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Lam B, Kajderowicz KM, Keys HR, Roessler JM, Frenkel EM, Kirkland A, Bisht P, El-Brolosy MA, Jaenisch R, Bell GW, Weissman JS, Griffith EC, Hrvatin S. Multi-species genome-wide CRISPR screens identify conserved suppressors of cold-induced cell death. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.25.605098. [PMID: 39091747 PMCID: PMC11291167 DOI: 10.1101/2024.07.25.605098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Cells must adapt to environmental changes to maintain homeostasis. One of the most striking environmental adaptations is entry into hibernation during which core body temperature can decrease from 37C to as low at 4C. How mammalian cells, which evolved to optimally function within a narrow range of temperatures, adapt to this profound decrease in temperature remains poorly understood. In this study, we conducted the first genome-scale CRISPR-Cas9 screen in cells derived from Syrian hamster, a facultative hibernator, as well as human cells to investigate the genetic basis of cold tolerance in a hibernator and a non-hibernator in an unbiased manner. Both screens independently revealed glutathione peroxidase 4 (GPX4), a selenium-containing enzyme, and associated proteins as critical for cold tolerance. We utilized genetic and pharmacological approaches to demonstrate that GPX4 is active in the cold and its catalytic activity is required for cold tolerance. Furthermore, we show that the role of GPX4 as a suppressor of cold-induced cell death extends across hibernating species, including 13-lined ground squirrels and greater horseshoe bats, highlighting the evolutionary conservation of this mechanism of cold tolerance. This study identifies GPX4 as a central modulator of mammalian cold tolerance and advances our understanding of the evolved mechanisms by which cells mitigate cold-associated damage - one of the most common challenges faced by cells and organisms in nature.
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Affiliation(s)
- Breanna Lam
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kathrin M. Kajderowicz
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Heather R. Keys
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Julian M. Roessler
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Evgeni M. Frenkel
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Adina Kirkland
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Punam Bisht
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Mohamed A. El-Brolosy
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Harvard Society of Fellows, Cambridge, MA, 02138, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - George W. Bell
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jonathan S. Weissman
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Eric C. Griffith
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Sinisa Hrvatin
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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Galbraith JD, Hayward A. The influence of transposable elements on animal colouration. Trends Genet 2023:S0168-9525(23)00091-4. [PMID: 37183153 DOI: 10.1016/j.tig.2023.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/16/2023]
Abstract
Transposable elements (TEs) are mobile genetic sequences present within host genomes. TEs can contribute to the evolution of host traits, since transposition is mutagenic and TEs often contain host regulatory and protein coding sequences. We review cases where TEs influence animal colouration, reporting major patterns and outstanding questions. TE-induced colouration phenotypes typically arise via introduction of novel regulatory sequences and splice sites, affecting pigment cell development or pigment synthesis. We discuss if particular TE types may be more frequently involved in the evolution of colour variation in animals, given that examples involving long terminal repeat (LTR) elements appear to dominate. Currently, examples of TE-induced colouration phenotypes in animals mainly concern model and domesticated insect and mammal species. However, several influential recent examples, coupled with increases in genome sequencing, suggest cases reported from wild species will increase considerably.
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Affiliation(s)
- James D Galbraith
- Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, UK.
| | - Alexander Hayward
- Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, UK.
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Harris RA, Raveendran M, Lyfoung DT, Sedlazeck FJ, Mahmoud M, Prall TM, Karl JA, Doddapaneni H, Meng Q, Han Y, Muzny D, Wiseman RW, O'Connor DH, Rogers J. Construction of a new chromosome-scale, long-read reference genome assembly for the Syrian hamster, Mesocricetus auratus. Gigascience 2022; 11:6594469. [PMID: 35640223 PMCID: PMC9155146 DOI: 10.1093/gigascience/giac039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/03/2021] [Accepted: 03/29/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The Syrian hamster (Mesocricetus auratus) has been suggested as a useful mammalian model for a variety of diseases and infections, including infection with respiratory viruses such as SARS-CoV-2. The MesAur1.0 genome assembly was generated in 2013 using whole-genome shotgun sequencing with short-read sequence data. Current more advanced sequencing technologies and assembly methods now permit the generation of near-complete genome assemblies with higher quality and greater continuity. FINDINGS Here, we report an improved assembly of the M. auratus genome (BCM_Maur_2.0) using Oxford Nanopore Technologies long-read sequencing to produce a chromosome-scale assembly. The total length of the new assembly is 2.46 Gb, similar to the 2.50-Gb length of a previous assembly of this genome, MesAur1.0. BCM_Maur_2.0 exhibits significantly improved continuity, with a scaffold N50 that is 6.7 times greater than MesAur1.0. Furthermore, 21,616 protein-coding genes and 10,459 noncoding genes are annotated in BCM_Maur_2.0 compared to 20,495 protein-coding genes and 4,168 noncoding genes in MesAur1.0. This new assembly also improves the unresolved regions as measured by nucleotide ambiguities, where ∼17.11% of bases in MesAur1.0 were unresolved compared to BCM_Maur_2.0, in which the number of unresolved bases is reduced to 3.00%. CONCLUSIONS Access to a more complete reference genome with improved accuracy and continuity will facilitate more detailed, comprehensive, and meaningful research results for a wide variety of future studies using Syrian hamsters as models.
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Affiliation(s)
- R Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dustin T Lyfoung
- Wisconsin National Primate Research Center, University of Wisconsin, 1220 Capitol Court, Madison, WI 53711, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Trent M Prall
- Department of Pathology and Laboratory Medicine, University of Wisconsin, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53711, USA
| | - Julie A Karl
- Department of Pathology and Laboratory Medicine, University of Wisconsin, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53711, USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qingchang Meng
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi Han
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Roger W Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin, 1220 Capitol Court, Madison, WI 53711, USA,Department of Pathology and Laboratory Medicine, University of Wisconsin, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53711, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, University of Wisconsin, 1220 Capitol Court, Madison, WI 53711, USA,Department of Pathology and Laboratory Medicine, University of Wisconsin, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53711, USA
| | - Jeffrey Rogers
- Correspondence address. Jeffrey Rogers, Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Tel.: 713-798-7783; E-mail:
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