1
|
Bae YA. In silico identification and structural characterization of telomerase reverse transcriptases in parasitic platyhelminths. Gene 2025; 962:149558. [PMID: 40360013 DOI: 10.1016/j.gene.2025.149558] [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: 03/21/2025] [Revised: 04/28/2025] [Accepted: 05/08/2025] [Indexed: 05/15/2025]
Abstract
Telomere shortening during eukaryotic cell division can lead to severe problems such as inactivation of neighboring genes and aberrant chromosomal fusion. To protect chromosome ends from the replicative errors, most eukaryotes have evolved an enzymatic defense mechanism called telomerase, in which telomerase reverse transcriptase (TERT) plays a central role. This enzymatic activity is highly elevated in consecutively dividing somatic cells of regenerating and probably asexually reproducing, platyhelminths. Therefore, flatworms can be powerful models to investigate the biological implications of TERT in these non-embryonic developments. Current information on the protein is largely limited to a handful of representative species within the phylum Platyhelminthes. This study characterizes the structural features of TERT proteins and their encoding genes in flatworms, aiming to expand our knowledge of the telomere-protecting protein in this lower animal taxon. The platyhelminth genes exhibited exon-intron architectures that were highly divergent from their orthologs in the other lophotrochozoans, and their protein products lacked some TERT-specific domains such as the telomerase essential N-terminal and repeat addition processivity domains. Nevertheless, the unique gene and protein structures were tightly conserved among the flatworm homologs. Analysis of the tert transcripts showed that use of alternative splice acceptors or donors in a minor AT-AC intron, as well as intron retention and exon exclusion, contribute to the generation of aberrant mRNAs. The present findings demonstrate that the tert gene has undergone structural changes soon after the emergence of the platyhelminth lineage, which might have been coordinated with those of its functional counterpart, the telomerase RNA molecule.
Collapse
Affiliation(s)
- Young-An Bae
- Department of Microbiology and Lee Gil Ya Cancer and Diabetes Institute, Gachon University College of Medicine, Incheon 21999, Korea.
| |
Collapse
|
2
|
Kemal RA, O’Keefe RT. Addressing the tissue specificity of U5 snRNP spliceosomopathies. Front Cell Dev Biol 2025; 13:1572188. [PMID: 40264708 PMCID: PMC12011746 DOI: 10.3389/fcell.2025.1572188] [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: 02/06/2025] [Accepted: 03/20/2025] [Indexed: 04/24/2025] Open
Abstract
Precursor mRNA (pre-mRNA) must undergo splicing to remove intron sequences and join exons. This splicing process is catalysed by an RNA/protein complex called the spliceosome. At the centre of the catalytic spliceosome is the U5 small nuclear ribonucleoprotein (snRNP). Pathogenic variants in U5 snRNP core proteins are associated with various diseases commonly known as spliceosomopathies. Variants in TXNL4A and EFTUD2 manifest in craniofacial malformations while variants in PRPF8 and SNRNP200 manifest in retinitis pigmentosa. This perspective highlights research addressing how these specific manifestations come about as the spliceosome is required in all cells and at all developmental stages. Cell and animal models can replicate the human clinical specificity providing explanations for the specificity of the disorders. We propose that future research could benefit from models originating from patient-derived induced pluripotent stem cells (iPSCs) and isogenic controls to compare the coding and non-coding transcriptomic perturbations. Analysis of spliceosomal protein complexes and their interactome could also uncover novel insights on molecular pathogenesis. Finally, as studies highlight changes in metabolic processes, metabolomic studies could become a new venture in studying the consequences of U5 snRNP variants.
Collapse
Affiliation(s)
- Rahmat Azhari Kemal
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine, and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
- Department of Medical Biology, Faculty of Medicine, Universitas Riau, Pekanbaru, Indonesia
| | - Raymond T. O’Keefe
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine, and Health, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| |
Collapse
|
3
|
Wang J, Ruan GX, Li Y, Xiao X, Zhu Z, Chen W, Huang H, Zhang R, Wang R, Chen M, Guo L, Li Y, Xu S, Ou X. Minor Splicing Factor RNPC3 Is Essential for the Germinal Center B Cell Response. Eur J Immunol 2025; 55:e202451508. [PMID: 40170400 DOI: 10.1002/eji.202451508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2024] [Revised: 03/07/2025] [Accepted: 03/18/2025] [Indexed: 04/03/2025]
Abstract
Germinal center (GC) response ensures the generation of diverse and high-affinity antibodies during the T cell-dependent (TD) immune response. This process is controlled by coordinated transcriptional and posttranscriptional gene regulatory mechanisms. Minor intron splicing is known to be involved in posttranscriptional regulation of gene expression. RNA-binding region (RNP1, RRM) containing 3 (RNPC3) is a minor spliceosome component involved in stabilizing the U11/U12 di-snRNP complex, which is essential for minor intron splicing. However, it remains unclear if RNPC3 and RNPC3-related gene regulatory mechanisms are important for the TD immune response. In this study, we conditionally ablated RNPC3 in activated B cells and showed that the mutant mice had defective antibody generation due to impaired GC B cell response. We demonstrate that RNPC3 deficiency inhibits the proliferation and promotes the apoptosis of activated B cells. Mechanistically, we show that RNPC3 regulates the development of GC B cells in a minor spliceosome-dependent manner by controlling the removal of minor introns from minor intron-containing genes associated with cell proliferation and apoptosis. Our study thus uncovers a previously unappreciated role for RNPC3 in regulating GC B cell response.
