1
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Li J, Li C, Xu W. Liver cancer-specific mutations in functional domains of ADAR2 lead to the elevation of coding and non-coding RNA editing in multiple tumor-related genes. Mol Genet Genomics 2024; 299:1. [PMID: 38170228 DOI: 10.1007/s00438-023-02091-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/17/2023] [Indexed: 01/05/2024]
Abstract
Mutation is the major cause of phenotypic innovations. Apart from DNA mutations, the alteration on RNA such as the ADAR-mediated A-to-I RNA editing could also shape the phenotype. These two layers of variations have not been systematically combined to study their collective roles in cancers. We collected the high-quality transcriptomes of ten hepatocellular carcinoma (HCC) and the matched control samples. We systematically identified HCC-specific mutations in the exonic regions and profiled the A-to-I RNA editome in each sample. All ten HCC samples had mutations in the CDS of ADAR2 gene (dsRNA-binding domain or catalytic domain). The consequence of these mutations converged to the elevation of ADAR2 efficiency as reflected by the global increase of RNA editing levels in HCC. The up-regulated editing sites (UES) were enriched in the CDS and UTR of oncogenes and tumor suppressor genes (TSG), indicating the possible roles of these target genes in HCC oncogenesis. We present the mutation-ADAR2-UES-oncogene/TSG-HCC axis that explains how mutations at different layers would finally lead to abnormal phenotype. In the light of central dogma, our work provides novel insights into how to fully take advantage of the transcriptome data to decipher the consequence of mutations.
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Affiliation(s)
- Jian Li
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Chaowei Li
- Department of PET/CT, The Second Clinical Medical College of Qingdao University (Qingdao Center Hospital), Qingdao, 266042, China
| | - Wengui Xu
- Department of Molecular Imaging and Nuclear Medicine, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
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2
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Hou Q, Shang L, Chen X, Luo Q, Wei L, Zhang C. Convergent evolution of allele-specific gene expression that leads to non-small cell lung cancer in different human populations. J Appl Genet 2023:10.1007/s13353-023-00813-4. [PMID: 38036772 DOI: 10.1007/s13353-023-00813-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 12/02/2023]
Abstract
Phenotypical innovations during evolution are caused by novel mutations, which are usually heterozygous at the beginning. The gene expressions on two alleles of these mutation sites are not necessarily identical, leading to flexible allele-specific regulation in cell systems. We retrieve the transcriptome data of normal and non-small cell lung cancer (NSCLC) tissues from 47 African Americans (AA) and 50 European Americans (EA). We analyze the differentially expressed genes (DEGs) in NSCLC as well as the tumor-specific mutations. Expression and mutation profiles show convergent evolution in AA and EA populations. The tumor-specific mutations are poorly overlapped, but many of them are located in the same genes, mainly oncogenes and tumor suppressor genes. The DEGs in tumors are majorly caused by the mutated alleles rather than normal alleles. The relative expressions of mutated alleles are highly correlated between AA and EA. The differential expression in NSCLC is predominantly mediated by the mutated alleles on heterozygous sites. This molecular mechanism underlying NSCLC oncogenesis is conserved across different human populations, exhibiting convergent evolution. We present this novel angle that differential expression analysis should be performed separately for different alleles. Our ideas should greatly benefit the cancer community.
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Affiliation(s)
- Qiuyu Hou
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Lifeng Shang
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Xu Chen
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Qiang Luo
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Liang Wei
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China
| | - Chence Zhang
- Department of Thoracic Surgery, Qingdao Eighth People's Hospital, Qingdao, 266100, Shandong, China.
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3
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Wang Y, Li Z, Wang X, Jiang W, Jiang W. SARS-CoV-2 continuously optimizes its codon usage to adapt to human lung environment. J Appl Genet 2023; 64:831-837. [PMID: 37740828 DOI: 10.1007/s13353-023-00790-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 09/25/2023]
Abstract
Viruses need to utilize the resources from host cells to reproduce themselves. RNA translation rate, which is largely determined by codon usage, is the rate-limiting step across the life cycle of viruses. Adapting to the codon usage of hosts would help virus better proliferate. We retrieved the time-course mutation profile of millions of world-wide SARS-CoV-2 sequences. For synonymous mutations, we defined whether a mutation elevate or reduce the relative synonymous codon usage (RSCU). We found that if a synonymous mutation in SARS-CoV-2 increases the RSCU (calculated from human lungs), denoted as delta RSCU > 0, then this mutation is positively selected because the allele frequency (AF) of this mutation increases with time, and vice versa. The results suggest that in SARS-CoV-2, the synonymous mutations that increase codon optimality are beneficial to the virus and are favored by natural selection. For the first time, we used the dynamics of allele frequency to demonstrate that SARS-CoV-2 is continuously optimizing its codon usage to adapt to human lungs. Nevertheless, adaptation to other human tissues cannot be excluded. These results warn us that under this global pandemic, synonymous mutations in SARS-CoV-2 should not be automatically ignored since they indeed change the fitness of the virus.
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Affiliation(s)
- Yinglian Wang
- Institute of Integrated Medicine, Qingdao Medical College, Qingdao University, Qingdao, 266071, Shandong, China
- Changyi People's Hospital, Weifang, 261300, Shandong, China
| | - Zhenhua Li
- Pulmonary and Critical Care Medicine Department 2, Qingdao Municipal Hospital of Traditional Chinese Medicine (Qingdao Hiser Medical Group), Qingdao, 266033, China
- Department of Respiratory Diseases, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao Haici Hospital, Qingdao, 266033, Shandong, China
| | - Xiuxiu Wang
- Department of Respiratory Medicine, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, 266035, Shandong, China
| | - Wen Jiang
- Pulmonary and Critical Care Medicine Department 2, Qingdao Municipal Hospital of Traditional Chinese Medicine (Qingdao Hiser Medical Group), Qingdao, 266033, China
- Department of Respiratory Diseases, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao Haici Hospital, Qingdao, 266033, Shandong, China
| | - Wenqing Jiang
- Pulmonary and Critical Care Medicine Department 2, Qingdao Municipal Hospital of Traditional Chinese Medicine (Qingdao Hiser Medical Group), Qingdao, 266033, China.
