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Liu X, Xiao C, Xu X, Zhang J, Mo F, Chen JY, Delihas N, Zhang L, An NA, Li CY. Origin of functional de novo genes in humans from "hopeful monsters". WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1845. [PMID: 38605485 DOI: 10.1002/wrna.1845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
For a long time, it was believed that new genes arise only from modifications of preexisting genes, but the discovery of de novo protein-coding genes that originated from noncoding DNA regions demonstrates the existence of a "motherless" origination process for new genes. However, the features, distributions, expression profiles, and origin modes of these genes in humans seem to support the notion that their origin is not a purely "motherless" process; rather, these genes arise preferentially from genomic regions encoding preexisting precursors with gene-like features. In such a case, the gene loci are typically not brand new. In this short review, we will summarize the definition and features of human de novo genes and clarify their process of origination from ancestral non-coding genomic regions. In addition, we define the favored precursors, or "hopeful monsters," for the origin of de novo genes and present a discussion of the functional significance of these young genes in brain development and tumorigenesis in humans. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
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Affiliation(s)
- Xiaoge Liu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chunfu Xiao
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xinwei Xu
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jie Zhang
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Fan Mo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Nicholas Delihas
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | - Ni A An
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Chuan-Yun Li
- State Key Laboratory of Protein and Plant Gene Research, Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Southwest United Graduate School, Kunming, China
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Pinzon Cortes JA, El-Osta A, Fontemaggi G, Delihas N, Miyazaki K, Goel A, Brazane M, Carré C, Dama P, Bayraktar S, Castellano L, Enguita FJ, Mitic T, Caporali A, Gerber AP, Amodio N. The Non-Coding RNA Journal Club: Highlights on Recent Papers-10. Noncoding RNA 2022; 8:3. [PMID: 35076559 PMCID: PMC8788465 DOI: 10.3390/ncrna8010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/05/2022] [Indexed: 12/05/2022] Open
Abstract
We are delighted to share with you our seventh Journal Club and highlight some of the most interesting papers published recently [...].
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Affiliation(s)
- Jairo A. Pinzon Cortes
- Epigenetics in Human Health and Disease, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia;
| | - Assam El-Osta
- Epigenetics in Human Health and Disease, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3004, Australia;
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144 Rome, Italy
| | - Nicholas Delihas
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, NY 11794, USA
| | - Katsuki Miyazaki
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA 91016, USA;
- Department of Surgery, Tokushima University, Tokushima 7708503, Japan
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Biomedical Research Center, Monrovia, CA 91016, USA;
- City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Mira Brazane
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire Biologie du Développement, Institut de Biologie Paris-Seine, UMR7622, 75005 Paris, France
| | - Clément Carré
- Transgenerational Epigenetics & Small RNA Biology, Sorbonne Université, CNRS, Laboratoire Biologie du Développement, Institut de Biologie Paris-Seine, UMR7622, 75005 Paris, France
| | - Paola Dama
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Salih Bayraktar
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
| | - Leandro Castellano
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
- Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine (ICTEM), Imperial College London, London W12 0NN, UK
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisbon, Portugal
| | - Tijana Mitic
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK;
| | - Andrea Caporali
- University/British Heart Foundation Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK;
| | - André P. Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy
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