1
|
Hejla D, Huynh S, Samra S, Richmond PA, Dalmann J, Del Bel KL, Byres L, Lehman A, Turvey SE, Boerkoel CF. Naturally occurring splice variants dissect the functional domains of BHC80 and emphasize the need for RNA analysis. Am J Med Genet A 2024; 194:e63548. [PMID: 38264805 DOI: 10.1002/ajmg.a.63548] [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: 11/23/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 01/25/2024]
Abstract
Pathogenic PHF21A variation causes PHF21A-related neurodevelopmental disorders (NDDs). Although amorphic alleles, including haploinsufficiency, have been established as a disease mechanism, increasing evidence suggests that missense variants as well as frameshift variants extending the BHC80 carboxyl terminus also cause disease. Expanding on these, we report a proposita with intellectual disability and overgrowth and a novel de novo heterozygous PHF21A splice variant (NM_001352027.3:c.[153+1G>C];[=]) causing skipping of exon 6, which encodes an in-frame BHC80 deletion (p.(Asn30_Gln51del)). This deletion disrupts a predicted leucine zipper domain and implicates this domain in BHC80 function and as a target of variation causing PHF21A-related NDDs. This extension of understanding emphasizes the application of RNA analysis in precision genomic medicine practice.
Collapse
Affiliation(s)
- Duha Hejla
- Department of Pediatrics, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Stephanie Huynh
- Provincial Medical Genetics Program, B.C. Women's Hospital, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simran Samra
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
- Experimental Medicine Program, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Phillip A Richmond
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Joshua Dalmann
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Kate L Del Bel
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Loryn Byres
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Lehman
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Stuart E Turvey
- The Rare Disease Discovery Hub, BC Children's Hospital Research Institute, University of British Columbia and Children's Hospital of British Columbia, Vancouver, British Columbia, Canada
| | - Cornelius F Boerkoel
- Provincial Medical Genetics Program, B.C. Women's Hospital, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
2
|
Yustis JC, Devoucoux M, Côté J. The Functional Relationship between RNA Splicing and the Chromatin Landscape. J Mol Biol 2024:168614. [PMID: 38762032 DOI: 10.1016/j.jmb.2024.168614] [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: 03/04/2024] [Revised: 04/27/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Chromatin is a highly regulated and dynamic structure that has been shown to play an essential role in transcriptional and co-transcriptional regulation. In the context of RNA splicing, early evidence suggested a loose connection between the chromatin landscape and splicing. More recently, it has been shown that splicing occurs in a co-transcriptional manner, meaning that the splicing process occurs in the context of chromatin. Experimental and computational evidence have also shown that chromatin dynamics can influence the splicing process and vice versa. However, much of this evidence provides mainly correlative relationships between chromatin and splicing with just a few concrete examples providing defined molecular mechanisms by which these two processes are functionally related. Nevertheless, it is clear that chromatin and RNA splicing are tightly interconnected to one another. In this review, we highlight the current state of knowledge of the relationship between chromatin and splicing.
Collapse
Affiliation(s)
- Juan-Carlos Yustis
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada G1R 3S3
| | - Maëva Devoucoux
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada G1R 3S3
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada G1R 3S3.
| |
Collapse
|
3
|
Pohorilets I, Beard JP, Driscoll JL, Schmitz JC, Koide K. Synthesis and antiproliferative activity of a tetrahydrofuran analog of FR901464. Bioorg Med Chem Lett 2024; 104:129739. [PMID: 38599298 DOI: 10.1016/j.bmcl.2024.129739] [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: 01/24/2024] [Revised: 04/03/2024] [Accepted: 04/06/2024] [Indexed: 04/12/2024]
Abstract
FR901464 is a natural product that exhibits antiproliferative activity at single-digit nanomolar concentrations in cancer cells. Its tetrahydropyran-spiroepoxide covalently binds the spliceosome. Through our medicinal chemistry campaign, we serendipitously discovered that a bromoetherification formed a tetrahydrofuran. The tetrahydrofuran analog was three orders of magnitude less potent than the corresponding tetrahydropyran analogs. This study shows the significance of the tetrahydropyran ring that presents the epoxide toward the spliceosome.
Collapse
Affiliation(s)
- Ivanna Pohorilets
- Department of Chemistry, University of Pittsburgh 219 Parkman Avenue, Pittsburgh, PA 15260, United States
| | - Jacob P Beard
- Department of Chemistry, University of Pittsburgh 219 Parkman Avenue, Pittsburgh, PA 15260, United States
| | - Julia L Driscoll
- Department of Chemistry, University of Pittsburgh 219 Parkman Avenue, Pittsburgh, PA 15260, United States
| | - John C Schmitz
- Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh School of Medicine 5150 Centre Avenue, Pittsburgh, PA 15232, United States; Cancer Therapeutics Program, UPMC Hillman Cancer Center 5117 Centre Ave, Pittsburgh, PA 15232, United States
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh 219 Parkman Avenue, Pittsburgh, PA 15260, United States; Cancer Therapeutics Program, UPMC Hillman Cancer Center 5117 Centre Ave, Pittsburgh, PA 15232, United States.
| |
Collapse
|
4
|
Campagne S. U1 snRNP Biogenesis Defects in Neurodegenerative Diseases. Chembiochem 2024; 25:e202300864. [PMID: 38459794 DOI: 10.1002/cbic.202300864] [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: 12/22/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/10/2024]
Abstract
The U1 small ribonucleoprotein (U1 snRNP) plays a pivotal role in the intricate process of gene expression, specifically within nuclear RNA processing. By initiating the splicing reaction and modulating 3'-end processing, U1 snRNP exerts precise control over RNA metabolism and gene expression. This ribonucleoparticle is abundantly present, and its complex biogenesis necessitates shuttling between the nuclear and cytoplasmic compartments. Over the past three decades, extensive research has illuminated the crucial connection between disrupted U snRNP biogenesis and several prominent human diseases, notably various neurodegenerative conditions. The perturbation of U1 snRNP homeostasis has been firmly established in diseases such as Spinal Muscular Atrophy, Pontocerebellar hypoplasia, and FUS-mediated Amyotrophic Lateral Sclerosis. Intriguingly, compelling evidence suggests a potential correlation in Fronto-temporal dementia and Alzheimer's disease as well. Although the U snRNP biogenesis pathway is conserved across all eukaryotic cells, neurons, in particular, appear to be highly susceptible to alterations in spliceosome homeostasis. In contrast, other cell types exhibit a greater resilience to such disturbances. This vulnerability underscores the intricate relationship between U1 snRNP dynamics and the health of neuronal cells, shedding light on potential avenues for understanding and addressing neurodegenerative disorders.
Collapse
Affiliation(s)
- Sebastien Campagne
- University of Bordeaux, INSERM U1212, CNRS UMR5320, ARNA unit 146, rue Leo Saignat, 33077, Bordeaux
- Institut Européen de Chimie et de Biologie, 2, rue Robert Escarpit, 33600, Pessac
| |
Collapse
|
5
|
Wan X, Shi W, Ma L, Wang L, Zheng R, He J, Wang Y, Li X, Zha X, Wang J, Xu L. A 3'-pre-tRNA-derived small RNA tRF-1-Ser regulated by 25(OH)D promotes proliferation and stemness by inhibiting the function of MBNL1 in breast cancer. Clin Transl Med 2024; 14:e1681. [PMID: 38725048 PMCID: PMC11082093 DOI: 10.1002/ctm2.1681] [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: 01/19/2024] [Revised: 03/28/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND We explored the potential novel anticancer mechanisms of 25-hydroxyvitamin D (25(OH)D), a vitamin D metabolite with antitumour effects in breast cancer. It is stable in serum and is used to assess vitamin D levels in clinical practice. Transfer RNA-derived small RNAs are small noncoding RNAs that generate various distinct biological functions, but more research is needed on their role in breast cancer. METHODS Small RNA microarrays were used to explore the novel regulatory mechanism of 25(OH)D. High-throughput RNA-sequencing technology was used to detect transcriptome changes after 25(OH)D treatment and tRF-1-Ser knockdown. RNA pull-down and high-performance liquid chromatography-mass spectrometry/mass spectrometry were used to explore the proteins bound to tRF-1-Ser. In vitro and in vivo functional experiments were conducted to assess the influence of 25(OH)D and tRF-1-Ser on breast cancer. Semi-quantitative PCR was performed to detect alternative splicing events. Western blot assay and qPCR were used to assess protein and mRNA expression. RESULTS The expression of tRF-1-Ser is negatively regulated by 25(OH)D. In our breast cancer (BRCA) clinical samples, we found that the expression of tRF-1-Ser was higher in cancer tissues than in paired normal tissues, and was significantly associated with tumour invasion. Moreover, tRF-1-Ser inhibits the function of MBNL1 by hindering its nuclear translocation. Functional experiments and transcriptome data revealed that the downregulation of tRF-1-Ser plays a vital role in the anticancer effect of 25(OH)D. CONCLUSIONS In brief, our research revealed a novel anticancer mechanism of 25(OH)D, unveiled the vital function of tRF-1-Ser in BRCA progression, and suggested that tRF-1-Ser could emerge as a new therapeutic target for BRCA.
Collapse
Affiliation(s)
- Xinyu Wan
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Wenjie Shi
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lingjun Ma
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lexin Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Ran Zheng
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jinzhi He
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Ye Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Xuan Li
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Xiaoming Zha
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jue Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lu Xu
- Department of NutritionThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| |
Collapse
|
6
|
Kamiya Y, Aihara N, Shiga T, Horiuchi N, Kamiie J. Diversity of mutations in the dystrophin gene and details of muscular lesions in porcine dystrophinopathies. Vet Pathol 2024; 61:432-441. [PMID: 38006213 DOI: 10.1177/03009858231214028] [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] [Indexed: 11/26/2023]
Abstract
During meat inspections in pigs, dystrophinopathies are among the muscle lesions targeted for disposal. In this study, the authors examined the lesions and the distribution of dystrophin expression in 25 pigs with dystrophinopathy. In addition, complementary deoxyribonucleic acid (cDNA) sequencing and western blotting were performed in 6 of the 25 cases, all of which were characterized by degeneration, necrosis, and fat replacement of muscle fibers. Comparing the results of immunohistochemistry with anti-dystrophin antibodies that recognized at different sites in the protein, the authors noted that the loss of dystrophin expression was most pronounced in the C-terminus-recognizing antibody (19/25 cases). The authors detected 5 missense mutations and 3 types of shortened transcripts generated by the skipping of exons in the cDNA, which were associated with the pathogenesis. One missense mutation had been reported previously, whereas the remaining mutations identified had not been previously documented in pigs. In the cases with shortened transcripts, normal-sized transcripts were detected together with the defective transcripts, suggesting that these mutations were caused by splicing abnormalities. In addition, they were in-frame mutations, all of which have similar pathogeneses of Becker muscular dystrophy in humans. These cases were 6 months of age and exhibited macroscopic discoloration, fatty replacement, and muscle degeneration, suggesting that the effect of these mutations on skeletal muscle was significant.
