1
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Nemeth K, Bayraktar R, Ferracin M, Calin GA. Non-coding RNAs in disease: from mechanisms to therapeutics. Nat Rev Genet 2024; 25:211-232. [PMID: 37968332 DOI: 10.1038/s41576-023-00662-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 11/17/2023]
Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are not translated into proteins. Since their discovery, ncRNAs have emerged as important regulators of multiple biological functions across a range of cell types and tissues, and their dysregulation has been implicated in disease. Notably, much research has focused on the link between microRNAs (miRNAs) and human cancers, although other ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as relevant contributors to human disease. In this Review, we summarize our current understanding of the roles of miRNAs, lncRNAs and circRNAs in cancer and other major human diseases, notably cardiovascular, neurological and infectious diseases. Further, we discuss the potential use of ncRNAs as biomarkers of disease and as therapeutic targets.
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Affiliation(s)
- Kinga Nemeth
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | - George A Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The RNA Interference and Non-coding RNA Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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2
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Liu Y, Jiang M, Li Y, Chen P, Chen X. Advances in the study of ELABELA in renal physiological functions and related diseases. Front Pharmacol 2023; 14:1276488. [PMID: 38026926 PMCID: PMC10644379 DOI: 10.3389/fphar.2023.1276488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
ELABELA (ELA), also known as Toddler or Apela, is a novel endogenous ligand of the angiotensin receptor AT1-related receptor protein (APJ). ELA is highly expressed in human embryonic, cardiac, and renal tissues and involves various biological functions, such as embryonic development, blood circulation regulation, and maintaining body fluid homeostasis. ELA is also closely related to the occurrence and development of acute kidney injury, hypertensive kidney damage, diabetic nephropathy, renal tumors, and other diseases. Understanding the physiological role of ELA and its mechanism of action in kidney-related diseases would provide new targets and directions for the clinical treatment of kidney diseases.
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Affiliation(s)
- YuRong Liu
- Department of Physiology and Neurobiology, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, Shandong, China
| | - MingChun Jiang
- Department of Physiology and Neurobiology, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, Shandong, China
| | - Yue Li
- Department of Anatomy, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, Shandong, China
| | - Peng Chen
- Department of Physiology and Neurobiology, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, Shandong, China
| | - XiaoYu Chen
- Department of Physiology and Neurobiology, Shandong First Medical University (Shandong Academy of Medical Sciences), Taian, Shandong, China
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3
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Hashemi Karoii D, Azizi H. Functions and mechanism of noncoding RNA in regulation and differentiation of male mammalian reproduction. Cell Biochem Funct 2023; 41:767-778. [PMID: 37583312 DOI: 10.1002/cbf.3838] [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: 05/16/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/17/2023]
Abstract
Noncoding RNAs (ncRNAs) are active regulators of a wide range of biological and physiological processes, including the majority of mammalian reproductive events. Knowledge of the biological activities of ncRNAs in the context of mammalian reproduction will allow for a more comprehensive and comparative understanding of male sterility and fertility. In this review, we describe recent advances in ncRNA-mediated control of mammalian reproduction and emphasize the importance of ncRNAs in several aspects of mammalian reproduction, such as germ cell biogenesis and reproductive organ activity. Furthermore, we focus on gene expression regulatory feedback loops including hormones and ncRNA expression to better understand germ cell commitment and reproductive organ function. Finally, this study shows the role of ncRNAs in male reproductive failure and provides suggestions for further research.
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Affiliation(s)
- Danial Hashemi Karoii
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Hossein Azizi
- Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
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4
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Hosea R, Hillary S, Wu S, Kasim V. Targeting Transcription Factor YY1 for Cancer Treatment: Current Strategies and Future Directions. Cancers (Basel) 2023; 15:3506. [PMID: 37444616 DOI: 10.3390/cancers15133506] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/28/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Cancer represents a significant and persistent global health burden, with its impact underscored by its prevalence and devastating consequences. Whereas numerous oncogenes could contribute to cancer development, a group of transcription factors (TFs) are overactive in the majority of tumors. Targeting these TFs may also combat the downstream oncogenes activated by the TFs, making them attractive potential targets for effective antitumor therapeutic strategy. One such TF is yin yang 1 (YY1), which plays crucial roles in the development and progression of various tumors. In preclinical studies, YY1 inhibition has shown efficacy in inhibiting tumor growth, promoting apoptosis, and sensitizing tumor cells to chemotherapy. Recent studies have also revealed the potential of combining YY1 inhibition with immunotherapy for enhanced antitumor effects. However, clinical translation of YY1-targeted therapy still faces challenges in drug specificity and delivery. This review provides an overview of YY1 biology, its role in tumor development and progression, as well as the strategies explored for YY1-targeted therapy, with a focus on their clinical implications, including those using small molecule inhibitors, RNA interference, and gene editing techniques. Finally, we discuss the challenges and current limitations of targeting YY1 and the need for further research in this area.
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Affiliation(s)
- Rendy Hosea
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Sharon Hillary
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Shourong Wu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing 400030, China
| | - Vivi Kasim
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
- The 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing 400044, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing University, Chongqing 400030, China
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5
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Clauwaert J, McVey Z, Gupta R, Menschaert G. TIS Transformer: remapping the human proteome using deep learning. NAR Genom Bioinform 2023; 5:lqad021. [PMID: 36879896 PMCID: PMC9985340 DOI: 10.1093/nargab/lqad021] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/20/2023] [Accepted: 02/14/2023] [Indexed: 03/07/2023] Open
Abstract
The correct mapping of the proteome is an important step towards advancing our understanding of biological systems and cellular mechanisms. Methods that provide better mappings can fuel important processes such as drug discovery and disease understanding. Currently, true determination of translation initiation sites is primarily achieved by in vivo experiments. Here, we propose TIS Transformer, a deep learning model for the determination of translation start sites solely utilizing the information embedded in the transcript nucleotide sequence. The method is built upon deep learning techniques first designed for natural language processing. We prove this approach to be best suited for learning the semantics of translation, outperforming previous approaches by a large margin. We demonstrate that limitations in the model performance are primarily due to the presence of low-quality annotations against which the model is evaluated against. Advantages of the method are its ability to detect key features of the translation process and multiple coding sequences on a transcript. These include micropeptides encoded by short Open Reading Frames, either alongside a canonical coding sequence or within long non-coding RNAs. To demonstrate the use of our methods, we applied TIS Transformer to remap the full human proteome.
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Affiliation(s)
- Jim Clauwaert
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Oost-Vlaanderen 9000, Belgium
| | - Zahra McVey
- Novo Nordisk Research Centre Oxford, Novo Nordisk Ltd., Crawley, South East England, RH6 0PA, UK
| | - Ramneek Gupta
- Novo Nordisk Research Centre Oxford, Novo Nordisk Ltd., Crawley, South East England, RH6 0PA, UK
| | - Gerben Menschaert
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Oost-Vlaanderen 9000, Belgium
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6
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Ivanov MN, Stoyanov DS, Pavlov SP, Tonchev AB. Distribution, Function, and Expression of the Apelinergic System in the Healthy and Diseased Mammalian Brain. Genes (Basel) 2022; 13:2172. [PMID: 36421846 PMCID: PMC9690544 DOI: 10.3390/genes13112172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/14/2022] [Accepted: 11/14/2022] [Indexed: 07/27/2023] Open
Abstract
Apelin, a peptide initially isolated from bovine stomach extract, is an endogenous ligand for the Apelin Receptor (APLNR). Subsequently, a second peptide, ELABELA, that can bind to the receptor has been identified. The Apelin receptor and its endogenous ligands are widely distributed in mammalian organs. A growing body of evidence suggests that this system participates in various signaling cascades that can regulate cell proliferation, blood pressure, fluid homeostasis, feeding behavior, and pituitary hormone release. Additional research has been done to elucidate the system's potential role in neurogenesis, the pathophysiology of Glioblastoma multiforme, and the protective effects of apelin peptides on some neurological and psychiatric disorders-ischemic stroke, epilepsy, Parkinson's, and Alzheimer's disease. This review discusses the current knowledge on the apelinergic system's involvement in brain physiology in health and disease.
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Affiliation(s)
- Martin N. Ivanov
- Department of Anatomy and Cell Biology, Medical University-Varna, 9000 Varna, Bulgaria
- Department of Stem Cell Biology, Research Institute, Medical University-Varna, 9000 Varna, Bulgaria
| | - Dimo S. Stoyanov
- Department of Anatomy and Cell Biology, Medical University-Varna, 9000 Varna, Bulgaria
| | - Stoyan P. Pavlov
- Department of Anatomy and Cell Biology, Medical University-Varna, 9000 Varna, Bulgaria
| | - Anton. B. Tonchev
- Department of Anatomy and Cell Biology, Medical University-Varna, 9000 Varna, Bulgaria
- Department of Stem Cell Biology, Research Institute, Medical University-Varna, 9000 Varna, Bulgaria
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7
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Fu H, Wang T, Kong X, Yan K, Yang Y, Cao J, Yuan Y, Wang N, Kee K, Lu ZJ, Xi Q. A Nodal enhanced micropeptide NEMEP regulates glucose uptake during mesendoderm differentiation of embryonic stem cells. Nat Commun 2022; 13:3984. [PMID: 35810171 PMCID: PMC9271079 DOI: 10.1038/s41467-022-31762-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
TGF-β family proteins including Nodal are known as central regulators of early development in metazoans, yet our understanding of the scope of Nodal signaling’s downstream targets and associated physiological mechanisms in specifying developmentally appropriate cell fates is far from complete. Here, we identified a highly conserved, transmembrane micropeptide—NEMEP—as a direct target of Nodal signaling in mesendoderm differentiation of mouse embryonic stem cells (mESCs), and this micropeptide is essential for mesendoderm differentiation. We showed that NEMEP interacts with the glucose transporters GLUT1/GLUT3 and promotes glucose uptake likely through these interactions. Thus, beyond expanding the scope of known Nodal signaling targets in early development and showing that this target micropeptide augments the glucose uptake during mesendoderm differentiation, our study provides a clear example for the direct functional impact of altered glucose metabolism on cell fate determination. Fu et al. identify the highly conserved, transmembrane micropeptide, NEMEP, as a direct target of Nodal signaling, essential for mesendoderm differentiation. NEMEP interacts with the glucose transporters GLUT1/GLUT3 and promotes glucose uptake.
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Affiliation(s)
- Haipeng Fu
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Tingyu Wang
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaohui Kong
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Kun Yan
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yang Yang
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Joint Graduate Program of Peking-Tsinghua-NIBS, Tsinghua University, Beijing, 100084, China
| | - Jingyi Cao
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yafei Yuan
- State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Nan Wang
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Kehkooi Kee
- Center for Stem Cell Biology and Regenerative Medicine, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Zhi John Lu
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiaoran Xi
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Joint Graduate Program of Peking-Tsinghua-NIBS, Tsinghua University, Beijing, 100084, China.
