1
|
Beusch I, Madhani HD. Understanding the dynamic design of the spliceosome. Trends Biochem Sci 2024:S0968-0004(24)00078-1. [PMID: 38641465 DOI: 10.1016/j.tibs.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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
|
2
|
Zhang F, Liu S, Qiao Z, Li L, Han Y, Sun J, Ge C, Zhu J, Li D, Yao H, Zhang H, Dai J, Yan Y, Chen Z, Yin L, Ma F. Housekeeping U1 snRNA facilitates antiviral innate immunity by promoting TRIM25-mediated RIG-I activation. Cell Rep 2024; 43:113945. [PMID: 38483900 DOI: 10.1016/j.celrep.2024.113945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/24/2024] [Accepted: 02/27/2024] [Indexed: 04/02/2024] Open
Abstract
U1 small nuclear RNA (snRNA) is an abundant and evolutionarily conserved 164-nucleotide RNA species that functions in pre-mRNA splicing, and it is considered to be a housekeeping non-coding RNA. However, the role of U1 snRNA in regulating host antiviral immunity remains largely unexplored. Here, we find that RNVU1-18, a U1 pseudogene, is significantly upregulated in the host infected with RNA viruses, including influenza and respiratory syncytial virus. Overexpression of U1 snRNA protects cells against RNA viruses, while knockdown of U1 snRNA leads to more viral burden in vitro and in vivo. Knockout of RNVU1-18 is sufficient to impair the type I interferon-dependent antiviral innate immunity. U1 snRNA is required to fully activate the retinoic acid-inducible gene I (RIG-I)-dependent antiviral signaling, since it interacts with tripartite motif 25 (TRIM25) and enhances the RIG-I-TRIM25 interaction to trigger K63-linked ubiquitination of RIG-I. Our study reveals the important role of housekeeping U1 snRNA in regulating host antiviral innate immunity and restricting RNA virus infection.
Collapse
Affiliation(s)
- Fan Zhang
- National Key Laboratory of Immunity and Inflammation, and CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China; School of Pharmacy, Xi'an Jiaotong University, Xi'an 710061, China
| | - Siying Liu
- National Key Laboratory of Immunity and Inflammation, and CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Zigang Qiao
- National Key Laboratory of Immunity and Inflammation, and CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Liang Li
- National Key Laboratory of Immunity and Inflammation, and CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Yu Han
- National Key Laboratory of Immunity and Inflammation, and CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Jiya Sun
- National Key Laboratory of Immunity and Inflammation, and CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Chenglong Ge
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123, China
| | - Jingfei Zhu
- National Key Laboratory of Immunity and Inflammation, and CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Dapei Li
- National Key Laboratory of Immunity and Inflammation, and CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Haiping Yao
- National Key Laboratory of Immunity and Inflammation, and CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Huiying Zhang
- National Key Laboratory of Immunity and Inflammation, and CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China
| | - Jianfeng Dai
- Institute of Biology and Medical Sciences, Soochow University, Suzhou 215123, China
| | - Yongdong Yan
- Department of Respiratory Medicine, Children's Hospital of Soochow University, Suzhou 215025, China
| | - Zhengrong Chen
- Department of Respiratory Medicine, Children's Hospital of Soochow University, Suzhou 215025, China.
| | - Lichen Yin
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou 215123, China.
| | - Feng Ma
- National Key Laboratory of Immunity and Inflammation, and CAMS Key Laboratory of Synthetic Biology Regulatory Elements, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou 215123, China.
| |
Collapse
|
3
|
Stixová L, Tichý V, Bártová E. RNA-related DNA damage and repair: The role of N7-methylguanosine in the cell nucleus exposed to UV light. Heliyon 2024; 10:e25599. [PMID: 38370261 PMCID: PMC10869776 DOI: 10.1016/j.heliyon.2024.e25599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024] Open
Abstract
Background Chemical modifications in mRNAs, tRNAs, rRNAs, and non-coding RNAs stabilize these nucleic acids and regulate their function. In addition to regulating the translation of genetic information from mRNA to proteins, it has been revealed that modifications in RNAs regulate repair processes in the genome. Methods Using local laser microirradiation, confocal microscopy, dot blots, and mass spectrometry we studied the role of N7-methylguanosine (m7G), which is co-transcriptionally installed in RNA. Results Here, we show that after UVC and UVA irradiation, the level of m7G RNA is increased initially in the cytoplasm, and after local laser microirradiation, m7G RNA is highly abundant in UVA-damaged chromatin. This process is poly(ADP-ribose) polymerase (PARP)-dependent, but not accompanied by changes in the level of m7G-writers, including methyltransferases RNMT, METTL1, and WBSCR22. We also observed that METTL1 deficiency does not affect the recruitment of m7G RNA to microirradiated chromatin. Analyzing the levels of mRNA, let-7e, and miR-203a in both the cytoplasm and the cell nucleus, we revealed that UVC irradiation changed the level of mRNA, and significantly increased the pool of both let-7e and miR-203a, which correlated with radiation-induced m7G RNA increase in the cytoplasm. Conclusions Irradiation by UV light increases the m7G RNA pool in the cytoplasm and in the microirradiated genome. Thus, epigenetically modified RNAslikely contribute to DNA damage responses or m7G signals the presence of RNA damage.
Collapse
Affiliation(s)
- Lenka Stixová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
| | - Vlastimil Tichý
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
| | - Eva Bártová
- Department of Cell Biology and Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, Czech Republic
| |
Collapse
|
4
|
Hernández-Contreras KA, Martínez-Díaz JA, Hernández-Aguilar ME, Herrera-Covarrubias D, Rojas-Durán F, Chi-Castañeda LD, García-Hernández LI, Aranda-Abreu GE. Alterations of mRNAs and Non-coding RNAs Associated with Neuroinflammation in Alzheimer's Disease. Mol Neurobiol 2024:10.1007/s12035-023-03908-5. [PMID: 38236345 DOI: 10.1007/s12035-023-03908-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 12/27/2023] [Indexed: 01/19/2024]
Abstract
Alzheimer's disease is a neurodegenerative pathology whose pathognomonic hallmarks are increased generation of β-amyloid (Aβ) peptide, production of hyperphosphorylated (pTau), and neuroinflammation. The last is an alteration closely related to the progression of AD and although it is present in multiple neurodegenerative diseases, the pathophysiological events that characterize neuroinflammatory processes vary depending on the disease. In this article, we focus on mRNA and non-coding RNA alterations as part of the pathophysiological events characteristic of neuroinflammation in AD and the influence of these alterations on the course of the disease through interaction with multiple RNAs related to the generation of Aβ, pTau, and neuroinflammation itself.
Collapse
Affiliation(s)
- Karla Aketzalli Hernández-Contreras
- Doctorado en Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Jorge Antonio Martínez-Díaz
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - María Elena Hernández-Aguilar
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Deissy Herrera-Covarrubias
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Fausto Rojas-Durán
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Lizbeth Donají Chi-Castañeda
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Luis Isauro García-Hernández
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México
| | - Gonzalo Emiliano Aranda-Abreu
- Instituto de Investigaciones Cerebrales/Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, Carr. Xalapa-Veracruz, Km 3.5, C.P. 91190, Xalapa, Veracruz, México.
| |
Collapse
|
5
|
Ma T, Xiong ES, Lardelli RM, Lykke-Andersen J. Sm complex assembly and 5' cap trimethylation promote selective processing of snRNAs by the 3' exonuclease TOE1. Proc Natl Acad Sci U S A 2024; 121:e2315259121. [PMID: 38194449 PMCID: PMC10801842 DOI: 10.1073/pnas.2315259121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 12/06/2023] [Indexed: 01/11/2024] Open
Abstract
Competing exonucleases that promote 3' end maturation or degradation direct quality control of small non-coding RNAs, but how these enzymes distinguish normal from aberrant RNAs is poorly understood. The Pontocerebellar Hypoplasia 7 (PCH7)-associated 3' exonuclease TOE1 promotes maturation of canonical small nuclear RNAs (snRNAs). Here, we demonstrate that TOE1 achieves specificity toward canonical snRNAs through their Sm complex assembly and cap trimethylation, two features that distinguish snRNAs undergoing correct biogenesis from other small non-coding RNAs. Indeed, disruption of Sm complex assembly via snRNA mutations or protein depletions obstructs snRNA processing by TOE1, and in vitro snRNA processing by TOE1 is stimulated by a trimethylated cap. An unstable snRNA variant that normally fails to undergo maturation becomes fully processed by TOE1 when its degenerate Sm binding motif is converted into a canonical one. Our findings uncover the molecular basis for how TOE1 distinguishes snRNAs from other small non-coding RNAs and explain how TOE1 promotes maturation specifically of canonical snRNAs undergoing proper processing.
Collapse
Affiliation(s)
- Tiantai Ma
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Erica S. Xiong
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Rea M. Lardelli
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| | - Jens Lykke-Andersen
- Department of Molecular Biology, School of Biological Sciences, University of California, San Diego, La Jolla, CA92093
| |
Collapse
|
6
|
Zheng J, Liu F, Tuo J, Chen S, Su J, Ou X, Ding M, Chen H, Shi B, Li Y, Chen X, Wang C, Su C. Multidimensional Transcriptomics Unveils RNF34 as a Prognostic Biomarker and Potential Indicator of Chemotherapy Sensitivity in Wilms' Tumour. Mol Biotechnol 2024:10.1007/s12033-023-01008-2. [PMID: 38195816 DOI: 10.1007/s12033-023-01008-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024]
Abstract
Nephroblastoma, colloquially known as Wilms' tumour (WT), is the predominant malignant renal neoplasm arising in the paediatric population. Modern therapeutic approaches for WT incorporate a synergistic combination of surgical intervention, radiotherapy, and chemotherapy, which substantially ameliorate the overall patient survival rate. Despite this, the optimal sequence of chemotherapy and surgical intervention remains a matter of contention, with each strategy presenting its own strengths and weaknesses that could influence clinical decision-making. To make some headway on this clinical dilemma, we deployed a multidimensional transcriptomics integration approach by analysing bulk RNA sequencing data with 136 samples, as well as single-nucleus RNA sequencing (snRNA-seq) and paired spatial transcriptome sequencing (stRNA) data from 32 WT specimens. Our findings identified a distinct elevation of RNF34 expression within WT samples, which correlated with unfavourable prognostic outcomes. Leveraging the Genomics of Drug Sensitivity in Cancer (GDSC), we simultaneously revealed that patients with high expression of RNF34 have higher sensitivity to commonly used chemotherapy drugs for WT. Furthermore, our analysis of snRNA and stRNA data unveiled a reduced proportion of RNF34 expression in neoplastic cells after chemotherapy. Moreover, stRNA data delineated a significant association between a higher proportion of RNF34 expression in cancer cells and adverse features such as anaplastic histology and tumour recurrence. Intriguingly, we also observed a close association between elevated RNF34 expression and a characteristic exhausted tumour immune microenvironment. Collectively, our findings underscore the pivotal role of RNF34 in the prognostic prediction potential and treatment sensitivity of WT. This comprehensive analysis can potentially inform and refine clinical decision-making for WT patients and guide future studies towards the development of optimized, rational therapeutic strategies.