Collapse
|
7
|
Khalenkow D, Brandsma CA, Timens W, Choy DF, Grimbaldeston MA, Rosenberger CM, Slebos DJ, Kerstjens HAM, Faiz A, Koppelman GH, Nawijn MC, van den Berge M, Guryev V. Alternative Splicing Is a Major Factor Shaping Transcriptome Diversity in Mild and Severe Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2024; 70:414-423. [PMID: 38315810 DOI: 10.1165/rcmb.2023-0296oc] [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: 08/10/2023] [Accepted: 02/05/2024] [Indexed: 02/07/2024] Open
Abstract
The role of alternative splicing in chronic obstructive pulmonary disease (COPD) is still largely unknown. We aimed to investigate the differences in alternatively splicing events between patients with mild-to-moderate and severe COPD compared with non-COPD control subjects and to identify splicing factors associated with aberrant alternative splicing in COPD. For this purpose, we performed genome-wide RNA-sequencing analysis of bronchial brushings from 23 patients with mild-to-moderate COPD, 121 with severe COPD, and 23 non-COPD control subjects. We found a significant difference in the frequency of alternative splicing events in patients with mild-to-moderate and severe COPD compared with non-COPD control subjects. There were from two to eight times (depending on event type) more differential alternative splicing events in the severe than in the mild-to-moderate stage. The severe COPD samples showed less intron retention and more exon skipping. It is interesting that the transcript levels of the top 10 differentially expressed splicing factors were significantly correlated with the percentage of many alternatively spliced transcripts in severe COPD. The aberrant alternative splicing in severe COPD was predicted to increase the overall protein-coding capacity of gene products. In conclusion, we observed large and significant differences in alternative splicing between bronchial samples of patients with COPD and control subjects, with more events observed in severe than in mild-to-moderate COPD. The changes in the expression of several splicing factors correlated with prevalence of alternative splicing in severe COPD. Alternative splicing can indirectly impact gene expression by changing the relative abundance of protein-coding isoforms potentially influencing pathophysiological changes. The results provide a better understanding of COPD-related alternative splicing changes.
Collapse
Affiliation(s)
- Dmitry Khalenkow
- European Research Institute for the Biology of Ageing
- Groningen Research Institute for Asthma and COPD
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital
| | - Corry-Anke Brandsma
- Groningen Research Institute for Asthma and COPD
- Department of Pathology and Medical Biology
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD
- Department of Pathology and Medical Biology
| | - David F Choy
- Genentech, Inc., South San Francisco, California; and
| | | | | | | | - Huib A M Kerstjens
- Department of Pulmonology and Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alen Faiz
- Faculty of Science, Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, Australia
| | - Gerard H Koppelman
- Groningen Research Institute for Asthma and COPD
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD
- Department of Pathology and Medical Biology
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD
- Department of Pulmonary Diseases, and
| | - Victor Guryev
- European Research Institute for the Biology of Ageing
| |
Collapse
|
8
|
Gu J, Ma X, Ma Q, Xia Z, Lin Y, Yuan J, Li Y, Li C, Chen Y, Wang W, Zhang P, Wang ZY. RNA splicing modulates the postharvest physiological deterioration of cassava storage root. Plant Physiol 2024:kiae206. [PMID: 38635971 DOI: 10.1093/plphys/kiae206] [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: 01/08/2024] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
Rapid postharvest physiological deterioration (PPD) of cassava (Manihot esculenta Crantz) storage roots is a major constraint that limits the potential of this plant as a food and industrial crop. Extensive studies have been performed to explore the regulatory mechanisms underlying the PPD processes in cassava to understand their molecular and physiological responses. However, the exceptional functional versatility of alternative splicing (AS) remains to be explored during the PPD process in cassava. Here, we identified several aberrantly spliced genes during the early PPD stage. An in-depth analysis of AS revealed that the abscisic acid (ABA) biosynthesis pathway might serve as an additional molecular layer in attenuating the onset of PPD. Exogenous ABA application alleviated PPD symptoms through maintaining ROS generation and scavenging. Interestingly, the intron retention transcript of MeABA1 (ABA DEFICIENT 1) was highly correlated with PPD symptoms in cassava storage roots. RNA yeast three-hybrid and RNA immunoprecipitation assays showed that the serine/arginine-rich protein MeSCL33 (SC35-like splicing factor 33) binds to the precursor mRNA of MeABA1. Importantly, overexpressing MeSCL33 in cassava conferred improved PPD resistance by manipulating the AS and expression levels of MeABA1 and then modulating the endogenous ABA levels in cassava storage roots. Our results uncovered the pivotal role of the ABA biosynthesis pathway and RNA splicing in regulating cassava PPD resistance and proposed the essential roles of MeSCL33 for conferring PPD resistance, broadening our understanding of SR proteins in cassava development and stress responses.
Collapse
Affiliation(s)
- Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, P.R. China
- Zhanjiang Research Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang 524300, P.R. China
| | - Xiaowen Ma
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, P.R. China
| | - Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Science, Shanghai 200032, P.R. China
| | - Zhiqiang Xia
- Sanya Nanfan Research Institute from Hainan University, Sanya 572025, China
| | - Yan Lin
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, P.R. China
| | - Jianbo Yuan
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, P.R. China
| | - Yang Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, P.R. China
- Zhanjiang Research Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang 524300, P.R. China
| | - Cong Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, P.R. China
- Zhanjiang Research Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang 524300, P.R. China
| | - Yanhang Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, P.R. China
- Zhanjiang Research Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang 524300, P.R. China
| | - Wenquan Wang
- College of Tropical Agriculture and Forest, Hainan University, Haikou 570228, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Science, Shanghai 200032, P.R. China
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, P.R. China
- Zhanjiang Research Center, Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Zhanjiang 524300, P.R. China
| |
Collapse
|
9
|
Giraud G, El Achi K, Zoulim F, Testoni B. Co-Transcriptional Regulation of HBV Replication: RNA Quality Also Matters. Viruses 2024; 16:615. [PMID: 38675956 PMCID: PMC11053573 DOI: 10.3390/v16040615] [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: 03/25/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Chronic hepatitis B (CHB) virus infection is a major public health burden and the leading cause of hepatocellular carcinoma. Despite the efficacy of current treatments, hepatitis B virus (HBV) cannot be fully eradicated due to the persistence of its minichromosome, or covalently closed circular DNA (cccDNA). The HBV community is investing large human and financial resources to develop new therapeutic strategies that either silence or ideally degrade cccDNA, to cure HBV completely or functionally. cccDNA transcription is considered to be the key step for HBV replication. Transcription not only influences the levels of viral RNA produced, but also directly impacts their quality, generating multiple variants. Growing evidence advocates for the role of the co-transcriptional regulation of HBV RNAs during CHB and viral replication, paving the way for the development of novel therapies targeting these processes. This review focuses on the mechanisms controlling the different co-transcriptional processes that HBV RNAs undergo, and their contribution to both viral replication and HBV-induced liver pathogenesis.
Collapse
Affiliation(s)
- Guillaume Giraud
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
| | - Khadija El Achi
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
| | - Fabien Zoulim
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
- Hospices Civils de Lyon, Hôpital Croix Rousse, Service d’Hépato-Gastroentérologie, 69004 Lyon, France
| | - Barbara Testoni
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
| |
Collapse
|
10
|
Domanskyi S, Srivastava A, Kaster J, Li H, Herlyn M, Rubinstein JC, Chuang JH. Nextflow pipeline for Visium and H&E data from patient-derived xenograft samples. Cell Rep Methods 2024:100759. [PMID: 38626768 DOI: 10.1016/j.crmeth.2024.100759] [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] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/23/2024] [Accepted: 03/25/2024] [Indexed: 04/18/2024]
Abstract
We designed a Nextflow DSL2-based pipeline, Spatial Transcriptomics Quantification (STQ), for simultaneous processing of 10x Genomics Visium spatial transcriptomics data and a matched hematoxylin and eosin (H&E)-stained whole-slide image (WSI), optimized for patient-derived xenograft (PDX) cancer specimens. Our pipeline enables the classification of sequenced transcripts for deconvolving the mouse and human species and mapping the transcripts to reference transcriptomes. We align the H&E WSI with the spatial layout of the Visium slide and generate imaging and quantitative morphology features for each Visium spot. The pipeline design enables multiple analysis workflows, including single or dual reference genome input and stand-alone image analysis. We show the utility of our pipeline on a dataset from Visium profiling of four melanoma PDX samples. The clustering of Visium spots and clustering of H&E imaging features reveal similar patterns arising from the two data modalities.
Collapse
Affiliation(s)
- Sergii Domanskyi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Anuj Srivastava
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | | | - Haiyin Li
- The Wistar Institute, Philadelphia, PA 19104, USA
| | | | - Jill C Rubinstein
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Hartford HealthCare Cancer Institute at St. Vincent's Medical Center, Bridgeport, CT 06606, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; UCONN Health Department of Genetics and Genome Sciences, Farmington, CT 06032, USA.
| |
Collapse
|
11
|
Abeywardana T, Wu X, Huang ST, Aldana Masangkay G, Rodin AS, Branciamore S, Gogoshin G, Li A, Du L, Tharuka N, Tomaino R, Chen Y. Regulation of Enhancers by SUMOylation Through TFAP2C Binding and Recruitment of HDAC Complex to the Chromatin. Res Sq 2024:rs.3.rs-4201913. [PMID: 38645262 PMCID: PMC11030540 DOI: 10.21203/rs.3.rs-4201913/v1] [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] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Enhancers are fundamental to gene regulation. Post-translational modifications by the small ubiquitin-like modifiers (SUMO) modify chromatin regulation enzymes, including histone acetylases and deacetylases. However, it remains unclear whether SUMOylation regulates enhancer marks, acetylation at the 27th lysine residue of the histone H3 protein (H3K27Ac). To investigate whether SUMOylation regulates H3K27Ac, we performed genome-wide ChIP-seq analyses and discovered that knockdown (KD) of the SUMO activating enzyme catalytic subunit UBA2 reduced H3K27Ac at most enhancers. Bioinformatic analysis revealed that TFAP2C-binding sites are enriched in enhancers whose H3K27Ac was reduced by UBA2 KD. ChIP-seq analysis in combination with molecular biological methods showed that TFAP2C binding to enhancers increased upon UBA2 KD or inhibition of SUMOylation by a small molecule SUMOylation inhibitor. However, this is not due to the SUMOylation of TFAP2C itself. Proteomics analysis of TFAP2C interactome on the chromatin identified histone deacetylation (HDAC) and RNA splicing machineries that contain many SUMOylation targets. TFAP2C KD reduced HDAC1 binding to chromatin and increased H3K27Ac marks at enhancer regions, suggesting that TFAP2C is important in recruiting HDAC machinery. Taken together, our findings provide insights into the regulation of enhancer marks by SUMOylation and TFAP2C and suggest that SUMOylation of proteins in the HDAC machinery regulates their recruitments to enhancers.
Collapse
Affiliation(s)
| | - Xiwei Wu
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | | | | | - Andrei S Rodin
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | - Sergio Branciamore
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | - Grigoriy Gogoshin
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | - Arthur Li
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | - Li Du
- Toni Stephenson Lymphoma Center Beckman Research Institute, City of Hope
| | | | - Ross Tomaino
- Harvard Medical School Taplin Mass Spectrometry Facility
| | | |
Collapse
|
12
|
Sakamuri SSVP, Sure VN, Oruganti L, Wisen W, Chandra PK, Liu N, Fonseca VA, Wang X, Klein J, Katakam PVG. Acute severe hypoglycemia alters mouse brain microvascular proteome. J Cereb Blood Flow Metab 2024; 44:556-572. [PMID: 37944245 PMCID: PMC10981402 DOI: 10.1177/0271678x231212961] [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: 05/01/2023] [Revised: 09/12/2023] [Accepted: 10/05/2023] [Indexed: 11/12/2023]
Abstract
Hypoglycemia increases the risk related to stroke and neurodegenerative diseases, however, the underlying mechanisms are unclear. For the first time, we studied the effect of a single episode (acute) of severe (ASH) and mild (AMH) hypoglycemia on mouse brain microvascular proteome. After four-hour fasting, insulin was administered (i.p) to lower mean blood glucose in mice and induce ∼30 minutes of ASH (∼30 mg/dL) or AMH (∼75 mg/dL), whereas a similar volume of saline was given to control mice (∼130 mg/dL). Blood glucose was allowed to recover over 60 minutes either spontaneously or by 20% dextrose administration (i.p). Twenty-four hours later, the brain microvessels (BMVs) were isolated, and tandem mass tag (TMT)-based quantitative proteomics was performed using liquid chromatography-mass spectrometry (LC/MS). When compared to control, ASH significantly downregulated 13 proteins (p ≤ 0.05) whereas 23 proteins showed a strong trend toward decrease (p ≤ 0.10). When compared to AMH, ASH significantly induced the expression of 35 proteins with 13 proteins showing an increasing trend. AMH downregulated only 3 proteins. ASH-induced downregulated proteins are involved in actin cytoskeleton maintenance needed for cell shape and migration which are critical for blood-brain barrier maintenance and angiogenesis. In contrast, ASH-induced upregulated proteins are RNA-binding proteins involved in RNA splicing, transport, and stability. Thus, ASH alters BMV proteomics to impair cytoskeletal integrity and RNA processing which are critical for cerebrovascular function.