Collapse
Affiliation(s)
- Jing Wang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Gui-Xin Ruan
- Department of Basic Medicine, School of Medicine, Taizhou University, Taizhou, China
| | - Yuxing Li
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, China
| | - Xiong Xiao
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Zhijian Zhu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenjing Chen
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hengjun Huang
- Jiangxi Province Key Laboratory of Traditional Chinese Medicine Pharmacology, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical Sciences, Nanchang, China
- Jiangxi Health Industry Institute of Traditional Chinese Medicine, Nanchang, China
| | - Rui Zhang
- School of Medicine, Chengdu Women's and Children's Central Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruisi Wang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Meiyuan Chen
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ling Guo
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yan Li
- Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Shengli Xu
- Singapore Immunology Network (SIgN), Agency for Science, Technology, and Research (A*STAR), Singapore, Republic of Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Xijun Ou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| |
Collapse
|
4
|
Norppa AJ, Shcherbii MV, Frilander MJ. Connecting genotype and phenotype in minor spliceosome diseases. RNA (NEW YORK, N.Y.) 2025; 31:284-299. [PMID: 39761998 PMCID: PMC11874965 DOI: 10.1261/rna.080337.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Minor spliceosome is responsible for recognizing and excising a specific subset of divergent introns during the pre-mRNA splicing process. Mutations in the unique snRNA and protein components of the minor spliceosome are increasingly being associated with a variety of germline and somatic human disorders, collectively termed as minor spliceosomopathies. Understanding the mechanistic basis of these diseases has been challenging due to limited functional information on many minor spliceosome components. However, recently published cryo-electron microscopy (cryo-EM) structures of various minor spliceosome assembly intermediates have marked a significant advancement in elucidating the roles of these components during splicing. These structural breakthroughs have not only enhanced our comprehension of the minor spliceosome's functionality but also shed light on how disease-associated mutations disrupt its functions. Consequently, research focus is now shifting toward investigating how these splicing defects translate into broader pathological processes within gene expression pathways. Here we outline the current structural and functional knowledge of the minor spliceosome, explore the mechanistic consequences of its mutations, and discuss emerging challenges in connecting molecular dysfunctions to clinical phenotypes.
Collapse
Affiliation(s)
- Antto J Norppa
- Institute of Biotechnology, 000014 University of Helsinki, Finland
| | | | | |
Collapse
|
5
|
Kostygov AY, Skýpalová K, Kraeva N, Kalita E, McLeod C, Yurchenko V, Field MC, Lukeš J, Butenko A. Comprehensive analysis of the Kinetoplastea intron landscape reveals a novel intron-containing gene and the first exclusively trans-splicing eukaryote. BMC Biol 2024; 22:281. [PMID: 39627879 PMCID: PMC11613528 DOI: 10.1186/s12915-024-02080-z] [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: 09/14/2024] [Accepted: 11/26/2024] [Indexed: 12/08/2024] Open
Abstract
BACKGROUND In trypanosomatids, a group of unicellular eukaryotes that includes numerous important human parasites, cis-splicing has been previously reported for only two genes: a poly(A) polymerase and an RNA helicase. Conversely, trans-splicing, which involves the attachment of a spliced leader sequence, is observed for nearly every protein-coding transcript. So far, our understanding of splicing in this protistan group has stemmed from the analysis of only a few medically relevant species. In this study, we used an extensive dataset encompassing all described trypanosomatid genera to investigate the distribution of intron-containing genes and the evolution of splice sites. RESULTS We identified a new conserved intron-containing gene encoding an RNA-binding protein that is universally present in Kinetoplastea. We show that Perkinsela sp., a kinetoplastid endosymbiont of Amoebozoa, represents the first eukaryote completely devoid of cis-splicing, yet still preserving trans-splicing. We also provided evidence for reverse transcriptase-mediated intron loss in Kinetoplastea, extensive conservation of 5' splice sites, and the presence of non-coding RNAs within a subset of retained trypanosomatid introns. CONCLUSIONS All three intron-containing genes identified in Kinetoplastea encode RNA-interacting proteins, with a potential to fine-tune the expression of multiple genes, thus challenging the perception of cis-splicing in these protists as a mere evolutionary relic. We suggest that there is a selective pressure to retain cis-splicing in trypanosomatids and that this is likely associated with overall control of mRNA processing. Our study provides new insights into the evolution of introns and, consequently, the regulation of gene expression in eukaryotes.
Collapse
Affiliation(s)
- Alexei Yu Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
- Zoological Institute of the Russian Academy of Sciences, St. Petersburg, 199034, Russia
| | - Karolína Skýpalová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Natalia Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Elora Kalita
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Cameron McLeod
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic.
- Institute of Parasitology, Czech Academy of Sciences, České Budějovice, 370 05, Czech Republic.
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czech Republic.
| |
Collapse
|
6
|
Tseng CC, Obeng EA. RNA splicing as a therapeutic target in myelodysplastic syndromes. Semin Hematol 2024; 61:431-441. [PMID: 39542752 DOI: 10.1053/j.seminhematol.2024.10.005] [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: 10/10/2024] [Accepted: 10/18/2024] [Indexed: 11/17/2024]
Abstract
Myelodysplastic syndromes (MDS) represent a heterogeneous group of hematological disorders and are more commonly found in people over the age of 60. MDS patients exhibit peripheral blood cytopenias and carry an increased risk of disease progression to acute myeloid leukemia (AML). Splicing factor mutations (including genes SF3B1, SRSF2, U2AF1, and ZRSR2) are early events identified in more than 50% of MDS cases. These mutations cause aberrant pre-mRNA splicing and impact MDS pathophysiology. Emerging evidence shows that splicing factor-mutant cells are more sensitive to perturbations targeting the spliceosome, aberrantly spliced genes and/or their regulated molecular pathways. This review summarizes current therapeutic strategies and ongoing efforts targeting splicing factor mutations for the treatment of MDS.