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8
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Jayaraman V, Toledo‐Patiño S, Noda‐García L, Laurino P. Mechanisms of protein evolution. Protein Sci 2022; 31:e4362. [PMID: 35762715 PMCID: PMC9214755 DOI: 10.1002/pro.4362] [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: 02/28/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 11/06/2022]
Abstract
How do proteins evolve? How do changes in sequence mediate changes in protein structure, and in turn in function? This question has multiple angles, ranging from biochemistry and biophysics to evolutionary biology. This review provides a brief integrated view of some key mechanistic aspects of protein evolution. First, we explain how protein evolution is primarily driven by randomly acquired genetic mutations and selection for function, and how these mutations can even give rise to completely new folds. Then, we also comment on how phenotypic protein variability, including promiscuity, transcriptional and translational errors, may also accelerate this process, possibly via "plasticity-first" mechanisms. Finally, we highlight open questions in the field of protein evolution, with respect to the emergence of more sophisticated protein systems such as protein complexes, pathways, and the emergence of pre-LUCA enzymes.
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Affiliation(s)
- Vijay Jayaraman
- Department of Molecular Cell BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Saacnicteh Toledo‐Patiño
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Lianet Noda‐García
- Department of Plant Pathology and Microbiology, Institute of Environmental Sciences, Robert H. Smith Faculty of Agriculture, Food and EnvironmentHebrew University of JerusalemRehovotIsrael
| | - Paola Laurino
- Protein Engineering and Evolution UnitOkinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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9
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Bogaert A, Fijalkowska D, Staes A, Van de Steene T, Demol H, Gevaert K. Limited evidence for protein products of non-coding transcripts in the HEK293T cellular cytosol. Mol Cell Proteomics 2022; 21:100264. [PMID: 35788065 PMCID: PMC9396073 DOI: 10.1016/j.mcpro.2022.100264] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/22/2022] [Accepted: 06/30/2022] [Indexed: 10/25/2022] Open
Abstract
Ribosome profiling has revealed translation outside of canonical coding sequences (CDSs) including translation of short upstream ORFs, long non-coding RNAs, overlapping ORFs, ORFs in UTRs or ORFs in alternative reading frames. Studies combining mass spectrometry, ribosome profiling and CRISPR-based screens showed that hundreds of ORFs derived from non-coding transcripts produce (micro)proteins, while other studies failed to find evidence for such types of non-canonical translation products. Here, we attempted to discover translation products from non-coding regions by strongly reducing the complexity of the sample prior to mass spectrometric analysis. We used an extended database as the search space and applied stringent filtering of the identified peptides to find evidence for novel translation events. We show that, theoretically our strategy facilitates the detection of translation events of transcripts from non-coding regions, but experimentally only find 19 peptides that might originate from such translation events. Finally, Virotrap based interactome analysis of two N-terminal proteoforms originating from non-coding regions finally showed the functional potential of these novel proteins.
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Affiliation(s)
- Annelies Bogaert
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Daria Fijalkowska
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - An Staes
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Tessa Van de Steene
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Hans Demol
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, 9052, Belgium.
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10
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Cancer-related micropeptides encoded by ncRNAs: Promising drug targets and prognostic biomarkers. Cancer Lett 2022; 547:215723. [DOI: 10.1016/j.canlet.2022.215723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/14/2022] [Accepted: 05/01/2022] [Indexed: 02/07/2023]
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11
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Plasma Levels of Apelinergic System Components in Patients with Chronic and Acute Coronary Syndromes-A Pilot Study. J Clin Med 2021; 10:jcm10194420. [PMID: 34640437 PMCID: PMC8509670 DOI: 10.3390/jcm10194420] [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: 08/30/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 12/22/2022] Open
Abstract
The effects of the apelinergic system components apelin (AP) and elabela (ELA) in the regulation of human cardiovascular homeostasis, and data concerning the relationship between ELA and AP and coronary artery disease (CAD) are yet unknown. The aim of the study was the evaluation of AP, ELA and APJ-receptor levels in the plasma of patients with chronic coronary syndromes (CCS) and acute coronary syndromes (ACS). The study group consisted of 114 patients with CAD and 33 healthy controls. Patients were divided into two groups: with CCS (n = 30) and ACS (n = 84). Routine laboratory tests and plasma ELA, AP-17, AP-13 and APJ receptor levels were measured. Echocardiographic data were analyzed in all patients. Levels of AP-17 and ELA were significantly lower in CCS than in healthy controls and ACS patients. We demonstrated significant increase of levels of plasma apelinergic system peptides, especially ELA and AP-17 in ACS patients compared with healthy controls and CCS, suggestive of compensating up-regulation mechanisms. There is a relationship between circulating ELA and AP-17 levels and classical, biochemical markers of ischemia and left ventricular ejection faction as well.
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12
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Dib A, Zanet J, Mancheno-Ferris A, Gallois M, Markus D, Valenti P, Marques-Prieto S, Plaza S, Kageyama Y, Chanut-Delalande H, Payre F. Pri smORF Peptides Are Wide Mediators of Ecdysone Signaling, Contributing to Shape Spatiotemporal Responses. Front Genet 2021; 12:714152. [PMID: 34527021 DOI: 10.3389/fgene.2021.714152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/28/2021] [Indexed: 11/13/2022] Open
Abstract
There is growing evidence that peptides encoded by small open-reading frames (sORF or smORF) can fulfill various cellular functions and define a novel class regulatory molecules. To which extend transcripts encoding only smORF peptides compare with canonical protein-coding genes, yet remain poorly understood. In particular, little is known on whether and how smORF-encoding RNAs might need tightly regulated expression within a given tissue, at a given time during development. We addressed these questions through the analysis of Drosophila polished rice (pri, a.k.a. tarsal less or mille pattes), which encodes four smORF peptides (11-32 amino acids in length) required at several stages of development. Previous work has shown that the expression of pri during epidermal development is regulated in the response to ecdysone, the major steroid hormone in insects. Here, we show that pri transcription is strongly upregulated by ecdysone across a large panel of cell types, suggesting that pri is a core component of ecdysone response. Although pri is produced as an intron-less short transcript (1.5 kb), genetic assays reveal that the developmental functions of pri require an unexpectedly large array of enhancers (spanning over 50 kb), driving a variety of spatiotemporal patterns of pri expression across developing tissues. Furthermore, we found that separate pri enhancers are directly activated by the ecdysone nuclear receptor (EcR) and display distinct regulatory modes between developmental tissues and/or stages. Alike major developmental genes, the expression of pri in a given tissue often involves several enhancers driving apparently redundant (or shadow) expression, while individual pri enhancers can harbor pleiotropic functions across tissues. Taken together, these data reveal the broad role of Pri smORF peptides in ecdysone signaling and show that the cis-regulatory architecture of the pri gene contributes to shape distinct spatial and temporal patterns of ecdysone response throughout development.
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Affiliation(s)
- Azza Dib
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Jennifer Zanet
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Alexandra Mancheno-Ferris
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Maylis Gallois
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Damien Markus
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Philippe Valenti
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Simon Marques-Prieto
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Serge Plaza
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - Yuji Kageyama
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan.,Biosignal Research Center, Kobe University, Kobe, Japan
| | - Hélène Chanut-Delalande
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
| | - François Payre
- Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, Toulouse, France
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13
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Guerra-Almeida D, Tschoeke DA, da-Fonseca RN. Understanding small ORF diversity through a comprehensive transcription feature classification. DNA Res 2021; 28:6317669. [PMID: 34240112 PMCID: PMC8435553 DOI: 10.1093/dnares/dsab007] [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: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Small open reading frames (small ORFs/sORFs/smORFs) are potentially coding sequences smaller than 100 codons that have historically been considered junk DNA by gene prediction software and in annotation screening; however, the advent of next-generation sequencing has contributed to the deeper investigation of junk DNA regions and their transcription products, resulting in the emergence of smORFs as a new focus of interest in systems biology. Several smORF peptides were recently reported in noncanonical mRNAs as new players in numerous biological contexts; however, their relevance is still overlooked in coding potential analysis. Hence, this review proposes a smORF classification based on transcriptional features, discussing the most promising approaches to investigate smORFs based on their different characteristics. First, smORFs were divided into nonexpressed (intergenic) and expressed (genic) smORFs. Second, genic smORFs were classified as smORFs located in noncoding RNAs (ncRNAs) or canonical mRNAs. Finally, smORFs in ncRNAs were further subdivided into sequences located in small or long RNAs, whereas smORFs located in canonical mRNAs were subdivided into several specific classes depending on their localization along the gene. We hope that this review provides new insights into large-scale annotations and reinforces the role of smORFs as essential components of a hidden coding DNA world.
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Affiliation(s)
- Diego Guerra-Almeida
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Diogo Antonio Tschoeke
- Alberto Luiz Coimbra Institute of Graduate Studies and Engineering Research (COPPE), Biomedical Engineering Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodrigo Nunes- da-Fonseca
- Institute of Biodiversity and Sustainability, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,National Institute of Science and Technology in Molecular Entomology, Rio de Janeiro, Brazil
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14
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Gao X, Zhang K, Zhou H, Zellmer L, Yuan C, Huang H, Liao DJ. At elevated temperatures, heat shock protein genes show altered ratios of different RNAs and expression of new RNAs, including several novel HSPB1 mRNAs encoding HSP27 protein isoforms. Exp Ther Med 2021; 22:900. [PMID: 34257713 PMCID: PMC8243336 DOI: 10.3892/etm.2021.10332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/10/2021] [Indexed: 12/22/2022] Open
Abstract
Heat shock proteins (HSP) serve as chaperones to maintain the physiological conformation and function of numerous cellular proteins when the ambient temperature is increased. To determine how accurate the general assumption that HSP gene expression is increased in febrile situations is, the RNA levels of the HSF1 (heat shock transcription factor 1) gene and certain HSP genes were determined in three cell lines cultured at 37˚C or 39˚C for three days. At 39˚C, the expression of HSF1, HSPB1, HSP90AA1 and HSP70A1L genes demonstrated complex changes in the ratios of expression levels between different RNA variants of the same gene. Several older versions of the RNAs of certain HSP genes that have been replaced by a newer version in the National Center for Biotechnology Information database were also detected, indicating that the older versions are actually RNA variants of these genes. The present study cloned four new RNA variants of the HSP27-encoding HSPB1 gene, which together encode three short HSP27 peptides. Reanalysis of the proteomics data from our previous studies also demonstrated that proteins from certain HSP genes could be detected simultaneously at multiple positions using SDS-PAGE, suggesting that these genes may engender multiple protein isoforms. These results collectively suggested that, besides increasing their expression, certain HSP and associated genes also use alternative transcription start sites to produce multiple RNA transcripts and use alternative splicing of a transcript to produce multiple mature RNAs, as important mechanisms for responding to an increased ambient temperature in vitro.
