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Backofen R, Gorodkin J, Hofacker IL, Stadler PF. Comparative RNA Genomics. Methods Mol Biol 2024; 2802:347-393. [PMID: 38819565 DOI: 10.1007/978-1-0716-3838-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Over the last quarter of a century it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large-scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible non-coding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a-necessarily incomplete-overview of the current state of comparative analysis of non-coding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.
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Affiliation(s)
- Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Jan Gorodkin
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Ivo L Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria
- Bioinformatics and Computational Biology research group, University of Vienna, Vienna, Austria
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany.
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.
- Universidad National de Colombia, Bogotá, Colombia.
- Institute for Theoretical Chemistry, University of Vienna, Wien, Austria.
- Center for Non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark.
- Santa Fe Institute, Santa Fe, NM, USA.
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Li F, Deng Q, Pang X, Huang S, Zhang J, Zhu X, Chen H, Liu X. m 5C Regulator-Mediated Methylation Modification Patterns and Tumor Microenvironment Infiltration Characterization in Papillary Thyroid Carcinoma. Front Oncol 2021; 11:729887. [PMID: 34804923 PMCID: PMC8597900 DOI: 10.3389/fonc.2021.729887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/12/2021] [Indexed: 12/20/2022] Open
Abstract
Recently, immune response modulation at the epigenetic level is illustrated in studies, but the possible function of RNA 5-methylcytosine (m5C) modification in cell infiltration within the tumor microenvironment (TME) is still unclear. Three different m5C modification patterns were identified, and high differentiation degree was observed in the cell infiltration features within TME under the above three identified patterns. A low m5C-score, which was reflected in the activated immunity, predicted the relatively favorable prognostic outcome. A small amount of effective immune infiltration was seen in the high m5C-score subtype, indicating the dismal patient survival. Our study constructed a diagnostic model using the 10 signature genes highly related to the m5C-score, discovered that the model exhibited high diagnostic accuracy for PTC, and screened out five potential drugs for PTC based on this m5C-score model. m5C modification exerts an important part in forming the TME complexity and diversity. It is valuable to evaluate the m5C modification patterns in single tumors, so as to enhance our understanding towards the infiltration characterization in TME.
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Affiliation(s)
- Fei Li
- Department of Nuclear Medicine, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Qingmei Deng
- Department of Molecular Pathology, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
| | - Xiaoxi Pang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Shan Huang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Jingmiao Zhang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Xiaxia Zhu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Hong Chen
- Department of Nuclear Medicine, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Xiuxia Liu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
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Schumann U, Zhang HN, Sibbritt T, Pan A, Horvath A, Gross S, Clark SJ, Yang L, Preiss T. Multiple links between 5-methylcytosine content of mRNA and translation. BMC Biol 2020; 18:40. [PMID: 32293435 PMCID: PMC7158060 DOI: 10.1186/s12915-020-00769-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND 5-Methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of m5C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise. RESULTS We obtained ~ 1000 candidate m5C sites in the wider transcriptome, most of which were found in mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCaP and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m5C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in both mRNAs and noncoding RNAs. Candidate m5C sites in mRNAs are enriched in 5'UTRs and near start codons and are embedded in a local context reminiscent of the NSUN2-dependent m5C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that modification levels, at bulk and for many individual sites, were inversely correlated with ribosome association. CONCLUSIONS Our findings emphasise the major role of NSUN2 in placing the m5C mark transcriptome-wide. We further present evidence that substantiates a functional interdependence of cytosine methylation level with mRNA translation. Additionally, we identify several compelling candidate sites for future mechanistic analysis.
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Affiliation(s)
- Ulrike Schumann
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia
| | - He-Na Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Tennille Sibbritt
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia
| | - Anyu Pan
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia
| | - Attila Horvath
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia
| | - Simon Gross
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia
| | - Susan J Clark
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, New South Wales, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, New South Wales, 2010, Australia
| | - Li Yang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, John Curtin School of Medical Research, Australian National University, Canberra, 2601, Australian Captial Territory, Australia.
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, 2010, Australia.