Collapse
Affiliation(s)
- Siva SVP Sakamuri
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Venkata N Sure
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Lokanatha Oruganti
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - William Wisen
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Partha K Chandra
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, LA, USA
| | - Ning Liu
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, LA, USA
- Clinical Neuroscience Research Center, New Orleans, LA, USA
- Department of Neurosurgery, Tulane University School of Medicine, New Orleans, LA, USA
| | - Vivian A Fonseca
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
- Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | - Xiaoying Wang
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, LA, USA
- Clinical Neuroscience Research Center, New Orleans, LA, USA
- Department of Neurosurgery, Tulane University School of Medicine, New Orleans, LA, USA
| | - Jennifer Klein
- Department of Biochemistry & Molecular Biology, Louisiana State University School of Medicine, New Orleans, LA, USA
| | - Prasad VG Katakam
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA, USA
- Neuroscience Program, Tulane Brain Institute, Tulane University, New Orleans, LA, USA
- Clinical Neuroscience Research Center, New Orleans, LA, USA
| |
Collapse
|
13
|
Xu M, Zhang X, Cao J, Liu J, He Y, Guan Q, Tian X, Tang J, Li X, Ren D, Bu Q, Wang Z. OsPGL3A encodes a DYW-type pentatricopeptide repeat protein involved in chloroplast RNA processing and regulated chloroplast development. Mol Breed 2024; 44:29. [PMID: 38549701 PMCID: PMC10965880 DOI: 10.1007/s11032-024-01468-7] [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] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/19/2024] [Indexed: 04/24/2024]
Abstract
The chloroplast serves as the primary site of photosynthesis, and its development plays a crucial role in regulating plant growth and morphogenesis. The Pentatricopeptide Repeat Sequence (PPR) proteins constitute a vast protein family that function in the post-transcriptional modification of RNA within plant organelles. In this study, we characterized mutant of rice with pale green leaves (pgl3a). The chlorophyll content of pgl3a at the seedling stage was significantly reduced compared to the wild type (WT). Transmission electron microscopy (TEM) and quantitative PCR analysis revealed that pgl3a exhibited aberrant chloroplast development compared to the wild type (WT), accompanied by significant alterations in gene expression levels associated with chloroplast development and photosynthesis. The Mutmap analysis revealed that a single base deletionin the coding region of Os03g0136700 in pgl3a. By employing CRISPR/Cas9 mediated gene editing, two homozygous cr-pgl3a mutants were generated and exhibited a similar phenotype to pgl3a, thereby confirming that Os03g0136700 was responsible for pgl3a. Consequently, it was designated as OsPGL3A. OsPGL3A belongs to the DYW-type PPR protein family and is localized in chloroplasts. Furthermore, we demonstrated that the RNA editing efficiency of rps8-182 and rpoC2-4106, and the splicing efficiency of ycf3-1 were significantly decreased in pgl3a mutants compared to WT. Collectively, these results indicate that OsPGL3A plays a crucial role in chloroplast development by regulating the editing and splicing of chloroplast genes in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01468-7.
Collapse
Affiliation(s)
- Min Xu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xinying Zhang
- College of Life Science, Northeast Agricultural University, Harbin, 150030 Heilongjiang China
| | - Jinzhe Cao
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Jiali Liu
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Yiyuan He
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qingjie Guan
- Key Laboratory of the Ministry of Education for Ecological Restoration of Saline Vegetation, College of Life Sciences, Northeast Forestry University, Harbin, 150040 Heilongjiang China
| | - Xiaojie Tian
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Jiaqi Tang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Xiufeng Li
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Deyong Ren
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, 310006 People’s Republic of China
| | - Qingyun Bu
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| | - Zhenyu Wang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081 Heilongjiang China
| |
Collapse
|
14
|
Lee GY, Ham S, Sohn J, Kwon HC, Lee SJV. Meta-analysis of the transcriptome identifies aberrant RNA processing as common feature of aging in multiple species. Mol Cells 2024; 47:100047. [PMID: 38508494 PMCID: PMC11026732 DOI: 10.1016/j.mocell.2024.100047] [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: 02/07/2024] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
Aging is accompanied by the gradual deregulation of the transcriptome. However, whether age-dependent changes in the transcriptome are evolutionarily conserved or diverged remains largely unexplored. Here, we performed a meta-analysis examining the age-dependent changes in the transcriptome using publicly available datasets of 11 representative metazoans, ranging from Caenorhabditis elegans to humans. To identify the transcriptomic changes associated with aging, we analyzed various aspects of the transcriptome, including genome composition, RNA processing, and functional consequences. The use of introns and novel splice sites tended to increase with age, particularly in the brain. In addition, our analysis suggests that the age-dependent accumulation of premature termination codon-containing transcripts is a common feature of aging across multiple animal species. Using C. elegans as a test model, we showed that several splicing factors that are evolutionarily conserved and age-dependently downregulated were required to maintain a normal lifespan. Thus, aberrant RNA processing appears to be associated with aging and a short lifespan in various species.
Collapse
Affiliation(s)
- Gee-Yoon Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Seokjin Ham
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jooyeon Sohn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Hyunwoo C Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Seung-Jae V Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea.
| |
Collapse
|
15
|
Altina NH, Maranon DG, Anderson JR, Donaldson MK, Elmegerhi S, St Clair LA, Perera R, Geiss BJ, Wilusz J. The leader RNA of SARS-CoV-2 sequesters polypyrimidine tract binding protein (PTBP1) and influences pre-m RNA splicing in infected cells. Virology 2024; 592:109986. [PMID: 38290414 PMCID: PMC10923090 DOI: 10.1016/j.virol.2024.109986] [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: 07/27/2023] [Revised: 12/02/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
The large amount of viral RNA produced during infections has the potential to interact with and effectively sequester cellular RNA binding proteins, thereby influencing aspects of post-transcriptional gene regulation in the infected cell. Here we demonstrate that the abundant 5' leader RNA region of SARS-CoV-2 viral RNAs can interact with the cellular polypyrimidine tract binding protein (PTBP1). Interestingly, the effect of a knockdown of PTBP1 protein on cellular gene expression is also mimicked during SARS-CoV-2 infection, suggesting that this protein may be functionally sequestered by viral RNAs. Consistent with this model, the alternative splicing of mRNAs that is normally controlled by PTBP1 is dysregulated during SARS-CoV-2 infection. Collectively, these data suggest that the SARS-CoV-2 leader RNA sequesters the cellular PTBP1 protein during infection, resulting in significant impacts on the RNA biology of the host cell. These alterations in post-transcriptional gene regulation may play a role in SARS-CoV-2 mediated molecular pathogenesis.
Collapse
Affiliation(s)
- Noelia H Altina
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - David G Maranon
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - John R Anderson
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Meghan K Donaldson
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Suad Elmegerhi
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Laura A St Clair
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Rushika Perera
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Brian J Geiss
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA.
| |
Collapse
|
16
|
Sudhakar SRN, Khan SN, Clark A, Hendrickson-Rebizant T, Patel S, Lakowski TM, Davie JR. Protein arginine methyltransferase 1, a major regulator of biological processes. Biochem Cell Biol 2024; 102:106-126. [PMID: 37922507 DOI: 10.1139/bcb-2023-0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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] [Indexed: 11/05/2023] Open
Abstract
Protein arginine methyltransferase 1 (PRMT1) is a major type I arginine methyltransferase that catalyzes the formation of monomethyl and asymmetric dimethylarginine in protein substrates. It was first identified to asymmetrically methylate histone H4 at the third arginine residue forming the H4R3me2a active histone mark. However, several protein substrates are now identified as being methylated by PRMT1. As a result of its association with diverse classes of substrates, PRMT1 regulates several biological processes like chromatin dynamics, transcription, RNA processing, and signal transduction. The review provides an overview of PRMT1 structure, biochemical features, specificity, regulation, and role in cellular functions. We discuss the genomic distribution of PRMT1 and its association with tRNA genes. Further, we explore the different substrates of PRMT1 involved in splicing. In the end, we discuss the proteins that interact with PRMT1 and their downstream effects in diseased states.
Collapse
Affiliation(s)
- Sadhana R N Sudhakar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Shahper N Khan
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ariel Clark
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | | | - Shrinal Patel
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ted M Lakowski
- College of Pharmacy Pharmaceutical Analysis Laboratory, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| |
Collapse
|
17
|
Zhang Z, Zhang J. Purification of SRSF1 from E. coli for Biophysical and Biochemical Assays. Curr Protoc 2024; 4:e1017. [PMID: 38578012 DOI: 10.1002/cpz1.1017] [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] [Indexed: 04/06/2024]
Abstract
The Ser/Arg-rich splicing factors (SR proteins) constitute a crucial protein family in alternative splicing, comprising twelve members characterized by unique repetitive Arg-Ser dipeptide sequences (RS) and one to two RNA-recognition motifs (RRM). The RS regions of SR proteins undergo variable phosphorylation, resulting in unphosphorylated, partially phosphorylated, or hyper-phosphorylated states based on functional requirements. Despite the identification of the SR protein family over 30 years ago, the purification of native SR proteins in soluble form at large quantities has presented challenges due to their low solubility. This protocol delineates a method for acquiring soluble, full-length, unphosphorylated, hypo- and hyper-phosphorylated SRSF1, a prototypical SR family member. Notably, this protocol facilitates the purification of SRSF1 in ample quantities suitable for NMR, as well as various biophysical and biochemical studies. The methodologies and principles outlined herein are expected to extend beyond SRSF1 protein production and can be adapted for purifying other SR protein family members or SR-related proteins, such as snRNP70 and U2AF-35. Given the involvement of these proteins in numerous essential biological processes, this protocol will prove beneficial to researchers in related fields. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Purification of SRSF1 from E. coli Support Protocol: Purification of ULP1 Basic Protocol 2: Purification of hypo-phosphorylated SRSF1 from E. coli Basic Protocol 3: Purification of hyper-phosphorylated SRSF1 from E. coli.
Collapse
Affiliation(s)
- Zihan Zhang
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jun Zhang
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama
| |
Collapse
|
18
|
Shreim A, Gazzeri S, Eymin B. [Targeting the spliceosome: A new therapeutic strategy to counteract chemotherapy resistance in lung cancer?]. Rev Mal Respir 2024; 41:294-298. [PMID: 38461087 DOI: 10.1016/j.rmr.2024.02.013] [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: 02/05/2024] [Accepted: 02/05/2024] [Indexed: 03/11/2024]
Abstract
Lung cancer is the first cancer-related cause of death worldwide. This is in partially due to therapeutic resistance, which occurs in around 70% of patients, especially those receiving platinum salts, the gold-standard chemotherapy. The massive deregulation of alternative transcript splicing processes observed in many cancers has led to the development of a new class of pharmacological agents aimed at inhibiting the activity of the splicing machinery (spliceosome). The molecular mechanisms by which these inhibitors act remain largely unknown, as do the benefits of using them in combination with other therapies. In this context, our work is focused on an inhibitor of the SRPK1 kinase, a major regulator of the spliceosome.