Collapse
Affiliation(s)
- Chun-Chih Tseng
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Esther A Obeng
- Division of Molecular Oncology, Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN.
| |
Collapse
|
7
|
Bolikhova AK, Buyan AI, Mariasina SS, Rudenko AY, Chekh DS, Mazur AM, Prokhortchouk EB, Dontsova OA, Sergiev PV. Study of the RNA splicing kinetics via in vivo 5-EU labeling. RNA (NEW YORK, N.Y.) 2024; 30:1356-1373. [PMID: 39048310 PMCID: PMC11404452 DOI: 10.1261/rna.079937.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 07/08/2024] [Indexed: 07/27/2024]
Abstract
Splicing is an important step of gene expression in all eukaryotes. Splice sites might be used with different efficiency, giving rise to alternative splicing products. At the same time, splice sites might be used at a variable rate. We used 5-ethynyl uridine labeling to sequence a nascent transcriptome of HeLa cells and deduced the rate of splicing for each donor and acceptor splice site. The following correlation analysis showed a correspondence of primary transcript features with the rate of splicing. Some dependencies we revealed were anticipated, such as a splicing rate decrease with a decreased complementarity of the donor splice site to U1 and acceptor sites to U2 snRNAs. Other dependencies were more surprising, like a negative influence of a distance to the 5' end on the rate of the acceptor splicing site utilization, or the differences in splicing rate between long, short, and RBM17-dependent introns. We also observed a deceleration of last intron splicing with an increase of the distance to the poly(A) site, which might be explained by the cooperativity of the splicing and polyadenylation. Additional analysis of splicing kinetics of SF3B4 knockdown cells suggested the impairment of a U2 snRNA recognition step. As a result, we deconvoluted the effects of several examined features on the splicing rate into a single regression model. The data obtained here are useful for further studies in the field, as they provide general splicing rate dependencies as well as help to justify the existence of slowly removed splice sites.
Collapse
Affiliation(s)
- Anastasiia K Bolikhova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Andrey I Buyan
- Institute of Protein Research, Russian Academy of Sciences, Pushchino 142290, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Sofia S Mariasina
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Y Rudenko
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Daria S Chekh
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander M Mazur
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Egor B Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Olga A Dontsova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Functioning of Living Systems, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Petr V Sergiev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo 121205, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute of Functional Genomics, Lomonosov Moscow State University, Moscow 119991, Russia
| |
Collapse
|
8
|
Powell-Rodgers G, Pirzada MUR, Richee J, Jungers CF, Colijn S, Stratman AN, Djuranovic S. Role of U11/U12 minor spliceosome gene ZCRB1 in Ciliogenesis and WNT Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607392. [PMID: 39149385 PMCID: PMC11326282 DOI: 10.1101/2024.08.09.607392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Despite the fact that 0.5% of human introns are processed by the U11/U12 minor spliceosome, the latter influences gene expression across multiple cellular processes. The ZCRB1 protein is a recently described core component of the U12 mono-snRNP minor spliceosome, but its functional significance to minor splicing, gene regulation, and biological signaling cascades is poorly understood. Using CRISPR-Cas9 and siRNA targeted knockout and knockdown strategies, we show that human cell lines with a partial reduction in ZCRB1 expression exhibit significant dysregulation of the splicing and expression of U12-type genes, primarily due to dysregulation of U12 mono-snRNA. RNA-Seq and targeted analyses of minor intron-containing genes indicate a downregulation in the expression of genes involved in ciliogenesis, and consequentially an upregulation in WNT signaling. Additionally, zcrb1 CRISPR-Cas12a knockdown in zebrafish embryos led to gross developmental and body axis abnormalities, disrupted ciliogenesis, and upregulated WNT signaling, complementing our human cell studies. This work highlights a conserved and essential biological role of the minor spliceosome in general, and the ZCRB1 protein specifically in cellular and developmental processes across species, shedding light on the multifaceted relationship between splicing regulation, ciliogenesis, and WNT signaling.
Collapse
Affiliation(s)
- Geralle Powell-Rodgers
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Mujeeb Ur Rehman Pirzada
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Jahmiera Richee
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Courtney F. Jungers
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Sarah Colijn
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Amber N. Stratman
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Sergej Djuranovic
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| |
Collapse
|
9
|
Beusch I, Madhani HD. Understanding the dynamic design of the spliceosome. Trends Biochem Sci 2024; 49:583-595. [PMID: 38641465 DOI: 10.1016/j.tibs.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 04/21/2024]
Abstract
The spliceosome catalyzes the splicing of pre-mRNAs. Although the spliceosome evolved from a prokaryotic self-splicing intron and an associated protein, it is a vastly more complex and dynamic ribonucleoprotein (RNP) whose function requires at least eight ATPases and multiple RNA rearrangements. These features afford stepwise opportunities for multiple inspections of the intron substrate, coupled with spliceosome disassembly for substrates that fail inspection. Early work using splicing-defective pre-mRNAs or small nuclear (sn)RNAs in Saccharomyces cerevisiae demonstrated that such checks could occur in catalytically active spliceosomes. We review recent results on pre-mRNA splicing in various systems, including humans, suggesting that earlier steps in spliceosome assembly are also subject to such quality control. The inspection-rejection framework helps explain the dynamic nature of the spliceosome.
Collapse
Affiliation(s)
- Irene Beusch
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
10
|
Rawat C, Heemers HV. Alternative splicing in prostate cancer progression and therapeutic resistance. Oncogene 2024; 43:1655-1668. [PMID: 38658776 PMCID: PMC11136669 DOI: 10.1038/s41388-024-03036-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
Prostate cancer (CaP) remains the second leading cause of cancer deaths in western men. CaP mortality results from diverse molecular mechanisms that mediate resistance to the standard of care treatments for metastatic disease. Recently, alternative splicing has been recognized as a hallmark of CaP aggressiveness. Alternative splicing events cause treatment resistance and aggressive CaP behavior and are determinants of the emergence of the two major types of late-stage treatment-resistant CaP, namely castration-resistant CaP (CRPC) and neuroendocrine CaP (NEPC). Here, we review recent multi-omics data that are uncovering the complicated landscape of alternative splicing events during CaP progression and the impact that different gene transcript isoforms can have on CaP cell biology and behavior. We discuss renewed insights in the molecular machinery by which alternative splicing occurs and contributes to the failure of systemic CaP therapies. The potential for alternative splicing events to serve as diagnostic markers and/or therapeutic targets is explored. We conclude by considering current challenges and promises associated with splicing-modulating therapies, and their potential for clinical translation into CaP patient care.