- Department of Respiratory Diseases, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao Haici Hospital, Qingdao, 266033, Shandong, China.
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4
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Ge F, Cao X, Jiang Y. A-to-I RNA editing shows dramatic up-regulation in osteosarcoma and broadly regulates tumor-related genes by altering microRNA target regions. J Appl Genet 2023; 64:493-505. [PMID: 37542613 DOI: 10.1007/s13353-023-00777-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/07/2023]
Abstract
A-to-I RNA editing is a prevalent type of RNA modification in animals. The dysregulation of RNA editing has led to multiple human cancers. However, the role of RNA editing has never been studied in osteosarcoma, a complex bone cancer with unknown molecular basis. We retrieved the RNA-sequencing data from 24 primary osteosarcoma patients and 3 healthy controls. We systematically profiled the RNA editomes in these samples and quantitatively identified reliable differential editing sites (DES) between osteosarcoma and normal samples. RNA editing efficiency is dramatically increased in osteosarcoma, presumably due to the significant up-regulation of editing enzymes ADAR1 and ADAR2. Up-regulated DES in osteosarcoma are enriched in 3'UTRs. Strikingly, such 3'UTR sites are further enriched in microRNA binding regions of gene EMP2 and other oncogenes, abolishing the microRNA suppression on target genes. Accordingly, the expression of these tumor-promoting genes is elevated in osteosarcoma. There might be an RNA editing-dependent pathway leading to osteosarcoma. We expanded our knowledge on the potential roles of RNA editing in oncogenesis. Based on these molecular features, our work is valuable for future prognosis and diagnosis of osteosarcoma.
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Affiliation(s)
- Fuqun Ge
- Department of Joint Surgery, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Xinyue Cao
- School of Clinical Medicine, Qilu Medical University, Zibo, 255300, Shandong, China
| | - Yankai Jiang
- Department of Joint Surgery, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China.
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5
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Wei L. Retrospect of the Two-Year Debate: What Fuels the Evolution of SARS-CoV-2: RNA Editing or Replication Error? Curr Microbiol 2023; 80:151. [PMID: 36976379 PMCID: PMC10044072 DOI: 10.1007/s00284-023-03279-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/19/2023] [Indexed: 03/29/2023]
Abstract
Mutation is one of the mechanisms of the evolutionary divergence of an organism. Under this global COVID-19 pandemic, the fast evolution of SARS-CoV-2 became one of the most worrying issues. Some researchers believed that the hosts' RNA deamination systems (APOBECs and ADARs) are the major source of mutations and have driven the evolution of SARS-CoV-2. However, apart from RNA editing, the RDRP (RNA-dependent RNA polymerase)-mediated replication errors may also contribute to the mutation of SARS-CoV-2 (just like the single-nucleotide polymorphisms/variations in eukaryotes caused by DNA replication errors). Unfortunately, it is technically unable to distinguish RNA editing and replication errors (SNPs) in this RNA virus. Here comes a fundamental question: we indeed observed the fast evolution of SARS-CoV-2, but what exactly fuels its evolution: RNA editing or replication errors? This debate lasts for 2 years. In this piece, we will retrospect the 2-year debate on RNA editing versus SNPs.
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Affiliation(s)
- Lai Wei
- College of Life Sciences, Beijing Normal University, Beijing, China.
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6
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Bian Z, Wu Z, Liu N, Jiang X. The efficacy and safety of SARS-CoV-2 vaccines mRNA1273 and BNT162b2 might be complicated by rampant C-to-U RNA editing. J Appl Genet 2023; 64:361-365. [PMID: 36943642 PMCID: PMC10028319 DOI: 10.1007/s13353-023-00756-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/14/2023] [Accepted: 03/12/2023] [Indexed: 03/23/2023]
Abstract
The SARS-CoV-2 RNA vaccines are smartly designed to increase the synonymous codon usage by introducing multiple U-to-C mutations. This design would elevate the translation efficiency of vaccine RNAs. However, we found evidence to reason that the designed cytidines might be converted to uridines again by C-to-U RNA deamination in host cells. This C-to-U mechanism might be a main factor that affects the efficacy and safety of RNA vaccines.
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Affiliation(s)
- Zhongzheng Bian
- Department of Emergency Medicine, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Ziqian Wu
- Department of Emergency Medicine, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Nan Liu
- Department of Emergency Medicine, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China
| | - Xiao Jiang
- Department of Emergency Intensive Care Unit, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, China.
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7
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Evidence Supporting That C-to-U RNA Editing Is the Major Force That Drives SARS-CoV-2 Evolution. J Mol Evol 2023; 91:214-224. [PMID: 36799984 PMCID: PMC9936484 DOI: 10.1007/s00239-023-10097-1] [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: 11/16/2022] [Accepted: 02/03/2023] [Indexed: 02/18/2023]
Abstract
Mutations of DNA organisms are introduced by replication errors. However, SARS-CoV-2, as an RNA virus, is additionally subjected to rampant RNA editing by hosts. Both resources contributed to SARS-CoV-2 mutation and evolution, but the relative prevalence of the two origins is unknown. We performed comparative genomic analyses at intra-species (world-wide SARS-CoV-2 strains) and inter-species (SARS-CoV-2 and RaTG13 divergence) levels. We made prior predictions of the proportion of each mutation type (nucleotide substitution) under different scenarios and compared the observed versus the expected. C-to-T alteration, representing C-to-U editing, is far more abundant that all other mutation types. Derived allele frequency (DAF) as well as novel mutation rate of C-to-T are the highest in SARS-CoV-2 population, and C-T substitution dominates the divergence sites between SARS-CoV-2 and RaTG13. This is compelling evidence suggesting that C-to-U RNA editing is the major source of SARS-CoV-2 mutation. While replication errors serve as a baseline of novel mutation rate, the C-to-U editing has elevated the mutation rate for orders of magnitudes and accelerates the evolution of the virus.
