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Yusen Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Rui Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
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6
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Verwilt J, Mestdagh P, Vandesompele J. Artifacts and biases of the reverse transcription reaction in RNA sequencing. RNA (NEW YORK, N.Y.) 2023; 29:889-897. [PMID: 36990512 DOI: 10.1261/rna.079623.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
RNA sequencing has spurred a significant number of research areas in recent years. Most protocols rely on synthesizing a more stable complementary DNA (cDNA) copy of the RNA molecule during the reverse transcription reaction. The resulting cDNA pool is often wrongfully assumed to be quantitatively and molecularly similar to the original RNA input. Sadly, biases and artifacts confound the resulting cDNA mixture. These issues are often overlooked or ignored in the literature by those that rely on the reverse transcription process. In this review, we confront the reader with intra- and intersample biases and artifacts caused by the reverse transcription reaction during RNA sequencing experiments. To fight the reader's despair, we also provide solutions to most issues and inform on good RNA sequencing practices. We hope the reader can use this review to their advantage, thereby contributing to scientifically sound RNA studies.
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Affiliation(s)
- Jasper Verwilt
- OncoRNALab, Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
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7
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Tavares RDCA, Mahadeshwar G, Wan H, Pyle AM. MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542276. [PMID: 37292902 PMCID: PMC10245971 DOI: 10.1101/2023.05.25.542276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chemical modifications are essential regulatory elements that modulate the behavior and function of cellular RNAs. Despite recent advances in sequencing-based RNA modification mapping, methods combining accuracy and speed are still lacking. Here, we introduce MRT- ModSeq for rapid, simultaneous detection of multiple RNA modifications using MarathonRT. MRT-ModSeq employs distinct divalent cofactors to generate 2-D mutational profiles that are highly dependent on nucleotide identity and modification type. As a proof of concept, we use the MRT fingerprints of well-studied rRNAs to implement a general workflow for detecting RNA modifications. MRT-ModSeq rapidly detects positions of diverse modifications across a RNA transcript, enabling assignment of m1acp3Y, m1A, m3U, m7G and 2'-OMe locations through mutation-rate filtering and machine learning. m1A sites in sparsely modified targets, such as MALAT1 and PRUNE1 could also be detected. MRT-ModSeq can be trained on natural and synthetic transcripts to expedite detection of diverse RNA modification subtypes across targets of interest.
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Affiliation(s)
| | - Gandhar Mahadeshwar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA
| | - Han Wan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Anna Marie Pyle
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06511, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
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8
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Apostle A, Yin Y, Chillar K, Eriyagama AMDN, Arneson R, Burke E, Fang S, Yuan Y. Effects of Epitranscriptomic RNA Modifications on the Catalytic Activity of the SARS-CoV-2 Replication Complex. Chembiochem 2023; 24:e202300095. [PMID: 36752976 PMCID: PMC10121919 DOI: 10.1002/cbic.202300095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/09/2023]
Abstract
SARS-CoV-2 causes individualized symptoms. Many reasons have been given. We propose that an individual's epitranscriptomic system could be responsible as well. The viral RNA genome can be subject to epitranscriptomic modifications, which can be different for different individuals, and thus epitranscriptomics can affect many events including RNA replication differently. In this context, we studied the effects of modifications including pseudouridine (Ψ), 5-methylcytosine (m5 C), N6-methyladenosine (m6 A), N1-methyladenosine (m1 A) and N3-methylcytosine (m3 C) on the activity of SARS-CoV-2 replication complex (SC2RC). We found that Ψ, m5 C, m6 A and m3 C had little effect, whereas m1 A inhibited the enzyme. Both m1 A and m3 C disrupt canonical base pairing, but they had different effects. The fact that m1 A inhibits SC2RC implies that the modification can be difficult to detect. This fact also implies that individuals with upregulated m1 A including cancer, obesity and diabetes patients might have milder symptoms. However, this contradicts clinical observations. Relevant discussions are provided.
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Affiliation(s)
- Alexander Apostle
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Yipeng Yin
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Komal Chillar
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Adikari M D N Eriyagama
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Reed Arneson
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Emma Burke
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Shiyue Fang
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Yinan Yuan
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
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9
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Lei H, Zeng T, Ye X, Fan R, Xiong W, Tian T, Zhou X. Chemical Control of CRISPR Gene Editing via Conditional Diacylation Crosslinking of Guide RNAs. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206433. [PMID: 36737854 PMCID: PMC10074079 DOI: 10.1002/advs.202206433] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Conditional control of RNA structure and function has emerged as an effective toolkit. Here, a strategy based on a one-step introduction of diacylation linkers and azide groups on the 2'-OH of RNA is advance. Selected from eight phosphine reagents, it is found that 2-(diphenylphosphino)ethylamine has excellent performance in reducing azides via a Staudinger reduction to obtain the original RNA. It is demonstrated that the enzymatic activities of Cas13 and Cas9 can be regulated by chemically modified guide RNAs, and further achieved ligand-induced gene editing in living cells by a controllable CRISPR/Cas9 system.