Collapse
Affiliation(s)
- A Shreim
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, institut pour l'avancée des biosciences, site santé, Allée des Alpes, 38000, Grenoble, France.
| | - S Gazzeri
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, institut pour l'avancée des biosciences, site santé, Allée des Alpes, 38000, Grenoble, France
| | - B Eymin
- Université Grenoble Alpes, INSERM U1209, CNRS UMR5309, institut pour l'avancée des biosciences, site santé, Allée des Alpes, 38000, Grenoble, France
| |
Collapse
|
19
|
Chen K, Zhou Y, Ding M, Wang Y, Ren Z, Yang Y. Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction. Brief Bioinform 2024; 25:bbae163. [PMID: 38605640 PMCID: PMC11009468 DOI: 10.1093/bib/bbae163] [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: 01/04/2024] [Revised: 02/22/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Language models pretrained by self-supervised learning (SSL) have been widely utilized to study protein sequences, while few models were developed for genomic sequences and were limited to single species. Due to the lack of genomes from different species, these models cannot effectively leverage evolutionary information. In this study, we have developed SpliceBERT, a language model pretrained on primary ribonucleic acids (RNA) sequences from 72 vertebrates by masked language modeling, and applied it to sequence-based modeling of RNA splicing. Pretraining SpliceBERT on diverse species enables effective identification of evolutionarily conserved elements. Meanwhile, the learned hidden states and attention weights can characterize the biological properties of splice sites. As a result, SpliceBERT was shown effective on several downstream tasks: zero-shot prediction of variant effects on splicing, prediction of branchpoints in humans, and cross-species prediction of splice sites. Our study highlighted the importance of pretraining genomic language models on a diverse range of species and suggested that SSL is a promising approach to enhance our understanding of the regulatory logic underlying genomic sequences.
Collapse
Affiliation(s)
- Ken Chen
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yue Zhou
- Peng Cheng Laboratory, Shenzhen, China
| | - Maolin Ding
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yu Wang
- Peng Cheng Laboratory, Shenzhen, China
| | | | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Machine Intelligence and Advanced Computing (Sun Yat-sen University), Ministry of Education, China
| |
Collapse
|
20
|
Zhang X, Xu X, Shu J, Zhi X, Wang H, Dong Y, Sheng W, Li D, Meng Y, Cai C. A novel MMUT splicing variant causing mild methylmalonic acidemia phenotype. Heliyon 2024; 10:e26912. [PMID: 38455531 PMCID: PMC10918191 DOI: 10.1016/j.heliyon.2024.e26912] [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: 02/09/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
Objectives Methylmalonic acidemia (MMA) is a rare inborn genetic disorder that is characterized by increased levels of methylmalonic acid in blood plasma and urine. Isolated methylmalonic acidemia is one of the most common types of MMA and is caused by mutations in the gene encoding methyl-malonyl coenzyme A mutase (MMUT). In this study, we investigated the possible mechanisms underlying the symptoms of isolated MMA in a patient by molecular analysis. Methods PCR amplification and Sanger sequencing analysis was performed to identify variants in the MMUT gene in the proband and his family. Furthermore, minigene constructs were generated to validate the splicing defects in the MMUT gene variant identified in the proband. Results The 3-year-old patient was admitted to the hospital with symptoms of MMA, including fever, convulsions, and vomiting. He showed metabolic acidosis, high levels of methylmalonic acid in blood and urine, and normal blood homocysteine levels. Genetic analysis demonstrated that the patient was a compound heterozygous carrier of two variants in the MMUT gene: a missense c.278G > A variant that has already been reported in a patient with the severe mut⁰ phenotype; and a novel splice site variant c.2125-2A > G. RT-PCR analysis showed that, while the novel variant clearly alters splicing, a minor amount of a full-length transcript is generated, suggesting that a wild-type protein may be produced although at a lower quantitative level. The patient's condition improved after treatment with vitamin B12. Serious complications were not reported during follow-up at age 5. Conclusions We identified a novel splice site variant that partially disrupts normal splicing of the MMUT pre-mRNA. Production of a reduced amount of full-length transcript is responsible for the mild clinical phenotype observed in this patient. Functional studies have proven useful in exploring the genotype-phenotype association and in providing guidance for the genetic diagnosis of MMA.
Collapse
Affiliation(s)
- Xinjie Zhang
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Pediatric Research Institute, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Xiaowei Xu
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Pediatric Research Institute, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Jianbo Shu
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Pediatric Research Institute, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Xiufang Zhi
- Graduate College of Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300070, China
| | - Hong Wang
- Department of Neurology, Tianjin Children's Hospital, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Yan Dong
- Graduate College of Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300070, China
| | - Wenchao Sheng
- Graduate College of Tianjin Medical University, No. 22 Qixiangtai Road, Heping District, Tianjin, 300070, China
| | - Dong Li
- Department of Neurology, Tianjin Children's Hospital, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Yingtao Meng
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Pediatric Research Institute, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Chunquan Cai
- Tianjin Children's Hospital (Children's Hospital of Tianjin University), No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Pediatric Research Institute, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
- Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, No. 238 Longyan Road, Beichen District, Tianjin, 300134, China
| |
Collapse
|
21
|
Zhang Y, Zhang X, Tang Q, Li L, Jiang T, Fang Y, Zhang H, Zhai J, Ren G, Zheng B. A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants. Sci China Life Sci 2024:10.1007/s11427-023-2466-7. [PMID: 38489006 DOI: 10.1007/s11427-023-2466-7] [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: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 03/17/2024]
Abstract
Lariat RNA is concomitantly produced by excised intron during RNA splicing, which is usually debranched by DBR1, an RNA debranching enzyme. However, increasing evidence showed that some lariat RNA could escape debranching. Little is known about how and why these lariat RNAs could be retained. By comparing the atlas of lariat RNAs between the non-dividing cell (mature pollen) and three actively dividing tissues (young shoot apex, young seeds, and young roots), we identified hundreds to thousands of lariat RNA naturally retained in each tissue, and the incidence of lariat RNA retention is much less in shoot apex while much more in pollen. Many lariat RNAs derived from the same intron or different lariat RNAs from the same pre-mRNA could be retained in one tissue while degraded in the other tissues. By deciphering lariat RNA sequences, we identified an AG-rich (RAAAAVAAAR) motif and a UC-rich (UCUCUYUCUC) motif for pollen-specific and the other three tissues-retained lariat RNAs, respectively. Reconstitution of the pollen-specific AG-rich motif indeed enhanced lariat RNA retention in plants. Biologically, hundreds of lariat RNAs harbored miRNA binding sites, and dual-luciferase reporter assay showed that these natural lariat RNAs had the potential to protect expression of miRNA target genes. Collectively, our results uncover that selective retention of lariat RNA is an actively regulatory process, and provide new insights into understanding how lariat RNA metabolism may impact miRNA activity.
Collapse
Affiliation(s)
- Yong Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaotuo Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qi Tang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Li
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ting Jiang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yixiao Fang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hong Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| |
Collapse
|
22
|
Ding R, Yu X, Hu Z, Dong Y, Huang H, Zhang Y, Han Q, Ni ZY, Zhao R, Ye Y, Zou Q. Lactate modulates RNA splicing to promote CTLA-4 expression in tumor-infiltrating regulatory T cells. Immunity 2024; 57:528-540.e6. [PMID: 38417442 DOI: 10.1016/j.immuni.2024.01.019] [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: 10/30/2023] [Revised: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 03/01/2024]
Abstract
RNA splicing is involved in cancer initiation and progression, but how it influences host antitumor immunity in the metabolically abnormal tumor microenvironment (TME) remains unclear. Here, we demonstrate that lactate modulates Foxp3-dependent RNA splicing to maintain the phenotypic and functional status of tumor-infiltrating regulatory T (Treg) cells via CTLA-4. RNA splicing in Treg cells was correlated with the Treg cell signatures in the TME. Ubiquitin-specific peptidase 39 (USP39), a component of the RNA splicing machinery, maintained RNA-splicing-mediated CTLA-4 expression to control Treg cell function. Mechanistically, lactate promoted USP39-mediated RNA splicing to facilitate CTLA-4 expression in a Foxp3-dependent manner. Moreover, the efficiency of CTLA-4 RNA splicing was increased in tumor-infiltrating Treg cells from patients with colorectal cancer. These findings highlight the immunological relevance of RNA splicing in Treg cells and provide important insights into the environmental mechanism governing CTLA-4 expression in Treg cells.
Collapse
Affiliation(s)
- Rui Ding
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaoyan Yu
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhilin Hu
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease, the School of Basic Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Yu Dong
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Haiyan Huang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuerong Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qiaoqiao Han
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhi-Yu Ni
- Clinical Medical College, Hebei University of Engineering, Handan 056038, Hebei, China; Central Laboratory, Hebei Collaborative Innovation Center of Tumor Microecological Metabolism Regulation, Affiliated Hospital of Hebei University, Baoding 071000, Hebei, China; Affiliated Hospital of Hebei Engineering University, Handan 056002, Hebei, China.
| | - Ren Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Youqiong Ye
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Qiang Zou
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| |
Collapse
|
23
|
Huo Y, Cheng M, Tang M, Zhang M, Yang X, Zheng Y, Zhao T, He P, Yu J. GhCTSF1, a short PPR protein with a conserved role in chloroplast development and photosynthesis, participates in intron splicing of rpoC1 and ycf3-2 transcripts in cotton. Plant Commun 2024:100858. [PMID: 38444162 DOI: 10.1016/j.xplc.2024.100858] [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: 07/08/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
Abstract
Cotton is one of the most important textile fibers worldwide. As crucial agronomic traits, leaves play an essential role in the growth, disease resistance, fiber quality, and yield of cotton plants. Pentatricopeptide repeat (PPR) proteins are a large family of nuclear-encoded proteins involved in organellar or nuclear RNA metabolism. Using a virus-induced gene silencing assay, we found that cotton plants displayed variegated yellow leaf phenotypes with decreased chlorophyll content when expression of the PPR gene GhCTSF1 was silenced. GhCTSF1 encodes a chloroplast-localized protein that contains only two PPR motifs. Disruption of GhCTSF1 substantially reduces the splicing efficiency of rpoC1 intron 1 and ycf3 intron 2. Loss of function of the GhCTSF1 ortholog EMB1417 causes splicing defects in rpoC1 and ycf3-2, leading to impaired chloroplast structure and decreased photosynthetic rates in Arabidopsis. We also found that GhCTSF1 interacts with two splicing factors, GhCRS2 and GhWTF1. Defects in GhCRS2 and GhWTF1 severely affect intron splicing of rpoC1 and ycf3-2 in cotton, leading to defects in chloroplast development and a reduction in photosynthesis. Our results suggest that GhCTSF1 is specifically required for splicing rpoC1 and ycf3-2 in cooperation with GhCRS2 and GhWTF1.