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Affiliation(s)
- Xia Gao
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China.,Key Lab of Endemic and Ethnic Diseases of The Ministry of Education of China in Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Keyin Zhang
- Department of Pathology, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China.,Key Lab of Endemic and Ethnic Diseases of The Ministry of Education of China in Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Haiyan Zhou
- Clinical Research Center, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China
| | - Lucas Zellmer
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Chengfu Yuan
- Department of Biochemistry, China Three Gorges University, Yichang, Hubei 443002, P.R. China
| | - Hai Huang
- Center for Clinical Laboratories, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China
| | - Dezhong Joshua Liao
- Key Lab of Endemic and Ethnic Diseases of The Ministry of Education of China in Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Center for Clinical Laboratories, Guizhou Medical University Hospital, Guiyang, Guizhou 550004, P.R. China
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15
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Zhang Q, Wu E, Tang Y, Cai T, Zhang L, Wang J, Hao Y, Zhang B, Zhou Y, Guo X, Luo J, Chen R, Yang F. Deeply Mining a Universe of Peptides Encoded by Long Noncoding RNAs. Mol Cell Proteomics 2021; 20:100109. [PMID: 34129944 PMCID: PMC8335655 DOI: 10.1016/j.mcpro.2021.100109] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/16/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022] Open
Abstract
Many small ORFs embedded in long noncoding RNA (lncRNA) transcripts have been shown to encode biologically functional polypeptides (small ORF-encoded polypeptides [SEPs]) in different organisms. Despite some novel SEPs have been found, the identification is still hampered by their poor predictability, diminutive size, and low relative abundance. Here, we take advantage of NONCODE, a repository containing the most complete collection and annotation of lncRNA transcripts from different species, to build a novel database that attempts to maximize a collection of SEPs from human and mouse lncRNA transcripts. In order to further improve SEP discovery, we implemented two effective and complementary polypeptide enrichment strategies using 30-kDa molecular weight cutoff filter and C8 solid-phase extraction column. These combined strategies enabled us to discover 353 SEPs from eight human cell lines and 409 SEPs from three mouse cell lines and eight mouse tissues. Importantly, 19 of them were then verified through in vitro expression, immunoblotting, parallel reaction monitoring, and synthetic peptides. Subsequent bioinformatics analysis revealed that some of the physical and chemical properties of these novel SEPs, including amino acid composition and codon usage, are different from those commonly found in canonical proteins. Intriguingly, nearly 65% of the identified SEPs were found to be initiated with non-AUG start codons. The 762 novel SEPs probably represent the largest number of SEPs detected by MS reported to date. These novel SEPs might not only provide new clues for the annotation of noncoding elements in the genome but also serve as a valuable resource for functional study.
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Affiliation(s)
- Qing Zhang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Erzhong Wu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yiheng Tang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Tanxi Cai
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lili Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jifeng Wang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yajing Hao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Bao Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yue Zhou
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Thermofisher Scientific, Shanghai, China
| | - Xiaojing Guo
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jianjun Luo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Runsheng Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Guangdong Geneway Decoding Bio-Tech Co Ltd, Foshan, China.
| | - Fuquan Yang
- Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
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16
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Fuchs S, Kucklick M, Lehmann E, Beckmann A, Wilkens M, Kolte B, Mustafayeva A, Ludwig T, Diwo M, Wissing J, Jänsch L, Ahrens CH, Ignatova Z, Engelmann S. Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach. PLoS Genet 2021; 17:e1009585. [PMID: 34061833 PMCID: PMC8195425 DOI: 10.1371/journal.pgen.1009585] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 06/11/2021] [Accepted: 05/07/2021] [Indexed: 01/08/2023] Open
Abstract
Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results. We used the workflow to identify high quality peptide spectrum matches (PSMs) for small proteins (≤ 100 aa, SP100) in Staphylococcus aureus Newman. Protein extracts from S. aureus were subjected to different experimental workflows for protein digestion and prefractionation and measured with highly sensitive mass spectrometers. In total, 175 proteins with up to 100 aa (SP100) were identified. Out of these 24 (ranging from 9 to 99 aa) were novel and not contained in the used genome annotation.144 SP100 are highly conserved and were found in at least 50% of the publicly available S. aureus genomes, while 127 are additionally conserved in other staphylococci. Almost half of the identified SP100 were basic, suggesting a role in binding to more acidic molecules such as nucleic acids or phospholipids.
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Affiliation(s)
- Stephan Fuchs
- Robert Koch Institute, Methodenentwicklung und Forschungsinfrastruktur (MF), Berlin, Germany
| | - Martin Kucklick
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Erik Lehmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Alexander Beckmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Maya Wilkens
- Robert Koch Institute, Methodenentwicklung und Forschungsinfrastruktur (MF), Berlin, Germany
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Baban Kolte
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Ayten Mustafayeva
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Tobias Ludwig
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Maurice Diwo
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
| | - Josef Wissing
- Helmholtz Center for Infection Research GmbH, Cellular Proteomics, Braunschweig, Germany
| | - Lothar Jänsch
- Helmholtz Center for Infection Research GmbH, Cellular Proteomics, Braunschweig, Germany
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Zoya Ignatova
- University of Hamburg, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Susanne Engelmann
- University of Technical Sciences Braunschweig, Institute for Microbiology, Braunschweig, Germany
- Helmholtz Center for Infection Research GmbH, Microbial Proteomics, Braunschweig, Germany
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17
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Montigny A, Tavormina P, Duboe C, San Clémente H, Aguilar M, Valenti P, Lauressergues D, Combier JP, Plaza S. Drosophila primary microRNA-8 encodes a microRNA-encoded peptide acting in parallel of miR-8. Genome Biol 2021; 22:118. [PMID: 33892772 PMCID: PMC8063413 DOI: 10.1186/s13059-021-02345-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 04/09/2021] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Recent genome-wide studies of many species reveal the existence of a myriad of RNAs differing in size, coding potential and function. Among these are the long non-coding RNAs, some of them producing functional small peptides via the translation of short ORFs. It now appears that any kind of RNA presumably has a potential to encode small peptides. Accordingly, our team recently discovered that plant primary transcripts of microRNAs (pri-miRs) produce small regulatory peptides (miPEPs) involved in auto-regulatory feedback loops enhancing their cognate microRNA expression which in turn controls plant development. Here we investigate whether this regulatory feedback loop is present in Drosophila melanogaster. RESULTS We perform a survey of ribosome profiling data and reveal that many pri-miRNAs exhibit ribosome translation marks. Focusing on miR-8, we show that pri-miR-8 can produce a miPEP-8. Functional assays performed in Drosophila reveal that miPEP-8 affects development when overexpressed or knocked down. Combining genetic and molecular approaches as well as genome-wide transcriptomic analyses, we show that miR-8 expression is independent of miPEP-8 activity and that miPEP-8 acts in parallel to miR-8 to regulate the expression of hundreds of genes. CONCLUSION Taken together, these results reveal that several Drosophila pri-miRs exhibit translation potential. Contrasting with the mechanism described in plants, these data shed light on the function of yet undescribed primary-microRNA-encoded peptides in Drosophila and their regulatory potential on genome expression.
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Affiliation(s)
- Audrey Montigny
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Patrizia Tavormina
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Carine Duboe
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Hélène San Clémente
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Marielle Aguilar
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Philippe Valenti
- Laboratoire MCD, Centre de Biologie Intégrative, Université de Toulouse 3, CNRS UMR5077, Bat 4R4, 118 route de Narbonne, 31062, Toulouse, France
| | - Dominique Lauressergues
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse 3, CNRS UMR5546, 31320, Auzeville-Tolosane, France.
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18
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Vitorino R, Guedes S, Amado F, Santos M, Akimitsu N. The role of micropeptides in biology. Cell Mol Life Sci 2021; 78:3285-3298. [PMID: 33507325 PMCID: PMC11073438 DOI: 10.1007/s00018-020-03740-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022]
Abstract
Micropeptides are small polypeptides coded by small open-reading frames. Progress in computational biology and the analyses of large-scale transcriptomes and proteomes have revealed that mammalian genomes produce a large number of transcripts encoding micropeptides. Many of these have been previously annotated as long noncoding RNAs. The role of micropeptides in cellular homeostasis maintenance has been demonstrated. This review discusses different types of micropeptides as well as methods to identify them, such as computational approaches, ribosome profiling, and mass spectrometry.
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Affiliation(s)
- Rui Vitorino
- Departamento de Cirurgia E Fisiologia, Faculdade de Medicina da Universidade Do Porto, UnIC, Porto, Portugal.
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal.
| | - Sofia Guedes
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Francisco Amado
- Departamento de Química, LAQV-REQUIMTE, Universidade de Aveiro, Aveiro, Portugal
- Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Manuel Santos
- Department of Medical Sciences, iBiMED, University of Aveiro, Aveiro, Portugal
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19
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Little RB, Norris DP. Right, left and cilia: How asymmetry is established. Semin Cell Dev Biol 2021; 110:11-18. [PMID: 32571625 DOI: 10.1016/j.semcdb.2020.06.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022]
Abstract
The initial breaking of left-right (L-R) symmetry in the embryo is controlled by a motile-cilia-driven leftward fluid flow in the left-right organiser (LRO), resulting in L-R asymmetric gene expression flanking the LRO. Ultimately this results in left- but not right-sided activation of the Nodal-Pitx2 pathway in more lateral tissues. While aspects of the initial breaking event clearly vary between vertebrates, events in the Lateral Plate Mesoderm (LPM) are conserved through the vertebrate lineage. Evidence from model systems and humans highlights the role of cilia both in the initial symmetry breaking and in the ability of more lateral tissues to exhibit asymmetric gene expression. In this review we concentrate on the process of L-R determination in mouse and humans.
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Affiliation(s)
- Rosie B Little
- MRC Harwell Institute, Harwell Campus, Oxfordshire, OX11 0RD, UK
| | - Dominic P Norris
- MRC Harwell Institute, Harwell Campus, Oxfordshire, OX11 0RD, UK.
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20
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Zhang S, Chen Y, Wang Y, Zhang P, Chen G, Zhou Y. Insights Into Translatomics in the Nervous System. Front Genet 2021; 11:599548. [PMID: 33408739 PMCID: PMC7779767 DOI: 10.3389/fgene.2020.599548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
Most neurological disorders are caused by abnormal gene translation. Generally, dysregulation of elements involved in the translational process disrupts homeostasis in neurons and neuroglia. Better understanding of how the gene translation process occurs requires detailed analysis of transcriptomic and proteomic profile data. However, a lack of strictly direct correlations between mRNA and protein levels limits translational investigation by combining transcriptomic and proteomic profiling. The much better correlation between proteins and translated mRNAs than total mRNAs in abundance and insufficiently sensitive proteomics approach promote the requirement of advances in translatomics technology. Translatomics which capture and sequence the mRNAs associated with ribosomes has been effective in identifying translational changes by genetics or projections, ribosome stalling, local translation, and transcript isoforms in the nervous system. Here, we place emphasis on the main three translatomics methods currently used to profile mRNAs attached to ribosome-nascent chain complex (RNC-mRNA). Their prominent applications in neurological diseases including glioma, neuropathic pain, depression, fragile X syndrome (FXS), neurodegenerative disorders are outlined. The content reviewed here expands our understanding on the contributions of aberrant translation to neurological disease development.
