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Sun YH, Cui H, Song C, Shen JT, Zhuo X, Wang RH, Yu X, Ndamba R, Mu Q, Gu H, Wang D, Murthy GG, Li P, Liang F, Liu L, Tao Q, Wang Y, Orlowski S, Xu Q, Zhou H, Jagne J, Gokcumen O, Anthony N, Zhao X, Li XZ. Amniotes co-opt intrinsic genetic instability to protect germ-line genome integrity. Nat Commun 2023; 14:812. [PMID: 36781861 PMCID: PMC9925758 DOI: 10.1038/s41467-023-36354-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/27/2023] [Indexed: 02/15/2023] Open
Abstract
Unlike PIWI-interacting RNA (piRNA) in other species that mostly target transposable elements (TEs), >80% of piRNAs in adult mammalian testes lack obvious targets. However, mammalian piRNA sequences and piRNA-producing loci evolve more rapidly than the rest of the genome for unknown reasons. Here, through comparative studies of chickens, ducks, mice, and humans, as well as long-read nanopore sequencing on diverse chicken breeds, we find that piRNA loci across amniotes experience: (1) a high local mutation rate of structural variations (SVs, mutations ≥ 50 bp in size); (2) positive selection to suppress young and actively mobilizing TEs commencing at the pachytene stage of meiosis during germ cell development; and (3) negative selection to purge deleterious SV hotspots. Our results indicate that genetic instability at pachytene piRNA loci, while producing certain pathogenic SVs, also protects genome integrity against TE mobilization by driving the formation of rapid-evolving piRNA sequences.
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Affiliation(s)
- Yu H Sun
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Hongxiao Cui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chi Song
- College of Public Health, Division of Biostatistics, The Ohio State University, Columbus, OH, 43210, USA
| | - Jiafei Teng Shen
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, 322000, China
| | - Xiaoyu Zhuo
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ruoqiao Huiyi Wang
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiaohui Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Rudo Ndamba
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Qian Mu
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Hanwen Gu
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Duolin Wang
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Gayathri Guru Murthy
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA
| | - Pidong Li
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Fan Liang
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Lei Liu
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Qing Tao
- Grandomics Biosciences Co., Ltd, Beijing, 102206, China
| | - Ying Wang
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Sara Orlowski
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Qi Xu
- Department of Animal Science, McGill University, Quebec, H9X 3V9, Canada
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, CA, 95616, USA
| | - Jarra Jagne
- Animal Health Diagnostic Center, Cornell University College of Veterinary Medicine, Ithaca, NY, 14850, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Nick Anthony
- Department of Poultry Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Xin Zhao
- Department of Animal Science, McGill University, Quebec, H9X 3V9, Canada.
| | - Xin Zhiguo Li
- Center for RNA Biology: From Genome to Therapeutics, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, 14642, USA.
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Larsson L, Degens H, Li M, Salviati L, Lee YI, Thompson W, Kirkland JL, Sandri M. Sarcopenia: Aging-Related Loss of Muscle Mass and Function. Physiol Rev 2019; 99:427-511. [PMID: 30427277 PMCID: PMC6442923 DOI: 10.1152/physrev.00061.2017] [Citation(s) in RCA: 859] [Impact Index Per Article: 143.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/14/2018] [Accepted: 06/15/2018] [Indexed: 12/11/2022] Open
Abstract
Sarcopenia is a loss of muscle mass and function in the elderly that reduces mobility, diminishes quality of life, and can lead to fall-related injuries, which require costly hospitalization and extended rehabilitation. This review focuses on the aging-related structural changes and mechanisms at cellular and subcellular levels underlying changes in the individual motor unit: specifically, the perikaryon of the α-motoneuron, its neuromuscular junction(s), and the muscle fibers that it innervates. Loss of muscle mass with aging, which is largely due to the progressive loss of motoneurons, is associated with reduced muscle fiber number and size. Muscle function progressively declines because motoneuron loss is not adequately compensated by reinnervation of muscle fibers by the remaining motoneurons. At the intracellular level, key factors are qualitative changes in posttranslational modifications of muscle proteins and the loss of coordinated control between contractile, mitochondrial, and sarcoplasmic reticulum protein expression. Quantitative and qualitative changes in skeletal muscle during the process of aging also have been implicated in the pathogenesis of acquired and hereditary neuromuscular disorders. In experimental models, specific intervention strategies have shown encouraging results on limiting deterioration of motor unit structure and function under conditions of impaired innervation. Translated to the clinic, if these or similar interventions, by saving muscle and improving mobility, could help alleviate sarcopenia in the elderly, there would be both great humanitarian benefits and large cost savings for health care systems.