Collapse
Affiliation(s)
- Yuzhu Huo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Mengxue Cheng
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Meiju Tang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Meng Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Xiaofan Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Yating Zheng
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Tong Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Peng He
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| | - Jianing Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China.
| |
Collapse
|
24
|
Ma X, Liu B, Gong Z, Wang J, Qu Z, Cai J. Comparative proteomic analysis across the developmental stages of the Eimeria tenella. Genomics 2024; 116:110792. [PMID: 38215860 DOI: 10.1016/j.ygeno.2024.110792] [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: 10/17/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Eimeria tenella is the main pathogen responsible for coccidiosis in chickens. The life cycle of E. tenella is, arguably, the least complex of all Coccidia, with only one host. However, it presents different developmental stages, either in the environment or in the host and either intracellular or extracellular. Its signaling and metabolic pathways change with its different developmental stages. Until now, little is known about the developmental regulation and transformation mechanisms of its life cycle. In this study, protein profiles from the five developmental stages, including unsporulated oocysts (USO), partially sporulated (7 h) oocysts (SO7h), sporulated oocysts (SO), sporozoites (S) and second-generation merozoites (M2), were harvested using the label-free quantitative proteomics approach. Then the differentially expressed proteins (DEPs) for these stages were identified. A total of 314, 432, 689, and 665 DEPs were identified from the comparison of SO7h vs USO, SO vs SO7h, S vs SO, and M2 vs S, respectively. By conducting weighted gene coexpression network analysis (WGCNA), six modules were dissected. Proteins in blue and brown modules were calculated to be significantly positively correlated with the E. tenella developmental stages of sporozoites (S) and second-generation merozoites (M2), respectively. In addition, hub proteins with high intra-module degree were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes (KEGG) pathway enrichment analyses revealed that hub proteins in blue modules were involved in electron transport chain and oxidative phosphorylation. Hub proteins in the brown module were involved in RNA splicing. These findings provide new clues and ideas to enhance our fundamental understanding of the molecular mechanisms underlying parasite development.
Collapse
Affiliation(s)
- Xueting Ma
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Baohong Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China.
| | - Zhenxing Gong
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia Province 750021, China
| | - Jing Wang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Zigang Qu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China
| | - Jianping Cai
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730000, China; Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou 730046, China.
| |
Collapse
|
25
|
Borisevich SS, Aksinina TE, Ilyina MG, Shender VO, Anufrieva KS, Arapidi GP, Antipova NV, Anizon F, Esvan YJ, Giraud F, Tatarskiy VV, Moreau P, Shakhparonov MI, Pavlyukov MS, Shtil AA. The Nitro Group Reshapes the Effects of Pyrido[3,4- g]quinazoline Derivatives on DYRK/CLK Activity and RNA Splicing in Glioblastoma Cells. Cancers (Basel) 2024; 16:834. [PMID: 38398225 PMCID: PMC10886777 DOI: 10.3390/cancers16040834] [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: 12/30/2023] [Revised: 02/10/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Serine-threonine protein kinases of the DYRK and CLK families regulate a variety of vital cellular functions. In particular, these enzymes phosphorylate proteins involved in pre-mRNA splicing. Targeting splicing with pharmacological DYRK/CLK inhibitors emerged as a promising anticancer strategy. Investigation of the pyrido[3,4-g]quinazoline scaffold led to the discovery of DYRK/CLK binders with differential potency against individual enzyme isoforms. Exploring the structure-activity relationship within this chemotype, we demonstrated that two structurally close compounds, pyrido[3,4-g]quinazoline-2,10-diamine 1 and 10-nitro pyrido[3,4-g]quinazoline-2-amine 2, differentially inhibited DYRK1-4 and CLK1-3 protein kinases in vitro. Unlike compound 1, compound 2 efficiently inhibited DYRK3 and CLK4 isoenzymes at nanomolar concentrations. Quantum chemical calculations, docking and molecular dynamic simulations of complexes of 1 and 2 with DYRK3 and CLK4 identified a dramatic difference in electron donor-acceptor properties critical for preferential interaction of 2 with these targets. Subsequent transcriptome and proteome analyses of patient-derived glioblastoma (GBM) neurospheres treated with 2 revealed that this compound impaired CLK4 interactions with spliceosomal proteins, thereby altering RNA splicing. Importantly, 2 affected the genes that perform critical functions for cancer cells including DNA damage response, p53 signaling and transcription. Altogether, these results provide a mechanistic basis for the therapeutic efficacy of 2 previously demonstrated in in vivo GBM models.
Collapse
Affiliation(s)
- Sophia S Borisevich
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, Ufa 450054, Russia
- Institute of Cyber Intelligence Systems, National Research Nuclear University MEPhI, Moscow 115409, Russia
| | - Tatiana E Aksinina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Margarita G Ilyina
- Ufa Institute of Chemistry, Ufa Federal Research Center of the Russian Academy of Sciences, Ufa 450054, Russia
- Institute of Cyber Intelligence Systems, National Research Nuclear University MEPhI, Moscow 115409, Russia
| | - Victoria O Shender
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia
| | - Ksenia S Anufrieva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia
| | - Georgij P Arapidi
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow 119435, Russia
| | - Nadezhda V Antipova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Fabrice Anizon
- Université Clermont Auvergne, Centre National de la Recherche Scientifique, Clermont Auvergne Institut National Polytechnique, Institute of Chemistry of Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Yannick J Esvan
- Université Clermont Auvergne, Centre National de la Recherche Scientifique, Clermont Auvergne Institut National Polytechnique, Institute of Chemistry of Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Francis Giraud
- Université Clermont Auvergne, Centre National de la Recherche Scientifique, Clermont Auvergne Institut National Polytechnique, Institute of Chemistry of Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Pascale Moreau
- Université Clermont Auvergne, Centre National de la Recherche Scientifique, Clermont Auvergne Institut National Polytechnique, Institute of Chemistry of Clermont-Ferrand, F-63000 Clermont-Ferrand, France
| | - Mikhail I Shakhparonov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Marat S Pavlyukov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Alexander A Shtil
- Blokhin National Medical Research Center of Oncology, Moscow 115522, Russia
- Department of Chemistry, Moscow State University, Moscow 119234, Russia
| |
Collapse
|
26
|
Tushir S, Jhanwar P, Benda M, Horáčková V, Doležal P, Tatu U. In vivo Validation of Hsp90 Trans-splicing in Giardia lamblia: Highlighting the Role of Cis-elements. J Mol Biol 2024; 436:168440. [PMID: 38218367 DOI: 10.1016/j.jmb.2024.168440] [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: 10/23/2023] [Revised: 12/24/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024]
Abstract
Giardia lambliacauses giardiasis, one of the most common human infectious diseases globally. Previous studies from our lab have shown that hsp90 gene ofGiardia is split into two halves, namely hspN and hspC. The independent pre-mRNAs of these split genes join by trans-splicing, producing a full-length Hsp90 (FlHsp90) mRNA. Genetic manipulation of the participating genes is necessary to understand the mechanism and significance of such trans-splicing based expression of Hsp90. In this study, we have performed transfection based exogenous expression of hspN and/or hspC in G. lamblia. We electroporated a plasmid containing the Avi-tagged hspN component of Hsp90 and examined its fate in G. lamblia. We show that the exogenously expressed hspN RNA gets trans-spliced to endogenously expressed hspC RNA, giving rise to a hybrid-FlHsp90. We highlight the importance of cis-elements in this trans-splicing reaction through mutational analysis. The episomal plasmid carrying deletions in the intronic region of hspN, showed inhibition of the trans-splicing reaction.Additionally, exogenous hspC RNA also followed the same fate as of exogenous hspN, while upon co-transfection with episomal hspN, they underwent trans-splicing with each other. Using eGFP as a test protein, we have shown that intronic sequences of hsp90 gene can guide trans-splicing mediated repair of any associated exonic sequences. Our study provides in vivo validation of Hsp90 trans-splicing, showing crucial role of cis-elements and importantly highlights the potential of hsp90 intronic sequences to function as a minimal splicing tool.
Collapse
Affiliation(s)
- Sheetal Tushir
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Pratima Jhanwar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Martin Benda
- Dept. of Parasitology, Faculty of Science, BIOCEV, Charles University, Czech Republic
| | - Vendula Horáčková
- Dept. of Parasitology, Faculty of Science, BIOCEV, Charles University, Czech Republic
| | - Pavel Doležal
- Dept. of Parasitology, Faculty of Science, BIOCEV, Charles University, Czech Republic
| | - Utpal Tatu
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
27
|
Anderson R, Das MR, Chang Y, Farenhem K, Schmitz CO, Jain A. CAG repeat expansions create splicing acceptor sites and produce aberrant repeat-containing RNAs. Mol Cell 2024; 84:702-714.e10. [PMID: 38295802 PMCID: PMC10923110 DOI: 10.1016/j.molcel.2024.01.006] [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: 08/20/2023] [Revised: 11/07/2023] [Accepted: 01/08/2024] [Indexed: 02/04/2024]
Abstract
Expansions of CAG trinucleotide repeats cause several rare neurodegenerative diseases. The disease-causing repeats are translated in multiple reading frames and without an identifiable initiation codon. The molecular mechanism of this repeat-associated non-AUG (RAN) translation is not known. We find that expanded CAG repeats create new splice acceptor sites. Splicing of proximal donors to the repeats produces unexpected repeat-containing transcripts. Upon splicing, depending on the sequences surrounding the donor, CAG repeats may become embedded in AUG-initiated open reading frames. Canonical AUG-initiated translation of these aberrant RNAs may account for proteins that have been attributed to RAN translation. Disruption of the relevant splice donors or the in-frame AUG initiation codons is sufficient to abrogate RAN translation. Our findings provide a molecular explanation for the abnormal translation products observed in CAG trinucleotide repeat expansion disorders and add to the repertoire of mechanisms by which repeat expansion mutations disrupt cellular functions.
Collapse
Affiliation(s)
- Rachel Anderson
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Michael R Das
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Yeonji Chang
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA
| | - Kelsey Farenhem
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Cameron O Schmitz
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Ankur Jain
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA.
| |
Collapse
|
28
|
Li X, Jiang Y. Research Progress of Group II Intron Splicing Factors in Land Plant Mitochondria. Genes (Basel) 2024; 15:176. [PMID: 38397166 PMCID: PMC10887915 DOI: 10.3390/genes15020176] [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: 12/11/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondria are important organelles that provide energy for the life of cells. Group II introns are usually found in the mitochondrial genes of land plants. Correct splicing of group II introns is critical to mitochondrial gene expression, mitochondrial biological function, and plant growth and development. Ancestral group II introns are self-splicing ribozymes that can catalyze their own removal from pre-RNAs, while group II introns in land plant mitochondria went through degenerations in RNA structures, and thus they lost the ability to self-splice. Instead, splicing of these introns in the mitochondria of land plants is promoted by nuclear- and mitochondrial-encoded proteins. Many proteins involved in mitochondrial group II intron splicing have been characterized in land plants to date. Here, we present a summary of research progress on mitochondrial group II intron splicing in land plants, with a major focus on protein splicing factors and their probable functions on the splicing of mitochondrial group II introns.
Collapse
Affiliation(s)
| | - Yueshui Jiang
- School of Life Sciences, Qufu Normal University, Qufu 273165, China;
| |
Collapse
|
29
|
Duan C, Mooney T, Buerer L, Bowers C, Rong S, Kim SW, Fredericks AM, Monaghan SF, Fairbrother WG. The unusual gene architecture of polyubiquitin is created by dual-specific splice sites. Genome Biol 2024; 25:33. [PMID: 38268025 PMCID: PMC10809524 DOI: 10.1186/s13059-023-03157-8] [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] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND The removal of introns occurs through the splicing of a 5' splice site (5'ss) with a 3' splice site (3'ss). These two elements are recognized by distinct components of the spliceosome. However, introns in higher eukaryotes contain many matches to the 5' and 3' splice-site motifs that are presumed not to be used. RESULTS Here, we find that many of these sites can be used. We also find occurrences of the AGGT motif that can function as either a 5'ss or a 3'ss-previously referred to as dual-specific splice sites (DSSs)-within introns. Analysis of the Sequence Read Archive reveals a 3.1-fold enrichment of DSSs relative to expectation, implying synergy between the ability to function as a 5'ss and 3'ss. Despite this suggested mechanistic advantage, DSSs are 2.7- and 4.7-fold underrepresented in annotated 5' and 3' splice sites. A curious exception is the polyubiquitin gene UBC, which contains a tandem array of DSSs that precisely delimit the boundary of each ubiquitin monomer. The resulting isoforms splice stochastically to include a variable number of ubiquitin monomers. We found no evidence of tissue-specific or feedback regulation but note the 8.4-fold enrichment of DSS-spliced introns in tandem repeat genes suggests a driving role in the evolution of genes like UBC. CONCLUSIONS We find an excess of unannotated splice sites and the utilization of DSSs in tandem repeats supports the role of splicing in gene evolution. These findings enhance our understanding of the diverse and complex nature of the splicing process.