Collapse
Affiliation(s)
- Jie Zheng
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Fengling Liu
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jinwei Tuo
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Siyu Chen
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Jinxia Su
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiuyi Ou
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Min Ding
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Haoran Chen
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Bo Shi
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Yong Li
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xun Chen
- Department of Pediatrics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.
| | - Congjun Wang
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.
| | - Cheng Su
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China.
| |
Collapse
|
7
|
Fujiwara R, Zhai SN, Liang D, Shah AP, Tracey M, Ma XK, Fields CJ, Mendoza-Figueroa MS, Meline MC, Tatomer DC, Yang L, Wilusz JE. IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events. Mol Cell 2023; 83:4445-4460.e7. [PMID: 37995689 PMCID: PMC10841813 DOI: 10.1016/j.molcel.2023.10.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 10/12/2023] [Accepted: 10/25/2023] [Indexed: 11/25/2023]
Abstract
The metazoan-specific Integrator complex catalyzes 3' end processing of small nuclear RNAs (snRNAs) and premature termination that attenuates the transcription of many protein-coding genes. Integrator has RNA endonuclease and protein phosphatase activities, but it remains unclear if both are required for complex function. Here, we show IntS6 (Integrator subunit 6) over-expression blocks Integrator function at a subset of Drosophila protein-coding genes, although having no effect on snRNAs or attenuation of other loci. Over-expressed IntS6 titrates protein phosphatase 2A (PP2A) subunits, thereby only affecting gene loci where phosphatase activity is necessary for Integrator function. IntS6 functions analogous to a PP2A regulatory B subunit as over-expression of canonical B subunits, which do not bind Integrator, is also sufficient to inhibit Integrator activity. These results show that the phosphatase module is critical at only a subset of Integrator-regulated genes and point to PP2A recruitment as a tunable step that modulates transcription termination efficiency.
Collapse
Affiliation(s)
- Rina Fujiwara
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Si-Nan Zhai
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Dongming Liang
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Aayushi P Shah
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew Tracey
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Xu-Kai Ma
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Christopher J Fields
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - María Saraí Mendoza-Figueroa
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Michele C Meline
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA.
| |
Collapse
|
8
|
Staněk D. Coilin and Cajal bodies. Nucleus 2023; 14:2256036. [PMID: 37682044 PMCID: PMC10494742 DOI: 10.1080/19491034.2023.2256036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/09/2023] Open
Abstract
The nucleus of higher eukaryotes contains a number of structures that concentrate specific biomolecules and play distinct roles in nuclear metabolism. In recent years, the molecular mechanisms controlling their formation have been intensively studied. In this brief review, I focus on coilin and Cajal bodies. Coilin is a key scaffolding protein of Cajal bodies that is evolutionarily conserved in metazoans. Cajal bodies are thought to be one of the archetypal nuclear structures involved in the metabolism of several short non-coding nuclear RNAs. Yet surprisingly little is known about the structure and function of coilin, and a comprehensive model to explain the origin of Cajal bodies is also lacking. Here, I summarize recent results on Cajal bodies and coilin and discuss them in the context of the last three decades of research in this field.
Collapse
Affiliation(s)
- David Staněk
- Laboratory of RNA Biology, Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| |
Collapse
|
9
|
Wang H, Cai G, Yu F, Li D, Wang C, Ma D, Han X, Chen J, Wang C, He J. Changes in the small noncoding RNA transcriptome in osteosarcoma cells. J Orthop Surg Res 2023; 18:898. [PMID: 38001513 PMCID: PMC10675919 DOI: 10.1186/s13018-023-04362-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Osteosarcoma has the highest incidence among bone malignant tumors and mainly occurs in adolescents and the elderly, but the pathological mechanism is still unclear, which makes early diagnosis and treatment very difficult. Bone marrow mesenchymal stem cells (BMSCs) are considered to be one of the sources of osteosarcoma cells. Therefore, a full understanding of the gene expression differences between BMSCs and osteosarcoma cells is very important to explore the pathogenesis of osteosarcoma and facilitate the early diagnosis and treatment of osteosarcoma. Small noncoding RNAs (sncRNAs) are a class of RNAs that do not encode proteins but directly play biological functions at the RNA level. SncRNAs mainly include Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), repeat RNAs and microRNAs (miRNAs). METHODS In this study, we compared the expression of sncRNAs in BMSCs and osteosarcoma cells by high-throughput sequencing and qPCR and looked for differentially expressed sncRNAs. CCK-8, clone formation and transwell assay were used to detect the effect of sncRNA in MG63 cells. RESULTS We found that 66 piRNAs were significantly upregulated and 70 piRNAs were significantly downregulated in MG63 cells. As for snoRNAs, 71 snoRNAs were significantly upregulated and 117 snoRNAs were significantly downregulated in MG63 cells. As for snRNAs, 35 snRNAs were significantly upregulated and 17 snRNAs were significantly downregulated in MG63 cells. As for repeat RNAs, 6 repeat RNAs were significantly upregulated and 7 repeat RNAs were significantly downregulated in MG63 cells. As for miRNAs, 326 miRNAs were significantly upregulated and 281 miRNAs were significantly downregulated in MG63 cells. Overexpression of piRNA DQ596225, snoRNA ENST00000364830.2, snRNA ENST00000410533.1 and miRNA hsa-miR-369-5p inhibited the proliferation and migration of MG63 cells. CONCLUSIONS Our results provide a theoretical basis for the pathogenesis, early diagnosis and treatment of osteosarcoma.
Collapse
Affiliation(s)
- Hui Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Guiquan Cai
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Fengbin Yu
- Department of Orthopaedics, The 72nd Group Army Hospital of PLA, Huzhou, 313000, Zhejiang, People's Republic of China
| | - De Li
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Chenglong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Ding Ma
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Xiuguo Han
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China
| | - Jiajia Chen
- Department of Spine Surgery, The Second Affiliated Hospital of Nantong University, Nantong University, Nantong, 226001, Jiangsu, People's Republic of China
| | - Chuandong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China.
| | - Jiye He
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, People's Republic of China.
| |
Collapse
|
10
|
Chen Q, Zhou T. Emerging functional principles of tRNA-derived small RNAs and other regulatory small RNAs. J Biol Chem 2023; 299:105225. [PMID: 37673341 PMCID: PMC10562873 DOI: 10.1016/j.jbc.2023.105225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Recent advancements in small RNA sequencing have unveiled a previously hidden world of regulatory small noncoding RNAs (sncRNAs) that extend beyond the well-studied small interfering RNAs, microRNAs, and piwi-interacting RNAs. This exploration, starting with tRNA-derived small RNAs, has led to the discovery of a diverse universe of sncRNAs derived from various longer structured RNAs such as rRNAs, small nucleolar RNAs, small nuclear RNAs, Y RNAs, and vault RNAs, with exciting uncharted functional possibilities. In this perspective, we discuss the emerging functional principles of sncRNAs beyond the well-known RNAi-like mechanisms, focusing on those that operate independent of linear sequence complementarity but rather function in an aptamer-like fashion. Aptamers use 3D structure for specific interactions with ligands and are modulated by RNA modifications and subcellular environments. Given that aptamer-like sncRNA functions are widespread and present in species lacking RNAi, they may represent an ancient functional principle that predates RNAi. We propose a rethinking of the origin of RNAi and its relationship with these aptamer-like functions in sncRNAs and how these complementary mechanisms shape biological processes. Lastly, the aptamer-like function of sncRNAs highlights the need for caution in using small RNA mimics in research and therapeutics, as their specificity is not restricted solely to linear sequence.
Collapse
Affiliation(s)
- Qi Chen
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah, USA; Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA.
| |
Collapse
|
11
|
Kabzinski J, Kucharska-Lusina A, Majsterek I. RNA-Based Liquid Biopsy in Head and Neck Cancer. Cells 2023; 12:1916. [PMID: 37508579 PMCID: PMC10377854 DOI: 10.3390/cells12141916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Head and neck cancer (HNC) is a prevalent and diverse group of malignancies with substantial morbidity and mortality rates. Early detection and monitoring of HNC are crucial for improving patient outcomes. Liquid biopsy, a non-invasive diagnostic approach, has emerged as a promising tool for cancer detection and monitoring. In this article, we review the application of RNA-based liquid biopsy in HNC. Various types of RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), circular RNA (circRNA) and PIWI-interacting RNA (piRNA), are explored as potential biomarkers in HNC liquid-based diagnostics. The roles of RNAs in HNC diagnosis, metastasis, tumor resistance to radio and chemotherapy, and overall prognosis are discussed. RNA-based liquid biopsy holds great promise for the early detection, prognosis, and personalized treatment of HNC. Further research and validation are necessary to translate these findings into clinical practice and improve patient outcomes.
Collapse
Affiliation(s)
- Jacek Kabzinski
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Aleksandra Kucharska-Lusina
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| |
Collapse
|
12
|
Fornaini NR, Bergelová B, Gvoždík V, Černohorská H, Krylov V, Kubíčková S, Fokam EB, Badjedjea G, Evans BJ, Knytl M. Consequences of polyploidy and divergence as revealed by cytogenetic mapping of tandem repeats in African clawed frogs ( Xenopus, Pipidae). EUR J WILDLIFE RES 2023; 69:81. [PMID: 37483536 PMCID: PMC10361878 DOI: 10.1007/s10344-023-01709-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/13/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Repetitive elements have been identified in several amphibian genomes using whole genome sequencing, but few studies have used cytogenetic mapping to visualize these elements in this vertebrate group. Here, we used fluorescence in situ hybridization and genomic data to map the U1 and U2 small nuclear RNAs and histone H3 in six species of African clawed frog (genus Xenopus), including, from subgenus Silurana, the diploid Xenopus tropicalis and its close allotetraploid relative X. calcaratus and, from subgenus Xenopus, the allotetraploid species X. pygmaeus, X. allofraseri, X. laevis, and X. muelleri. Results allowed us to qualitatively evaluate the relative roles of polyploidization and divergence in the evolution of repetitive elements because our focal species include allotetraploid species derived from two independent polyploidization events - one that is relatively young that gave rise to X. calcaratus and another that is older that gave rise to the other (older) allotetraploids. Our results demonstrated conserved loci number and position of signals in the species from subgenus Silurana; allotetraploid X. calcaratus has twice as many signals as diploid X. tropicalis. However, the content of repeats varied among the other allotetraploid species. We detected almost same number of signals in X. muelleri as in X. calcaratus and same number of signals in X. pygmaeus, X. allofraseri, X. laevis as in the diploid X. tropicalis. Overall, these results are consistent with the proposal that allopolyploidization duplicated these tandem repeats and that variation in their copy number was accumulated over time through reduction and expansion in a subset of the older allopolyploids.