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Affiliation(s)
- Shuxia Zhang
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yeru Chen
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongjie Wang
- Key Laboratory of Elemene Anti-Cancer Medicine of Zhejiang Province and Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou, China.,Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, Holistic Integrative Pharmacy Institutes, Hangzhou Normal University, Hangzhou, China
| | - Piao Zhang
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Gang Chen
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Youfa Zhou
- Department of Anesthesiology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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21
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Pang Y, Liu Z, Han H, Wang B, Li W, Mao C, Liu S. Peptide SMIM30 promotes HCC development by inducing SRC/YES1 membrane anchoring and MAPK pathway activation. J Hepatol 2020; 73:1155-1169. [PMID: 32461121 DOI: 10.1016/j.jhep.2020.05.028] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Growing evidence shows that some non-coding RNAs (ncRNAs) contain small open reading frames (smORFs) that are translated into short peptides. Herein, we aimed to determine where and how these short peptides might promote hepatocellular carcinoma (HCC) development. METHODS We performed an RNA-immunoprecipitation followed by high-throughput sequencing (RIP-seq) assay with an antibody against ribosomal protein S6 (RPS6) on 4 cancer cell lines. Focusing on 1 long non-coding RNA (lncRNA), LINC00998, we used qPCR and public databases to evaluate its expression level in patients with HCC. Special vectors were constructed to confirm its coding potential. We also explored the function and mechanism of LINC00998-encoded peptide in tumor growth and metastasis. RESULTS We discovered that many lncRNAs bind to RPS6 in cancer cells. One of these lncRNAs, LINC00998, encoded a small endogenous peptide, termed SMIM30. SMIM30, rather than the RNA itself, promoted HCC tumorigenesis by modulating cell proliferation and migration, and its level was correlated with poor survival in patients with HCC. Furthermore, SMIM30 was transcribed by c-Myc and then drove the membrane anchoring of the non-receptor tyrosine kinases SRC/YES1. Moreover, the downstream MAPK signaling pathway was activated by SRC/YES1. CONCLUSIONS Our results not only unravel a new mechanism of HCC tumorigenesis promoted by ncRNA-encoded peptides, but also suggest that these peptides can serve as a new target for HCC cancer therapy and a new biomarker for HCC diagnosis and prognosis. LAY SUMMARY Very little is known about how peptides activate signaling pathways that play a crucial role in diseases such as cancer. Specifically, we reported on a conserved peptide encoded by LINC00998, SMIM30. This peptide promoted the tumorigenesis of hepatocellular carcinoma (HCC) by modulating cell proliferation and migration. Of note, it bound the non-receptor tyrosine kinases, SRC/YES1, to drive their membrane anchoring and phosphorylation, activating the downstream MAPK signaling pathway. Our work not only unravels a new mechanism of HCC tumorigenesis promoted by peptides, but also demonstrates how the peptide works to activate a signaling pathway.
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Affiliation(s)
- Yanan Pang
- Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Zhiyong Liu
- Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Huan Han
- Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Beilei Wang
- Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Wei Li
- Changzheng Hospital, Second Military Medical University, Shanghai 200433, China
| | - Chuanbin Mao
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5300, USA; School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang 310027, PR China.
| | - Shanrong Liu
- Changhai Hospital, Second Military Medical University, Shanghai 200433, China.
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22
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Seyler L, Kujawinski EB, Azua-Bustos A, Lee MD, Marlow J, Perl SM, Cleaves II HJ. Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers. ASTROBIOLOGY 2020; 20:1251-1261. [PMID: 32551936 PMCID: PMC7116171 DOI: 10.1089/ast.2019.2135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
It is now routinely possible to sequence and recover microbial genomes from environmental samples. To the degree it is feasible to assign transcriptional and translational functions to these genomes, it should be possible, in principle, to largely understand the complete molecular inputs and outputs of a microbial community. However, gene-based tools alone are presently insufficient to describe the full suite of chemical reactions and small molecules that compose a living cell. Metabolomic tools have developed quickly and now enable rapid detection and identification of small molecules within biological and environmental samples. The convergence of these technologies will soon facilitate the detection of novel enzymatic activities, novel organisms, and potentially extraterrestrial life-forms on solar system bodies. This review explores the methodological problems and scientific opportunities facing researchers who hope to apply metabolomic methods in astrobiology-related fields, and how present challenges might be overcome.
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Affiliation(s)
- Lauren Seyler
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Address correspondence to: Lauren Seyler, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, 86 Water Street, Woods Hole, MA 02543, USA
| | - Elizabeth B. Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Armando Azua-Bustos
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Michael D. Lee
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Exobiology Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - Jeffrey Marlow
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Scott M. Perl
- Geological and Planetary Sciences, California Institute of Technology/NASA Jet Propulsion Laboratory, Pasadena, California, USA
- Mineral Sciences, Los Angeles Natural History Museum, Los Angeles, California, USA
| | - Henderson James Cleaves II
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- School of Natural Sciences, Institute for Advanced Study, Princeton, New Jersey, USA
- Geographical Research Laboratory, Carnegie Institution of Washington
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23
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Zhou Y, Chen B. GAS5‑mediated regulation of cell signaling (Review). Mol Med Rep 2020; 22:3049-3056. [PMID: 32945519 PMCID: PMC7453608 DOI: 10.3892/mmr.2020.11435] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
In recent years, an increasing number of long non-coding RNAs (lncRNAs) have been discovered using microarrays and nucleic acid sequencing technology. LncRNAs exert crucial biological functions by regulating signaling pathways. In particular, the lncRNA growth arrest-specific transcript 5 (GAS5) has been documented to serve a crucial role in numerous signaling pathways. This article discusses the latest developments in the association between GAS5 and microRNA (miRNA), p53, mTOR, glucocorticoid response element (GRE) and AKT in order to investigate the roles served by GAS5. miRNAs can activate related signaling pathways and GAS5 can combine with miRNA to regulate related signaling pathways. GAS5 may regulate p53 expression via derivation of snoRNA, but the underlying mechanism requires further investigation. GAS5 overxpresion reduces the expression level of mTOR, which is induced by inhibiting miR-106a-5p expression. GAS5 is a sponge of GR, and serves a role in controlling and maintaining glucocorticoid sensitivity and drug resistance via competitive combination with GR. GAS5 can interact with miRNAs, such as miR-21 and miR-532-5p, to regulate the expression of AKT signaling pathway, affecting cell survival and apoptosis. Collectively, the data indicate that GAS5 serves a key role in the miRNA, p53, mTOR, GRE, and AKT signaling pathways. GAS5 regulates complex intracellular signaling pathways primarily through three modes of action, all of which are interrelated: Signal, decoy and guide. In the present article, latest developments in the association between GAS5 and a number of cellular signaling pathways are discussed to examine the tumor suppressive role of GAS5.
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Affiliation(s)
- Yang Zhou
- Department of Urology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212000, P.R. China
| | - Binghai Chen
- Department of Urology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212000, P.R. China
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24
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Li M, Li X, Zhang Y, Wu H, Zhou H, Ding X, Zhang X, Jin X, Wang Y, Yin X, Li C, Yang P, Xu H. Micropeptide MIAC Inhibits HNSCC Progression by Interacting with Aquaporin 2. J Am Chem Soc 2020; 142:6708-6716. [PMID: 32176498 DOI: 10.1021/jacs.0c00706] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Several important micropeptides encoded by noncoding RNAs have been identified in recent years; however, there have never been any reports of micropeptides in head and neck squamous cell carcinoma (HNSCC). Here we report the discovery and characterization of a human endogenous peptide named micropeptide inhibiting actin cytoskeleton (MIAC). Comprehensive analysis of the TCGA (The Cancer Genome Atlas) database (n = 500), clinical fresh samples (n = 94), and tissue microarrays (n = 60) revealed that lower MIAC expression is correlated with poor overall survival of HNSCC patients. Meanwhile, RNA-sequencing analysis of 9657 human tissues across 32 cancer types from TCGA cohorts found that MIAC is significantly associated with the progression of 5 other different tumors. Mechanistically, MIAC directly interacts with AQP2 (Aquaporin 2) to inhibit the actin cytoskeleton by regulating SEPT2 (Septin 2)/ITGB4 (Integrin Beta 4) and ultimately suppressing the tumor growth and metastasis of HNSCC. Collectively, the mechanism investigation and evaluation of MIAC activity in vivo and in vitro highlights that MIAC plays an important role in HNSCC tumorigenesis.
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Affiliation(s)
| | | | | | - Heming Wu
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing 210029, P. R. China
| | | | - Xu Ding
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing 210029, P. R. China
| | - Xiaomin Zhang
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing 210029, P. R. China
| | | | | | | | - Chencheng Li
- Nanjing Anji Biotechnology Co. Ltd., Nanjing, Jiangsu 210009, P. R. China
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25
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Narita K, Nagatomo H, Kozuka-Hata H, Oyama M, Takeda S. Discovery of a Vertebrate-Specific Factor that Processes Flagellar Glycolytic Enolase during Motile Ciliogenesis. iScience 2020; 23:100992. [PMID: 32248064 PMCID: PMC7132099 DOI: 10.1016/j.isci.2020.100992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 01/13/2020] [Accepted: 03/12/2020] [Indexed: 12/13/2022] Open
Abstract
Motile cilia and flagella require ATP for their formation and function. Although glycolytic enzymes are components of flagellar proteomes, how they translocate to flagella is unknown. Here we show that the expression pattern of the functionally nonannotated gene 4833427G06Rik (C11orf88), which is found only in vertebrates and is designated here as Hoatzin (Hoatz), suggests a functional association of its product with motile cilia and flagella. Hoatz knockout (KO) mice developed hydrocephalus and male infertility in an autosomal recessive manner, and the ependymal cilia frequently showed disorganized axonemes, reducing motility associated with collapsed spermatid flagella during cytodifferentiation. HOATZ was associated with certain proteins, including the flagellar glycolytic enzyme ENO4. In the testes of the Hoatz KO mice, the immature form of ENO4 accumulated in abnormal cytoplasmic puncta of developing spermatids. These data indicate that HOATZ is required for motile ciliogenesis and flagellar genesis in vertebrates by mediating the maturation of ENO4. Knockout of Hoatz causes hydrocephalus and oligo-astheno-terato-zoospermia Motile cilia are variably affected by the Hoatz mutation depending on tissue type Candidate HOATZ-interacting proteins including ENO4 are identified Knockout of Hoatz alters the western blot profile of ENO4
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Affiliation(s)
- Keishi Narita
- Department of Anatomy and Cell Biology, Faculty of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan.
| | - Hiroaki Nagatomo
- Center for Life Science Research, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Sen Takeda
- Department of Anatomy and Cell Biology, Faculty of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan.