Collapse
Affiliation(s)
- Chaorui Duan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Truman Mooney
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Luke Buerer
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Cory Bowers
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Stephen Rong
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02903, USA
| | - Seong Won Kim
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | | | - Sean F Monaghan
- Division of Surgical Research, Department of Surgery, Alpert Medical School of Brown University/Rhode Island Hospital, Providence, RI, 02903, USA
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA.
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02903, USA.
| |
Collapse
|
30
|
Kaempfer R. RNA Activators of Stress Kinase PKR within Human Genes That Control Splicing or Translation Create Novel Targets for Hereditary Diseases. Int J Mol Sci 2024; 25:1323. [PMID: 38279321 PMCID: PMC10816128 DOI: 10.3390/ijms25021323] [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: 12/24/2023] [Revised: 01/14/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
Specific sequences within RNA encoded by human genes essential for survival possess the ability to activate the RNA-dependent stress kinase PKR, resulting in phosphorylation of its substrate, eukaryotic translation initiation factor-2α (eIF2α), either to curb their mRNA translation or to enhance mRNA splicing. Thus, interferon-γ (IFNG) mRNA activates PKR through a 5'-terminal 203-nucleotide pseudoknot structure, thereby strongly downregulating its own translation and preventing a harmful hyper-inflammatory response. Tumor necrosis factor-α (TNF) pre-mRNA encodes within the 3'-untranslated region (3'-UTR) a 104-nucleotide RNA pseudoknot that activates PKR to enhance its splicing by an order of magnitude while leaving mRNA translation intact, thereby promoting effective TNF protein expression. Adult and fetal globin genes encode pre-mRNA structures that strongly activate PKR, leading to eIF2α phosphorylation that greatly enhances spliceosome assembly and splicing, yet also structures that silence PKR activation upon splicing to allow for unabated globin mRNA translation essential for life. Regulatory circuits resulting in each case from PKR activation were reviewed previously. Here, we analyze mutations within these genes created to delineate the RNA structures that activate PKR and to deconvolute their folding. Given the critical role of intragenic RNA activators of PKR in gene regulation, such mutations reveal novel potential RNA targets for human disease.
Collapse
Affiliation(s)
- Raymond Kaempfer
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem 9112102, Israel
| |
Collapse
|
31
|
Zhang R, Wang D, Ruan GX, Wang R, Li Y, Chen W, Huang H, Wang J, Meng L, Zhu Z, Lei D, Xu S, Ou X. Spliceosome component PHD finger 5A is essential for early B lymphopoiesis. Development 2024; 151:dev202247. [PMID: 38095286 DOI: 10.1242/dev.202247] [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: 08/08/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
The spliceosome, a multi-megadalton ribonucleoprotein complex, is essential for pre-mRNA splicing in the nucleus and ensuring genomic stability. Its precise and dynamic assembly is pivotal for its function. Spliceosome malfunctions can lead to developmental abnormalities and potentially contribute to tumorigenesis. The specific role of the spliceosome in B cell development is poorly understood. Here, we reveal that the spliceosomal U2 snRNP component PHD finger protein 5A (Phf5a) is vital for early B cell development. Loss of Phf5a results in pronounced defects in B cell development, causing an arrest at the transition from pre-pro-B to early pro-B cell stage in the bone marrow of mutant mice. Phf5a-deficient B cells exhibit impaired immunoglobulin heavy (IgH) chain expression due to defective V-to-DJ gene rearrangement. Mechanistically, our findings suggest that Phf5a facilitates IgH gene rearrangement by regulating the activity of recombination-activating gene endonuclease and influencing chromatin interactions at the Igh locus.
Collapse
Affiliation(s)
- Rui Zhang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Daoqin Wang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Gui-Xin Ruan
- Medical School, Taizhou University, Taizhou 318000, China
| | - Ruisi Wang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuxing Li
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wenjing Chen
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hengjun Huang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jing Wang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Limin Meng
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhijian Zhu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dengfeng Lei
- Department of Ophthalmology, Southern University of Science and Technology Hospital, Shenzhen 518055, China
| | - Shengli Xu
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Singapore 138648, Republic of Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive MD9, Singapore 117593, Republic of Singapore
| | - Xijun Ou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
32
|
Hao L, Chen M, Li D, Lijavetzky D. Editorial: Plant RNA processing: discovery, mechanism and function. Front Plant Sci 2024; 15:1359415. [PMID: 38282821 PMCID: PMC10809176 DOI: 10.3389/fpls.2024.1359415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024]
Affiliation(s)
- Lili Hao
- China National Center for Bioinformation, Beijing, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Dayong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Diego Lijavetzky
- Instituto de Biología Agrícola de Mendoza (IBAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (FCA-UNCuyo), Mendoza, Argentina
| |
Collapse
|
33
|
Polido SA, Stuani C, Voigt A, Banik P, Kamps J, Bader V, Grover P, Krause LJ, Zerr I, Matschke J, Glatzel M, Winklhofer KF, Buratti E, Tatzelt J. Cross-seeding by prion protein inactivates TDP-43. Brain 2024; 147:240-254. [PMID: 37669322 DOI: 10.1093/brain/awad289] [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: 01/30/2023] [Revised: 07/14/2023] [Accepted: 08/03/2023] [Indexed: 09/07/2023] Open
Abstract
A common pathological denominator of various neurodegenerative diseases is the accumulation of protein aggregates. Neurotoxic effects are caused by a loss of the physiological activity of the aggregating protein and/or a gain of toxic function of the misfolded protein conformers. In transmissible spongiform encephalopathies or prion diseases, neurodegeneration is caused by aberrantly folded isoforms of the prion protein (PrP). However, it is poorly understood how pathogenic PrP conformers interfere with neuronal viability. Employing in vitro approaches, cell culture, animal models and patients' brain samples, we show that misfolded PrP can induce aggregation and inactivation of TAR DNA-binding protein-43 (TDP-43). Purified PrP aggregates interact with TDP-43 in vitro and in cells and induce the conversion of soluble TDP-43 into non-dynamic protein assemblies. Similarly, mislocalized PrP conformers in the cytosol bind to and sequester TDP-43 in cytosolic aggregates. As a consequence, TDP-43-dependent splicing activity in the nucleus is significantly decreased, leading to altered protein expression in cells with cytosolic PrP aggregates. Finally, we present evidence for cytosolic TDP-43 aggregates in neurons of transgenic flies expressing mammalian PrP and Creutzfeldt-Jakob disease patients. Our study identified a novel mechanism of how aberrant PrP conformers impair physiological pathways by cross-seeding.
Collapse
Affiliation(s)
- Stella A Polido
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Cristiana Stuani
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Aaron Voigt
- Department of Neurology, Medical Faculty, University Hospital, RWTH Aachen University, 52074 Aachen, Germany
| | - Papiya Banik
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Janine Kamps
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Cluster of Excellence RESOLV, Ruhr University Bochum, 44801 Bochum, Germany
| | - Verian Bader
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Prerna Grover
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Laura J Krause
- Cluster of Excellence RESOLV, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Inga Zerr
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jakob Matschke
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Konstanze F Winklhofer
- Cluster of Excellence RESOLV, Ruhr University Bochum, 44801 Bochum, Germany
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy
| | - Jörg Tatzelt
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- Cluster of Excellence RESOLV, Ruhr University Bochum, 44801 Bochum, Germany
| |
Collapse
|
34
|
Yan Q, Fang X, Liu X, Guo S, Chen S, Luo M, Lan P, Guan XY. Loss of ESRP2 Activates TAK1-MAPK Signaling through the Fetal RNA-Splicing Program to Promote Hepatocellular Carcinoma Progression. Adv Sci (Weinh) 2024; 11:e2305653. [PMID: 37985644 PMCID: PMC10767434 DOI: 10.1002/advs.202305653] [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: 08/13/2023] [Indexed: 11/22/2023]
Abstract
Tumors usually display fetal-like characteristics, and many oncofetal proteins have been identified. However, fetal-like reprogramming of RNA splicing in hepatocellular carcinoma (HCC) is poorly understood. Here, it is demonstrated that the expression of epithelial splicing regulatory protein 2 (ESRP2), an RNA splicing factor, is suppressed in fetal hepatocytes and HCC, in parallel with tumor progression. By combining RNA-Seq with splicing analysis, it is identified that ESRP2 controls the fetal-to-adult switch of multiple splice isoforms in HCC. Functionally, ESRP2 suppressed cell proliferation and migration by specifically switching the alternative splicing (AS) of the TAK1 gene and restraining the expression of the fetal and oncogenic isoform, TAK1_ΔE12. Notably, aberrant TAK1 splicing led to the activation of p38MAPK signaling and predicted poor prognosis in HCC patients. Further investigation revealed that TAK1_ΔE12 protein interacted closely with TAB3 and formed liquid condensation in HCC cells, resulting in p38MAPK activation, enhanced cell migration, and accelerated tumorigenesis. Loss of ESRP2 sensitized HCC cells to TAK1 kinase inhibitor (TAK1i), promoting pyroptotic cell death and CD8+ T cell infiltration. Combining TAK1i with immune checkpoint therapy achieved potent tumor regression in mice. Overall, the findings reveal a previously unexplored onco-fetal reprogramming of RNA splicing and provide novel therapeutic avenues for HCC.
Collapse
Affiliation(s)
- Qian Yan
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
| | - Xiaona Fang
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
- Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Xiaoxia Liu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
| | - Sai Guo
- Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, China
| | - Siqi Chen
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
| | - Min Luo
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Shenzhen Key Laboratory of recurrent metastatic cancer and personalized therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Ping Lan
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
- State Key Laboratory of Oncology in South China, Guangzhou, China
| | - Xin-Yuan Guan
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Shenzhen Key Laboratory of recurrent metastatic cancer and personalized therapy, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Clinical Oncology, State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China
| |
Collapse
|
35
|
Tshilenge KT, Bons J, Aguirre CG, Geronimo-Olvera C, Shah S, Rose J, Gerencser AA, Mak SK, Ehrlich ME, Bragg DC, Schilling B, Ellerby LM. Proteomic analysis of X-linked dystonia parkinsonism disease striatal neurons reveals altered RNA metabolism and splicing. Neurobiol Dis 2024; 190:106367. [PMID: 38042508 PMCID: PMC11103251 DOI: 10.1016/j.nbd.2023.106367] [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: 09/22/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a rare neurodegenerative disease endemic to the Philippines. The genetic cause for XDP is an insertion of a SINE-VNTR-Alu (SVA)-type retrotransposon within intron 32 of TATA-binding protein associated factor 1 (TAF1) that causes an alteration of TAF1 splicing, partial intron retention, and decreased transcription. Although TAF1 is expressed in all organs, medium spiny neurons (MSNs) within the striatum are one of the cell types most affected in XDP. To define how mutations in the TAF1 gene lead to MSN vulnerability, we carried out a proteomic analysis of human XDP patient-derived neural stem cells (NSCs) and MSNs derived from induced pluripotent stem cells. NSCs and MSNs were grown in parallel and subjected to quantitative proteomic analysis in data-independent acquisition mode on the Orbitrap Eclipse Tribrid mass spectrometer. Subsequent functional enrichment analysis demonstrated that neurodegenerative disease-related pathways, such as Huntington's disease, spinocerebellar ataxia, cellular senescence, mitochondrial function and RNA binding metabolism, were highly represented. We used weighted coexpression network analysis (WGCNA) of the NSC and MSN proteomic data set to uncover disease-driving network modules. Three of the modules significantly correlated with XDP genotype when compared to the non-affected control and were enriched for DNA helicase and nuclear chromatin assembly, mitochondrial disassembly, RNA location and mRNA processing. Consistent with aberrant mRNA processing, we found splicing and intron retention of TAF1 intron 32 in XDP MSN. We also identified TAF1 as one of the top enriched transcription factors, along with YY1, ATF2, USF1 and MYC. Notably, YY1 has been implicated in genetic forms of dystonia. Overall, our proteomic data set constitutes a valuable resource to understand mechanisms relevant to TAF1 dysregulation and to identify new therapeutic targets for XDP.