Collapse
Affiliation(s)
- Nicola R. Fornaini
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
| | - Barbora Bergelová
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Zoology, National Museum of the Czech Republic, Prague, Czech Republic
| | - Halina Černohorská
- Department of Genetics and Reproduction, CEITEC - Veterinary Research Institute, Hudcova 296/70, Brno, 62100 Czech Republic
| | - Vladimír Krylov
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
| | - Svatava Kubíčková
- Department of Genetics and Reproduction, CEITEC - Veterinary Research Institute, Hudcova 296/70, Brno, 62100 Czech Republic
| | - Eric B. Fokam
- Department of Animal Biology and Conservation, University of Buea, PO Box 63, Buea, 00237 Cameroon
| | - Gabriel Badjedjea
- Department of Aquatic Ecology, Biodiversity Monitoring Center, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Ben J. Evans
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S4K1 Canada
| | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843 Czech Republic
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, ON L8S4K1 Canada
| |
Collapse
|
13
|
Happi Mbakam C, Tremblay JP. Gene therapy for Duchenne muscular dystrophy: an update on the latest clinical developments. Expert Rev Neurother 2023; 23:905-920. [PMID: 37602688 DOI: 10.1080/14737175.2023.2249607] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/15/2023] [Indexed: 08/22/2023]
Abstract
INTRODUCTION Duchenne muscular dystrophy (DMD) is one of the most severe and devastating neuromuscular hereditary diseases with a male newborn incidence of 20 000 cases each year. The disease caused by mutations (exon deletions, nonsense mutations, intra-exonic insertions or deletions, exon duplications, splice site defects, and deep intronic mutations) in the DMD gene, progressively leads to muscle wasting and loss of ambulation. This situation is painful for both patients and their families, calling for an emergent need for effective treatments. AREAS COVERED In this review, the authors describe the state of the gene therapy approach in clinical trials for DMD. This therapeutics included gene replacement, gene substitution, RNA-based therapeutics, readthrough mutation, and the CRISPR approach. EXPERT OPINION Only a few drug candidates have yet been granted conditional approval for the treatment of DMD. Most of these therapies have only a modest capability to restore the dystrophin or improve muscle function, suggesting an important unmet need in the development of DMD therapeutics. Complementary genes and cellular therapeutics need to be explored to both restore dystrophin, improve muscle function, and efficiently reconstitute the muscle fibers in the advanced stage of the disease.
Collapse
Affiliation(s)
- Cedric Happi Mbakam
- CHU de Québec research centre, Laval University, Québec, Canada
- Molecular Medicine Department, Faculty of Medicine, Laval University, Québec, Canada
| | - Jacques P Tremblay
- CHU de Québec research centre, Laval University, Québec, Canada
- Molecular Medicine Department, Faculty of Medicine, Laval University, Québec, Canada
| |
Collapse
|
14
|
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
|
15
|
Wang Y, Liu T, Xiao W, Bai Y, Yue D, Feng L. Ox-LDL induced profound changes of small non-coding RNA in rat endothelial cells. Front Cardiovasc Med 2023; 10:1060719. [PMID: 36824457 PMCID: PMC9941181 DOI: 10.3389/fcvm.2023.1060719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
Introduction Atherosclerosis (AS) is a common cardiovascular disease with a high incidence rate and mortality. Endothelial cell injury and dysfunction are early markers of AS. Oxidative low-density lipoprotein (Ox-LDL) is a key risk factor for the development of AS. Ox-LDL promotes endothelial cell apoptosis and induces inflammation and oxidative stress in endothelial cells. Small non-coding RNAs (sncRNAs) mainly include Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), microRNAs (miRNAs) and repeat-associated RNAs. Studies have shown that small non-coding RNAs play an increasingly important role in diseases. Methods We used ox-LDL to treat rat endothelial cells to simulate endothelial cell injury. The expression changes of sncRNA were analyzed by small RNA high-throughput sequencing, and the expression changes of piRNA, snoRNA, snRNA, miRNA and repeat-associated RNA were verified by quantitative polymerase chain reaction (qPCR). Results Small RNA sequencing showed that 42 piRNAs were upregulated and 38 piRNAs were downregulated in endothelial cells treated with ox-LDL. PiRNA DQ614630 promoted the apoptosis of endothelial cells. The snoRNA analysis results showed that 80 snoRNAs were upregulated and 68 snoRNAs were downregulated in endothelial cells with ox-LDL treatment, and snoRNA ENSRNOT00000079032.1 inhibited the apoptosis of endothelial cells. For snRNA, we found that 20 snRNAs were upregulated and 26 snRNAs were downregulated in endothelial cells with ox-LDL treatment, and snRNA ENSRNOT00000081005.1 increased the apoptosis of endothelial cells. Analysis of miRNAs indicated that 106 miRNAs were upregulated and 91 miRNAs were downregulated in endothelial cells with ox-LDL treatment, and miRNA rno-novel-136-mature promoted the apoptosis of endothelial cells. The repeat RNA analysis results showed that 4 repeat RNAs were upregulated and 6 repeat RNAs were downregulated in endothelial cells treated with ox-LDL. Discussion This study first reported the expression changes of sncRNAs in endothelial cells with ox-LDL treatment, which provided new markers for the diagnosis and treatment of endothelial cell injury.
Collapse
Affiliation(s)
| | | | - Wenying Xiao
- Department of Cardiology, Shidong Hospital, Shidong Hospital Affiliated to University of Shanghai for Science and Technology, Shanghai, China
| | | | | | | |
Collapse
|
16
|
Tseng CK, Cheng SC. Arresting Spliceosome Intermediates at Various Stages of the Splicing Pathway. Methods Mol Biol 2023; 2666:193-211. [PMID: 37166667 DOI: 10.1007/978-1-0716-3191-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The spliceosome is a dynamic ribonucleoprotein particle and is assembled via sequential binding of five snRNAs and numerous protein factors. To understand the molecular mechanism of the splicing reaction, it is necessary to dissect the spliceosome pathway and isolate spliceosome intermediates in various stages of the pathway for biochemical and structural analysis. Here, we describe protocols for preparing intron-containing transcripts, cell-free splicing extracts, and in vitro splicing reactions, as well as procedures to arrest the spliceosome at different stages of the pathway for characterization of specific splicing complexes from the budding yeast Saccharomyces cerevisiae. Methods for arresting spliceosomes at specific stages include depletion with antibodies against factors required for specific steps of the pathway, use of extracts prepared from temperature-sensitive mutants, use of dominant negative mutants of DExD/H-box proteins, and use of mutant substrates.
Collapse
Affiliation(s)
- Chi-Kang Tseng
- Graduate Institute of Microbiology, National Taiwan University, College of Medicine, Taipei, Taiwan, Republic of China
| | - Soo-Chen Cheng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China.
| |
Collapse
|
17
|
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 Interdiscip Rev RNA 2023; 14:e1761. [PMID: 36056453 DOI: 10.1002/wrna.1761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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
|
18
|
Love SL, Emerson JD, Koide K, Hoskins AA. Pre-mRNA splicing-associated diseases and therapies. RNA Biol 2023; 20:525-538. [PMID: 37528617 PMCID: PMC10399480 DOI: 10.1080/15476286.2023.2239601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023] Open
Abstract
Precursor mRNA (pre-mRNA) splicing is an essential step in human gene expression and is carried out by a large macromolecular machine called the spliceosome. Given the spliceosome's role in shaping the cellular transcriptome, it is not surprising that mutations in the splicing machinery can result in a range of human diseases and disorders (spliceosomopathies). This review serves as an introduction into the main features of the pre-mRNA splicing machinery in humans and how changes in the function of its components can lead to diseases ranging from blindness to cancers. Recently, several drugs have been developed that interact directly with this machinery to change splicing outcomes at either the single gene or transcriptome-scale. We discuss the mechanism of action of several drugs that perturb splicing in unique ways. Finally, we speculate on what the future may hold in the emerging area of spliceosomopathies and spliceosome-targeted treatments.
Collapse
Affiliation(s)
- Sierra L Love
- Genetics Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Joseph D Emerson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
19
|
Guglas K, Kozłowska-Masłoń J, Kolenda T, Paszkowska A, Teresiak A, Bliźniak R, Lamperska K. Midsize noncoding RNAs in cancers: a new division that clarifies the world of noncoding RNA or an unnecessary chaos? Rep Pract Oncol Radiother 2022; 27:1077-93. [PMID: 36632289 DOI: 10.5603/RPOR.a2022.0123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/18/2022] [Indexed: 12/31/2022] Open
Abstract
Most of the human genome is made out of noncoding RNAs (ncRNAs). These ncRNAs do not code for proteins but carry a vast number of important functions in human cells such as: modification and processing other RNAs (tRNAs, rRNAs, snRNAs, snoRNAs, miRNAs), help in the synthesis of ribosome proteins, initiation of DNA replication, regulation of transcription, processing of pre-messenger mRNA during its maturation and much more. The ncRNAs also have a significant impact on many events that occur during carcinogenesis in cancer cells, such as: regulation of cell survival, cellular signaling, apoptosis, proliferation or even influencing the metastasis process. The ncRNAs may be divided based on their length, into short and long, where 200 nucleotides is the "magic" border. However, a new division was proposed, suggesting the creation of the additional group called midsize noncoding RNAs, with the length ranging from 50-400 nucleotides. This new group may include: transfer RNA (tRNA), small nuclear RNAs (snRNAs) with 7SK and 7SL, small nucleolar RNAs (snoRNAs), small Cajal body-specific RNAs (scaRNAs) and YRNAs. In this review their structure, biogenesis, function and influence on carcinogenesis process will be evaluated. What is more, a question will be answered of whether this new division is a necessity that clears current knowledge or just creates an additional misunderstanding in the ncRNA world?
Collapse
|
20
|
Lipinski KA, Chi J, Chen X, Hoskins AA, Brow DA. Yeast U6 snRNA made by RNA polymerase II is less stable but functional. RNA 2022; 28:1606-1620. [PMID: 36195346 PMCID: PMC9670810 DOI: 10.1261/rna.079328.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
U6 small nuclear (sn)RNA is the shortest and most conserved snRNA in the spliceosome and forms a substantial portion of its active site. Unlike the other four spliceosomal snRNAs, which are synthesized by RNA polymerase (RNAP) II, U6 is made by RNAP III. To determine if some aspect of U6 function is incompatible with synthesis by RNAP II, we created a U6 snRNA gene with RNAP II promoter and terminator sequences. This "U6-II" gene is functional as the sole source of U6 snRNA in yeast, but its transcript is much less stable than U6 snRNA made by RNAP III. Addition of the U4 snRNA Sm protein binding site to U6-II increased its stability and led to formation of U6-II•Sm complexes. We conclude that synthesis of U6 snRNA by RNAP III is not required for its function and that U6 snRNPs containing the Sm complex can form in vivo. The ability to synthesize U6 snRNA with RNAP II relaxes sequence restraints imposed by intragenic RNAP III promoter and terminator elements and allows facile control of U6 levels via regulators of RNAP II transcription.