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8
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Li Y, Hou F, Zhou M, Yang X, Yin B, Jiang W, Xu H. C-to-U RNA deamination is the driving force accelerating SARS-CoV-2 evolution. Life Sci Alliance 2023; 6:6/1/e202201688. [PMID: 36347544 PMCID: PMC9644418 DOI: 10.26508/lsa.202201688] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/09/2022] Open
Abstract
Understanding the molecular mechanism underlying the rampant mutation of SARS-CoV-2 would help us control the COVID-19 pandemic. The APOBEC-mediated C-to-U deamination is a major mutation type in the SARS-CoV-2 genome. However, it is unclear whether the novel mutation rate u is higher for C-to-U than for other mutation types, and what the detailed driving force is. By analyzing the time course SARS-CoV-2 global population data, we found that C-to-U has the highest novel mutation rate u among all mutation types and that this u is still increasing with time (du/dt > 0). Novel C-to-U events, rather than other mutation types, have a preference over particular genomic regions. A less local RNA structure is correlated with a high novel C-to-U mutation rate. A cascade model nicely explains the du/dt > 0 for C-to-U deamination. In SARS-CoV-2, the RNA structure serves as the molecular basis of the extremely high and continuously accelerating C-to-U deamination rate. This mechanism is the driving force of the mutation, adaptation, and evolution of SARS-CoV-2. Our findings help us understand the dynamic evolution of the virus mutation rate.
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Affiliation(s)
- Yan Li
- Cardiovasology Department I, Qingdao Center Hospital, Qingdao, China
| | - Fanghua Hou
- Cardiovasology Department I, Qingdao Center Hospital, Qingdao, China
| | - Meili Zhou
- Emergency Department, Qingdao Center Hospital, Qingdao, China
| | - Xiaoping Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Bin Yin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Huiqing Xu
- Department of Pathology, Qingdao Haici Hospital, Qingdao, China
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9
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Hepatitis B virus (HBV) codon adapts well to the gene expression profile of liver cancer: an evolutionary explanation for HBV's oncogenic role. J Microbiol 2022; 60:1106-1112. [PMID: 36251120 PMCID: PMC9574796 DOI: 10.1007/s12275-022-2371-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/02/2022]
Abstract
Due to the evolutionary arms race between hosts and viruses, viruses must adapt to host translation systems to rapidly synthesize viral proteins. Highly expressed genes in hosts have a codon bias related to tRNA abundance, the primary RNA translation rate determinant. We calculated the relative synonymous codon usage (RSCU) of three hepatitis viruses (HAV, HBV, and HCV), SARS-CoV-2, 30 human tissues, and hepatocellular carcinoma (HCC). After comparing RSCU between viruses and human tissues, we calculated the codon adaptation index (CAI) of viral and human genes. HBV and HCV showed the highest correlations with HCC and the normal liver, while SARS-CoV-2 had the strongest association with lungs. In addition, based on HCC RSCU, the CAI of HBV and HCV genes was the highest. HBV and HCV preferentially adapt to the tRNA pool in HCC, facilitating viral RNA translation. After an initial trigger, rapid HBV/HCV translation and replication may change normal liver cells into HCC cells. Our findings reveal a novel perspective on virus-mediated oncogenesis.
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10
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The Sponge Interaction Between Circular RNA and microRNA Serves as a Fast-Evolving Mechanism That Suppresses Non-small Cell Lung Cancer (NSCLC) in Humans. J Mol Evol 2022; 90:362-374. [PMID: 36036266 DOI: 10.1007/s00239-022-10067-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/19/2022] [Indexed: 10/15/2022]
Abstract
Non-small cell lung cancer (NSCLC) is one of the most lethal cancer types in the world. Currently, the molecular mechanisms and pathways underlying NSCLC oncogenesis are poorly understood. Using multiple Omics data, we systematically explored the differentially expressed circular RNAs (circRNAs) in NSCLC. We also investigated potential microRNA sponges (that absorb circRNAs) in NSCLC and downstream target genes with experimental verifications. hsa_circ_0003497 was down-regulated in NSCLC and played an inhibitory role in tumorigenesis. In contrast, miR-197-3p was up-regulated in NSCLC. hsa_circ_0003497 directly interacts with miR-197-3p and releases a target gene of miR-197-3p termed CTNND1 (a known tumor suppressor gene). Evolutionary analysis reveals fast evolution of this hsa_circ_0003497-miR-197-3p-CTNND1-NSCLC axis in mammals. This work clarified the biological functions and molecular mechanisms of how hsa_circ_0003497 suppresses NSCLC through miR-197-3p and CTNND1. We discovered molecular markers for the prognosis of NSCLC and provided potential intervention targets for its treatment.
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11
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Xiao W, Sun Y, Xu J, Zhang N, Dong L. uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response. J Mol Evol 2022; 90:375-388. [PMID: 35962830 PMCID: PMC9375200 DOI: 10.1007/s00239-022-10068-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022]
Abstract
Diseases and environmental stresses are two distinct challenges for virtually all living organisms. In light of evolution, cellular responses to diseases and stresses might share similar molecular mechanisms, but the detailed regulation pathway is not reported yet. We obtained the transcriptomes and translatomes from several NSCLC (non-small-cell lung cancer) patients as well as from different species under normal or stress conditions. We found that the translation level of gene ATF4 is remarkably enhanced in NSCLC due to the reduced number of ribosomes binding to its upstream open reading frames (uORFs). We also showed the evolutionary conservation of this uORF-ATF4 regulation in the stress response of other species. Molecular experiments showed that knockdown of ATF4 reduced the cell growth rate while overexpression of ATF4 enhanced cell growth, especially for the ATF4 allele with mutated uORFs. Population genetics analyses in multiple species verified that the mutations that abolish uATGs (start codon of uORFs) are highly deleterious, suggesting the functional importance of uORFs. Our study proposes an evolutionarily conserved pattern that enhances the ATF4 translation by uORFs upon stress or disease. We generalized the concept of cellular response to diseases and stresses. These two biological processes may share similar molecular mechanisms.