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Affiliation(s)
- Huajun Lei
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Tianying Zeng
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Xiaofang Ye
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Ruochen Fan
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Wei Xiong
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Tian Tian
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Xiang Zhou
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
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10
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The role of post-transcriptional modifications during development. Biol Futur 2022:10.1007/s42977-022-00142-3. [PMID: 36481986 DOI: 10.1007/s42977-022-00142-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
AbstractWhile the existence of post-transcriptional modifications of RNA nucleotides has been known for decades, in most RNA species the exact positions of these modifications and their physiological function have been elusive until recently. Technological advances, such as high-throughput next-generation sequencing (NGS) methods and nanopore-based mapping technologies, have made it possible to map the position of these modifications with single nucleotide accuracy, and genetic screens have uncovered the “writer”, “reader” and “eraser” proteins that help to install, interpret and remove such modifications, respectively. These discoveries led to intensive research programmes with the aim of uncovering the roles of these modifications during diverse biological processes. In this review, we assess novel discoveries related to the role of post-transcriptional modifications during animal development, highlighting how these discoveries can affect multiple aspects of development from fertilization to differentiation in many species.
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11
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Arzumanian VA, Dolgalev GV, Kurbatov IY, Kiseleva OI, Poverennaya EV. Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications. Int J Mol Sci 2022; 23:13851. [PMID: 36430347 PMCID: PMC9695239 DOI: 10.3390/ijms232213851] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
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Affiliation(s)
- Viktoriia A. Arzumanian
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | - Georgii V. Dolgalev
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
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12
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Su Z, Monshaugen I, Klungland A, Ougland R, Dutta A. Characterization of novel small non-coding RNAs and their modifications in bladder cancer using an updated small RNA-seq workflow. Front Mol Biosci 2022; 9:887686. [PMID: 35923465 PMCID: PMC9340255 DOI: 10.3389/fmolb.2022.887686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/27/2022] [Indexed: 01/03/2023] Open
Abstract
Background: Bladder cancer (BLCA) is one of the most common cancer types worldwide. The disease is responsible for about 200,000 deaths annually, thus improved diagnostics and therapy is needed. A large body of evidence reveal that small RNAs of less than 40 nucleotides may act as tumor suppressors, oncogenes, and disease biomarkers, with a major focus on microRNAs. However, the role of other families of small RNAs is not yet deciphered. Recent results suggest that small RNAs and their modification status, play a role in BLCA development and are promising biomarkers due to their high abundance in the exomes and body fluids (including urine). Moreover, free modified nucleosides have been detected at elevated levels from the urine of BLCA patients. A genome-wide view of small RNAs, and their modifications, will help pinpoint the molecules that could be used as biomarker or has important biology in BLCA development. Methods: BLCA tumor tissue specimens were obtained from 12 patients undergoing transurethral resection of non-muscle invasive papillary urothelial carcinomas. Genome-wide profiling of small RNAs less than 40 bases long was performed by a modified protocol with TGIRT (thermostable group II reverse transcriptase) to identify novel small RNAs and their modification status. Results: Comprehensive analysis identified not only microRNAs. Intriguingly, 57 ± 15% (mean ± S.D.) of sequencing reads mapped to non-microRNA-small RNAs including tRNA-derived fragments (tRFs), ribosomal RNA-derived fragments (rRFs) and YRNA-derived fragments (YRFs). Misincorporation (mismatch) sites identified potential base modification positions on the small RNAs, especially on tRFs, corresponding to m1A (N1-methyladenosine), m1G (N1-methylguanosine) and m2 2G (N2, N2-dimethylguanosine). We also detected mismatch sites on rRFs corresponding to known modifications on 28 and 18S rRNA. Conclusion: We found abundant non-microRNA-small RNAs in BLCA tumor samples. Small RNAs, especially tRFs and rRFs, contain modifications that can be captured as mismatch by TGIRT sequencing. Both the modifications and the non-microRNA-small RNAs should be explored as a biomarker for BLCA detection or follow-up.
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Affiliation(s)
- Zhangli Su
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Ida Monshaugen
- Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- Department of Surgery, Baerum Hospital Vestre Viken Hospital Trust, Gjettum, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Rune Ougland
- Department of Microbiology, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Department of Surgery, Baerum Hospital Vestre Viken Hospital Trust, Gjettum, Norway
| | - Anindya Dutta
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, United States
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Wang J, Xi Y, Ma S, Qi J, Li J, Zhang R, Han C, Li L, Wang J, Liu H. Single-molecule long-read sequencing reveals the potential impact of posttranscriptional regulation on gene dosage effects on the avian Z chromosome. BMC Genomics 2022; 23:122. [PMID: 35148676 PMCID: PMC8832729 DOI: 10.1186/s12864-022-08360-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 02/01/2022] [Indexed: 12/23/2022] Open
Abstract
Background Mammalian sex chromosomes provide dosage compensation, but avian lack a global mechanism of dose compensation. Herein, we employed nanopore sequencing to investigate the genetic basis of gene expression and gene dosage effects in avian Z chromosomes at the posttranscriptional level. Results In this study, the gonad and head skin of female and male duck samples (n = 4) were collected at 16 weeks of age for Oxford nanopore sequencing. Our results revealed a dosage effect and local regulation of duck Z chromosome gene expression. Additionally, AS and APA achieve tissue-specific gene expression, and male-biased lncRNA regulates its Z-linked target genes, with a positive regulatory role for gene dosage effects on the duck Z chromosome. In addition, GO enrichment and KEGG pathway analysis showed that the dosage effects of Z-linked genes were mainly associated with the cellular response to hormone stimulus, melanin biosynthetic, metabolic pathways, and melanogenesis, resulting in sex differences. Conclusions Our data suggested that post transcriptional regulation (AS, APA and lncRNA) has a potential impact on the gene expression effects of avian Z chromosomes. Our study provides a new view of gene regulation underlying the dose effects in avian Z chromosomes at the RNA post transcriptional level. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08360-8.
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Affiliation(s)
- Jianmei Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Yang Xi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Shengchao Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Jingjing Qi
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Junpeng Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Rongping Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 613000, China.
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