Collapse
Affiliation(s)
- Karli A Lipinski
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jing Chi
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - Xin Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Aaron A Hoskins
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| |
Collapse
|
21
|
Hatch ST, Smargon AA, Yeo GW. Engineered U1 snRNAs to modulate alternatively spliced exons. Methods 2022; 205:140-148. [PMID: 35764245 DOI: 10.1016/j.ymeth.2022.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/30/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022] Open
Abstract
Alternative splicing accounts for a considerable portion of transcriptomic diversity, as most protein-coding genes are spliced into multiple mRNA isoforms. However, errors in splicing patterns can give rise to mis-splicing with pathological consequences, such as the congenital diseases familial dysautonomia, Duchenne muscular dystrophy, and spinal muscular atrophy. Small nuclear RNA (snRNA) components of the U snRNP family have been proposed as a therapeutic modality for the treatment of mis-splicing. U1 snRNAs offer great promise, with prior studies demonstrating in vivo efficacy, suggesting additional preclinical development is merited. Improvements in enabling technologies, including screening methodologies, gene delivery vectors, and relevant considerations from gene editing approaches justify further advancement of U1 snRNA as a therapeutic and research tool. With the goal of providing a user-friendly protocol, we compile and demonstrate a methodological toolkit for sequence-specific targeted perturbation of alternatively spliced pre-mRNA with engineered U1 snRNAs. We observe robust modulation of endogenous pre-mRNA transcripts targeted in two contrasting splicing contexts, SMN2 exon 7 and FAS exon 6, exhibiting the utility and applicability of engineered U1 snRNA to both inclusion and exclusion of targeted exons. We anticipate that these demonstrations will contribute to the usability of U1 snRNA in investigating splicing modulation in eukaryotic cells, increasing accessibility to the broader research community.
Collapse
Affiliation(s)
- Samuel T Hatch
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Aaron A Smargon
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA; Stem Cell Program, University of California San Diego, Sanford Consortium for Regenerative Medicine, La Jolla, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
22
|
Buel SM, Debopadhaya S, De los Santos H, Edwards KM, David AM, Dao UH, Bennett KP, Hurley JM. The PAICE suite reveals circadian posttranscriptional timing of noncoding RNAs and spliceosome components in Mus musculus macrophages. G3 (Bethesda) 2022; 12:6649694. [PMID: 35876788 PMCID: PMC9434326 DOI: 10.1093/g3journal/jkac176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/27/2022] [Indexed: 01/07/2023]
Abstract
Circadian rhythms broadly regulate physiological functions by tuning oscillations in the levels of mRNAs and proteins to the 24-h day/night cycle. Globally assessing which mRNAs and proteins are timed by the clock necessitates accurate recognition of oscillations in RNA and protein data, particularly in large omics data sets. Tools that employ fixed-amplitude models have previously been used to positive effect. However, the recognition of amplitude change in circadian oscillations required a new generation of analytical software to enhance the identification of these oscillations. To address this gap, we created the Pipeline for Amplitude Integration of Circadian Exploration suite. Here, we demonstrate the Pipeline for Amplitude Integration of Circadian Exploration suite's increased utility to detect circadian trends through the joint modeling of the Mus musculus macrophage transcriptome and proteome. Our enhanced detection confirmed extensive circadian posttranscriptional regulation in macrophages but highlighted that some of the reported discrepancy between mRNA and protein oscillations was due to noise in data. We further applied the Pipeline for Amplitude Integration of Circadian Exploration suite to investigate the circadian timing of noncoding RNAs, documenting extensive circadian timing of long noncoding RNAs and small nuclear RNAs, which control the recognition of mRNA in the spliceosome complex. By tracking oscillating spliceosome complex proteins using the PAICE suite, we noted that the clock broadly regulates the spliceosome, particularly the major spliceosome complex. As most of the above-noted rhythms had damped amplitude changes in their oscillations, this work highlights the importance of the PAICE suite in the thorough enumeration of oscillations in omics-scale datasets.
Collapse
Affiliation(s)
| | | | | | - Kaelyn M Edwards
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Alexandra M David
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Uyen H Dao
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Kristin P Bennett
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA,Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA,Institute for Data Exploration and Applications, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jennifer M Hurley
- Corresponding author: Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| |
Collapse
|
23
|
Zhou S, Dong J, Xiong M, Gan S, Wen Y, Zhang J, Wang X, Yuan S, Gui Y. UHRF1 interacts with snRNAs and regulates alternative splicing in mouse spermatogonial stem cells. Stem Cell Reports 2022; 17:1859-1873. [PMID: 35905740 PMCID: PMC9391524 DOI: 10.1016/j.stemcr.2022.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 12/22/2022] Open
Abstract
Life-long male fertility relies on exquisite homeostasis and the development of spermatogonial stem cells (SSCs); however, the underlying molecular genetic and epigenetic regulation in this equilibrium process remains unclear. Here, we document that UHRF1 interacts with snRNAs to regulate pre-mRNA alternative splicing in SSCs and is required for the homeostasis of SSCs in mice. Genetic deficiency of UHRF1 in mouse prospermatogonia results in gradual loss of spermatogonial stem cells, eventually leading to Sertoli-cell-only syndrome (SCOS) and male infertility. Comparative RNA-seq data provide evidence that Uhrf1 ablation dysregulates previously reported SSC maintenance- and differentiation-related genes. We further found that UHRF1 could act as an alternative RNA splicing regulator and interact with Tle3 transcripts to regulate its splicing event in spermatogonia. Collectively, our data reveal a multifunctional role for UHRF1 in regulating gene expression programs and alternative splicing during SSC homeostasis, which may provide clues for treating human male infertility.
Collapse
Affiliation(s)
- Shumin Zhou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Juan Dong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mengneng Xiong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shiming Gan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yujiao Wen
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jin Zhang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuiqiao Yuan
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Laboratory Animal Center, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong 518057, China.
| | - Yaoting Gui
- Guangdong Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Shenzhen, Guangdong 518036, China.
| |
Collapse
|
24
|
Ma D, Zhou X, Wang Y, Dai L, Yuan J, Peng J, Zhang X, Wang C. Changes in the Small Noncoding RNAome During M1 and M2 Macrophage Polarization. Front Immunol 2022; 13:799733. [PMID: 35619693 PMCID: PMC9127141 DOI: 10.3389/fimmu.2022.799733] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/01/2022] [Indexed: 12/14/2022] Open
Abstract
Macrophages belong to a special phagocytic subgroup of human leukocytes and are one of the important cells of the human immune system. Small noncoding RNAs are a group of small RNA molecules that can be transcribed without the ability to encode proteins but could play a specific function in cells. SncRNAs mainly include microRNAs (miRNAs) and piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs) and repeat RNAs. We used high-throughput sequencing analysis and qPCR to detect the expression changes of the small noncoding RNAome during macrophage polarization. Our results showed that 84 miRNAs and 47 miRNAs with were downregulated during M1 macrophage polarization and that 11 miRNAs were upregulated and 19 miRNAs were downregulated during M2 macrophage polarization. MiR-novel-3-nature and miR-27b-5p could promote expression of TNF-α which was marker gene of M1 macrophages. The piRNA analysis results showed that 69 piRNAs were upregulated and 61 piRNAs were downregulated during M1 macrophage polarization and that 3 piRNAs were upregulated and 10 piRNAs were downregulated during M2 macrophage polarization. DQ551351 and DQ551308 could promote the mRNA expression of TNF-α and DQ551351overexpression promoted the antitumor activity of M1 macrophages. SnoRNA results showed that 62 snoRNAs were upregulated and 59 snoRNAs were downregulated during M1 macrophage polarization, whereas 6 snoRNAs were upregulated and 10 snoRNAs were downregulated during M2 macrophage polarization. Overexpression of snoRNA ENSMUST00000158683.2 could inhibit expression of TNF-α. For snRNA, we found that 12 snRNAs were upregulated and 15 snRNAs were downregulated during M1 macrophage polarization and that 2 snRNAs were upregulated during M2 macrophage polarization. ENSMUSG00000096786 could promote expression of IL-1 and iNOS and ENSMUSG00000096786 overexpression promoted the antitumor activity of M1 macrophages. Analysis of repeat RNAs showed that 7 repeat RNAs were upregulated and 9 repeat RNAs were downregulated during M1 macrophage polarization and that 2 repeat RNAs were downregulated during M2 macrophage polarization. We first reported the expression changes of piRNA, snoRNA, snRNA and repeat RNA during macrophage polarization, and preliminarily confirmed that piRNA, snoRNA and snRNA can regulate the function of macrophages.
Collapse
Affiliation(s)
- Ding Ma
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Xing Zhou
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, China
| | - Yu Wang
- Department of Cardiology, Shidong Hospital Affiliated to University of Shanghai for Science and Technology, Shanghai, China
| | - Liming Dai
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Jie Yuan
- Department of Orthopaedic Surgery, The Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Jianping Peng
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Xiaoling Zhang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Chuandong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| |
Collapse
|
25
|
Xiao F, Peng J, Li Y, Zhou X, Ma D, Dai L, Yuan J, Chen X, Wang C. Small Noncoding RNAome Changes During Human Bone Marrow Mesenchymal Stem Cells Senescence In Vitro. Front Endocrinol (Lausanne) 2022; 13:808223. [PMID: 35634512 PMCID: PMC9135970 DOI: 10.3389/fendo.2022.808223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Bone marrow mesenchymal stem cells (BMSCs) have been used in stem cell-based therapy for various diseases due to their self-renewing ability and differentiation potential to various types of cells and immunoprivileged properties. However, the proliferation capability and functionality of BMSCs are known to decline with aging, which severely limits the extensive applications of BMSC-based therapies. To date, the exact mechanism involved in the cellular senescence of BMSCs remains unclear. RNA is thought to be the initial molecular form of life on earth. It also acts as a transmitter and important regulator of genetic information expression. There are many kinds of small noncoding RNAs with different functions in cells that regulate important life activity processes in multiple dimensions, including development process, gene expression, genomic stability, and cellular senescence. In this study, a replicative senescence model of hBMSCs was established and the expression changes of small noncoding RNAs during senescence were detected by small RNA high-throughput sequencing analysis and qPCR. Small RNA sequencing results showed that there were significant differences in the expression of 203 miRNAs, 46 piRNAs, 63 snoRNAs, 12 snRNAs, and 7 rasiRNAs. The results of qPCR, which was performed for the verification of the sequencing results, showed that there were significant differences in the expression of 24 miRNAs, 34 piRNAs, 34 snoRNAs, and 2 snRNAs. These findings might provide a novel insight into hBMSC senescence and contribute to the development of new targeting senescence strategies.