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R Cerqueira F, Vasconcelos ATR. OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5989499. [PMID: 33206960 PMCID: PMC7673341 DOI: 10.1093/database/baaa067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/11/2020] [Accepted: 07/27/2020] [Indexed: 11/14/2022]
Abstract
Small open reading frames (ORFs) have been systematically disregarded by automatic genome annotation. The difficulty in finding patterns in tiny sequences is the main reason that makes small ORFs to be overlooked by computational procedures. However, advances in experimental methods show that small proteins can play vital roles in cellular activities. Hence, it is urgent to make progress in the development of computational approaches to speed up the identification of potential small ORFs. In this work, our focus is on bacterial genomes. We improve a previous approach to identify small ORFs in bacteria. Our method uses machine learning techniques and decoy subject sequences to filter out spurious ORF alignments. We show that an advanced multivariate analysis can be more effective in terms of sensitivity than applying the simplistic and widely used e-value cutoff. This is particularly important in the case of small ORFs for which alignments present higher e-values than usual. Experiments with control datasets show that the machine learning algorithms used in our method to curate significant alignments can achieve average sensitivity and specificity of 97.06% and 99.61%, respectively. Therefore, an important step is provided here toward the construction of more accurate computational tools for the identification of small ORFs in bacteria.
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Affiliation(s)
- Fabio R Cerqueira
- Department of Production Engineering, Universidade Federal Fluminense, Rua Domingos Silvério s/n, Petrópolis, 25 650-050, Rio de Janeiro, Brazil.,Graduate Program in Computer Science, Universidade Federal de Viçosa, 36570-900, Minas Gerais, Brazil
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27
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Clauwaert J, Menschaert G, Waegeman W. DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns. Nucleic Acids Res 2019; 47:e36. [PMID: 30753697 PMCID: PMC6451124 DOI: 10.1093/nar/gkz061] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/02/2019] [Accepted: 01/30/2019] [Indexed: 12/13/2022] Open
Abstract
Annotation of gene expression in prokaryotes often finds itself corrected due to small variations of the annotated gene regions observed between different (sub)-species. It has become apparent that traditional sequence alignment algorithms, used for the curation of genomes, are not able to map the full complexity of the genomic landscape. We present DeepRibo, a novel neural network utilizing features extracted from ribosome profiling information and binding site sequence patterns that shows to be a precise tool for the delineation and annotation of expressed genes in prokaryotes. The neural network combines recurrent memory cells and convolutional layers, adapting the information gained from both the high-throughput ribosome profiling data and ribosome binding translation initiation sequence region into one model. DeepRibo is designed as a single model trained on a variety of ribosome profiling experiments, used for the identification of open reading frames in prokaryotes without a priori knowledge of the translational landscape. Through extensive validation of the model trained on various sets of data, multiple species sequence similarity, mass spectrometry and Edman degradation verified proteins, the effectiveness of DeepRibo is highlighted.
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Affiliation(s)
- Jim Clauwaert
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Gerben Menschaert
- Biobix, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Willem Waegeman
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Coupure Links 653, 9000 Gent, Belgium
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Read C, Nyimanu D, Williams TL, Huggins DJ, Sulentic P, Macrae RGC, Yang P, Glen RC, Maguire JJ, Davenport AP. International Union of Basic and Clinical Pharmacology. CVII. Structure and Pharmacology of the Apelin Receptor with a Recommendation that Elabela/Toddler Is a Second Endogenous Peptide Ligand. Pharmacol Rev 2019; 71:467-502. [PMID: 31492821 PMCID: PMC6731456 DOI: 10.1124/pr.119.017533] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The predicted protein encoded by the APJ gene discovered in 1993 was originally classified as a class A G protein-coupled orphan receptor but was subsequently paired with a novel peptide ligand, apelin-36 in 1998. Substantial research identified a family of shorter peptides activating the apelin receptor, including apelin-17, apelin-13, and [Pyr1]apelin-13, with the latter peptide predominating in human plasma and cardiovascular system. A range of pharmacological tools have been developed, including radiolabeled ligands, analogs with improved plasma stability, peptides, and small molecules including biased agonists and antagonists, leading to the recommendation that the APJ gene be renamed APLNR and encode the apelin receptor protein. Recently, a second endogenous ligand has been identified and called Elabela/Toddler, a 54-amino acid peptide originally identified in the genomes of fish and humans but misclassified as noncoding. This precursor is also able to be cleaved to shorter sequences (32, 21, and 11 amino acids), and all are able to activate the apelin receptor and are blocked by apelin receptor antagonists. This review summarizes the pharmacology of these ligands and the apelin receptor, highlights the emerging physiologic and pathophysiological roles in a number of diseases, and recommends that Elabela/Toddler is a second endogenous peptide ligand of the apelin receptor protein.
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Affiliation(s)
- Cai Read
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Centre for Clinical Investigation, Addenbrooke's Hospital, Cambridge, United Kingdom (C.R., D.N., T.L.W., D.J.H., P.S., R.G.C.M., P.Y., J.J.M., A.P.D.); The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom (D.J.H., R.C.G.); and Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom (R.C.G.)
| | - Duuamene Nyimanu
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Centre for Clinical Investigation, Addenbrooke's Hospital, Cambridge, United Kingdom (C.R., D.N., T.L.W., D.J.H., P.S., R.G.C.M., P.Y., J.J.M., A.P.D.); The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom (D.J.H., R.C.G.); and Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom (R.C.G.)
| | - Thomas L Williams
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Centre for Clinical Investigation, Addenbrooke's Hospital, Cambridge, United Kingdom (C.R., D.N., T.L.W., D.J.H., P.S., R.G.C.M., P.Y., J.J.M., A.P.D.); The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom (D.J.H., R.C.G.); and Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom (R.C.G.)
| | - David J Huggins
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Centre for Clinical Investigation, Addenbrooke's Hospital, Cambridge, United Kingdom (C.R., D.N., T.L.W., D.J.H., P.S., R.G.C.M., P.Y., J.J.M., A.P.D.); The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom (D.J.H., R.C.G.); and Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom (R.C.G.)
| | - Petra Sulentic
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Centre for Clinical Investigation, Addenbrooke's Hospital, Cambridge, United Kingdom (C.R., D.N., T.L.W., D.J.H., P.S., R.G.C.M., P.Y., J.J.M., A.P.D.); The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom (D.J.H., R.C.G.); and Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom (R.C.G.)
| | - Robyn G C Macrae
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Centre for Clinical Investigation, Addenbrooke's Hospital, Cambridge, United Kingdom (C.R., D.N., T.L.W., D.J.H., P.S., R.G.C.M., P.Y., J.J.M., A.P.D.); The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom (D.J.H., R.C.G.); and Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom (R.C.G.)
| | - Peiran Yang
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Centre for Clinical Investigation, Addenbrooke's Hospital, Cambridge, United Kingdom (C.R., D.N., T.L.W., D.J.H., P.S., R.G.C.M., P.Y., J.J.M., A.P.D.); The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom (D.J.H., R.C.G.); and Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom (R.C.G.)
| | - Robert C Glen
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Centre for Clinical Investigation, Addenbrooke's Hospital, Cambridge, United Kingdom (C.R., D.N., T.L.W., D.J.H., P.S., R.G.C.M., P.Y., J.J.M., A.P.D.); The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom (D.J.H., R.C.G.); and Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom (R.C.G.)
| | - Janet J Maguire
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Centre for Clinical Investigation, Addenbrooke's Hospital, Cambridge, United Kingdom (C.R., D.N., T.L.W., D.J.H., P.S., R.G.C.M., P.Y., J.J.M., A.P.D.); The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom (D.J.H., R.C.G.); and Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom (R.C.G.)
| | - Anthony P Davenport
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Centre for Clinical Investigation, Addenbrooke's Hospital, Cambridge, United Kingdom (C.R., D.N., T.L.W., D.J.H., P.S., R.G.C.M., P.Y., J.J.M., A.P.D.); The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom (D.J.H., R.C.G.); and Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, United Kingdom (R.C.G.)
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29
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Xu Z, Hu L, Shi B, Geng S, Xu L, Wang D, Lu ZJ. Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events. Nucleic Acids Res 2019; 46:e109. [PMID: 29945224 PMCID: PMC6182183 DOI: 10.1093/nar/gky533] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/31/2018] [Indexed: 02/06/2023] Open
Abstract
Translation is dynamically regulated during cell development and stress response. In order to detect actively translated open reading frames (ORFs) and dynamic cellular translation events, we have developed a computational method, RiboWave, to process ribosome profiling data. RiboWave utilizes wavelet transform to denoise the original signal by extracting 3-nt periodicity of ribosomes and precisely locate their footprint denoted as Periodic Footprint P-site (PF P-site). Such high-resolution footprint is found to capture the full track of actively elongating ribosomes, from which translational landscape can be explicitly characterized. We compare RiboWave with several published methods, like RiboTaper, ORFscore and RibORF, and found that RiboWave outperforms them in both accuracy and usage when defining actively translated ORFs. Moreover, we show that PF P-site derived by RiboWave shows superior performance in characterizing the dynamics and complexity of cellular translatome by accurately estimating the abundance of protein levels, assessing differential translation and identifying dynamic translation frameshift.
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Affiliation(s)
- Zhiyu Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Long Hu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Binbin Shi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - SiSi Geng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Longchen Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dong Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhi J Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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30
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Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, Pruitt KD. Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation. Nucleic Acids Res 2019; 46:D221-D228. [PMID: 29126148 PMCID: PMC5753299 DOI: 10.1093/nar/gkx1031] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 10/20/2017] [Indexed: 01/29/2023] Open
Abstract
The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community.
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Affiliation(s)
- Shashikant Pujar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Nuala A O'Leary
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Catherine M Farrell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Jane E Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan M Mudge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Craig Wallin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Carlos G Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mark Diekhans
- University of California Santa Cruz Genomics Institute, Santa Cruz, CA 95064, USA
| | - If Barnes
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Andrew E Berry
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eric Cox
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tamara Goldfarb
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Jose M Gonzalez
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - John Jackson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Vinita Joardar
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mike P Kay
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Vamsi K Kodali
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Monica McAndrews
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Kelly M McGarvey
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Michael Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Bhanu Rajput
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sanjida H Rangwala
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lillian D Riddick
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Ruth L Seal
- HUGO Gene Nomenclature Committee, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Marthe Suner
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Webb
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sophia Zhu
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Bronwen L Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Elspeth A Bruford
- HUGO Gene Nomenclature Committee, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Carol J Bult
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Terence Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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31
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Volkova OA, Kondrakhin YV, Kashapov TA, Sharipov RN. Comparative analysis of protein-coding and long non-coding transcripts based on RNA sequence features. J Bioinform Comput Biol 2019; 16:1840013. [PMID: 29739305 DOI: 10.1142/s0219720018400139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
RNA plays an important role in the intracellular cell life and in the organism in general. Besides the well-established protein coding RNAs (messenger RNAs, mRNAs), long non-coding RNAs (lncRNAs) have gained the attention of recent researchers. Although lncRNAs have been classified as non-coding, some authors reported the presence of corresponding sequences in ribosome profiling data (Ribo-seq). Ribo-seq technology is a powerful experimental tool utilized to characterize RNA translation in cell with focus on initiation (harringtonine, lactimidomycin) and elongation (cycloheximide). By exploiting translation starts obtained from the Ribo-seq experiment, we developed a novel position weight matrix model for the prediction of translation starts. This model allowed us to achieve 96% accuracy of discrimination between human mRNAs and lncRNAs. When the same model was used for the prediction of putative ORFs in RNAs, we discovered that the majority of lncRNAs contained only small ORFs ([Formula: see text][Formula: see text]nt) in contrast to mRNAs.