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Affiliation(s)
- Wenjing Xiao
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
| | - Yang Sun
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jinpeng Xu
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Na Zhang
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Lina Dong
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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12
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Zhao M, Li C, Dong Y, Wang X, Jiang W, Chen Y. Nothing in SARS-CoV-2 makes sense except in the light of RNA modification? Future Virol 2022; 0. [PMID: 35873408 PMCID: PMC9302237 DOI: 10.2217/fvl-2022-0043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/04/2022] [Indexed: 01/03/2023]
Abstract
The expression pattern of RNA deaminases determines the mutation and evolution of SARS-CoV-2.
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Affiliation(s)
- Mingmei Zhao
- Department of Neurosurgery, Qingdao Center Hospital, Qingdao, Shandong, 266042, China
| | - Chunxiao Li
- Cardiovasology Department I, Qingdao Center Hospital, Qingdao, Shandong, 266042, China
| | - Yu Dong
- Interventional Catheterization Lab, Qingdao Center Hospital, Qingdao, Shandong, 266042, China
| | - Xuekun Wang
- Cardiovasology Department I, Qingdao Center Hospital, Qingdao, Shandong, 266042, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, 266033, China
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, 266033, China
| | - Yaogang Chen
- Department of Neurosurgery, Qingdao Center Hospital, Qingdao, Shandong, 266042, China
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13
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Cai H, Liu X, Zheng X. RNA editing detection in SARS-CoV-2 transcriptome should be different from traditional SNV identification. J Appl Genet 2022; 63:587-594. [PMID: 35661108 PMCID: PMC9166928 DOI: 10.1007/s13353-022-00706-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/24/2022] [Accepted: 05/31/2022] [Indexed: 10/31/2022]
Affiliation(s)
- Houhao Cai
- Shandong University of Traditional Chinese Medicine, Jinan, 250000, Shandong, China
| | - Xiantao Liu
- Pulmonary and Critical Care Medicine, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250014, Shandong, China
| | - Xin Zheng
- Department of Respiratory and Critical Care Medicine, The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, 266000, Shandong, China.
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14
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Wei L. Reconciling the debate on deamination on viral RNA. J Appl Genet 2022; 63:583-585. [PMID: 35507138 PMCID: PMC9065659 DOI: 10.1007/s13353-022-00698-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/27/2022] [Accepted: 04/29/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Lai Wei
- College of Life Sciences, Beijing Normal University, Beijing, China.
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15
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Poor evidence for host-dependent regular RNA editing in the transcriptome of SARS-CoV-2. J Appl Genet 2022; 63:413-421. [PMID: 35179717 PMCID: PMC8854479 DOI: 10.1007/s13353-022-00687-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/21/2021] [Accepted: 02/13/2022] [Indexed: 12/18/2022]
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16
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An evolutionarily conserved mechanism that amplifies the effect of deleterious mutations in osteosarcoma. Mol Genet Genomics 2022; 297:373-385. [DOI: 10.1007/s00438-021-01852-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 12/29/2021] [Indexed: 10/19/2022]
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17
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Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals. J Mol Evol 2022; 90:139-148. [DOI: 10.1007/s00239-022-10047-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 01/06/2022] [Indexed: 10/19/2022]
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18
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Zhu L, Wang Q, Zhang W, Hu H, Xu K. Evidence for selection on SARS-CoV-2 RNA translation revealed by the evolutionary dynamics of mutations in UTRs and CDSs. RNA Biol 2022; 19:866-876. [PMID: 35762570 PMCID: PMC9584556 DOI: 10.1080/15476286.2022.2092351] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA translation is the rate-limiting step when cells synthesize proteins. Elevating translation efficiency (TE) is intuitively beneficial. Particularly, when viruses invade host cells, how to compete with endogenous RNAs for efficient translation is a major issue to be resolved. We collected millions of worldwide SARS-CoV-2 sequences during the past year and traced the dynamics of allele frequency of every mutation. We defined adaptive and deleterious mutations according to the rise and fall of their frequencies along time. For 5ʹUTR and synonymous mutations in SARS-CoV-2, the selection on TE is evident near start codons. Adaptive mutations generally decrease GC content while deleterious mutations increase GC content. This trend fades away with increasing distance to start codons. Mutations decreasing GC content near start codons would unravel the complex RNA structure and facilitate translation initiation, which are beneficial to SARS-CoV-2, and vice versa. During this evolutionary arms race between human and virus, SARS-CoV-2 tries to improve its cis elements to compete with host RNAs for rapid translation.
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Affiliation(s)
- Lin Zhu
- Department of Urology, Peking University People's Hospital, Xicheng, Beijing, China
| | - Qi Wang
- Department of Urology, Peking University People's Hospital, Xicheng, Beijing, China
| | - Weiyu Zhang
- Department of Urology, Peking University People's Hospital, Xicheng, Beijing, China.,Peking University Applied Lithotripsy Institute, Peking University People's Hospital, Xicheng, Beijing, China
| | - Hao Hu
- Department of Urology, Peking University People's Hospital, Xicheng, Beijing, China
| | - Kexin Xu
- Department of Urology, Peking University People's Hospital, Xicheng, Beijing, China
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19
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Inverted repeats in coronavirus SARS-CoV-2 genome manifest the evolution events. J Theor Biol 2021; 530:110885. [PMID: 34478743 PMCID: PMC8406619 DOI: 10.1016/j.jtbi.2021.110885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/13/2021] [Accepted: 08/25/2021] [Indexed: 11/24/2022]
Abstract
The world faces a great unforeseen challenge through the COVID-19 pandemic caused by coronavirus SARS-CoV-2. The virus genome structure and evolution are positioned front and center for further understanding insights on vaccine development, monitoring of transmission trajectories, and prevention of zoonotic infections of new coronaviruses. Of particular interest are genomic elements Inverse Repeats (IRs), which maintain genome stability, regulate gene expressions, and are the targets of mutations. However, little research attention is given to the IR content analysis in the SARS-CoV-2 genome. In this study, we propose a geometric analysis method and using the method to investigate the distributions of IRs in SARS-CoV-2 and its related coronavirus genomes. The method represents each genomic IR sequence pair as a single point and constructs the geometric shape of the genome using the IRs. Thus, the IR shape can be considered as the signature of the genome. The genomes of different coronaviruses are then compared using the constructed IR shapes. The results demonstrate that SARS-CoV-2 genome, specifically, has an abundance of IRs, and the IRs in coronavirus genomes show an increase during evolution events.