Collapse
Affiliation(s)
- Fei Xiao
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Jianping Peng
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Yang Li
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Xing Zhou
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University Nanning, Guangxi, China
| | - Ding Ma
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Liming Dai
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
| | - Jie Yuan
- Department of Orthopaedic Surgery, The Second Hospital of Shanxi Medical University, TaiYuan, China
| | - Xiaodong Chen
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
- *Correspondence: Xiaodong Chen, ; Chuandong Wang,
| | - Chuandong Wang
- Department of Orthopedic Surgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
- *Correspondence: Xiaodong Chen, ; Chuandong Wang,
| |
Collapse
|
26
|
Santos da Silva K, de Souza ACP, Pety AM, Noronha RCR, Vicari MR, Pieczarka JC, Nagamachi CY. Comparative Cytogenetics Analysis Among Peckoltia Species (Siluriformes, Loricariidae): Insights on Karyotype Evolution and Biogeography in the Amazon Region. Front Genet 2021; 12:779464. [PMID: 34777486 PMCID: PMC8581261 DOI: 10.3389/fgene.2021.779464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Peckoltia is widely distributed genus in the Amazon and Orinoco basins and the Guiana Shield, containing 18 valid species, and distinct morphotypes still needing description in the scientific literature due to its great taxonomic complexity. This study performed a comparative chromosomal analysis of two undescribed Peckoltia species (Peckoltia sp. 3 Jarumã and Peckoltia sp. 4 Caripetuba) from the Brazilian Amazon using conventional chromosome bands methods and in situ localization of the repetitive DNA (5S and 18S rRNA and U1 snRNA genes and telomeric sequences). Both species presented 2n = 52 but differed in their karyotype formula, probably due to inversions or translocations. The nucleolus organizer regions (NORs) showed distal location on a probably homeologous submetacentric pair in both species, besides an extra signal in a subtelocentric chromosome in Peckoltia sp. 4 Caripetuba. Heterochromatin occurred in large blocks, with different distributions in the species. The mapping of the 18S and 5S rDNA, and U1 snDNA showed differences in locations and number of sites. No interstitial telomeric sites were detected using the (TTAGGG)n probes. Despite 2n conservationism in Peckoltia species, the results showed variation in karyotype formulas, chromosomal bands, and locations of repetitive sites, demonstrating great chromosomal diversity. A proposal for Peckoltia karyotype evolution was inferred in this study based on the diversity of location and number of chromosomal markers analyzed. A comparative analysis with other Peckoltia karyotypes described in the literature, their biogeography patterns, and molecular phylogeny led to the hypothesis that the derived karyotype was raised in the left bank of the Amazon River.
Collapse
Affiliation(s)
- Kevin Santos da Silva
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, Brazil
| | - Augusto Cesar Paes de Souza
- Laboratório de Estudos da Ictiofauna da Amazônia, Instituto Federal de Educação Ciência e Tecnologia Do Pará, Abaetetuba, Brazil
| | - Ananda Marques Pety
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, Brazil
| | - Renata Coelho Rodrigues Noronha
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, Brazil
| | - Marcelo Ricardo Vicari
- Laboratório de Biologia Cromossômica, Estrutura e Função, Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Julio Cesar Pieczarka
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, Brazil
| | - Cleusa Yoshiko Nagamachi
- Laboratório de Citogenética, Centro de Estudos Avançados da Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal Do Pará, Belém, Brazil
| |
Collapse
|
27
|
Pfleiderer MM, Galej WP. Emerging insights into the function and structure of the Integrator complex. Transcription 2021; 12:251-265. [PMID: 35311473 PMCID: PMC9006982 DOI: 10.1080/21541264.2022.2047583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/03/2022] Open
Abstract
The Integrator was originally discovered as a specialized 3'-end processing endonuclease complex required for maturation of RNA polymerase II (RNAPII)-dependent small nuclear RNAs (snRNAs). Since its discovery, Integrator's spectrum of substrates was significantly expanded to include non-polyadenylated long noncoding RNAs (lncRNA), enhancer RNAs (eRNAs), telomerase RNA (tertRNA), several Herpesvirus transcripts, and messenger RNAs (mRNAs). Recently emerging transcriptome-wide studies reveled an important role of the Integrator in protein-coding genes, where it contributes to gene expression regulation through promoter-proximal transcription attenuation. These new functional data are complemented by several structures of Integrator modules and higher-order complexes, providing mechanistic insights into Integrator-mediated processing events. In this work, we summarize recent progress in our understanding of the structure and function of the Integrator complex.
Collapse
|
28
|
Mabin JW, Lewis PW, Brow DA, Dvinge H. Human spliceosomal snRNA sequence variants generate variant spliceosomes. RNA 2021; 27:1186-1203. [PMID: 34234030 PMCID: PMC8457000 DOI: 10.1261/rna.078768.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/29/2021] [Indexed: 06/02/2023]
Abstract
Human pre-mRNA splicing is primarily catalyzed by the major spliceosome, comprising five small nuclear ribonucleoprotein complexes, U1, U2, U4, U5, and U6 snRNPs, each of which contains the corresponding U-rich snRNA. These snRNAs are encoded by large gene families exhibiting significant sequence variation, but it remains unknown if most human snRNA genes are untranscribed pseudogenes or produce variant snRNAs with the potential to differentially influence splicing. Since gene duplication and variation are powerful mechanisms of evolutionary adaptation, we sought to address this knowledge gap by systematically profiling human U1, U2, U4, and U5 snRNA variant gene transcripts. We identified 55 transcripts that are detectably expressed in human cells, 38 of which incorporate into snRNPs and spliceosomes in 293T cells. All U1 snRNA variants are more than 1000-fold less abundant in spliceosomes than the canonical U1, whereas at least 1% of spliceosomes contain a variant of U2 or U4. In contrast, eight U5 snRNA sequence variants occupy spliceosomes at levels of 1% to 46%. Furthermore, snRNA variants display distinct expression patterns across five human cell lines and adult and fetal tissues. Different RNA degradation rates contribute to the diverse steady state levels of snRNA variants. Our findings suggest that variant spliceosomes containing noncanonical snRNAs may contribute to different tissue- and cell-type-specific alternative splicing patterns.
Collapse
Affiliation(s)
- Justin W Mabin
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - Peter W Lewis
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - Heidi Dvinge
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| |
Collapse
|
29
|
Lin C, Feng Y, Peng X, Wu J, Wang W, Liu Y. U2.3 Precursor Small Nuclear RNA in vitro Processing Assay. Bio Protoc 2021; 11:e4142. [PMID: 34604448 DOI: 10.21769/bioprotoc.4142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/17/2021] [Accepted: 05/17/2021] [Indexed: 11/02/2022] Open
Abstract
Small nuclear RNAs (snRNAs) are vital for eukaryotic cell activities and play important roles in pre-mRNA splicing. The molecular mechanism underlying the transcription of snRNA, regulated via upstream/downstream cis-elements and relevant trans-elements, has been investigated in detail using cell-free extracts. However, the processing of precursor snRNA (pre-snRNA), which is required by 3' end maturation of pre-snRNA, remains unclear as a proper processing assay is difficult to develop in vitro. Here, we present an in vitro method using synthetic labeled RNA as substrates to study the 3' cleavage of pre-snRNA.
Collapse
Affiliation(s)
- Chan Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Yujie Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Xueyan Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Jiaming Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Weili Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| |
Collapse
|
30
|
Lin TY, Mehta R, Glatt S. Pseudouridines in RNAs: switching atoms means shifting paradigms. FEBS Lett 2021; 595:2310-2322. [PMID: 34468991 PMCID: PMC9290505 DOI: 10.1002/1873-3468.14188] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 01/21/2023]
Abstract
The structure, stability, and function of various coding and noncoding RNAs are influenced by chemical modifications. Pseudouridine (Ψ) is one of the most abundant post‐transcriptional RNA base modifications and has been detected at individual positions in tRNAs, rRNAs, mRNAs, and snRNAs, which are referred to as Ψ‐sites. By allowing formation of additional bonds with neighboring atoms, Ψ strengthens RNA–RNA and RNA–protein interactions. Although many aspects of the underlying modification reactions remain unclear, the advent of new transcriptome‐wide methods to quantitatively detect Ψ‐sites has recently changed our perception of the functional roles and importance of Ψ. For instance, it is now clear that the occurrence of Ψs appears to be directly linked to the lifetime and the translation efficiency of a given mRNA molecule. Furthermore, the administration of Ψ‐containing RNAs reduces innate immune responses, which appears strikingly advantageous for the development of generations of mRNA‐based vaccines. In this review, we aim to comprehensively summarize recent discoveries that highlight the impact of Ψ on various types of RNAs and outline possible novel biomedical applications of Ψ.
Collapse
Affiliation(s)
- Ting-Yu Lin
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Rahul Mehta
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Sebastian Glatt
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| |
Collapse
|
31
|
Bizarro J, Deryusheva S, Wacheul L, Gupta V, Ernst FGM, Lafontaine DLJ, Gall JG, Meier UT. Nopp140-chaperoned 2'-O-methylation of small nuclear RNAs in Cajal bodies ensures splicing fidelity. Genes Dev 2021; 35:1123-1141. [PMID: 34301768 PMCID: PMC8336889 DOI: 10.1101/gad.348660.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/29/2021] [Indexed: 12/27/2022]
Abstract
In this study, Bizarro et al. sought to understand the function and subcellular site of snRNA modification, and found that Cajal body (CB) localization of the protein Nopp140 is essential for concentration of small Cajal body-specific ribonucleoproteins (scaRNPs) in nuclear condensate and that phosphorylation by casein kinase 2 (CK2) at ∼80 serines targets Nopp140 to CBs. Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2′-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Spliceosomal small nuclear RNAs (snRNAs) are modified by small Cajal body (CB)-specific ribonucleoproteins (scaRNPs) to ensure snRNP biogenesis and pre-mRNA splicing. However, the function and subcellular site of snRNA modification are largely unknown. We show that CB localization of the protein Nopp140 is essential for concentration of scaRNPs in that nuclear condensate; and that phosphorylation by casein kinase 2 (CK2) at ∼80 serines targets Nopp140 to CBs. Transiting through CBs, snRNAs are apparently modified by scaRNPs. Indeed, Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2′-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Additionally, alternative splicing patterns change indicating that these modifications in U1, U2, U5, and U12 snRNAs safeguard splicing fidelity. Given the importance of CK2 in this pathway, compromised splicing could underlie the mode of action of small molecule CK2 inhibitors currently considered for therapy in cholangiocarcinoma, hematological malignancies, and COVID-19.
Collapse
Affiliation(s)
| | | | - Ludivine Wacheul
- RNA Molecular Biology, Fonds National de la Recherche Scientifique (FRS/FNRS), Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Varun Gupta
- Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Felix G M Ernst
- RNA Molecular Biology, Fonds National de la Recherche Scientifique (FRS/FNRS), Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds National de la Recherche Scientifique (FRS/FNRS), Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Joseph G Gall
- Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - U Thomas Meier
- Albert Einstein College of Medicine, Bronx, New York 10461, USA
| |
Collapse
|
32
|
Lester E, Ooi FK, Bakkar N, Ayers J, Woerman AL, Wheeler J, Bowser R, Carlson GA, Prusiner SB, Parker R. Tau aggregates are RNA-protein assemblies that mislocalize multiple nuclear speckle components. Neuron 2021; 109:1675-1691.e9. [PMID: 33848474 PMCID: PMC8141031 DOI: 10.1016/j.neuron.2021.03.026] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 02/05/2021] [Accepted: 03/18/2021] [Indexed: 12/13/2022]
Abstract
Tau aggregates contribute to neurodegenerative diseases, including frontotemporal dementia and Alzheimer's disease (AD). Although RNA promotes tau aggregation in vitro, whether tau aggregates in cells contain RNA is unknown. We demonstrate, in cell culture and mouse brains, that cytosolic and nuclear tau aggregates contain RNA with enrichment for small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). Nuclear tau aggregates colocalize with and alter the composition, dynamics, and organization of nuclear speckles, membraneless organelles involved in pre-mRNA splicing. Moreover, several nuclear speckle components, including SRRM2, mislocalize to cytosolic tau aggregates in cells, mouse brains, and brains of individuals with AD, frontotemporal dementia (FTD), and corticobasal degeneration (CBD). Consistent with these alterations, we observe that the presence of tau aggregates is sufficient to alter pre-mRNA splicing. This work identifies tau alteration of nuclear speckles as a feature of tau aggregation that may contribute to the pathology of tau aggregates.