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Affiliation(s)
- Oxana A Volkova
- * Laboratory of Gene Engineering, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Prosp. Acad. Lavrentyeva, 10, Novosibirsk 630090, Russia
| | - Yury V Kondrakhin
- † Laboratory of Bioinformatics, Institute of Computational Technologies, The Siberian Branch of the Russian Academy of Sciences, Ul. Acad. Rzhanova, 6, Novosibirsk 630090, Russia.,‡ BIOSOFT.RU, Ltd, Ul. Russkaya, 41/1 Novosibirsk 630058, Russia
| | - Timur A Kashapov
- ‡ BIOSOFT.RU, Ltd, Ul. Russkaya, 41/1 Novosibirsk 630058, Russia
| | - Ruslan N Sharipov
- ‡ BIOSOFT.RU, Ltd, Ul. Russkaya, 41/1 Novosibirsk 630058, Russia.,§ Novosibirsk State University, Ul. Pirogova, 2, Novosibirsk 630090, Russia
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Abstract
The aim of the review is to examine the role of growth factors and cytokines in the management of Diabetic Foot Ulcers, such as platelet derived growth factor (PDGF), vascular endothelial growth factor (VEGF), fibroblast growth factor (FGF) and Insulin like growth factor (IGF). Taking this a step further, the role of Hypoxia-inducible factors (HIFs), Transforming growth factor beta 1 (TGF-β-1) and other growth factors have also been examined, with regard to the treatment of diabetic foot ulcers. The roles of these above-mentioned growth cytokines have been analyzed by studying various scholastic articles. The complete process of wound healing is implemented and regulated by numerous cytokines and human growth factors. The findings of the study indicate that wound healing of diabetic foot ulcers is a complex and extremely challenging biological and molecular process that involves coordinated efforts of multiple cell types. The therapeutic effects of various growth factors in the clinical management of wounds are chronic venous ulcers, pressure ulcers, and diabetic foot ulcers. It has been concluded that altercations of various cytokines are found in patients enduring diabetic foot ulcers. In a similar way, changes in the level of cytokines are also found in patients suffering from other diabetic complications such as diabetic nephropathy, retinopathy, and neuropathy. Subsequently, the diabetic wound healing process can be accelerated by regulating the levels of the cytokines.
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Affiliation(s)
- Mohammad Zubair
- Department of Medical Microbiology, Faculty of Medicine, University of Tabuk, Tabuk, 71491, Kingdom of Saudi Arabia.
| | - Jamal Ahmad
- Rajiv Gandhi Centre for Diabetes and Endocrinology, Faculty of Medicine, J.N. Medical College, Aligarh Muslim University, Aligarh, 202002, India
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33
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Abstract
PURPOSE OF REVIEW Human genome is pervasively transcribed, producing coding and noncoding RNAs. Recent studies have revealed the roles of a class of noncoding RNAs, the long noncoding RNAs (lncRNAs), in heart failure and other cardiovascular diseases. This review provides a brief summary of recent findings on lncRNA function. RECENT FINDINGS Recent studies have documented the roles of lncRNAs in cardiac regeneration, conduction, hypertrophy/dysfunction, and endothelial function. LncRNAs perform these functions through acting as competing RNA (by binding and sequestering MicroRNAs) or acting as guides to protein targeting. A few lncRNAs also encode small peptides (e.g., Dwarf Open Reading Frame RNA) and in the context of heart regulate cardiac calcium homeostasis. SUMMARY Noncoding RNA provides a versatile mechanism of gene regulation and thereby present as novel targets for intervention in various cardiovascular disease. Future studies aimed at defining the context-dependent lncRNA mechanisms will be required to advance our understanding and relish the goal of RNA therapeutics.
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Affiliation(s)
- Priyatansh Gurha
- Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine, University of Texas Health Sciences Center at Houston, and Texas Heart Institute, Houston, TX 77030., Tel: +1 713-500-2335,
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Li A, Sun Y, Drummer C, Lu Y, Yu D, Zhou Y, Li X, Pearson SJ, Johnson C, Yu C, Yang WY, Mastascusa K, Jiang X, Sun J, Rogers T, Hu W, Wang H, Yang X. Increasing Upstream Chromatin Long-Range Interactions May Favor Induction of Circular RNAs in LysoPC-Activated Human Aortic Endothelial Cells. Front Physiol 2019; 10:433. [PMID: 31057422 PMCID: PMC6482593 DOI: 10.3389/fphys.2019.00433] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 03/28/2019] [Indexed: 01/10/2023] Open
Abstract
Circular RNAs (circRNAs) are non-coding RNAs that form covalently closed continuous loops, and act as gene regulators in physiological and disease conditions. To test our hypothesis that proatherogenic lipid lysophosphatidylcholine (LPC) induce a set of circRNAs in human aortic endothelial cell (HAEC) activation, we performed circRNA analysis by searching our RNA-Seq data from LPC-activated HAECs, and found: (1) LPC induces significant modulation of 77 newly characterized cirRNAs, among which 47 circRNAs (61%) are upregulated; (2) 34 (72%) out of 47 upregulated circRNAs are upregulated when the corresponding mRNAs are downregulated, suggesting that the majority of circRNAs are upregulated presumably via LPC-induced “abnormal splicing” when the canonical splicing for generation of corresponding mRNAs is suppressed; (3) Upregulation of 47 circRNAs is temporally associated with mRNAs-mediated LPC-upregulated cholesterol synthesis-SREBP2 pathway and LPC-downregulated TGF-β pathway; (4) Increase in upstream chromatin long-range interaction sites to circRNA related genes is associated with preferred circRNA generation over canonical splicing for mRNAs, suggesting that shifting chromatin long-range interaction sites from downstream to upstream may promote induction of a list of circRNAs in lysoPC-activated HAECs; (5) Six significantly changed circRNAs may have sponge functions for miRNAs; and (6) 74% significantly changed circRNAs contain open reading frames, suggesting that putative short proteins may interfere with the protein interaction-based signaling. Our findings have demonstrated for the first time that a new set of LPC-induced circRNAs may contribute to homeostasis in LPC-induced HAEC activation. These novel insights may lead to identifications of new therapeutic targets for treating metabolic cardiovascular diseases, inflammations, and cancers.
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Affiliation(s)
- Angus Li
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States.,Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States
| | - Yu Sun
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Charles Drummer
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Yifan Lu
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Daohai Yu
- Department of Clinical Sciences, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Yan Zhou
- Biostatistics and Bioinformatics Facility, Fox Chase Cancer Center, Temple Health, Philadelphia, PA, United States
| | - Xinyuan Li
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Simone J Pearson
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Candice Johnson
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Catherine Yu
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
| | - William Y Yang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Kevin Mastascusa
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Xiaohua Jiang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Jianxin Sun
- Center for Translational Medicine, Department of Medicine, Sidney Kimmel Medical College, Philadelphia University - Thomas Jefferson University, Philadelphia, PA, United States
| | - Thomas Rogers
- Center for Inflammation, Translational and Clinical Lung Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Wenhui Hu
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Hong Wang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| | - Xiaofeng Yang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States.,Center for Inflammation, Translational and Clinical Lung Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
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35
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Scheidler CM, Kick LM, Schneider S. Ribosomal Peptides and Small Proteins on the Rise. Chembiochem 2019; 20:1479-1486. [PMID: 30648812 DOI: 10.1002/cbic.201800715] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Indexed: 11/05/2022]
Abstract
Genetically encoded and ribosomally synthesised peptides and small proteins act as important regulators in fundamental cellular processes, including gene expression, development, signalling and metabolism. Moreover, they also play a crucial role in eukaryotic and prokaryotic defence against microorganisms. Extremely diverse in size and structure, they are often subject to extensive post-translational modification. Recent technological advances are now allowing the analysis of the whole cellular transcriptome and proteome, revealing the presence of hundreds of long-overlooked alternative and short open reading frames (short ORFs, or sORFs) in mRNA and supposedly noncoding RNAs. However, in many instances the biological roles of their translational products remain to be elucidated. Here we provide an overview on the intriguing structural and functional diversity of ribosomally synthesised peptides and newly discovered peptides and small proteins.
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Affiliation(s)
- Christopher M Scheidler
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Leonhard M Kick
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Sabine Schneider
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
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36
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Zhao J, Qin B, Nikolay R, Spahn CMT, Zhang G. Translatomics: The Global View of Translation. Int J Mol Sci 2019; 20:ijms20010212. [PMID: 30626072 PMCID: PMC6337585 DOI: 10.3390/ijms20010212] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/19/2018] [Accepted: 01/02/2019] [Indexed: 01/01/2023] Open
Abstract
In all kingdoms of life, proteins are synthesized by ribosomes in a process referred to as translation. The amplitude of translational regulation exceeds the sum of transcription, mRNA degradation and protein degradation. Therefore, it is essential to investigate translation in a global scale. Like the other “omics”-methods, translatomics investigates the totality of the components in the translation process, including but not limited to translating mRNAs, ribosomes, tRNAs, regulatory RNAs and nascent polypeptide chains. Technical advances in recent years have brought breakthroughs in the investigation of these components at global scale, both for their composition and dynamics. These methods have been applied in a rapidly increasing number of studies to reveal multifaceted aspects of translation control. The process of translation is not restricted to the conversion of mRNA coding sequences into polypeptide chains, it also controls the composition of the proteome in a delicate and responsive way. Therefore, translatomics has extended its unique and innovative power to many fields including proteomics, cancer research, bacterial stress response, biological rhythmicity and plant biology. Rational design in translation can enhance recombinant protein production for thousands of times. This brief review summarizes the main state-of-the-art methods of translatomics, highlights recent discoveries made in this field and introduces applications of translatomics on basic biological and biomedical research.
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Affiliation(s)
- Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China.