Collapse
Affiliation(s)
- Chitra Rawat
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Hannelore V Heemers
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
| |
Collapse
|
11
|
Bauer M, Schöbel CM, Wickenhauser C, Seliger B, Jasinski-Bergner S. Deciphering the role of alternative splicing in neoplastic diseases for immune-oncological therapies. Front Immunol 2024; 15:1386993. [PMID: 38736877 PMCID: PMC11082354 DOI: 10.3389/fimmu.2024.1386993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024] Open
Abstract
Alternative splicing (AS) is an important molecular biological mechanism regulated by complex mechanisms involving a plethora of cis and trans-acting elements. Furthermore, AS is tissue specific and altered in various pathologies, including infectious, inflammatory, and neoplastic diseases. Recently developed immuno-oncological therapies include monoclonal antibodies (mAbs) and chimeric antigen receptor (CAR) T cells targeting, among others, immune checkpoint (ICP) molecules. Despite therapeutic successes have been demonstrated, only a limited number of patients showed long-term benefit from these therapies with tumor entity-related differential response rates were observed. Interestingly, splice variants of common immunotherapeutic targets generated by AS are able to completely escape and/or reduce the efficacy of mAb- and/or CAR-based tumor immunotherapies. Therefore, the analyses of splicing patterns of targeted molecules in tumor specimens prior to therapy might help correct stratification, thereby increasing therapy success by antibody panel selection and antibody dosages. In addition, the expression of certain splicing factors has been linked with the patients' outcome, thereby highlighting their putative prognostic potential. Outstanding questions are addressed to translate the findings into clinical application. This review article provides an overview of the role of AS in (tumor) diseases, its molecular mechanisms, clinical relevance, and therapy response.
Collapse
Affiliation(s)
- Marcus Bauer
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Chiara-Maria Schöbel
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
| | - Claudia Wickenhauser
- Institute of Pathology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Barbara Seliger
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
- Department of Good Manufacturing Practice (GMP) Development & Advanced Therapy Medicinal Products (ATMP) Design, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Leipzig, Germany
- Institute for Medical Immunology, Medical Faculty, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Simon Jasinski-Bergner
- Institute for Translational Immunology, Brandenburg Medical School (MHB), Theodor Fontane, Brandenburg an der Havel, Germany
| |
Collapse
|
12
|
Wuchty S, White AK, Olthof AM, Drake K, Hume AJ, Olejnik J, Aguiar-Pulido V, Mühlberger E, Kanadia RN. Minor intron-containing genes as an ancient backbone for viral infection? PNAS NEXUS 2024; 3:pgad479. [PMID: 38274120 PMCID: PMC10810330 DOI: 10.1093/pnasnexus/pgad479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024]
Abstract
Minor intron-containing genes (MIGs) account for <2% of all human protein-coding genes and are uniquely dependent on the minor spliceosome for proper excision. Despite their low numbers, we surprisingly found a significant enrichment of MIG-encoded proteins (MIG-Ps) in protein-protein interactomes and host factors of positive-sense RNA viruses, including SARS-CoV-1, SARS-CoV-2, MERS coronavirus, and Zika virus. Similarly, we observed a significant enrichment of MIG-Ps in the interactomes and sets of host factors of negative-sense RNA viruses such as Ebola virus, influenza A virus, and the retrovirus HIV-1. We also found an enrichment of MIG-Ps in double-stranded DNA viruses such as Epstein-Barr virus, human papillomavirus, and herpes simplex viruses. In general, MIG-Ps were highly connected and placed in central positions in a network of human-host protein interactions. Moreover, MIG-Ps that interact with viral proteins were enriched with essential genes. We also provide evidence that viral proteins interact with ancestral MIGs that date back to unicellular organisms and are mainly involved in basic cellular functions such as cell cycle, cell division, and signal transduction. Our results suggest that MIG-Ps form a stable, evolutionarily conserved backbone that viruses putatively tap to invade and propagate in human host cells.
Collapse
Affiliation(s)
- Stefan Wuchty
- Department of Computer Science, University of Miami, Coral Gables, FL 33146, USA
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
- Institute of Data Science and Computing, University of Miami, Coral Gables, FL 33146, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33134, USA
| | - Alisa K White
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Kyle Drake
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Adam J Hume
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
- Center for Emerging Infectious Diseases Policy and Research, Boston University, Boston, MA 02118, USA
| | - Judith Olejnik
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | | | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02118, USA
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| |
Collapse
|
13
|
Jobbins AM, Yu S, Paterson HAB, Maude H, Kefala-Stavridi A, Speck C, Cebola I, Vernia S. Pre-RNA splicing in metabolic homeostasis and liver disease. Trends Endocrinol Metab 2023; 34:823-837. [PMID: 37673766 DOI: 10.1016/j.tem.2023.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/07/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
The liver plays a key role in sensing nutritional and hormonal inputs to maintain metabolic homeostasis. Recent studies into pre-mRNA splicing and alternative splicing (AS) and their effects on gene expression have revealed considerable transcriptional complexity in the liver, both in health and disease. While the contribution of these mechanisms to cell and tissue identity is widely accepted, their role in physiological and pathological contexts within tissues is just beginning to be appreciated. In this review, we showcase recent studies on the splicing and AS of key genes in metabolic pathways in the liver, the effect of metabolic signals on the spliceosome, and therapeutic intervention points based on RNA splicing.