Collapse
Affiliation(s)
- Evan Lester
- Department of Biochemistry, University of Colorado, Boulder, CO, USA; Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Felicia K Ooi
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Nadine Bakkar
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Jacob Ayers
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Amanda L Woerman
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Joshua Wheeler
- Department of Biochemistry, University of Colorado, Boulder, CO, USA; Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Robert Bowser
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - George A Carlson
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA.
| |
Collapse
|
33
|
Wong DK, Stark MS, Rader SD, Fast NM. Characterization of Pre-mRNA Splicing and Spliceosomal Machinery in Porphyridium purpureum and Evolutionary Implications for Red Algae. J Eukaryot Microbiol 2021; 68:e12844. [PMID: 33569840 DOI: 10.1111/jeu.12844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Abstract
Pre-mRNA splicing is a highly conserved eukaryotic process, but our understanding of it is limited by a historical focus on well-studied organisms such as humans and yeast. There is considerable diversity in mechanisms and components of pre-mRNA splicing, especially in lineages that have evolved under the pressures of genome reduction. The ancestor of red algae is thought to have undergone genome reduction prior to the lineage's radiation, resulting in overall gene and intron loss in extant groups. Previous studies on the extremophilic red alga Cyanidioschyzon merolae revealed an intron-sparse genome with a highly reduced spliceosome. To determine whether these features applied to other red algae, we investigated multiple aspects of pre-mRNA splicing in the mesophilic red alga Porphyridium purpureum. Through strand-specific RNA-Seq, we observed high levels of intron retention across a large number of its introns, and nearly half of the transcripts for these genes are not spliced at all. We also discovered a relationship between variability of 5' splice site sequences and levels of splicing. To further investigate the connections between intron retention and splicing machinery, we bioinformatically assembled the P. purpureum spliceosome, and biochemically verified the presence of snRNAs. While most other core spliceosomal components are present, our results suggest highly divergent or missing U1 snRNP proteins, despite the presence of an uncharacteristically long U1 snRNA. These unusual aspects highlight the diverse nature of pre-mRNA splicing that can be seen in lesser-studied eukaryotes, raising the importance of investigating fundamental eukaryotic processes outside of model organisms.
Collapse
Affiliation(s)
- Donald K Wong
- Department of Botany, University of British Columbia, 3156-6270 University Boulevard, Vancouver, BC, Canada
| | - Martha S Stark
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George, BC, Canada
| | - Stephen D Rader
- Department of Chemistry, University of Northern British Columbia, 3333 University Way, Prince George, BC, Canada
| | - Naomi M Fast
- Department of Botany, University of British Columbia, 3156-6270 University Boulevard, Vancouver, BC, Canada
| |
Collapse
|
34
|
Abstract
AS (alternative splicing) is a fundamental process by which a gene can generate multiple distinct mRNA transcripts to increase protein diversity. Defects in AS influence the occurrence and development of many diseases, including cancers, and are frequently found to participate in various aspects of cancer biology, such as promoting invasion, metastasis, apoptosis resistance and drug resistance. NcRNAs (noncoding RNAs) are an abundant class of RNAs that do not encode proteins. NcRNAs include miRNAs (microRNAs), lncRNAs (long noncoding RNAs), circRNAs (circular RNAs) and snRNAs (small nuclear RNAs) and have been proven to act as regulatory molecules that mediate cancer processes through AS. NcRNAs can directly or indirectly influence a plethora of molecular targets to regulate cis-acting elements, trans-acting factors, or pre-mRNA transcription at multiple levels, affecting the AS process and generating alternatively spliced isoforms. Consequently, ncRNA-mediated AS outcomes affect multiple cellular signaling pathways that promote or suppress cancer progression. In this review, we summarize the current mechanisms by which ncRNAs regulate AS in cancers and discuss their potential clinical applications as biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Yunze Liu
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Xin Liu
- Department of Endocrinology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Changwei Lin
- Department of Gastrointestinal Surgery, the Third XiangYa Hospital of Central South University, Changsha, 410013, China
| | - Xianhong Jia
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Hongmei Zhu
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Jun Song
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China.
| | - Yi Zhang
- Department of General Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China.
| |
Collapse
|
35
|
Rashnonejad A, Amini-Chermahini G, Taylor NK, Wein N, Harper SQ. Designed U7 snRNAs inhibit DUX4 expression and improve FSHD-associated outcomes in DUX4 overexpressing cells and FSHD patient myotubes. Mol Ther Nucleic Acids 2020; 23:476-486. [PMID: 33510937 PMCID: PMC7807095 DOI: 10.1016/j.omtn.2020.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/06/2020] [Indexed: 12/21/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) arises from epigenetic changes that de-repress the DUX4 gene in muscle. The full-length DUX4 protein causes cell death and muscle toxicity, and therefore we hypothesize that FSHD therapies should center on inhibiting full-length DUX4 expression. In this study, we developed a strategy to accomplish DUX4 inhibition using U7-small nuclear RNA (snRNA) antisense expression cassettes (called U7-asDUX4). These non-coding RNAs were designed to inhibit production or maturation of the full-length DUX4 pre-mRNA by masking the DUX4 start codon, splice sites, or polyadenylation signal. In so doing, U7-asDUX4 snRNAs operate similarly to antisense oligonucleotides. However, in contrast to oligonucleotides, which are limited by poor uptake in muscle and a requirement for lifelong repeated dosing, U7-asDUX4 snRNAs can be packaged within myotropic gene therapy vectors and may require only a single administration when delivered to post-mitotic cells in vivo. We tested several U7-asDUX4s that reduced DUX4 expression in vitro and improved DUX4-associated outcomes. Inhibition of DUX4 expression via U7-snRNAs could be a new prospective gene therapy approach for FSHD or be used in combination with other strategies, like RNAi therapy, to maximize DUX4 silencing in individuals with FSHD.
Collapse
Affiliation(s)
- Afrooz Rashnonejad
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Gholamhossein Amini-Chermahini
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Noah K Taylor
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA
| | - Nicolas Wein
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Scott Q Harper
- Center for Gene Therapy, The Abigail Wexner Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
36
|
Davidson L, Francis L, Eaton JD, West S. Integrator-Dependent and Allosteric/Intrinsic Mechanisms Ensure Efficient Termination of snRNA Transcription. Cell Rep 2020; 33:108319. [PMID: 33113359 PMCID: PMC7610016 DOI: 10.1016/j.celrep.2020.108319] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/25/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
Many RNA polymerases terminate transcription using allosteric/intrinsic mechanisms, whereby protein alterations or nucleotide sequences promote their release from DNA. RNA polymerase II (Pol II) is somewhat different based on its behavior at protein-coding genes where termination additionally requires endoribonucleolytic cleavage and subsequent 5'→3' exoribonuclease activity. The Pol-II-transcribed small nuclear RNAs (snRNAs) also undergo endoribonucleolytic cleavage by the Integrator complex, which promotes their transcriptional termination. Here, we confirm the involvement of Integrator but show that Integrator-independent processes can terminate snRNA transcription both in its absence and naturally. This is often associated with exosome degradation of snRNA precursors that long-read sequencing analysis reveals as frequently terminating at T-runs located downstream of some snRNAs. This finding suggests a unifying vulnerability of RNA polymerases to such sequences given their well-known roles in terminating Pol III and bacterial RNA polymerase.
Collapse
Affiliation(s)
- Lee Davidson
- The Living Systems Institute, University of Exeter, Stocker Rd, Exeter EX4 4QD, UK
| | - Laura Francis
- The Living Systems Institute, University of Exeter, Stocker Rd, Exeter EX4 4QD, UK
| | - Joshua D Eaton
- The Living Systems Institute, University of Exeter, Stocker Rd, Exeter EX4 4QD, UK
| | - Steven West
- The Living Systems Institute, University of Exeter, Stocker Rd, Exeter EX4 4QD, UK.
| |
Collapse
|
37
|
Dulz TA, Azambuja M, Nascimento VD, Lorscheider CA, Noleto RB, Moreira-Filho O, Nogaroto V, Diniz D, Affonso PRADM, Vicari MR. Karyotypic Diversification in Two Megaleporinus Species (Characiformes, Anostomidae) Inferred from In Situ Localization of Repetitive DNA Sequences. Zebrafish 2020; 17:333-341. [PMID: 32990531 DOI: 10.1089/zeb.2020.1918] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Anostomidae species have conserved diploid numbers (2n = 54), although comparative cytogenetic studies have demonstrated chromosomal rearrangements occurrence among them, especially in repetitive DNA rich regions. The location and distribution of ribosomal DNA (rDNA) and small nuclear RNAs (snRNAs) multigene families are highly dynamic in the genomes of several organisms. In this study, we in situ located the rDNA and snRNA sites in two populations of Megaleporinus obtusidens and a sample of Megaleporinus reinhardti to infer their chromosomal changes in the evolutionary lineages. Both species of Megaleporinus shared 2n = 54 chromosomes with the presence of ZZ/ZW sex chromosome system, but they diverged in relationship to the location of 5S and 45S rDNAs as well as the distribution of snRNAs sites. The characterization of the analyzed sequences revealed the presence of complete rDNA and snRNAs sequences as well as snRNAs containing transposable elements (TEs) and microsatellite repeats. After chromosomal mapping, the sequences encompassing TEs proved to be dispersed through autosomes and accumulated on sex chromosomes. The data demonstrate that intra- and interspecific chromosomal changes occurred involving the multigene family's sites in Megaleporinus karyotypes. Furthermore, we detected TE-like sequences in the differentiation of sex chromosome systems in M. obtusidens and M. reinhardti.
Collapse
Affiliation(s)
- Thais Aparecida Dulz
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual do Paraná, União da Vitória, Brazil
| | - Matheus Azambuja
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | | | | | - Rafael Bueno Noleto
- Departamento de Ciências Biológicas, Universidade Estadual do Paraná, União da Vitória, Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| | - Débora Diniz
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | | | - Marcelo Ricardo Vicari
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil.,Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
| |
Collapse
|
38
|
Abstract
Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.