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37
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Exaptation at the molecular genetic level. SCIENCE CHINA-LIFE SCIENCES 2018; 62:437-452. [PMID: 30798493 DOI: 10.1007/s11427-018-9447-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 12/01/2018] [Indexed: 12/22/2022]
Abstract
The realization that body parts of animals and plants can be recruited or coopted for novel functions dates back to, or even predates the observations of Darwin. S.J. Gould and E.S. Vrba recognized a mode of evolution of characters that differs from adaptation. The umbrella term aptation was supplemented with the concept of exaptation. Unlike adaptations, which are restricted to features built by selection for their current role, exaptations are features that currently enhance fitness, even though their present role was not a result of natural selection. Exaptations can also arise from nonaptations; these are characters which had previously been evolving neutrally. All nonaptations are potential exaptations. The concept of exaptation was expanded to the molecular genetic level which aided greatly in understanding the enormous potential of neutrally evolving repetitive DNA-including transposed elements, formerly considered junk DNA-for the evolution of genes and genomes. The distinction between adaptations and exaptations is outlined in this review and examples are given. Also elaborated on is the fact that such distinctions are sometimes more difficult to determine; this is a widespread phenomenon in biology, where continua abound and clear borders between states and definitions are rare.
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38
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Abstract
Ribosome profiling involves sequencing of approximately 30-base-long stretches of ribosome-protected mRNA. The technique enables genome-wide mapping of RNA undergoing active translation. Numerous small open reading frames have been identified by using ribosome profiling, leading researchers to question the assumed non-functional character of sORFs and to the identification of various important sORF translation products. sORFs.org (https://www.sorfs.org) is a public repository of small open reading frames identified by ribosome profiling in a database of over 3 million sORFs across 78 datasets from six species. sORFs.org is a multi-omics endeavor providing tools and metrics to assess the coding potential of the delineated sORFs. A pipeline is also in place to systematically rescan public mass spectrometry datasets to acquire new experimental evidence for sORF-encoded polypeptides. sORFs.org provides two distinct query interfaces, export functionality, and various visualization tools to enable inspection of the available information. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Volodimir Olexiouk
- Department of Mathematical Modelling, Statistics and Bioinformatics, Universiteit Gent Faculteit Bio-Ingenieurswetenschappen, Gent, Belgium
| | - Gerben Menschaert
- Department of Mathematical Modelling, Statistics and Bioinformatics, Universiteit Gent Faculteit Bio-Ingenieurswetenschappen, Gent, Belgium
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39
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High resolution annotation of zebrafish transcriptome using long-read sequencing. Genome Res 2018; 28:1415-1425. [PMID: 30061115 PMCID: PMC6120630 DOI: 10.1101/gr.223586.117] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 07/05/2018] [Indexed: 12/13/2022]
Abstract
With the emergence of zebrafish as an important model organism, a concerted effort has been made to study its transcriptome. This effort is limited, however, by gaps in zebrafish annotation, which are especially pronounced concerning transcripts dynamically expressed during zygotic genome activation (ZGA). To date, short-read sequencing has been the principal technology for zebrafish transcriptome annotation. In part because these sequence reads are too short for assembly methods to resolve the full complexity of the transcriptome, the current annotation is rudimentary. By providing direct observation of full-length transcripts, recently refined long-read sequencing platforms can dramatically improve annotation coverage and accuracy. Here, we leveraged the SMRT platform to study the transcriptome of zebrafish embryos before and after ZGA. Our analysis revealed additional novelty and complexity in the zebrafish transcriptome, identifying 2539 high-confidence novel transcripts that originated from previously unannotated loci and 1835 high-confidence new isoforms in previously annotated genes. We validated these findings using a suite of computational approaches including structural prediction, sequence homology, and functional conservation analyses, as well as by confirmatory transcript quantification with short-read sequencing data. Our analyses provided insight into new homologs and paralogs of functionally important proteins and noncoding RNAs, isoform switching occurrences, and different classes of novel splicing events. Several novel isoforms representing distinct splicing events were validated through PCR experiments, including the discovery and validation of a novel 8-kb transcript spanning multiple mir-430 elements, an important driver of early development. Our study provides a significantly improved zebrafish transcriptome annotation resource.
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40
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Freyer L, Hsu CW, Nowotschin S, Pauli A, Ishida J, Kuba K, Fukamizu A, Schier AF, Hoodless PA, Dickinson ME, Hadjantonakis AK. Loss of Apela Peptide in Mice Causes Low Penetrance Embryonic Lethality and Defects in Early Mesodermal Derivatives. Cell Rep 2018; 20:2116-2130. [PMID: 28854362 DOI: 10.1016/j.celrep.2017.08.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 06/22/2017] [Accepted: 08/01/2017] [Indexed: 01/22/2023] Open
Abstract
Apela (also known as Elabela, Ende, and Toddler) is a small signaling peptide that activates the G-protein-coupled receptor Aplnr to stimulate cell migration during zebrafish gastrulation. Here, using CRISPR/Cas9 to generate a null, reporter-expressing allele, we study the role of Apela in the developing mouse embryo. We found that loss of Apela results in low-penetrance cardiovascular defects that manifest after the onset of circulation. Three-dimensional micro-computed tomography revealed a higher penetrance of vascular remodeling defects, from which some mutants recover, and identified extraembryonic anomalies as the earliest morphological distinction in Apela mutant embryos. Transcriptomics at late gastrulation identified aberrant upregulation of erythroid and myeloid markers in mutant embryos prior to the appearance of physical malformations. Double-mutant analyses showed that loss of Apela signaling impacts early Aplnr-expressing mesodermal populations independently of the alternative ligand Apelin, leading to lethal cardiac defects in some Apela null embryos.
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Affiliation(s)
- Laina Freyer
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Chih-Wei Hsu
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sonja Nowotschin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Andrea Pauli
- The Research Institute of Molecular Pathology, Vienna BioCenter, 1030 Vienna, Austria
| | - Junji Ishida
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8577, Japan
| | - Keiji Kuba
- Department of Biochemistry and Metabolic Science, Akita University, Akita 010-8543, Japan
| | - Akiyoshi Fukamizu
- Life Science Center, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba 305-8577, Japan
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada
| | - Mary E Dickinson
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
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41
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Yeasmin F, Yada T, Akimitsu N. Micropeptides Encoded in Transcripts Previously Identified as Long Noncoding RNAs: A New Chapter in Transcriptomics and Proteomics. Front Genet 2018; 9:144. [PMID: 29922328 PMCID: PMC5996887 DOI: 10.3389/fgene.2018.00144] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Abstract
Integrative analysis using omics-based technologies results in the identification of a large number of putative short open reading frames (sORFs) with protein-coding capacity within transcripts previously identified as long noncoding RNAs (lncRNAs) or transcripts of unknown function (TUFs). sORFs were previously overlooked because of their diminutive size and the difficulty of identification by bioinformatics analyses. There is now growing evidence of the existence of potentially functional micropeptides produced from sORFs within cells of diverse species. Recent characterization of a few of these revealed their significant divergent roles in many fundamental biological processes, where some also show important relationships with pathogenesis. Recent works therefore provide new insights for exploring the wealth of information that may lie within sORF-encoded short proteins. Here, we summarize the current progress and view of micropeptides encoded in sORFs of protein-coding genes.
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Affiliation(s)
- Fouzia Yeasmin
- Isotope Science Centre, The University of Tokyo, Tokyo, Japan
| | - Tetsushi Yada
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan
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42
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Brunet MA, Levesque SA, Hunting DJ, Cohen AA, Roucou X. Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship. Genome Res 2018; 28:609-624. [PMID: 29626081 PMCID: PMC5932603 DOI: 10.1101/gr.230938.117] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/27/2018] [Indexed: 12/12/2022]
Abstract
Technological advances promise unprecedented opportunities for whole exome sequencing and proteomic analyses of populations. Currently, data from genome and exome sequencing or proteomic studies are searched against reference genome annotations. This provides the foundation for research and clinical screening for genetic causes of pathologies. However, current genome annotations substantially underestimate the proteomic information encoded within a gene. Numerous studies have now demonstrated the expression and function of alternative (mainly small, sometimes overlapping) ORFs within mature gene transcripts. This has important consequences for the correlation of phenotypes and genotypes. Most alternative ORFs are not yet annotated because of a lack of evidence, and this absence from databases precludes their detection by standard proteomic methods, such as mass spectrometry. Here, we demonstrate how current approaches tend to overlook alternative ORFs, hindering the discovery of new genetic drivers and fundamental research. We discuss available tools and techniques to improve identification of proteins from alternative ORFs and finally suggest a novel annotation system to permit a more complete representation of the transcriptomic and proteomic information contained within a gene. Given the crucial challenge of distinguishing functional ORFs from random ones, the suggested pipeline emphasizes both experimental data and conservation signatures. The addition of alternative ORFs in databases will render identification less serendipitous and advance the pace of research and genomic knowledge. This review highlights the urgent medical and research need to incorporate alternative ORFs in current genome annotations and thus permit their inclusion in hypotheses and models, which relate phenotypes and genotypes.
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Affiliation(s)
- Marie A Brunet
- Biochemistry Department, Université de Sherbrooke, Quebec J1E 4K8, Canada.,Groupe de recherche PRIMUS, Department of Family and Emergency Medicine, Quebec J1H 5N4, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec G1V 0A6, Canada
| | - Sébastien A Levesque
- Pediatric Department, Centre Hospitalier de l'Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Darel J Hunting
- Department of Nuclear Medicine & Radiobiology, Université de Sherbrooke, Quebec J1H 5N4, Canada
| | - Alan A Cohen
- Groupe de recherche PRIMUS, Department of Family and Emergency Medicine, Quebec J1H 5N4, Canada
| | - Xavier Roucou
- Biochemistry Department, Université de Sherbrooke, Quebec J1E 4K8, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec G1V 0A6, Canada
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43
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Pang Y, Mao C, Liu S. Encoding activities of non-coding RNAs. Am J Cancer Res 2018; 8:2496-2507. [PMID: 29721095 PMCID: PMC5928905 DOI: 10.7150/thno.24677] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 02/25/2018] [Indexed: 12/14/2022] Open
Abstract
The universal expression of various non-coding RNAs (ncRNAs) is now considered the main feature of organisms' genomes. Many regions in the genome are transcribed but not annotated to encode proteins, yet contain small open reading frames (smORFs). A widely accepted opinion is that a vast majority of ncRNAs are not further translated. However, increasing evidence underlines a series of intriguing translational events from the ncRNAs, which were previously considered to lack coding potential. Recent studies also suggest that products derived from such novel translational events display important regulatory functions in many fundamental biological and pathological processes. Here we give a critical review on the potential coding capacity of ncRNAs, in particular, about what is known and unknown in this emerging area. We also discuss the possible underlying coding mechanisms of these extraordinary ncRNAs and possible roles of peptides or proteins derived from the ncRNAs in disease development and theranostics. Our review offers an extensive resource for studying the biology of ncRNAs and sheds light into the use of ncRNAs and their corresponding peptides or proteins for disease diagnosis and therapy.