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Affiliation(s)
- Lars Larsson
- Department of Physiology and Pharmacology, Basic and Clinical Muscle Biology Group, Karolinska Institutet , Stockholm , Sweden ; Section of Clinical Neurophysiology, Department of Clinical Neuroscience, Karolinska Institutet , Stockholm , Sweden ; Department of Biobehavioral Health, The Pennsylvania State University , University Park, Pennsylvania ; School of Healthcare Science, Metropolitan University , Manchester , United Kingdom ; Institute of Sport Science and Innovations, Lithuanian Sports University , Kaunas , Lithuania ; Clinical Genetics Unit, Department of Woman and Child Health, University of Padova , Padova , Italy ; IRP Città della Speranza, Padova , Italy ; Department of Biology, Texas A&M University , College Station, Texas ; Robert and Arlene Kogod Center on Aging, Mayo Clinic , Rochester, Minnesota ; Department of Biomedical Science, Venetian Institute of Molecular Medicine, University of Padova , Padova , Italy
| | - Hans Degens
- Department of Physiology and Pharmacology, Basic and Clinical Muscle Biology Group, Karolinska Institutet , Stockholm , Sweden ; Section of Clinical Neurophysiology, Department of Clinical Neuroscience, Karolinska Institutet , Stockholm , Sweden ; Department of Biobehavioral Health, The Pennsylvania State University , University Park, Pennsylvania ; School of Healthcare Science, Metropolitan University , Manchester , United Kingdom ; Institute of Sport Science and Innovations, Lithuanian Sports University , Kaunas , Lithuania ; Clinical Genetics Unit, Department of Woman and Child Health, University of Padova , Padova , Italy ; IRP Città della Speranza, Padova , Italy ; Department of Biology, Texas A&M University , College Station, Texas ; Robert and Arlene Kogod Center on Aging, Mayo Clinic , Rochester, Minnesota ; Department of Biomedical Science, Venetian Institute of Molecular Medicine, University of Padova , Padova , Italy
| | - Meishan Li
- Department of Physiology and Pharmacology, Basic and Clinical Muscle Biology Group, Karolinska Institutet , Stockholm , Sweden ; Section of Clinical Neurophysiology, Department of Clinical Neuroscience, Karolinska Institutet , Stockholm , Sweden ; Department of Biobehavioral Health, The Pennsylvania State University , University Park, Pennsylvania ; School of Healthcare Science, Metropolitan University , Manchester , United Kingdom ; Institute of Sport Science and Innovations, Lithuanian Sports University , Kaunas , Lithuania ; Clinical Genetics Unit, Department of Woman and Child Health, University of Padova , Padova , Italy ; IRP Città della Speranza, Padova , Italy ; Department of Biology, Texas A&M University , College Station, Texas ; Robert and Arlene Kogod Center on Aging, Mayo Clinic , Rochester, Minnesota ; Department of Biomedical Science, Venetian Institute of Molecular Medicine, University of Padova , Padova , Italy
| | - Leonardo Salviati
- Department of Physiology and Pharmacology, Basic and Clinical Muscle Biology Group, Karolinska Institutet , Stockholm , Sweden ; Section of Clinical Neurophysiology, Department of Clinical Neuroscience, Karolinska Institutet , Stockholm , Sweden ; Department of Biobehavioral Health, The Pennsylvania State University , University Park, Pennsylvania ; School of Healthcare Science, Metropolitan University , Manchester , United Kingdom ; Institute of Sport Science and Innovations, Lithuanian Sports University , Kaunas , Lithuania ; Clinical Genetics Unit, Department of Woman and Child Health, University of Padova , Padova , Italy ; IRP Città della Speranza, Padova , Italy ; Department of Biology, Texas A&M University , College Station, Texas ; Robert and Arlene Kogod Center on Aging, Mayo Clinic , Rochester, Minnesota ; Department of Biomedical Science, Venetian Institute of Molecular Medicine, University of Padova , Padova , Italy