Collapse
Affiliation(s)
- Erin K Borchardt
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Nicole M Martinez
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| |
Collapse
|
39
|
Wang W, Pu X, Yang S, Feng Y, Lin C, Li M, Li X, Li H, Meng C, Xie Q, Yu B, Liu Y. Alternative splicing of DSP1 enhances snRNA accumulation by promoting transcription termination and recycle of the processing complex. Proc Natl Acad Sci U S A 2020; 117:20325-33. [PMID: 32747542 DOI: 10.1073/pnas.2002115117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small nuclear RNAs (snRNAs) are the basal components of the spliceosome and play crucial roles in splicing. Their biogenesis is spatiotemporally regulated. However, related mechanisms are still poorly understood. Defective in snRNA processing (DSP1) is an essential component of the DSP1 complex that catalyzes plant snRNA 3'-end maturation by cotranscriptional endonucleolytic cleavage of the primary snRNA transcripts (presnRNAs). Here, we show that DSP1 is subjected to alternative splicing in pollens and embryos, resulting in two splicing variants, DSP1α and DSP1β. Unlike DSP1α, DSP1β is not required for presnRNA 3'-end cleavage. Rather, it competes with DSP1α for the interaction with CPSF73-I, the catalytic subunit of the DSP1 complex, which promotes efficient release of CPSF73-I and the DNA-dependent RNA polymerease II (Pol II) from the 3' end of snRNA loci thereby facilitates snRNA transcription termination, resulting in increased snRNA levels in pollens. Taken together, this study uncovers a mechanism that spatially regulates snRNA accumulation.
Collapse
|
40
|
Zimta AA, Sigurjonsson OE, Gulei D, Tomuleasa C. The Malignant Role of Exosomes as Nanocarriers of Rare RNA Species. Int J Mol Sci 2020; 21:ijms21165866. [PMID: 32824183 PMCID: PMC7461500 DOI: 10.3390/ijms21165866] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 12/19/2022] Open
Abstract
Nowadays, advancements in the oncology sector regarding diagnosis methods allow us to specifically detect an increased number of cancer patients, some of them in incipient stages. However, one of the main issues consists of the invasive character of most of the diagnosis protocols or complex medical procedures associated with it, that impedes part of the patients to undergo routine checkups. Therefore, in order to increase the number of cancer cases diagnosed in incipient stages, other minimally invasive alternatives must be considered. The current review paper presents the value of rare RNA species isolated from circulatory exosomes as biomarkers of diagnosis, prognosis or even therapeutic intervention. Rare RNAs are most of the time overlooked in current research in favor of the more abundant RNA species like microRNAs. However, their high degree of stability, low variability and, for most of them, conservation across species could shift the interest toward these types of RNAs. Moreover, due to their low abundance, the variation interval in terms of the number of sequences with differential expression between samples from healthy individuals and cancer patients is significantly diminished and probably easier to interpret in a clinical context.
Collapse
Affiliation(s)
- Alina-Andreea Zimta
- Research Center for Advanced Medicine-Medfuture, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (A.-A.Z.); (C.T.)
| | - Olafur Eysteinn Sigurjonsson
- The Blood Bank, Landspitali University Hospital, 121 Reykjavik, Iceland;
- School of Science and Engineering, Reykjavik University, 107 Reykjavik, Iceland
| | - Diana Gulei
- Research Center for Advanced Medicine-Medfuture, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (A.-A.Z.); (C.T.)
- Correspondence: or
| | - Ciprian Tomuleasa
- Research Center for Advanced Medicine-Medfuture, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania; (A.-A.Z.); (C.T.)
- Department of Hematology, Oncology Institute Prof. Dr. Ion Chiricuta, 400015 Cluj-Napoca, Romania
| |
Collapse
|
41
|
Bhandawat A, Sharma H, Pundir N, Madhawan A, Roy J. Genome-wide identification and characterization of novel non-coding RNA-derived SSRs in wheat. Mol Biol Rep 2020; 47:6111-25. [PMID: 32794134 DOI: 10.1007/s11033-020-05687-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/26/2020] [Indexed: 02/02/2023]
Abstract
Expression of eukaryotic genes is largely regulated by non-coding RNAs (ncRNA). Sequence variations in the regulatory RNAs may have critical biological consequences including transcriptional and post-transcriptional gene regulation. ncRNA-derived markers thus can be proved useful in molecular breeding, QTL mapping and association studies for trait dissection. In present study, we identified a total of 661 SSRs dwelling in pre-miRNA (15), small nuclear RNA (25) and lncRNA (621). Of these, 46 were validated and 100% amplification success was observed in selected wheat genotypes. A set of 36 ncRNA-SSRs markers was utilized for genetic variability assessment in forty-eight Indian wheat genotypes (which includes bread wheat, durum wheat and relatives). Number of alleles ranged from 1 to 4 with an average of two alleles per SSR locus. Mean PIC, observed heterozygosity and Shannon information index were found to be 0.258, 0.37 and 0.476 which suggests ncRNA-SSRs show higher polymorphism compared to genic SSRs but lower polymorphism compared to genomic SSRs. Thirty-six ncRNA-SSRs showed transferability ranging from 42.1% to 100%. Average genetic dissimilarity among wheat genotypes was found to be 0.29 based on Jaccard's dissimilarity. This is the first report of ncRNA-SSRs in wheat which will be useful for molecular breeding and genetic improvement of wheat.
Collapse
|
42
|
Mendoza-Figueroa MS, Tatomer DC, Wilusz JE. The Integrator Complex in Transcription and Development. Trends Biochem Sci 2020; 45:923-934. [PMID: 32800671 DOI: 10.1016/j.tibs.2020.07.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/03/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
Abstract
The Integrator complex is conserved across metazoans and controls the fate of many nascent RNAs transcribed by RNA polymerase II (RNAPII). Among the 14 subunits of Integrator is an RNA endonuclease that is crucial for the biogenesis of small nuclear RNAs and enhancer RNAs. Integrator is further employed to trigger premature transcription termination at many protein-coding genes, thereby attenuating gene expression. Integrator thus helps to shape the transcriptome and ensure that genes can be robustly induced when needed. The molecular functions of Integrator subunits beyond the RNA endonuclease remain poorly understood, but some can act independently of the multisubunit complex. We highlight recent molecular insights into Integrator and propose how misregulation of this complex may lead to developmental defects and disease.
Collapse
Affiliation(s)
- María Saraí Mendoza-Figueroa
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Deirdre C Tatomer
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeremy E Wilusz
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| |
Collapse
|
43
|
Oshiquiri LH, Gomes SL, Georg RC. Blastocladiella emersonii spliceosome is regulated in response to the splicing inhibition caused by the metals cadmium, cobalt and manganese. Fungal Biol 2020; 124:468-474. [PMID: 32389309 DOI: 10.1016/j.funbio.2020.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 01/08/2023]
Abstract
Blastocladiella emersonii is an aquatic fungus of the phylum Blastocladiomycota, localized near the base of the fungal tree. Previous studies have shown that B. emersonii responds to heat shock and cadmium exposure inducing the transcription of a high number of genes. EST sequencing from heat shocked and cadmium exposed B. emersonii cells has shown that exposure to cadmium causes strong splicing inhibition. Despite the knowledge about splicing inhibition by cadmium, it is still unclear if other metal contaminants can cause the same response. In the present study, we have demonstrated that the effect of cadmium exposure on splicing inhibition is much stronger than that of other divalent metals such as cobalt and manganese. Data presented here also indicate that intron retention occurs randomly among the fungal transcripts, as verified by analyzing differently affected transcripts. In addition, we identified in the genome of B. emersonii the genes encoding the snRNA splicing components U1, U2, U4, U5 and U6 and observed that spliceosome snRNAs are upregulated in the presence of metals, in particular snRNA U1 in cells under cadmium exposure. This observation suggests that snRNA upregulation might be a defense of the fungal cell against the metal stress condition.
Collapse
Affiliation(s)
- Letícia Harumi Oshiquiri
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Suely Lopes Gomes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Raphaela Castro Georg
- Departamento de Bioquímica e Biologia Molecular, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, Brazil; Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
| |
Collapse
|
44
|
Rahman MM, Lai YC, Husna AA, Chen HW, Tanaka Y, Kawaguchi H, Hatai H, Miyoshi N, Nakagawa T, Fukushima R, Miura N. Aberrantly expressed snoRNA, snRNA, piRNA and tRFs in canine melanoma. Vet Comp Oncol 2019; 18:353-361. [PMID: 31769925 DOI: 10.1111/vco.12558] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 12/13/2022]
Abstract
Among small non-coding RNAs (sncRNAs/sRNAs), the functional regulation of microRNAs (miRNAs) has been studied in canine oral melanoma (COM). However, the expression level of other sncRNAs, like small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), transfer RNA-derived fragments (tRFs) and PIWI-interacting RNAs (piRNAs), in COM is unknown. The aim of this study was to investigate sncRNAs other than miRNAs in COM from our small RNA sequencing project (PRJNA516252). We found that several snRNAs and piRNAs were upregulated, whereas tRFs and snoRNAs were downregulated in COM. Upregulation of U1 snRNA and piR-972, and downregulation of tRNA-ser (1) and snoRA24 was confirmed in dog melanoma tissue and cell lines by quantitative reverse transcription PCR. Consistently, the expression of tRNA-ser (1) and snoRA24 in plasma of COM cases was also decreased. Finally, we found a similar expression trend of U1 and snoRA24 in the human cutaneous melanoma cell line, MEWO, compared with human epidermal melanocyte cells (HEMa-Lp). In our study, snRNA, snoRNA, tRFs and piRNA were dysregulated during melanoma progression. Moreover, the melanoma-associated expression of U1 and snoRA24 was similar in human and dog melanoma.
Collapse
Affiliation(s)
- Md Mahfuzur Rahman
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Yu-Chang Lai
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Al Asmaul Husna
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan
| | - Hui-Wen Chen
- Joint Graduate School of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Yuiko Tanaka
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Kawaguchi
- Hygiene and Health Promotion Medicine, Kagoshima University Graduate School of Medicine and Dental Science, Kagoshima, Japan
| | - Hitoshi Hatai
- Department of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Noriaki Miyoshi
- Department of Veterinary Histopathology, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Takayuki Nakagawa
- Laboratory of Veterinary Surgery, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryuji Fukushima
- Animal Medical Centre, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Naoki Miura
- Veterinary Teaching Hospital, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan.,The United Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, Japan.,Joint Graduate School of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| |
Collapse
|
45
|
de Araujo LS, Ribeiro-Alves M, Leal-Calvo T, Leung J, Durán V, Samir M, Talbot S, Tallam A, Mello FCQ, Geffers R, Saad MHF, Pessler F. Reprogramming of Small Noncoding RNA Populations in Peripheral Blood Reveals Host Biomarkers for Latent and Active Mycobacterium tuberculosis Infection. mBio 2019; 10:e01037-19. [PMID: 31796535 DOI: 10.1128/mBio.01037-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Tuberculosis is the infectious disease with the worldwide largest disease burden and there remains a great need for better diagnostic biomarkers to detect latent and active M. tuberculosis infection. RNA molecules hold great promise in this regard, as their levels of expression may differ considerably between infected and uninfected subjects. We have measured expression changes in the four major classes of small noncoding RNAs in blood samples from patients with different stages of TB infection. We found that, in addition to miRNAs (which are known to be highly regulated in blood cells from TB patients), expression of piRNA and snoRNA is greatly altered in both latent and active TB, yielding promising biomarkers. Even though the functions of many sncRNA other than miRNA are still poorly understood, our results strongly suggest that at least piRNA and snoRNA populations may represent hitherto underappreciated players in the different stages of TB infection. In tuberculosis (TB), as in other infectious diseases, studies of small noncoding RNAs (sncRNA) in peripheral blood have focused on microRNAs (miRNAs) but have neglected the other major sncRNA classes in spite of their potential functions in host gene regulation. Using RNA sequencing of whole blood, we have therefore determined expression of miRNA, PIWI-interacting RNA (piRNA), small nucleolar RNA (snoRNA), and small nuclear RNA (snRNA) in patients with TB (n = 8), latent TB infection (LTBI; n = 21), and treated LTBI (LTBItt; n = 6) and in uninfected exposed controls (ExC; n = 14). As expected, sncRNA reprogramming was greater in TB than in LTBI, with the greatest changes seen in miRNA populations. However, substantial dynamics were also evident in piRNA and snoRNA populations. One miRNA and 2 piRNAs were identified as moderately accurate (area under the curve [AUC] = 0.70 to 0.74) biomarkers for LTBI, as were 1 miRNA, 1 piRNA, and 2 snoRNAs (AUC = 0.79 to 0.91) for accomplished LTBI treatment. Logistic regression identified the combination of 4 sncRNA (let-7a-5p, miR-589-5p, miR-196b-5p, and SNORD104) as a highly sensitive (100%) classifier to discriminate TB from all non-TB groups. Notably, it reclassified 8 presumed LTBI cases as TB cases, 5 of which turned out to have features of Mycobacterium tuberculosis infection on chest radiographs. SNORD104 expression decreased during M. tuberculosis infection of primary human peripheral blood mononuclear cells (PBMC) and M2-like (P = 0.03) but not M1-like (P = 0.31) macrophages, suggesting that its downregulation in peripheral blood in TB is biologically relevant. Taken together, the results demonstrate that snoRNA and piRNA should be considered in addition to miRNA as biomarkers and pathogenesis factors in the various stages of TB.