Collapse
Affiliation(s)
- Andrew M Jobbins
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Sijia Yu
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Helen A B Paterson
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Hannah Maude
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Antonia Kefala-Stavridi
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Christian Speck
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Santiago Vernia
- MRC (Medical Research Council) London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK.
| |
Collapse
|
14
|
Berta D, Girma M, Melku M, Adane T, Birke B, Yalew A. Role of RNA Splicing Mutations in Diffuse Large B Cell Lymphoma. Int J Gen Med 2023; 16:2469-2480. [PMID: 37342407 PMCID: PMC10278864 DOI: 10.2147/ijgm.s414106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Ribonucleic acid splicing is a crucial process to create a mature mRNA molecule by removing introns and ligating exons. This is a highly regulated process, but any alteration in splicing factors, splicing sites, or auxiliary components affects the final products of the gene. In diffuse large B-cell lymphoma, splicing mutations such as mutant splice sites, aberrant alternative splicing, exon skipping, and intron retention are detected. The alteration affects tumor suppression, DNA repair, cell cycle, cell differentiation, cell proliferation, and apoptosis. As a result, malignant transformation, cancer progression, and metastasis occurred in B cells at the germinal center. B-cell lymphoma 7 protein family member A (BCL7A), cluster of differentiation 79B (CD79B), myeloid differentiation primary response gene 88 (MYD88), tumor protein P53 (TP53), signal transducer and activator of transcription (STAT), serum- and glucose-regulated kinase 1 (SGK1), Pou class 2 associating factor 1 (POU2AF1), and neurogenic locus notch homolog protein 1 (NOTCH) are the most common genes affected by splicing mutations in diffuse large B cell lymphoma.
Collapse
Affiliation(s)
- Dereje Berta
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mekonnen Girma
- Department of Quality Assurance and Laboratory Management, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mulugeta Melku
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tiruneh Adane
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Bisrat Birke
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Aregawi Yalew
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| |
Collapse
|
15
|
Petrillo E. Do not panic: An intron-centric guide to alternative splicing. THE PLANT CELL 2023; 35:1752-1761. [PMID: 36648241 PMCID: PMC10226583 DOI: 10.1093/plcell/koad009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/05/2022] [Accepted: 01/11/2023] [Indexed: 05/30/2023]
Abstract
This review is an attempt to establish concepts of splicing and alternative splicing giving proper relevance to introns, the key actors in this mechanism. It might also work as a guide for those who found their favorite gene undergoes alternative splicing and could benefit from gaining a theoretical framework to understand the possible impacts of this process. This is not a thorough review of all the work in the field, but rather a critical review of some of the most relevant work done to understand the underlying mechanisms of splicing and the key questions that remain unanswered such as: What is the physiological relevance of alternative splicing? What are the functions of the different outcomes? To what extent do different alternative splicing types contribute to the proteome? Intron retention is the most frequent alternative splicing event in plants and, although scientifically neglected, it is also common in animals. This is a heterogeneous type of alternative splicing that includes different sub-types with features that have distinctive consequences in the resulting transcripts. Remarkably, intron retention can be a dead end for a transcript, but it could also be a stable intermediate whose processing is resumed upon a particular signal or change in the cell status. New sequencing technologies combined with the study of intron lariats in different conditions might help to answer key questions and could help us to understand the actual relevance of introns in gene expression regulation.
Collapse
Affiliation(s)
- Ezequiel Petrillo
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología, Molecular, y Celular, Universidad de Buenos Aires, 1428 Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA Buenos Aires, Argentina
| |
Collapse
|
16
|
Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
Collapse
Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
| |
Collapse
|
17
|
Di Nunzio F, Uversky VN, Mouland AJ. Biomolecular condensates: insights into early and late steps of the HIV-1 replication cycle. Retrovirology 2023; 20:4. [PMID: 37029379 PMCID: PMC10081342 DOI: 10.1186/s12977-023-00619-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/16/2023] [Indexed: 04/09/2023] Open
Abstract
A rapidly evolving understanding of phase separation in the biological and physical sciences has led to the redefining of virus-engineered replication compartments in many viruses with RNA genomes. Condensation of viral, host and genomic and subgenomic RNAs can take place to evade the innate immunity response and to help viral replication. Divergent viruses prompt liquid-liquid phase separation (LLPS) to invade the host cell. During HIV replication there are several steps involving LLPS. In this review, we characterize the ability of individual viral and host partners that assemble into biomolecular condensates (BMCs). Of note, bioinformatic analyses predict models of phase separation in line with several published observations. Importantly, viral BMCs contribute to function in key steps retroviral replication. For example, reverse transcription takes place within nuclear BMCs, called HIV-MLOs while during late replication steps, retroviral nucleocapsid acts as a driver or scaffold to recruit client viral components to aid the assembly of progeny virions. Overall, LLPS during viral infections represents a newly described biological event now appreciated in the virology field, that can also be considered as an alternative pharmacological target to current drug therapies especially when viruses become resistant to antiviral treatment.
Collapse
Affiliation(s)
- Francesca Di Nunzio
- Advanced Molecular Virology Unit, Department of Virology, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Andrew J Mouland
- Lady Davis Institute at the Jewish General Hospital, Montréal, QC, H3T 1E2, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada.
- Department of Medicine, McGill University, Montréal, QC, H4A 3J1, Canada.
| |
Collapse
|
18
|
Abstract
Dysregulated RNA splicing is a molecular feature that characterizes almost all tumour types. Cancer-associated splicing alterations arise from both recurrent mutations and altered expression of trans-acting factors governing splicing catalysis and regulation. Cancer-associated splicing dysregulation can promote tumorigenesis via diverse mechanisms, contributing to increased cell proliferation, decreased apoptosis, enhanced migration and metastatic potential, resistance to chemotherapy and evasion of immune surveillance. Recent studies have identified specific cancer-associated isoforms that play critical roles in cancer cell transformation and growth and demonstrated the therapeutic benefits of correcting or otherwise antagonizing such cancer-associated mRNA isoforms. Clinical-grade small molecules that modulate or inhibit RNA splicing have similarly been developed as promising anticancer therapeutics. Here, we review splicing alterations characteristic of cancer cell transcriptomes, dysregulated splicing's contributions to tumour initiation and progression, and existing and emerging approaches for targeting splicing for cancer therapy. Finally, we discuss the outstanding questions and challenges that must be addressed to translate these findings into the clinic.