Collapse
Affiliation(s)
| | - Joanna Bons
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Carlos Galicia Aguirre
- The Buck Institute for Research on Aging, Novato, California 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA
| | | | - Samah Shah
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Jacob Rose
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Akos A Gerencser
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Sally K Mak
- The Buck Institute for Research on Aging, Novato, California 94945, USA
| | - Michelle E Ehrlich
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - D Cristopher Bragg
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Neurology, The Collaborative Center for X-linked Dystonia-Parkinsonism, Massachusetts General Hospital, Charlestown, MA, USA
| | - Birgit Schilling
- The Buck Institute for Research on Aging, Novato, California 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA.
| | - Lisa M Ellerby
- The Buck Institute for Research on Aging, Novato, California 94945, USA; University of Southern California, Leonard Davis School of Gerontology, 3715 McClintock Ave, Los Angeles, CA 90893, USA.
| |
Collapse
|
36
|
Jaiswal AK, Thaxton ML, Scherer GM, Sorrentino JP, Garg NK, Rao DS. Small molecule inhibition of RNA binding proteins in haematologic cancer. RNA Biol 2024; 21:1-14. [PMID: 38329136 PMCID: PMC10857685 DOI: 10.1080/15476286.2024.2303558] [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] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
In recent years, advances in biomedicine have revealed an important role for post-transcriptional mechanisms of gene expression regulation in pathologic conditions. In cancer in general and leukaemia specifically, RNA binding proteins have emerged as important regulator of RNA homoeostasis that are often dysregulated in the disease state. Having established the importance of these pathogenetic mechanisms, there have been a number of efforts to target RNA binding proteins using oligonucleotide-based strategies, as well as with small organic molecules. The field is at an exciting inflection point with the convergence of biomedical knowledge, small molecule screening strategies and improved chemical methods for synthesis and construction of sophisticated small molecules. Here, we review the mechanisms of post-transcriptional gene regulation, specifically in leukaemia, current small-molecule based efforts to target RNA binding proteins, and future prospects.
Collapse
Affiliation(s)
- Amit K. Jaiswal
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
| | - Michelle L. Thaxton
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
| | - Georgia M. Scherer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Jacob P. Sorrentino
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Neil K. Garg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Dinesh S. Rao
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, CA, USA
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
| |
Collapse
|
37
|
Kuijper EC, Overzier M, Suidgeest E, Dzyubachyk O, Maguin C, Pérot JB, Flament J, Ariyurek Y, Mei H, Buijsen RAM, van der Weerd L, van Roon-Mom W. Antisense oligonucleotide-mediated disruption of HTT caspase-6 cleavage site ameliorates the phenotype of YAC128 Huntington disease mice. Neurobiol Dis 2024; 190:106368. [PMID: 38040383 DOI: 10.1016/j.nbd.2023.106368] [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: 09/08/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
In Huntington disease, cellular toxicity is particularly caused by toxic protein fragments generated from the mutant huntingtin (HTT) protein. By modifying the HTT protein, we aim to reduce proteolytic cleavage and ameliorate the consequences of mutant HTT without lowering total HTT levels. To that end, we use an antisense oligonucleotide (AON) that targets HTT pre-mRNA and induces partial skipping of exon 12, which contains the critical caspase-6 cleavage site. Here, we show that AON-treatment can partially restore the phenotype of YAC128 mice, a mouse model expressing the full-length human HTT gene including 128 CAG-repeats. Wild-type and YAC128 mice were treated intracerebroventricularly with AON12.1, scrambled AON or vehicle starting at 6 months of age and followed up to 12 months of age, when MRI was performed and mice were sacrificed. AON12.1 treatment induced around 40% exon skip and protein modification. The phenotype on body weight and activity, but not rotarod, was restored by AON treatment. Genes differentially expressed in YAC128 striatum changed toward wild-type levels and striatal volume was preserved upon AON12.1 treatment. However, scrambled AON also showed a restorative effect on gene expression and appeared to generally increase brain volume.
Collapse
Affiliation(s)
- Elsa C Kuijper
- Department of Human Genetics, Leiden University Medical Center, the Netherlands.
| | - Maurice Overzier
- Department of Human Genetics, Leiden University Medical Center, the Netherlands
| | - Ernst Suidgeest
- Department of Radiology, Leiden University Medical Center, the Netherlands
| | - Oleh Dzyubachyk
- Department of Radiology, Leiden University Medical Center, the Netherlands
| | - Cécile Maguin
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, Molecular Imaging Research Center, Laboratoire des Maladies Neurodégénératives, France
| | - Jean-Baptiste Pérot
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, Molecular Imaging Research Center, Laboratoire des Maladies Neurodégénératives, France; Institut du Cerveau - Paris Brain Institute, Sorbonne Université, France
| | - Julien Flament
- Université Paris-Saclay, Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, Molecular Imaging Research Center, Laboratoire des Maladies Neurodégénératives, France
| | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Center, the Netherlands
| | - Hailiang Mei
- Department of Biomedical Data Sciences, Leiden University Medical Center, the Netherlands
| | - Ronald A M Buijsen
- Department of Human Genetics, Leiden University Medical Center, the Netherlands
| | - Louise van der Weerd
- Department of Human Genetics, Leiden University Medical Center, the Netherlands; Department of Radiology, Leiden University Medical Center, the Netherlands
| | | |
Collapse
|
38
|
Baker CA. Spying on specific splicing in spinal nerve injury. Neurotherapeutics 2024; 21:e00315. [PMID: 38216398 PMCID: PMC10903080 DOI: 10.1016/j.neurot.2024.e00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 01/01/2024] [Indexed: 01/14/2024] Open
Affiliation(s)
- Christopher A Baker
- Howard Hughes Medical Institute, Department of Immunobiology, Yale School of Medicine, United States.
| |
Collapse
|
39
|
Cheng C, Yang F, Zhao S, Chen X. A novel de novo CLTC variant altering RNA splicing causes fetal developmental abnormalities. BMC Med Genomics 2023; 16:331. [PMID: 38111042 PMCID: PMC10729518 DOI: 10.1186/s12920-023-01778-3] [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: 08/01/2023] [Accepted: 12/14/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND About 31 individuals with CLTC variants have been reported worldwide, and all reported individuals have motor and mental retardation. CLTC is known to lead to intellectual developmental disorder, autosomal dominant 56. Few studies are focusing on the prenatal stage of the disease. METHOD An ultrasound examination was performed to obtain the prenatal phenotype. Whole-exome sequencing was used to find the pathogenic variant. Multiple computational tools predicted the conservation and deleteriousness. Minigene assay and western blot were utilized to investigate the effect on splicing of mRNA and protein expression. RESULT Here we found a novel de novo variant of CLTC in a fetus. The fetus manifested bilateral choroid plexus cysts of the brain, hyperechogenic kidneys, and ventricular septal defect. A heterozygous variant c.3249 + 1G > C was identified in the fetus. This position was conserved and the variant was predicted to be deleterious. Minigene assay revealed the presence of a truncating transcript with the retention of intron 20. Western blot result showed the c.3249 + 1G > C variant elicited degradation of the protein. CONCLUSION To the best of our knowledge, our study identified a novel de novo variant of CLTC and provided the earliest clinical characteristic of the CLTC variant at the prenatal stage. The functional experiment suggested the variant caused the altering of the RNA splicing and the protein expression. We extended the mutational spectrum of CLTC and provided guidance on genetic counseling.
Collapse
Affiliation(s)
- Chen Cheng
- Ultrasound Diagnosis Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, China
| | - Fan Yang
- Ultrasound Diagnosis Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, China
| | - Sheng Zhao
- Ultrasound Diagnosis Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, China.
| | - Xinlin Chen
- Ultrasound Diagnosis Department, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, China.
| |
Collapse
|
40
|
Dutta DJ, Sasaki J, Bansal A, Sugai K, Yamashita S, Li G, Lazarski C, Wang L, Sasaki T, Yamashita C, Carryl H, Suzuki R, Odawara M, Imamura Kawasawa Y, Rakic P, Torii M, Hashimoto-Torii K. Alternative splicing events as peripheral biomarkers for motor learning deficit caused by adverse prenatal environments. Proc Natl Acad Sci U S A 2023; 120:e2304074120. [PMID: 38051767 PMCID: PMC10723155 DOI: 10.1073/pnas.2304074120] [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: 03/13/2023] [Accepted: 10/25/2023] [Indexed: 12/07/2023] Open
Abstract
Severity of neurobehavioral deficits in children born from adverse pregnancies, such as maternal alcohol consumption and diabetes, does not always correlate with the adversity's duration and intensity. Therefore, biological signatures for accurate prediction of the severity of neurobehavioral deficits, and robust tools for reliable identification of such biomarkers, have an urgent clinical need. Here, we demonstrate that significant changes in the alternative splicing (AS) pattern of offspring lymphocyte RNA can function as accurate peripheral biomarkers for motor learning deficits in mouse models of prenatal alcohol exposure (PAE) and offspring of mother with diabetes (OMD). An aptly trained deep-learning model identified 29 AS events common to PAE and OMD as superior predictors of motor learning deficits than AS events specific to PAE or OMD. Shapley-value analysis, a game-theory algorithm, deciphered the trained deep-learning model's learnt associations between its input, AS events, and output, motor learning performance. Shapley values of the deep-learning model's input identified the relative contribution of the 29 common AS events to the motor learning deficit. Gene ontology and predictive structure-function analyses, using Alphafold2 algorithm, supported existing evidence on the critical roles of these molecules in early brain development and function. The direction of most AS events was opposite in PAE and OMD, potentially from differential expression of RNA binding proteins in PAE and OMD. Altogether, this study posits that AS of lymphocyte RNA is a rich resource, and deep-learning is an effective tool, for discovery of peripheral biomarkers of neurobehavioral deficits in children of diverse adverse pregnancies.