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20
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Zhang Y, Jiang W, Li Y, Jin X, Yang X, Zhang P, Jiang W, Yin B. Fast evolution of SARS-CoV-2 driven by deamination systems in hosts. Future Virol 2021; 16:587-590. [PMID: 34721652 DOI: 10.2217/fvl-2021-0181] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/25/2021] [Indexed: 11/21/2022]
Abstract
As an RNA virus, the fast evolution of SARS-CoV-2 is driven by the extensive RNA deamination by the host cells.
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Affiliation(s)
- Yanping Zhang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Shandong, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Wen Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Shandong, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yan Li
- Department of Cardiology, Qingdao Center Hospital, Shandong, China
| | - Xiaojie Jin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Shandong, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiaoping Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Shandong, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Pirun Zhang
- College of Basic Medicine, Shandong University of Traditional Chinese Medicine, Shandong, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Shandong, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Bin Yin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Shandong, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
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21
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Li J, Yu CP, Li Q, Chang S, Xie LL, Wang S. Large-scale omics data reveal the cooperation of mutation-circRNA-miRNA-target gene network in liver cancer oncogenesis. Future Oncol 2021; 18:163-178. [PMID: 34677082 DOI: 10.2217/fon-2021-0940] [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] [Indexed: 12/14/2022] Open
Abstract
Aims: Clarifying the initial trigger of the differentially expressed genes in cancers helps researchers understand the cellular system as a whole network. Materials & methods: We retrieve the transcriptome and translatome of tumor and normal tissues from ten liver cancer patients and define differentially expressed genes and tumor-specific mutations. We associate the oncogenesis with the mutations by target prediction and experimental verification. Results: Upregulated genes have tumor-specific mutations in 3'UTRs that abolish the binding of miRNAs. For downregulated genes, their corresponding miRNAs are mutually targeted by two circRNAs, with mutations in base-pairing regions. Transfection experiments support the oncogenic role of these mutations. Conclusions: The tumor-specific mutations serve as the initial trigger of liver cancer. The mutation-circRNA-miRNA-target gene chain is completed.
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Affiliation(s)
- Jian Li
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Chun-Peng Yu
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Qun Li
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Shuai Chang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Ling-Ling Xie
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
| | - Song Wang
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, 266011, China
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22
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Zhang Y, Jin X, Wang H, Miao Y, Yang X, Jiang W, Yin B. SARS-CoV-2 competes with host mRNAs for efficient translation by maintaining the mutations favorable for translation initiation. J Appl Genet 2021; 63:159-167. [PMID: 34655422 PMCID: PMC8520108 DOI: 10.1007/s13353-021-00665-w] [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: 08/10/2021] [Revised: 09/24/2021] [Accepted: 10/03/2021] [Indexed: 11/05/2022]
Abstract
During SARS-CoV-2 proliferation, the translation of viral RNAs is usually the rate-limiting step. Understanding the molecular details of this step is beneficial for uncovering the origin and evolution of SARS-CoV-2 and even for controlling the pandemic. To date, it is unclear how SARS-CoV-2 competes with host mRNAs for ribosome binding and efficient translation. We retrieved the coding sequences of all human genes and SARS-CoV-2 genes. We systematically profiled the GC content and folding energy of each CDS. Considering that some fixed or polymorphic mutations exist in SARS-CoV-2 and human genomes, all algorithms and analyses were applied to both pre-mutate and post-mutate versions. In SARS-CoV-2 but not human, the 5-prime end of CDS had lower GC content and less RNA structure than the 3-prime part, which was favorable for ribosome binding and efficient translation initiation. Globally, the fixed and polymorphic mutations in SARS-CoV-2 had created an even lower GC content at the 5-prime end of CDS. In contrast, no similar patterns were observed for the fixed and polymorphic mutations in human genome. Compared with human RNAs, the SARS-CoV-2 RNAs have less RNA structure in the 5-prime end and thus are more favorable of fast translation initiation. The fixed and polymorphic mutations in SARS-CoV-2 are further amplifying this advantage. This might serve as a strategy for SARS-CoV-2 to adapt to the human host.
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Affiliation(s)
- Yanping Zhang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Xiaojie Jin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Haiyan Wang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Yaoyao Miao
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Xiaoping Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China
| | - Bin Yin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China. .,The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, China.
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23
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Zhang Y, Jin X, Wang H, Miao Y, Yang X, Jiang W, Yin B. Compelling Evidence Suggesting the Codon Usage of SARS-CoV-2 Adapts to Human After the Split From RaTG13. Evol Bioinform Online 2021; 17:11769343211052013. [PMID: 34646060 PMCID: PMC8504689 DOI: 10.1177/11769343211052013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 09/17/2021] [Indexed: 11/17/2022] Open
Abstract
SARS-CoV-2 needs to efficiently make use of the resources from hosts in order to survive and propagate. Among the multiple layers of regulatory network, mRNA translation is the rate-limiting step in gene expression. Synonymous codon usage usually conforms with tRNA concentration to allow fast decoding during translation. It is acknowledged that SARS-CoV-2 has adapted to the codon usage of human lungs so that the virus could rapidly proliferate in the lung environment. While this notion seems to nicely explain the adaptation of SARS-CoV-2 to lungs, it is unable to tell why other viruses do not have this advantage. In this study, we retrieve the GTEx RNA-seq data for 30 tissues (belonging to over 17 000 individuals). We calculate the RSCU (relative synonymous codon usage) weighted by gene expression in each human sample, and investigate the correlation of RSCU between the human tissues and SARS-CoV-2 or RaTG13 (the closest coronavirus to SARS-CoV-2). Lung has the highest correlation of RSCU to SARS-CoV-2 among all tissues, suggesting that the lung environment is generally suitable for SARS-CoV-2. Interestingly, for most tissues, SARS-CoV-2 has higher correlations with the human samples compared with the RaTG13-human correlation. This difference is most significant for lungs. In conclusion, the codon usage of SARS-CoV-2 has adapted to human lungs to allow fast decoding and translation. This adaptation probably took place after SARS-CoV-2 split from RaTG13 because RaTG13 is less perfectly correlated with human. This finding depicts the trajectory of adaptive evolution from ancestral sequence to SARS-CoV-2, and also well explains why SARS-CoV-2 rather than other viruses could perfectly adapt to human lung environment.