Collapse
Affiliation(s)
- Robert K Bradley
- Computational Biology Program, Public Health Sciences Division and Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
| |
Collapse
|
19
|
Khatri D, Putoux A, Cologne A, Kaltenbach S, Besson A, Bertiaux E, Guguin J, Fendler A, Dupont MA, Benoit-Pilven C, Qebibo L, Ahmed-Elie S, Audebert-Bellanger S, Blanc P, Rambaud T, Castelle M, Cornen G, Grotto S, Guët A, Guibaud L, Michot C, Odent S, Ruaud L, Sacaze E, Hamel V, Bordonné R, Leutenegger AL, Edery P, Burglen L, Attié-Bitach T, Mazoyer S, Delous M. Deficiency of the minor spliceosome component U4atac snRNA secondarily results in ciliary defects in human and zebrafish. Proc Natl Acad Sci U S A 2023; 120:e2102569120. [PMID: 36802443 PMCID: PMC9992838 DOI: 10.1073/pnas.2102569120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 12/12/2022] [Indexed: 02/23/2023] Open
Abstract
In the human genome, about 750 genes contain one intron excised by the minor spliceosome. This spliceosome comprises its own set of snRNAs, among which U4atac. Its noncoding gene, RNU4ATAC, has been found mutated in Taybi-Linder (TALS/microcephalic osteodysplastic primordial dwarfism type 1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes. These rare developmental disorders, whose physiopathological mechanisms remain unsolved, associate ante- and post-natal growth retardation, microcephaly, skeletal dysplasia, intellectual disability, retinal dystrophy, and immunodeficiency. Here, we report bi-allelic RNU4ATAC mutations in five patients presenting with traits suggestive of the Joubert syndrome (JBTS), a well-characterized ciliopathy. These patients also present with traits typical of TALS/RFMN/LWS, thus widening the clinical spectrum of RNU4ATAC-associated disorders and indicating ciliary dysfunction as a mechanism downstream of minor splicing defects. Intriguingly, all five patients carry the n.16G>A mutation, in the Stem II domain, either at the homozygous or compound heterozygous state. A gene ontology term enrichment analysis on minor intron-containing genes reveals that the cilium assembly process is over-represented, with no less than 86 cilium-related genes containing at least one minor intron, among which there are 23 ciliopathy-related genes. The link between RNU4ATAC mutations and ciliopathy traits is supported by alterations of primary cilium function in TALS and JBTS-like patient fibroblasts, as well as by u4atac zebrafish model, which exhibits ciliopathy-related phenotypes and ciliary defects. These phenotypes could be rescued by WT but not by pathogenic variants-carrying human U4atac. Altogether, our data indicate that alteration of cilium biogenesis is part of the physiopathological mechanisms of TALS/RFMN/LWS, secondarily to defects of minor intron splicing.
Collapse
Affiliation(s)
- Deepak Khatri
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Audrey Putoux
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Department of Genetics, Clinical Genetics Unit, Centre de Référence Maladies Rares des Anomalies du Développement, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Audric Cologne
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Institut national de recherche en sciences et technologies du numérique Erable, Laboratoire de Biométrie et Biologie Evolutive, UMR5558 CNRS, Université Claude Bernard Lyon 1, 69622Villeurbanne, France
| | - Sophie Kaltenbach
- Department of Histology Embryology and Cytogenetics, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, University of Paris, 75015Paris, France
| | - Alicia Besson
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Eloïse Bertiaux
- Department of Cell Biology, Sciences III, University of Geneva, 1211-Geneva, Switzerland
| | - Justine Guguin
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Adèle Fendler
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Marie A. Dupont
- Laboratory of hereditary kidney diseases, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Clara Benoit-Pilven
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Institut national de recherche en sciences et technologies du numérique Erable, Laboratoire de Biométrie et Biologie Evolutive, UMR5558 CNRS, Université Claude Bernard Lyon 1, 69622Villeurbanne, France
| | - Leila Qebibo
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
| | - Samira Ahmed-Elie
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
| | - Séverine Audebert-Bellanger
- Department of Genetics, Clinical Genetics Unit, Centre de Compétence Anomalies du Développement et Syndromes Polymalformatifs, Centre Hospitalier Universitaire Morvan, 29200Brest, France
| | | | | | - Martin Castelle
- Hematology-Immunology Unit, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, 75015Paris, France
| | - Gaëlle Cornen
- Pediatric service, Centre Hospitalier Morlaix, 29600Morlaix, France
| | - Sarah Grotto
- Clinical Genetics Unit, Maternité Port-Royal, Assistance Publique - Hôpitaux de Paris, Cochin Broca Hôtel-Dieu Hospitals75014Paris, France
| | - Agnès Guët
- Neonatal and Pediatric Units, Louis-Mourier Hospital, 92700Colombes, France
| | - Laurent Guibaud
- Pediatric and Fetal Imaging, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Caroline Michot
- Clinical Genetics Department, Centre de Référence Maladies Rares–Maladies Osseuses Constitutionnelles, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, 75015Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre Hospitalier Universitaire Rennes, Centre de référence Anomalies du développement et syndromes malformatifs, Univ Rennes, CNRS, INSERM, Institut de Génétique et Développement de Rennes UMR 6290/ Equipe de Recherche Labellisée 1305, 35000Rennes, France
| | - Lyse Ruaud
- NeuroDiderot, UMR1141, University of Paris, 75019Paris, France
- Departement of Genetics, Assistance Publique - Hôpitaux de Paris, Robert Debré Hospital, 75019Paris, France
| | - Elise Sacaze
- Pediatric Service, Centre Hospitalier Régional Universitaire Brest, 29200Brest, France
| | - Virginie Hamel
- Department of Cell Biology, Sciences III, University of Geneva, 1211-Geneva, Switzerland
| | - Rémy Bordonné
- Institute of Molecular Genetics of Montpellier, UMR5535 CNRS, University of Montpellier, 34000Montpellier, France
| | | | - Patrick Edery
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Department of Genetics, Clinical Genetics Unit, Centre de Référence Maladies Rares des Anomalies du Développement, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Lydie Burglen
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Tania Attié-Bitach
- Department of Histology Embryology and Cytogenetics, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, University of Paris, 75015Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Sylvie Mazoyer
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Marion Delous
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| |
Collapse
|
20
|
Ivanova OM, Anufrieva KS, Kazakova AN, Malyants IK, Shnaider PV, Lukina MM, Shender VO. Non-canonical functions of spliceosome components in cancer progression. Cell Death Dis 2023; 14:77. [PMID: 36732501 PMCID: PMC9895063 DOI: 10.1038/s41419-022-05470-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 02/04/2023]
Abstract
Dysregulation of pre-mRNA splicing is a common hallmark of cancer cells and it is associated with altered expression, localization, and mutations of the components of the splicing machinery. In the last few years, it has been elucidated that spliceosome components can also influence cellular processes in a splicing-independent manner. Here, we analyze open source data to understand the effect of the knockdown of splicing factors in human cells on the expression and splicing of genes relevant to cell proliferation, migration, cell cycle regulation, DNA repair, and cell death. We supplement this information with a comprehensive literature review of non-canonical functions of splicing factors linked to cancer progression. We also specifically discuss the involvement of splicing factors in intercellular communication and known autoregulatory mechanisms in restoring their levels in cells. Finally, we discuss strategies to target components of the spliceosome machinery that are promising for anticancer therapy. Altogether, this review greatly expands understanding of the role of spliceosome proteins in cancer progression.