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On-line trapping/capillary hydrophilic-interaction liquid chromatography/mass spectrometry for sensitive determination of RNA modifications from human blood. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.11.029] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Li Y, Li J, Luo M, Zhou C, Shi X, Yang W, Lu Z, Chen Z, Sun N, He J. Novel long noncoding RNA NMR promotes tumor progression via NSUN2 and BPTF in esophageal squamous cell carcinoma. Cancer Lett 2018; 430:57-66. [PMID: 29763634 DOI: 10.1016/j.canlet.2018.05.013] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/05/2018] [Accepted: 05/10/2018] [Indexed: 01/20/2023]
Abstract
Long noncoding RNAs (lncRNA) have been implicated in cancer but most of them remain largely unstudied. Here, we identified a novel NSUN2 methylated lncRNA (NMR), which was significantly upregulated in esophageal squamous cell carcinoma (ESCC), functioned as a key regulator of ESCC tumor metastasis and drug resistance. Upregulation of NMR correlated with tumor metastasis and indicated poor overall survival in ESCC patients. Functionally, NMR could promote tumor cell migration and invasion, inhibit cisplatin-induced apoptosis and increase drug resistance in ESCC cells. Mechanistically, transcription of NMR could be upregulated by NF-κB activation after IL-1β and TNF-α treatment. NMR was methylated by NSUN2 and might competitively inhibit methylation of potential mRNAs. NMR could directly bind to chromatin regulator BPTF, and potentially promote MMP3 and MMP10 expression by ERK1/2 pathway through recruiting BPTF to chromatin. Taken together, NMR functions as an oncogenic gene and may serve as new biomarker and therapeutic target in ESCC.
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Affiliation(s)
- Yuan Li
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jiagen Li
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Mei Luo
- Central Laboratory, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Chengcheng Zhou
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xuejiao Shi
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Wenhui Yang
- Department of Biochemistry and Molecular Biology, Shanxi Medical University, Taiyuan, Shanxi, 030001, China; Tumor Hospital of Shanxi Province, Taiyuan, Shanxi, 030013, China
| | - Zhiliang Lu
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhaoli Chen
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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Statistical Methods for Transcriptome-Wide Analysis of RNA Methylation by Bisulfite Sequencing. Methods Mol Biol 2018; 1562:155-167. [PMID: 28349460 DOI: 10.1007/978-1-4939-6807-7_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
For the transcriptome-wide detection and quantification of the 5-methylcytosine (m5C) methylation modification of RNA, one experimental approach is via bisulfite conversion. In this chapter we discuss statistical methods, and a corresponding computational pipeline, to perform transcriptome-wide differential m5C methylation analysis between RNA samples, specialized for this assay.
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7
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Abstract
Over the last two decades it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures. Large scale sequencing projects, on the other hand, have profoundly changed our understanding of eukaryotic genomes. Pervasively transcribed, they give rise to a plethora of large and evolutionarily extremely flexible noncoding RNAs that exert a vastly diverse array of molecule functions. In this chapter we provide a-necessarily incomplete-overview of the current state of comparative analysis of noncoding RNAs, emphasizing computational approaches as a means to gain a global picture of the modern RNA world.
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Affiliation(s)
- Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany.,Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark
| | - Ivo L Hofacker
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.,Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.,Bioinformatics and Computational Biology Research Group, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
| | - Peter F Stadler
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark. .,Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria. .,Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany. .,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany. .,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, D-04103 Leipzig, Germany. .,Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM 87501, USA.
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Shafik A, Schumann U, Evers M, Sibbritt T, Preiss T. The emerging epitranscriptomics of long noncoding RNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:59-70. [PMID: 26541084 DOI: 10.1016/j.bbagrm.2015.10.019] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/15/2015] [Accepted: 10/28/2015] [Indexed: 01/08/2023]
Abstract
The pervasive transcription of genomes into long noncoding RNAs has been amply demonstrated in recent years and garnered much attention. Similarly, emerging 'epitranscriptomics' research has shown that chemically modified nucleosides, thought to be largely the domain of tRNAs and other infrastructural RNAs, are far more widespread and can exert unexpected influence on RNA utilization. Both areas are characterized by the often-ephemeral nature of the subject matter in that few individual examples have been fully assessed for their molecular or cellular function, and effects might often be subtle and cumulative. Here we review available information at the intersection of these two exciting areas of biology, by focusing on four RNA modifications that have been mapped transcriptome-wide: 5-methylcytidine, N6-methyladenosine, pseudouridine as well as adenosine to inosine (A-to-I) editing, and their incidence and function in long noncoding RNAs. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.
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Affiliation(s)
- Andrew Shafik
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Ulrike Schumann
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Maurits Evers
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Tennille Sibbritt
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia.
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research (JCSMR), The Australian National University, Building 131 Garran Road, Acton, Canberra, Australian Capital Territory 2601, Australia; Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst (Sydney), New South Wales 2010, Australia.
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