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Affiliation(s)
- Yanping Zhang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiaojie Jin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Haiyan Wang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yaoyao Miao
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiaoping Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
| | - Bin Yin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
- The Affiliated Qingdao Hiser Hospital of Qingdao University, Qingdao, Shandong, China
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24
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Jiang Y, Cao X, Wang H. Comparative genomic analysis of a naturally born serpentized pig reveals putative mutations related to limb and bone development. BMC Genomics 2021; 22:629. [PMID: 34454433 PMCID: PMC8399796 DOI: 10.1186/s12864-021-07925-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 08/08/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND It is believed that natural selection acts on the phenotypical changes caused by mutations. Phenotypically, from fishes to amphibians to reptiles, the emergence of limbs greatly facilitates the landing of ancient vertebrates, but the causal mutations and evolutionary trajectory of this process remain unclear. RESULTS We serendipitously obtained a pig of limbless phenotype. Mutations specific to this handicapped pig were identified using genome re-sequencing and comparative genomic analysis. We narrowed down the causal mutations to particular chromosomes and even several candidate genes and sites, such like a mutation-containing codon in gene BMP7 (bone morphogenetic protein) which was conserved in mammals but variable in lower vertebrates. CONCLUSIONS We parsed the limbless-related mutations in the light of evolution. The limbless pig shows phenocopy of the clades before legs were evolved. Our findings might help deduce the emergence of limbs during vertebrate evolution and should be appealing to the broad community of human genetics and evolutionary biology.
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Affiliation(s)
- Yankai Jiang
- Department of Joint Surgery, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Xinyue Cao
- School of Medicine and Nursing, Dezhou University, Dezhou, 253023, Shandong, China
| | - Haibin Wang
- Department of Joint Surgery, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China.
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25
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Mutation profiling of a limbless pig reveals genome-wide regulation of RNA processing related to bone development. J Appl Genet 2021; 62:643-653. [PMID: 34278546 DOI: 10.1007/s13353-021-00653-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 10/20/2022]
Abstract
Mutation is the basis of phenotypic changes and serves as the source of natural selection. The development of limbs has been the milestone in vertebrate evolution. Several limb and bone-related genes were verified experimentally, but other indirect and regulatory factors of limb development remained untested, especially very few cases were observed in natural environment. We report a naturally born serpentized pig without hindlimbs. Whole genome sequencing followed by comparative genomic analysis revealed multiple interesting patterns on the handicapped pig-specific mutations. Although the bone-related genes are not directly subjected to mutations, other regulatory factors such as the RNA deaminase genes Adar are damaged in the handicapped pig, leading to the abolished A-to-I deamination in many functional, conserved genes as well as the bone-related genes. This is a precious case that the limbless phenotype is observed in naturally born non-model organisms. Our study broadened the generality of the limbless phenotype across mammals and extended the regulation of hindlimb development to other non-bone-related genes. Our knowledge of limb and bone-related mutations and regulation would also contribute to human genetics.
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26
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Yu Y, Li Y, Dong Y, Wang X, Li C, Jiang W. Natural selection on synonymous mutations in SARS-CoV-2 and the impact on estimating divergence time. Future Virol 2021. [PMCID: PMC8132620 DOI: 10.2217/fvl-2021-0078] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To adapt to human host environment, synonymous mutations in SARS-CoV-2 are shaped by tRNA selection, energy cost and RNA structure.
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Affiliation(s)
- Yuanyuan Yu
- Department of Anesthesiology, Qingdao Haici Hospital, Qingdao, Shandong, China
| | - Yan Li
- Department of Cardiology, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Yu Dong
- Department of Intervention, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Xuekun Wang
- Department of Cardiology, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Chunxiao Li
- Department of Cardiology, Qingdao Center Hospital, Qingdao, Shandong, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, Shandong, China
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27
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Mohammed MEA. The percentages of SARS-CoV-2 protein similarity and identity with SARS-CoV and BatCoV RaTG13 proteins can be used as indicators of virus origin. ACTA ACUST UNITED AC 2021; 12:81-91. [PMID: 33850392 PMCID: PMC8033097 DOI: 10.1007/s42485-021-00060-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/08/2021] [Accepted: 03/22/2021] [Indexed: 02/08/2023]
Abstract
There are three types of proteins in coronaviruses: nonstructural, structural, and accessory proteins. Coronavirus proteins are essential for viral replication and for the binding and invasion of hosts and the regulation of host cell metabolism and immunity. This study investigated the amino acid sequence similarity and identity percentages of 10 proteins in SARS-CoV-2, SARS-CoV and the Rhinolophus affinis bat coronavirus (BatCoV RaTG13). The investigated proteins were the 1ab polyprotein, spike protein, orf3a, the envelope protein, the membrane protein, orf6, orf7a, orf7b, orf8, and the nucleocapsid protein. The online sequence alignment service of The European Molecular Biology Open Software Suite (EMBOSS) was used to determine the percentages of protein similarity and identity in the three viruses. The results showed that the similarity and identity percentages of the SARS-CoV-2 and BatCoV RaTG13 proteins were both greater than 95%, while the identity and similarity percentages of SARS-CoV-2 and SARS-CoV were both greater than 38%. The proteins of SARS-CoV-2 and BatCoV RaTG13 have high identity and similarity compared to those of SARS-CoV-2 and SARS-CoV.