Collapse
Affiliation(s)
- Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Institute for Regenerative Medicine, Sechenov University, Moscow, 119991, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Irina K Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
| |
Collapse
|
21
|
Luo J, Chen C, Liu Z, Wang X. The mutation in splicing factor genes correlates with unfavorable prognosis, genomic instability, anti-tumor immunosuppression and increased immunotherapy response in pan-cancer. Front Cell Dev Biol 2023; 10:1045130. [PMID: 36684432 PMCID: PMC9852835 DOI: 10.3389/fcell.2022.1045130] [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: 09/15/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
Splicing abnormality resulting from somatic mutations in key splicing factor genes (SFG) has been detected in various cancers. Hence, an in-depth study of splicing factor genes mutations' impact on pan-cancer is meaningful. This study investigated associations of splicing factor genes mutations with clinical features, tumor progression phenotypes, genomic integrity, anti-tumor immune responses, and immunotherapy response in 12 common cancer types from the TCGA database. Compared to SFG-wildtype cancers, SFG-mutated cancers displayed worse survival prognosis, higher tumor mutation burden and aneuploidy levels, higher expression of immunosuppressive signatures, and higher levels of tumor stemness, proliferation potential, and intratumor heterogeneity (ITH). However, splicing factor genes-mutated cancers showed higher response rates to immune checkpoint inhibitors than splicing factor genes-wildtype cancers in six cancer cohorts. Single-cell data analysis confirmed that splicing factor genes mutations were associated with increased tumor stemness, proliferation capacity, PD-L1 expression, intratumor heterogeneity, and aneuploidy levels. Our data suggest that the mutation in key splicing factor genes correlates with unfavorable clinical outcomes and disease progression, genomic instability, anti-tumor immunosuppression, and increased immunotherapy response in pan-cancer. Thus, the splicing factor genes mutation is an adverse prognostic factor and a positive marker for immunotherapy response in cancer.
Collapse
Affiliation(s)
- Jiangti Luo
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China,Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Canping Chen
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China,Big Data Research Institute, China Pharmaceutical University, Nanjing, China
| | - Zhixian Liu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China,*Correspondence: Zhixian Liu, ; Xiaosheng Wang,
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China,Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China,Big Data Research Institute, China Pharmaceutical University, Nanjing, China,*Correspondence: Zhixian Liu, ; Xiaosheng Wang,
| |
Collapse
|
22
|
Ding Z, Meng YR, Fan YJ, Xu YZ. Roles of minor spliceosome in intron recognition and the convergence with the better understood major spliceosome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1761. [PMID: 36056453 DOI: 10.1002/wrna.1761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/06/2022] [Accepted: 08/06/2022] [Indexed: 01/31/2023]
Abstract
Catalyzed by spliceosomes in the nucleus, RNA splicing removes intronic sequences from precursor RNAs in eukaryotes to generate mature RNA, which also significantly increases proteome complexity and fine-tunes gene expression. Most metazoans have two coexisting spliceosomes; the major spliceosome, which removes >99.5% of introns, and the minor spliceosome, which removes far fewer introns (only 770 at present have been predicted in the human genome). Both spliceosomes are large and dynamic machineries, each consisting of five small nuclear RNAs (snRNAs) and more than 100 proteins. However, the dynamic assembly, catalysis, and protein composition of the minor spliceosome are still poorly understood. With different splicing signals, minor introns are rare and usually distributed alone and flanked by major introns in genes, raising questions of how they are recognized by the minor spliceosome and how their processing deals with the splicing of neighboring major introns. Due to large numbers of introns and close similarities between the two machinery, cooperative, and competitive recognition by the two spliceosomes has been investigated. Functionally, many minor-intron-containing genes are evolutionarily conserved and essential. Mutations in the minor spliceosome exhibit a variety of developmental defects in plants and animals and are linked to numerous human diseases. Here, we review recent progress in the understanding of minor splicing, compare currently known components of the two spliceosomes, survey minor introns in a wide range of organisms, discuss cooperation and competition of the two spliceosomes in splicing of minor-intron-containing genes, and contributions of minor splicing mutations in development and diseases. This article is categorized under: RNA Processing > Processing of Small RNAs RNA Processing > Splicing Mechanisms RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
Collapse
Affiliation(s)
- Zhan Ding
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan-Ran Meng
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| |
Collapse
|
23
|
Appelbaum T, Aguirre GD, Beltran WA. Identification of circular RNAs hosted by the RPGR ORF15 genomic locus. RNA Biol 2023; 20:31-47. [PMID: 36593651 PMCID: PMC9817113 DOI: 10.1080/15476286.2022.2159165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/23/2022] [Accepted: 12/07/2022] [Indexed: 01/04/2023] Open
Abstract
Mutations in the retina-specific isoform of the gene encoding retinitis pigmentosa GTPase regulator (RPGRorf15) cause X-linked retinitis pigmentosa, a severe and early onset inherited retinal degeneration. The underlying pathogenic mechanisms and variability in disease severity remain to be fully elucidated. The present study examines structural features of the ORF15 exonic region to provide new insights into the disease pathogenesis. Using canine and human RNA samples, we identified several novel RPGR ORF15-like linear RNA transcripts containing cryptic introns (exitrons) within the annotated exon ORF15. Furthermore, using outward-facing primers designed inside exitrons in the ORF15 exonic region, we found many of previously unidentified circular RNAs (circRNAs) that formed via back fusion of linear parts of the RPGRorf15 pre-mRNAs. These circRNAs (resistant to RNAse R treatment) were found in all studied cells and tissues. Notably, some circRNAs were present in cytoplasmic and polysomal RNA fractions. Although certain RPGR circRNAs may be cell type specific, we found some of the same circRNAs expressed in different cell types, suggesting similarities in their biogenesis and functions. Sequence analysis of RPGR circRNAs revealed several remarkable features, including identification of N6-methyladenosine (m6A) consensus sequence motifs and high prevalence of predictive microRNA binding sites pointing to the functional roles of these circRNAs. Our findings also illustrate the presence of non-canonical RPGR circRNA biogenesis pathways independent of the known back splicing mechanism. The obtained data on novel RPGR circRNAs further underline structural complexity of the RPGR ORF15 region and provide a potential molecular basis for the disease phenotypic heterogeneity.