| | - Young Il Lee
- Department of Physiology and Pharmacology, Basic and Clinical Muscle Biology Group, Karolinska Institutet , Stockholm , Sweden ; Section of Clinical Neurophysiology, Department of Clinical Neuroscience, Karolinska Institutet , Stockholm , Sweden ; Department of Biobehavioral Health, The Pennsylvania State University , University Park, Pennsylvania ; School of Healthcare Science, Metropolitan University , Manchester , United Kingdom ; Institute of Sport Science and Innovations, Lithuanian Sports University , Kaunas , Lithuania ; Clinical Genetics Unit, Department of Woman and Child Health, University of Padova , Padova , Italy ; IRP Città della Speranza, Padova , Italy ; Department of Biology, Texas A&M University , College Station, Texas ; Robert and Arlene Kogod Center on Aging, Mayo Clinic , Rochester, Minnesota ; Department of Biomedical Science, Venetian Institute of Molecular Medicine, University of Padova , Padova , Italy
| | - Wesley Thompson
- Department of Physiology and Pharmacology, Basic and Clinical Muscle Biology Group, Karolinska Institutet , Stockholm , Sweden ; Section of Clinical Neurophysiology, Department of Clinical Neuroscience, Karolinska Institutet , Stockholm , Sweden ; Department of Biobehavioral Health, The Pennsylvania State University , University Park, Pennsylvania ; School of Healthcare Science, Metropolitan University , Manchester , United Kingdom ; Institute of Sport Science and Innovations, Lithuanian Sports University , Kaunas , Lithuania ; Clinical Genetics Unit, Department of Woman and Child Health, University of Padova , Padova , Italy ; IRP Città della Speranza, Padova , Italy ; Department of Biology, Texas A&M University , College Station, Texas ; Robert and Arlene Kogod Center on Aging, Mayo Clinic , Rochester, Minnesota ; Department of Biomedical Science, Venetian Institute of Molecular Medicine, University of Padova , Padova , Italy
| | - James L Kirkland
- Department of Physiology and Pharmacology, Basic and Clinical Muscle Biology Group, Karolinska Institutet , Stockholm , Sweden ; Section of Clinical Neurophysiology, Department of Clinical Neuroscience, Karolinska Institutet , Stockholm , Sweden ; Department of Biobehavioral Health, The Pennsylvania State University , University Park, Pennsylvania ; School of Healthcare Science, Metropolitan University , Manchester , United Kingdom ; Institute of Sport Science and Innovations, Lithuanian Sports University , Kaunas , Lithuania ; Clinical Genetics Unit, Department of Woman and Child Health, University of Padova , Padova , Italy ; IRP Città della Speranza, Padova , Italy ; Department of Biology, Texas A&M University , College Station, Texas ; Robert and Arlene Kogod Center on Aging, Mayo Clinic , Rochester, Minnesota ; Department of Biomedical Science, Venetian Institute of Molecular Medicine, University of Padova , Padova , Italy
| | - Marco Sandri
- Department of Physiology and Pharmacology, Basic and Clinical Muscle Biology Group, Karolinska Institutet , Stockholm , Sweden ; Section of Clinical Neurophysiology, Department of Clinical Neuroscience, Karolinska Institutet , Stockholm , Sweden ; Department of Biobehavioral Health, The Pennsylvania State University , University Park, Pennsylvania ; School of Healthcare Science, Metropolitan University , Manchester , United Kingdom ; Institute of Sport Science and Innovations, Lithuanian Sports University , Kaunas , Lithuania ; Clinical Genetics Unit, Department of Woman and Child Health, University of Padova , Padova , Italy ; IRP Città della Speranza, Padova , Italy ; Department of Biology, Texas A&M University , College Station, Texas ; Robert and Arlene Kogod Center on Aging, Mayo Clinic , Rochester, Minnesota ; Department of Biomedical Science, Venetian Institute of Molecular Medicine, University of Padova , Padova , Italy
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