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Affiliation(s)
- Mohammed Elimam Ahamed Mohammed
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia.,Unit of Bee Research and Honey Production, Faculty of Science, King Khalid University, Abha, Saudi Arabia
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28
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Li Q, Li J, Yu CP, Chang S, Xie LL, Wang S. Synonymous mutations that regulate translation speed might play a non-negligible role in liver cancer development. BMC Cancer 2021; 21:388. [PMID: 33836673 PMCID: PMC8033552 DOI: 10.1186/s12885-021-08131-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/30/2021] [Indexed: 01/11/2023] Open
Abstract
Background Synonymous mutations do not change the protein sequences. Automatically, they have been regarded as neutral events and are ignored in the mutation-based cancer studies. However, synonymous mutations will change the codon optimality, resulting in altered translational velocity. Methods We fully utilized the transcriptome and translatome of liver cancer and normal tissue from ten patients. We profiled the mutation spectrum and examined the effect of synonymous mutations on translational velocity. Results Synonymous mutations that increase the codon optimality significantly enhanced the translational velocity, and were enriched in oncogenes. Meanwhile, synonymous mutations decreasing codon optimality slowed down translation, and were enriched in tumor suppressor genes. These synonymous mutations significantly contributed to the translational changes in tumor samples compared to normal samples. Conclusions Synonymous mutations might play a role in liver cancer development by altering codon optimality and translational velocity. Synonymous mutations should no longer be ignored in the genome-wide studies.
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Affiliation(s)
- Qun Li
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jian Li
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chun-Peng Yu
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Shuai Chang
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ling-Ling Xie
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Song Wang
- Department of interventional radiology, The Affiliated Hospital of Qingdao University, Qingdao, China.
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29
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Sengupta A, Hassan SS, Choudhury PP. Clade GR and clade GH isolates of SARS-CoV-2 in Asia show highest amount of SNPs. INFECTION GENETICS AND EVOLUTION 2021; 89:104724. [PMID: 33476804 PMCID: PMC7816605 DOI: 10.1016/j.meegid.2021.104724] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 02/06/2023]
Abstract
Clades are monophyletic groups composed of a common ancestor and all its lineal descendants. As the propensity of virulence of a disease depends upon the type of clade the virus belongs to and it causes different fatality rates of disease in different countries, so the clade-wise analysis of SARS-CoV-2 isolates collected from different countries can illuminate the actual evolutionary relationships between them. In this study, 1566 SARS-CoV-2 genome sequences across ten Asian countries are collected, clustered, and characterized based on the clade they belong to. The isolates are compared to the Wuhan reference sequence” hCoV-19/Wuhan/WIV04/19″ to identify the mutations that occurred at different protein regions. Structural changes in amino acids due to mutations lead to functional instability of the proteins. Detailed clade-wise functional assessments are carried out to quantify the stability and vulnerability of the mutations occurring in SARS-CoV-2 genomes which can shade light on personalized prevention and treatment of the disease and encourage towards the invention of clade-specific vaccines.
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Affiliation(s)
- Antara Sengupta
- Department of Computer Science and Engineering, University of Calcutta, West Bengal, India.
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, West Bengal, India
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30
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Henry A. Welcome to the 16th volume of Future Virology. Future Virol 2021. [DOI: 10.2217/fvl-2020-0408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Atiya Henry
- Commissioning Department, Future Science Group, Unitec House, 2 Albert Place, Finchley, London N3 1QB, UK
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31
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Ahmed F, Sharma M, Al-Ghamdi AA, Al-Yami SM, Al-Salami AM, Refai MY, Warsi MK, Howladar SM, Baeshen MN. A Comprehensive Analysis of cis-Acting RNA Elements in the SARS-CoV-2 Genome by a Bioinformatics Approach. Front Genet 2020; 11:572702. [PMID: 33424918 PMCID: PMC7786107 DOI: 10.3389/fgene.2020.572702] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/14/2020] [Indexed: 01/08/2023] Open
Abstract
The emergence of a new coronavirus (CoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for severe respiratory disease in humans termed coronavirus disease of 2019 (COVID-19), became a new global threat for health and the economy. The SARS-CoV-2 genome is about a 29,800-nucleotide-long plus-strand RNA that can form functionally important secondary and higher-order structures called cis-acting RNA elements. These elements can interact with viral proteins, host proteins, or other RNAs and be involved in regulating translation and replication processes of the viral genome and encapsidation of the virus. However, the cis-acting RNA elements and their biological roles in SARS-CoV-2 as well as their comparative analysis in the closely related viral genome have not been well explored, which is very important to understand the molecular mechanism of viral infection and pathogenies. In this study, we used a bioinformatics approach to identify the cis-acting RNA elements in the SARS-CoV-2 genome. Initially, we aligned the full genomic sequence of six different CoVs, and a phylogenetic analysis was performed to understand their evolutionary relationship. Next, we predicted the cis-acting RNA elements in the SARS-CoV-2 genome using the structRNAfinder tool. Then, we annotated the location of these cis-acting RNA elements in different genomic regions of SARS-CoV-2. After that, we analyzed the sequence conservation patterns of each cis-acting RNA element among the six CoVs. Finally, the presence of cis-acting RNA elements across different CoV genomes and their comparative analysis was performed. Our study identified 12 important cis-acting RNA elements in the SARS-CoV-2 genome; among them, Corona_FSE, Corona_pk3, and s2m are highly conserved across most of the studied CoVs, and Thr_leader, MAT2A_D, and MS2 are uniquely present in SARS-CoV-2. These RNA structure elements can be involved in viral translation, replication, and encapsidation and, therefore, can be potential targets for better treatment of COVID-19. It is imperative to further characterize these cis-acting RNA elements experimentally for a better mechanistic understanding of SARS-CoV-2 infection and therapeutic intervention.