Collapse
|
46
|
Wu CW, Wimberly K, Pietras A, Dodd W, Atlas MB, Choe KP. RNA processing errors triggered by cadmium and integrator complex disruption are signals for environmental stress. BMC Biol 2019; 17:56. [PMID: 31311534 PMCID: PMC6631800 DOI: 10.1186/s12915-019-0675-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 06/24/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Adaptive responses to stress are essential for cell and organismal survival. In metazoans, little is known about the impact of environmental stress on RNA homeostasis. RESULTS By studying the regulation of a cadmium-induced gene named numr-1 in Caenorhabditis elegans, we discovered that disruption of RNA processing acts as a signal for environmental stress. We find that NUMR-1 contains motifs common to RNA splicing factors and influences RNA splicing in vivo. A genome-wide screen reveals that numr-1 is strongly and specifically induced by silencing of genes that function in basal RNA metabolism including subunits of the metazoan integrator complex. Human integrator processes snRNAs for functioning with splicing factors, and we find that silencing of C. elegans integrator subunits disrupts snRNA processing, causes aberrant pre-mRNA splicing, and induces the heat shock response. Cadmium, which also strongly induces numr-1, has similar effects on RNA and the heat shock response. Lastly, we find that heat shock factor-1 is required for full numr-1 induction by cadmium. CONCLUSION Our results are consistent with a model in which disruption of integrator processing of RNA acts as a molecular damage signal initiating an adaptive stress response mediated by heat shock factor-1. When numr-1 is induced via this pathway in C. elegans, its function in RNA metabolism may allow it to mitigate further damage and thereby promote tolerance to cadmium.
Collapse
Affiliation(s)
- Cheng-Wei Wu
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK, S7N 5B4, Canada.
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK, S7N 5B3, Canada.
| | - Keon Wimberly
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Adele Pietras
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - William Dodd
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - M Blake Atlas
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Keith P Choe
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.
| |
Collapse
|
47
|
Becker D, Hirsch AG, Bender L, Lingner T, Salinas G, Krebber H. Nuclear Pre- snRNA Export Is an Essential Quality Assurance Mechanism for Functional Spliceosomes. Cell Rep 2019; 27:3199-3214.e3. [PMID: 31189105 DOI: 10.1016/j.celrep.2019.05.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 04/03/2019] [Accepted: 05/09/2019] [Indexed: 02/05/2023] Open
Abstract
Removal of introns from pre-mRNAs is an essential step in eukaryotic gene expression, mediated by spliceosomes that contain snRNAs as key components. Although snRNAs are transcribed in the nucleus and function in the same compartment, all except U6 shuttle to the cytoplasm. Surprisingly, the physiological relevance for shuttling is unclear, in particular because the snRNAs in Saccharomyces cerevisiae were reported to remain nuclear. Here, we show that all yeast pre-snRNAs including U6 undergo a stepwise maturation process after nuclear export by Mex67 and Xpo1. Sm- and Lsm-ring attachment occurs in the cytoplasm and is important for the snRNA re-import, mediated by Cse1 and Mtr10. Finally, nuclear pre-snRNA cleavage and trimethylation of the 5'-cap finalizes shuttling. Importantly, preventing pre-snRNAs from being exported or processed results in faulty spliceosome assembly and subsequent genome-wide splicing defects. Thus, pre-snRNA export is obligatory for functional splicing and resembles an essential evolutionarily conserved quality assurance step.
Collapse
Affiliation(s)
- Daniel Becker
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Anna Greta Hirsch
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Lysann Bender
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany
| | - Thomas Lingner
- Transkriptomanalyselabor, Institut für Entwicklungsbiochemie, Georg-August Universität Göttingen, Göttingen, Germany
| | - Gabriela Salinas
- Transkriptomanalyselabor, Institut für Entwicklungsbiochemie, Georg-August Universität Göttingen, Göttingen, Germany
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften (GZMB), Georg-August Universität Göttingen, Göttingen, Germany.
| |
Collapse
|
48
|
Vijayakumari D, Sharma AK, Bawa PS, Kumar R, Srinivasan S, Vijayraghavan U. Early splicing functions of fission yeast Prp16 and its unexpected requirement for gene Silencing is governed by intronic features. RNA Biol 2019; 16:754-769. [PMID: 30810475 DOI: 10.1080/15476286.2019.1585737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Prp16 is a DEAH box pre-mRNA splicing factor that triggers a key spliceosome conformational switch to facilitate second step splicing in Saccharomyces cerevisiae. However, Prp16 functions are largely unexplored in Schizosaccharomyces pombe, an attractive model with exon-intron architecture more relevant to several other eukaryotes. Here, we generated mis-sense alleles in SpPrp16 whose consequences on genome-wide splicing uncover its nearly global splicing role with only a small subset of unaffected introns. Prp16 dependent and independent intron categories displayed a striking difference in the strength of intronic 5' splice site (5'SS)-U6 snRNA and branch site (BS)-U2 snRNA interactions. Selective weakening of these interactions could convert a Prp16 dependent intron into an independent one. These results point to the role of SpPrp16 in destabilizing 5'SS-U6snRNA and BS-U2snRNA interactions which plausibly trigger structural alterations in the spliceosome to facilitate first step catalysis. Our data suggest that SpPrp16 interactions with early acting factors, its enzymatic activities and association with intronic elements collectively account for efficient and accurate first step catalysis. In addition to splicing derangements in the spprp16F528S mutant, we show that SpPrp16 influences cell cycle progression and centromeric heterochromatinization. We propose that strong 5'SS-U6 snRNA and BS-U2 snRNA complementarity of intron-like elements in non-coding RNAs which lead to complete splicing arrest and impaired Seb1 functions at the pericentromeric loci may cumulatively account for the heterochromatin defects in spprp16F528S cells. These findings suggest that the diverse Prp16 functions within a genome are likely governed by its intronic features that influence splice site-snRNA interaction strength.
Collapse
Affiliation(s)
- Drisya Vijayakumari
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | - Amit Kumar Sharma
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | | | - Rakesh Kumar
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | | | - Usha Vijayraghavan
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| |
Collapse
|
49
|
Boivin V, Faucher-Giguère L, Scott M, Abou-Elela S. The cellular landscape of mid-size noncoding RNA. Wiley Interdiscip Rev RNA 2019; 10:e1530. [PMID: 30843375 PMCID: PMC6619189 DOI: 10.1002/wrna.1530] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 02/08/2019] [Accepted: 02/09/2019] [Indexed: 01/06/2023]
Abstract
Noncoding RNA plays an important role in all aspects of the cellular life cycle, from the very basic process of protein synthesis to specialized roles in cell development and differentiation. However, many noncoding RNAs remain uncharacterized and the function of most of them remains unknown. Mid-size noncoding RNAs (mncRNAs), which range in length from 50 to 400 nucleotides, have diverse regulatory functions but share many fundamental characteristics. Most mncRNAs are produced from independent promoters although others are produced from the introns of other genes. Many are found in multiple copies in genomes. mncRNAs are highly structured and carry many posttranscriptional modifications. Both of these facets dictate their RNA-binding protein partners and ultimately their function. mncRNAs have already been implicated in translation, catalysis, as guides for RNA modification, as spliceosome components and regulatory RNA. However, recent studies are adding new mncRNA functions including regulation of gene expression and alternative splicing. In this review, we describe the different classes, characteristics and emerging functions of mncRNAs and their relative expression patterns. Finally, we provide a portrait of the challenges facing their detection and annotation in databases. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
Collapse
Affiliation(s)
- Vincent Boivin
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Laurence Faucher-Giguère
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Michelle Scott
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Sherif Abou-Elela
- Department of Microbiology and Infectious Disease, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| |
Collapse
|
50
|
Pirouz M, Ebrahimi AG, Gregory RI. Unraveling 3'-end RNA uridylation at nucleotide resolution. Methods 2019; 155:10-19. [PMID: 30395968 PMCID: PMC6387850 DOI: 10.1016/j.ymeth.2018.10.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022] Open
Abstract
Post-transcriptional modification of RNA, the so-called 'Epitranscriptome', can regulate RNA structure, stability, localization, and function. Numerous modifications have been identified in virtually all classes of RNAs, including messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), microRNAs (miRNAs), and other noncoding RNAs (ncRNAs). These modifications may occur internally (by base or sugar modifications) and include RNA methylation at different nucleotide positions, or by the addition of various nucleotides at the 3'-end of certain transcripts by a family of terminal nucleotidylyl transferases. Developing methods to specifically and accurately detect and map these modifications is essential for understanding the molecular function(s) of individual RNA modifications and also for identifying and characterizing the proteins that may read, write, or erase them. Here, we focus on the characterization of RNA species targeted by 3' terminal uridylyl transferases (TUTases) (TUT4/7, also known as Zcchc11/6) and a 3'-5' exoribonuclease, Dis3l2, in the recently identified Dis3l2-mediated decay (DMD) pathway - a dedicated quality control pathway for a subset of ncRNAs. We describe the detailed methods used to precisely identify 3'-end modifications at nucleotide level resolution with a particular focus on the U1 and U2 small nuclear RNA (snRNA) components of the Spliceosome. These tools can be applied to investigate any RNA of interest and should facilitate studies aimed at elucidating the functional relevance of 3'-end modifications.
Collapse
Affiliation(s)
- Mehdi Pirouz
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Aref G Ebrahimi
- Section on Islet Cell and Regenerative Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA 02115, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Harvard Initiative for RNA Medicine, Boston, MA 02115, USA.
| |
Collapse
|