Collapse
Affiliation(s)
- Tatyana Appelbaum
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gustavo D. Aguirre
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - William A. Beltran
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
24
|
Jacquier V, Prévot M, Gostan T, Bordonné R, Benkhelifa-Ziyyat S, Barkats M, Soret J. Splicing efficiency of minor introns in a mouse model of SMA predominantly depends on their branchpoint sequence and can involve the contribution of major spliceosome components. RNA (NEW YORK, N.Y.) 2022; 28:303-319. [PMID: 34893560 PMCID: PMC8848931 DOI: 10.1261/rna.078329.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Spinal muscular atrophy (SMA) is a devastating neurodegenerative disease caused by reduced amounts of the ubiquitously expressed Survival of Motor Neuron (SMN) protein. In agreement with its crucial role in the biogenesis of spliceosomal snRNPs, SMN-deficiency is correlated to numerous splicing alterations in patient cells and various tissues of SMA mouse models. Among the snRNPs whose assembly is impacted by SMN-deficiency, those involved in the minor spliceosome are particularly affected. Importantly, splicing of several, but not all U12-dependent introns has been shown to be affected in different SMA models. Here, we have investigated the molecular determinants of this differential splicing in spinal cords from SMA mice. We show that the branchpoint sequence (BPS) is a key element controlling splicing efficiency of minor introns. Unexpectedly, splicing of several minor introns with suboptimal BPS is not affected in SMA mice. Using in vitro splicing experiments and oligonucleotides targeting minor or major snRNAs, we show for the first time that splicing of these introns involves both the minor and major machineries. Our results strongly suggest that splicing of a subset of minor introns is not affected in SMA mice because components of the major spliceosome compensate for the loss of minor splicing activity.
Collapse
Affiliation(s)
- Valentin Jacquier
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Manon Prévot
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Thierry Gostan
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Rémy Bordonné
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Sofia Benkhelifa-Ziyyat
- Centre de Recherche en Myologie (CRM), Institut de Myologie, Sorbonne Universités, UPMC Univ Paris 06, Inserm UMRS974, GH Pitié Salpêtrière, Paris 75013, France
| | - Martine Barkats
- Centre de Recherche en Myologie (CRM), Institut de Myologie, Sorbonne Universités, UPMC Univ Paris 06, Inserm UMRS974, GH Pitié Salpêtrière, Paris 75013, France
| | - Johann Soret
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| |
Collapse
|
25
|
Li S, Zhao S, Hu C, Mao C, Guo L, Yu H, Yu H. Whole Genome Sequence of an Edible Mushroom Stropharia rugosoannulata (Daqiugaigu). J Fungi (Basel) 2022; 8:99. [PMID: 35205854 PMCID: PMC8880121 DOI: 10.3390/jof8020099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
Stropharia rugosoannulata, also known as Daqiugaigu in China, is a well-known edible mushroom that has been widely cultivated in China in recent years. Many studies have focused on its nutrients, bioactive compounds, and lignin degradation capacity, although there are few molecular and genetic breeding studies due to the lack of genomic information. Here, we present the 47.9 Mb genome sequence of an S. rugosoannulata monokaryotic strain (A15), which has 20 contigs and an N50 of 3.64 Mb, which was obtained by a combination of Illumina and Nanopore sequencing platforms. Further analysis predicted 12,752 protein-coding genes, including 486 CAZyme-encoding genes. Phylogenetic analysis revealed a close evolutionary relationship between S. rugosoannulata and Hypholoma sublateritium, Psilocybe cyanescens, and Galerina marginata based on single-copy orthologous genes. Proteomic analysis revealed different protein expression profiles between the cap and the stipe of the S. rugosoannulata fruiting body. The proteins of the stipe associated with carbon metabolism, energy production, and stress-response-related biological processes had higher abundance, whereas proteins involved in fatty acid synthesis and mRNA splicing showed higher expression in the cap than in the stipe. The genome of S. rugosoannulata will provide valuable genetic resources not only for comparative genomic analyses and evolutionary studies among Basidiomycetes but also for alleviating the bottlenecks that restrict the molecular breeding of this edible mushroom.
Collapse
Affiliation(s)
- Shuwen Li
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Shuxue Zhao
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Chunhui Hu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Chengzhi Mao
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Lizhong Guo
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| | - Hailong Yu
- National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Hao Yu
- Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, China; (S.L.); (S.Z.); (C.H.); (C.M.); (L.G.)
| |
Collapse
|