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Affiliation(s)
- Firoz Ahmed
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
- University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | | | | | | | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
- University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohiuddin Khan Warsi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
- University of Jeddah Center for Scientific and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
| | - Saad M. Howladar
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Mohammed N. Baeshen
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
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32
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Rahman MS, Hoque MN, Islam MR, Islam I, Mishu ID, Rahaman MM, Sultana M, Hossain MA. Mutational insights into the envelope protein of SARS-CoV-2. GENE REPORTS 2020; 22:100997. [PMID: 33319124 PMCID: PMC7723457 DOI: 10.1016/j.genrep.2020.100997] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/23/2020] [Accepted: 12/02/2020] [Indexed: 01/03/2023]
Abstract
The ongoing mutations in the structural proteins of SARS-CoV-2 are the major impediment for prevention and control of the COVID-19 disease. Presently we focused on evolution of the envelope (E) protein, one of the most enigmatic and less studied protein among the four structural proteins (S, E, M and N) associated with multitude of immunopathological functions of SARS-CoV-2. In the present study, we comprehensively analyzed 81,818 high quality E protein sequences of SARS-CoV-2 globally available in the GISAID database as of 20 August 2020. Compared to Wuhan reference strain, our mutational analysis explored only 1.2 % (982/81818) mutant strains undergoing a total of 115 unique amino acid (aa) substitutions in the E protein, highlighting the fact that most (98.8 %) of the E protein of SARS-CoV-2 strains are highly conserved. Moreover, we found 58.77 % (134 of 228) nucleotides (nt) positions of SARS-CoV-2 E gene encountering a total of 176 unique nt-level mutations globally, which may affect the efficacy of real time RT-PCR-based molecular detection of COVID-19. Importantly, higher aa variations observed in the C-terminal domain (CTD) of the E protein, particularly at Ser55-Phe56, Arg69 and the C-terminal end (DLLV: 72–75) may alter the binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 and thus could play a key role in COVID-19 pathogenesis. Furthermore, this study revealed the V25A mutation in the transmembrane domain which is a key factor for the homopentameric conformation of E protein. Our analysis also observed a triple cysteine motif harboring mutation (L39M, A41S, A41V, C43F, C43R, C43S, C44Y, N45R) which may hinder the binding of E protein with spike glycoprotein. These results therefore suggest the continuous monitoring of the structural proteins including the envelope protein of SARS-CoV-2 since the number of genome sequences from across the world are continuously increasing.
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Key Words
- CTD, C-terminal domain
- E, envelope
- Envelope protein
- M, membrane
- Mutations
- N, nucleocapsid
- NC, negatively charged
- NP, non-polar
- PC, positively charged
- S, spike
- SARS-CoV-2
- SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus-2
- TMD, transmembrane domain
- Transmembrane domain
- Triple cysteine motif
- aa, amino acid
- nt, nucleotide
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Affiliation(s)
- M Shaminur Rahman
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - M Nazmul Hoque
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - M Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | | | | | - Munawar Sultana
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - M Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
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Berrio A, Gartner V, Wray GA. Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function. PeerJ 2020; 8:e10234. [PMID: 33088633 PMCID: PMC7571416 DOI: 10.7717/peerj.10234] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/04/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. METHODS Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. RESULTS We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein structure relative to the most recent common ancestor. These SARS-CoV-2-specific mutations may affect molecular processes mediated by the positive or negative RNA molecules, including transcription, translation, RNA stability, and evasion of the host innate immune system. Our results highlight the importance of considering mutations in viral genomes not only from the perspective of their impact on protein structure, but also how they may impact other molecular processes critical to the viral life cycle.
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Affiliation(s)
| | - Valerie Gartner
- Department of Biology, Duke University, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Gregory A. Wray
- Department of Biology, Duke University, Durham, NC, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
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Li Y, Yang X, Wang N, Wang H, Yin B, Yang X, Jiang W. GC usage of SARS-CoV-2 genes might adapt to the environment of human lung expressed genes. Mol Genet Genomics 2020; 295:1537-1546. [PMID: 32888056 PMCID: PMC7473593 DOI: 10.1007/s00438-020-01719-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/20/2020] [Indexed: 12/13/2022]
Abstract
Understanding how SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) efficiently reproduces itself by taking resources from the human host could facilitate the development of drugs against the virus. SARS-CoV-2 translates its own proteins by using the host tRNAs, so that its GC or codon usage should fit that of the host cells. It is necessary to study both the virus and human genomes in the light of evolution and adaptation. The SARS-CoV-2 virus has significantly lower GC content and GC3 as compared to human. However, when we selected a set of human genes that have similar GC properties to SARS-CoV-2, we found that these genes were enriched in particular pathways. Moreover, these human genes have the codon composition perfectly correlated with the SARS-CoV-2, and were extraordinarily highly expressed in human lung tissues, demonstrating that the SARS-CoV-2 genes have similar GC usage as compared to the lung expressed human genes. RSCU (relative synonymous codon usage) and CAI (codon adaptation index) profiles further support the matching between SARS-CoV-2 and lungs. Our study indicates that SARS-CoV-2 might have adapted to the human lung environment by observing the high correlation between GC usage of SARS-CoV-2 and human lung genes, which suggests the GC content of SARS-CoV-2 is optimized to take advantage of human lung tissues.
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Affiliation(s)
- Yue Li
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Xinai Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Na Wang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Haiyan Wang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Bin Yin
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Xiaoping Yang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China
| | - Wenqing Jiang
- Department of Respiratory Diseases, Qingdao Haici Hospital, Qingdao, China.
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Affiliation(s)
- Stefano Rusconi
- Associate Professor in Infectious Diseases, DIBIC Luigi Sacco, University of Milan, Milano 20157, Italy
| | - Frederick G Hayden
- Stuart S. Richardson Professor Emeritus of Clinical Virology & Professor Emeritus of Medicine, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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