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44
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García-Padilla C, Aránega A, Franco D. The role of long non-coding RNAs in cardiac development and disease. AIMS GENETICS 2018; 5:124-140. [PMID: 31435517 PMCID: PMC6698576 DOI: 10.3934/genet.2018.2.124] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/15/2018] [Indexed: 12/12/2022]
Abstract
Cells display a set of RNA molecules at one time point, reflecting thus the cellular transcriptional steady state, configuring therefore its transcriptome. It is basically composed of two different classes of RNA molecules; protein-coding RNAs (cRNAs) and protein non-coding RNAs (ncRNAs). Sequencing of the human genome and subsequently the ENCODE project identified that more than 80% of the genome is transcribed in some type of RNA. Importantly, only 3% of these transcripts correspond to protein-coding RNAs, pointing that ncRNAs are as important or even more as cRNAs. ncRNAs have pivotal roles in development, differentiation and disease. Non-coding RNAs can be classified into two distinct classes according to their length; i.e., small (<200 nt) and long (>200 nt) noncoding RNAs. The structure, biogenesis and functional roles of small non-coding RNA have been widely studied, particularly for microRNAs (miRNAs). In contrast to microRNAs, our current understanding of long non-coding RNAs (lncRNAs) is limited. In this manuscript, we provide state-of-the art review of the functional roles of long non-coding RNAs during cardiac development as well as an overview of the emerging role of these ncRNAs in distinct cardiac diseases.
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Affiliation(s)
| | | | - Diego Franco
- Cardiovascular Development Group, Department of Experimental Biology, University of Jaén, Jaén, Spain
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45
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Holdt LM, Kohlmaier A, Teupser D. Molecular roles and function of circular RNAs in eukaryotic cells. Cell Mol Life Sci 2018; 75:1071-1098. [PMID: 29116363 PMCID: PMC5814467 DOI: 10.1007/s00018-017-2688-5] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 09/29/2017] [Accepted: 10/17/2017] [Indexed: 12/27/2022]
Abstract
Protein-coding and noncoding genes in eukaryotes are typically expressed as linear messenger RNAs, with exons arranged colinearly to their genomic order. Recent advances in sequencing and in mapping RNA reads to reference genomes have revealed that thousands of genes express also covalently closed circular RNAs. Many of these circRNAs are stable and contain exons, but are not translated into proteins. Here, we review the emerging understanding that both, circRNAs produced by co- and posttranscriptional head-to-tail "backsplicing" of a downstream splice donor to a more upstream splice acceptor, as well as circRNAs generated from intronic lariats during colinear splicing, may exhibit physiologically relevant regulatory functions in eukaryotes. We describe how circRNAs impact gene expression of their host gene locus by affecting transcriptional initiation and elongation or splicing, and how they partake in controlling the function of other molecules, for example by interacting with microRNAs and proteins. We conclude with an outlook how circRNA dysregulation affects disease, and how the stability of circRNAs might be exploited in biomedical applications.
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Affiliation(s)
- Lesca M Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.
| | - Alexander Kohlmaier
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
- Faculty of Biology, Genetics, LMU Munich, Großhaderner Str. 2-4, 82152, Martinsried, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
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46
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Lakhotia SC. From Heterochromatin to Long Noncoding RNAs in Drosophila: Expanding the Arena of Gene Function and Regulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1008:75-118. [PMID: 28815537 DOI: 10.1007/978-981-10-5203-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc. There has been a rapid increase in the number of identified lncRNAs, although a much larger number still remains unknown. The diversity of modes of actions and functions of the limited number of Drosophila lncRNAs, which have been examined, already reflects the profound roles of such RNAs in generating and sustaining the biological complexities of eukaryotes. Several of the known Drosophila lncRNAs originate as independent sense or antisense transcripts from promoter or intergenic, intronic, or 5'/3'-UTR regions, while many of them are independent genes that produce only lncRNAs or coding as well as noncoding RNAs. The different lncRNAs affect chromatin organization (local or large-scale pan-chromosomal), transcription, RNA processing/stability, or translation either directly through interaction with their target DNA sequences or indirectly by acting as intermediary molecules for specific regulatory proteins or may act as decoys/sinks, or storage sites for specific proteins or groups of proteins, or may provide a structural framework for the assembly of substructures in nucleus/cytoplasm. It is interesting that many of the "functions" alluded to heterochromatin in earlier cytogenetic studies appear to find correlates with the known subtle as well as far-reaching actions of the different small and long noncoding RNAs. Further studies exploiting the very rich and powerful genetic and molecular resources available for the Drosophila model are expected to unravel the mystery underlying the long reach of ncRNAs.
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Affiliation(s)
- Subhash C Lakhotia
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221005, India.
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He Y, Yuan C, Chen L, Lei M, Zellmer L, Huang H, Liao DJ. Transcriptional-Readthrough RNAs Reflect the Phenomenon of "A Gene Contains Gene(s)" or "Gene(s) within a Gene" in the Human Genome, and Thus Are Not Chimeric RNAs. Genes (Basel) 2018; 9:E40. [PMID: 29337901 PMCID: PMC5793191 DOI: 10.3390/genes9010040] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/29/2017] [Accepted: 01/07/2018] [Indexed: 02/06/2023] Open
Abstract
Tens of thousands of chimeric RNAs, i.e., RNAs with sequences of two genes, have been identified in human cells. Most of them are formed by two neighboring genes on the same chromosome and are considered to be derived via transcriptional readthrough, but a true readthrough event still awaits more evidence and trans-splicing that joins two transcripts together remains as a possible mechanism. We regard those genomic loci that are transcriptionally read through as unannotated genes, because their transcriptional and posttranscriptional regulations are the same as those of already-annotated genes, including fusion genes formed due to genetic alterations. Therefore, readthrough RNAs and fusion-gene-derived RNAs are not chimeras. Only those two-gene RNAs formed at the RNA level, likely via trans-splicing, without corresponding genes as genomic parents, should be regarded as authentic chimeric RNAs. However, since in human cells, procedural and mechanistic details of trans-splicing have never been disclosed, we doubt the existence of trans-splicing. Therefore, there are probably no authentic chimeras in humans, after readthrough and fusion-gene derived RNAs are all put back into the group of ordinary RNAs. Therefore, it should be further determined whether in human cells all two-neighboring-gene RNAs are derived from transcriptional readthrough and whether trans-splicing truly exists.
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Affiliation(s)
- Yan He
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou, China.
| | - Chengfu Yuan
- Department of Biochemistry, China Three Gorges University, Yichang City 443002, Hubei, China.
| | - Lichan Chen
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
| | - Mingjuan Lei
- Hormel Institute, University of Minnesota, Austin, MN 55912, USA.
| | - Lucas Zellmer
- Masonic Cancer Center, University of Minnesota, 435 E. River Road, Minneapolis, MN 55455, USA.
| | - Hai Huang
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang 550004, Guizhou, China.
| | - Dezhong Joshua Liao
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou, China.
- Department of Pathology, Guizhou Medical University Hospital, Guiyang 550004, Guizhou, China.
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48
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Olexiouk V, Van Criekinge W, Menschaert G. An update on sORFs.org: a repository of small ORFs identified by ribosome profiling. Nucleic Acids Res 2018; 46:D497-D502. [PMID: 29140531 PMCID: PMC5753181 DOI: 10.1093/nar/gkx1130] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/25/2017] [Accepted: 10/26/2017] [Indexed: 12/13/2022] Open
Abstract
sORFs.org (http://www.sorfs.org) is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq). This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently includes 78 RIBO-seq datasets, a vast increase compared to the three that were processed in the initial release. Therefore, a novel pipeline was constructed that also enables sORF detection in RIBO-seq datasets comprising solely elongating RIBO-seq data while previously, matching initiating RIBO-seq data was necessary to delineate the sORFs. Furthermore, a novel noise filtering algorithm was designed, able to distinguish sORFs with true ribosomal activity from simulated noise, consequently reducing the false positive identification rate. The inclusion of other species also led to the development of an inner BLAST pipeline, assessing sequence similarity between sORFs in the repository. Building on the proof of concept model in the initial release of sORFs.org, a full PRIDE-ReSpin pipeline was now released, reprocessing publicly available MS-based proteomics PRIDE datasets, reporting on true translation events. Next to reporting those identified peptides, sORFs.org allows visual inspection of the annotated spectra within the Lorikeet MS/MS viewer, thus enabling detailed manual inspection and interpretation.
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Affiliation(s)
- Volodimir Olexiouk
- Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Wim Van Criekinge
- Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Gerben Menschaert
- Lab of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
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Karlik E, Marakli S, Gozukirmizi N. Two lncRNAs Expression Profiles in Salt Stressed Barley ( Hordeum vulgare L.) Roots. CYTOLOGIA 2018. [DOI: 10.1508/cytologia.83.37] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Elif Karlik
- Department of Biotechnology, Institution of Science, Istanbul University
| | - Sevgi Marakli
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University
| | - Nermin Gozukirmizi
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University
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50
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Umu SU, Langseth H, Bucher-Johannessen C, Fromm B, Keller A, Meese E, Lauritzen M, Leithaug M, Lyle R, Rounge TB. A comprehensive profile of circulating RNAs in human serum. RNA Biol 2017; 15:242-250. [PMID: 29219730 PMCID: PMC5798962 DOI: 10.1080/15476286.2017.1403003] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In this study, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed 10 billion Illumina reads from 477 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). We found that the core serum RNA repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting RNAs (piRNA), 411 transfer RNAs (tRNA), 24 small nucleolar RNAs (snoRNA), 125 small nuclear RNAs (snRNA) and 123 miscellaneous RNAs (misc-RNA). We also investigated biological and technical variation in expression, and the results suggest that many RNA molecules identified in serum contain signs of biological variation. They are therefore unlikely to be random degradation by-products. In addition, the presence of specific fragments of tRNA, snoRNA, Vault RNA and Y_RNA indicates protection from degradation. Our results suggest that many circulating RNAs in serum can be potential biomarkers.
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Affiliation(s)
- Sinan Uğur Umu
- a Department of Research , Cancer Registry of Norway , Oslo , Norway
| | - Hilde Langseth
- a Department of Research , Cancer Registry of Norway , Oslo , Norway
| | | | - Bastian Fromm
- b Department of Tumor Biology , Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital , Nydalen, Oslo , Norway
| | - Andreas Keller
- c Department of Clinical Bioinformatics , Saarland University , Saarbruecken , Germany
| | - Eckart Meese
- d Department of Human Genetics , Saarland University , Homburg/Saar , Germany
| | | | - Magnus Leithaug
- e Department of Medical Genetics , Oslo University Hospital and University of Oslo , Oslo , Norway
| | - Robert Lyle
- e Department of Medical Genetics , Oslo University Hospital and University of Oslo , Oslo , Norway.,f PharmaTox Strategic Research Initiative, School of Pharmacy, Faculty of Mathematics and Natural Sciences , University of Oslo , Oslo , Norway
| | - Trine B Rounge
- a Department of Research , Cancer Registry of Norway , Oslo , Norway
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