Collapse
Affiliation(s)
- Dipankar J. Dutta
- Center for Neuroscience Research, Children’s National Hospital,Washington, DC20010
| | - Junko Sasaki
- Center for Neuroscience Research, Children’s National Hospital,Washington, DC20010
- Department of Diabetes, Endocrinology and Metabolism, Tokyo Medical University, Tokyo160-8402, Japan
| | - Ankush Bansal
- Center for Neuroscience Research, Children’s National Hospital,Washington, DC20010
| | - Keiji Sugai
- Center for Neuroscience Research, Children’s National Hospital,Washington, DC20010
- Department of Diabetes, Endocrinology and Metabolism, Tokyo Medical University, Tokyo160-8402, Japan
| | - Satoshi Yamashita
- Center for Neuroscience Research, Children’s National Hospital,Washington, DC20010
| | - Guojiao Li
- Department of Diabetes, Endocrinology and Metabolism, Tokyo Medical University, Tokyo160-8402, Japan
| | - Christopher Lazarski
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC20010
| | - Li Wang
- Center for Neuroscience Research, Children’s National Hospital,Washington, DC20010
| | - Toru Sasaki
- Department of Obstetrics and Gynecology, Tokyo Medical University, Tokyo160-8402, Japan
| | - Chiho Yamashita
- Center for Neuroscience Research, Children’s National Hospital,Washington, DC20010
| | - Heather Carryl
- Center for Neuroscience Research, Children’s National Hospital,Washington, DC20010
| | - Ryo Suzuki
- Department of Diabetes, Endocrinology and Metabolism, Tokyo Medical University, Tokyo160-8402, Japan
| | - Masato Odawara
- Department of Diabetes, Endocrinology and Metabolism, Tokyo Medical University, Tokyo160-8402, Japan
| | - Yuka Imamura Kawasawa
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA17033
| | - Pasko Rakic
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT06520
| | - Masaaki Torii
- Center for Neuroscience Research, Children’s National Hospital,Washington, DC20010
- Department of Pediatrics, Pharmacology and Physiology, George Washington University, Washington, DC20010
| | - Kazue Hashimoto-Torii
- Center for Neuroscience Research, Children’s National Hospital,Washington, DC20010
- Department of Pediatrics, Pharmacology and Physiology, George Washington University, Washington, DC20010
| |
Collapse
|
41
|
Ma HL, Bizet M, Soares Da Costa C, Murisier F, de Bony EJ, Wang MK, Yoshimi A, Lin KT, Riching KM, Wang X, Beckman JI, Arya S, Droin N, Calonne E, Hassabi B, Zhang QY, Li A, Putmans P, Malbec L, Hubert C, Lan J, Mies F, Yang Y, Solary E, Daniels DL, Gupta YK, Deplus R, Abdel-Wahab O, Yang YG, Fuks F. SRSF2 plays an unexpected role as reader of m 5C on mRNA, linking epitranscriptomics to cancer. Mol Cell 2023; 83:4239-4254.e10. [PMID: 38065062 PMCID: PMC11090011 DOI: 10.1016/j.molcel.2023.11.003] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/06/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023]
Abstract
A common mRNA modification is 5-methylcytosine (m5C), whose role in gene-transcript processing and cancer remains unclear. Here, we identify serine/arginine-rich splicing factor 2 (SRSF2) as a reader of m5C and impaired SRSF2 m5C binding as a potential contributor to leukemogenesis. Structurally, we identify residues involved in m5C recognition and the impact of the prevalent leukemia-associated mutation SRSF2P95H. We show that SRSF2 binding and m5C colocalize within transcripts. Furthermore, knocking down the m5C writer NSUN2 decreases mRNA m5C, reduces SRSF2 binding, and alters RNA splicing. We also show that the SRSF2P95H mutation impairs the ability of the protein to read m5C-marked mRNA, notably reducing its binding to key leukemia-related transcripts in leukemic cells. In leukemia patients, low NSUN2 expression leads to mRNA m5C hypomethylation and, combined with SRSF2P95H, predicts poor outcomes. Altogether, we highlight an unrecognized mechanistic link between epitranscriptomics and a key oncogenesis driver.
Collapse
Affiliation(s)
- Hai-Li Ma
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Christelle Soares Da Costa
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Frédéric Murisier
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Eric James de Bony
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Meng-Ke Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Akihide Yoshimi
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Xing Wang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - John I Beckman
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Shailee Arya
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Nathalie Droin
- Université Paris-Saclay, INSERM U1287, and Department of Hematology, Gustave Roussy Cancer Center, Villejuif 94800, France
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Bouchra Hassabi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Qing-Yang Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Ang Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Lionel Malbec
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Céline Hubert
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Jie Lan
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Frédérique Mies
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Eric Solary
- Université Paris-Saclay, INSERM U1287, and Department of Hematology, Gustave Roussy Cancer Center, Villejuif 94800, France
| | | | - Yogesh K Gupta
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium
| | - Omar Abdel-Wahab
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics and Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China.
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Université libre de Bruxelles (ULB), Institut Jules Bordet, Brussels 1070, Belgium.
| |
Collapse
|
42
|
Huynh D, Wu CW. Identification of pararosaniline as a modifier of RNA splicing in Caenorhabditis elegans. G3 (Bethesda) 2023; 13:jkad241. [PMID: 37852248 DOI: 10.1093/g3journal/jkad241] [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] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/13/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
Posttranscriptional splicing of premessenger RNA (mRNA) is an evolutionarily conserved eukaryotic process for producing mature mRNA that is translated into proteins. Accurate splicing is necessary for normal growth and development, and aberrant splicing is increasingly evident in various human pathologies. To study environmental factors that influence RNA splicing, we employed a fluorescent Caenorhabditis elegans in vivo splicing reporter as a biomarker for splicing fidelity to screen against the US EPA ToxCast chemical library. We identified pararosaniline hydrochloride as a strong modifier of RNA splicing. Through gene expression analysis, we found that pararosaniline activates the oxidative stress response and alters the expression of key RNA splicing regulator genes. Physiological assays show that pararosaniline is deleterious to C. elegans development, reproduction, and aging. Through a targeted RNAi screen, we found that inhibiting protein translation can reverse pararosaniline's effect on the splicing reporter and provide significant protection against long-term pararosaniline toxicity. Together, this study reveals a new chemical modifier of RNA splicing and describes translation inhibition as a genetic mechanism to provide resistance.
Collapse
Affiliation(s)
- Dylan Huynh
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Cheng-Wei Wu
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
- Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| |
Collapse
|
43
|
Blázquez-Encinas R, García-Vioque V, Caro-Cuenca T, Moreno-Montilla MT, Mangili F, Alors-Pérez E, Ventura S, Herrera-Martínez AD, Moreno-Casado P, Calzado MA, Salvatierra Á, Gálvez-Moreno MA, Fernandez-Cuesta L, Foll M, Luque RM, Alcala N, Pedraza-Arevalo S, Ibáñez-Costa A, Castaño JP. Altered splicing machinery in lung carcinoids unveils NOVA1, PRPF8 and SRSF10 as novel candidates to understand tumor biology and expand biomarker discovery. J Transl Med 2023; 21:879. [PMID: 38049848 PMCID: PMC10696873 DOI: 10.1186/s12967-023-04754-8] [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] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/23/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Lung neuroendocrine neoplasms (LungNENs) comprise a heterogeneous group of tumors ranging from indolent lesions with good prognosis to highly aggressive cancers. Carcinoids are the rarest LungNENs, display low to intermediate malignancy and may be surgically managed, but show resistance to radiotherapy/chemotherapy in case of metastasis. Molecular profiling is providing new information to understand lung carcinoids, but its clinical value is still limited. Altered alternative splicing is emerging as a novel cancer hallmark unveiling a highly informative layer. METHODS We primarily examined the status of the splicing machinery in lung carcinoids, by assessing the expression profile of the core spliceosome components and selected splicing factors in a cohort of 25 carcinoids using a microfluidic array. Results were validated in an external set of 51 samples. Dysregulation of splicing variants was further explored in silico in a separate set of 18 atypical carcinoids. Selected altered factors were tested by immunohistochemistry, their associations with clinical features were assessed and their putative functional roles were evaluated in vitro in two lung carcinoid-derived cell lines. RESULTS The expression profile of the splicing machinery was profoundly dysregulated. Clustering and classification analyses highlighted five splicing factors: NOVA1, SRSF1, SRSF10, SRSF9 and PRPF8. Anatomopathological analysis showed protein differences in the presence of NOVA1, PRPF8 and SRSF10 in tumor versus non-tumor tissue. Expression levels of each of these factors were differentially related to distinct number and profiles of splicing events, and were associated to both common and disparate functional pathways. Accordingly, modulating the expression of NOVA1, PRPF8 and SRSF10 in vitro predictably influenced cell proliferation and colony formation, supporting their functional relevance and potential as actionable targets. CONCLUSIONS These results provide primary evidence for dysregulation of the splicing machinery in lung carcinoids and suggest a plausible functional role and therapeutic targetability of NOVA1, PRPF8 and SRSF10.
Collapse
Affiliation(s)
- Ricardo Blázquez-Encinas
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Víctor García-Vioque
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Teresa Caro-Cuenca
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Pathology Service, Reina Sofía University Hospital, Córdoba, Spain
| | - María Trinidad Moreno-Montilla
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Federica Mangili
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Emilia Alors-Pérez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Sebastian Ventura
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Computer Sciences, University of Córdoba, Córdoba, Spain
| | - Aura D Herrera-Martínez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Paula Moreno-Casado
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Thoracic Surgery and Lung Transplantation Unit, Reina Sofa University Hospital, Córdoba, Spain
| | - Marco A Calzado
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Ángel Salvatierra
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Thoracic Surgery and Lung Transplantation Unit, Reina Sofa University Hospital, Córdoba, Spain
| | - María A Gálvez-Moreno
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Lynnette Fernandez-Cuesta
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Matthieu Foll
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Raúl M Luque
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- CIBER Fisiopatología de La Obesidad y Nutrición (CIBERobn), Córdoba, Spain
| | - Nicolas Alcala
- Rare Cancers Genomics Team (RCG), Genomic Epidemiology Branch (GEM), International Agency for Research On Cancer (IARC/WHO), Lyon, France
| | - Sergio Pedraza-Arevalo
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Alejandro Ibáñez-Costa
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Reina Sofia University Hospital, Córdoba, Spain.
| | - Justo P Castaño
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Reina Sofia University Hospital, Córdoba, Spain.
- CIBER Fisiopatología de La Obesidad y Nutrición (CIBERobn), Córdoba, Spain.
| |
Collapse
|
44
|
Wahid M, Pratoomthai B, Egbuniwe IU, Evans HR, Babaei-Jadidi R, Amartey JO, Erdelyi V, Yacqub-Usman K, Jackson AM, Morris JC, Patel PM, Bates DO. Targeting alternative splicing as a new cancer immunotherapy-phosphorylation of serine arginine-rich splicing factor (SRSF1) by SR protein kinase 1 (SRPK1) regulates alternative splicing of PD1 to generate a soluble antagonistic isoform that prevents T cell exhaustion. Cancer Immunol Immunother 2023; 72:4001-4014. [PMID: 37973660 DOI: 10.1007/s00262-023-03534-z] [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: 06/07/2023] [Accepted: 08/21/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Regulation of alternative splicing is a new therapeutic approach in cancer. The programmed cell death receptor 1 (PD-1) is an immunoinhibitory receptor expressed on immune cells that binds to its ligands, PD-L1 and PD-L2 expressed by cancer cells forming a dominant immune checkpoint pathway in the tumour microenvironment. Targeting this pathway using blocking antibodies (nivolumab and pembrolizumab) is the mainstay of anti-cancer immunotherapies, restoring the function of exhausted T cells. PD-1 is alternatively spliced to form isoforms that are either transmembrane signalling receptors (flPD1) that mediate T cell death by binding to the ligand, PD-L1 or an alternatively spliced, soluble, variant that lacks the transmembrane domain. METHODS We used PCR and western blotting on primary peripheral blood mononuclear cells (PBMCs) and Jurkat T cells, IL-2 ELISA, flow cytometry, co-culture of melanoma and cholangiocarcinoma cells, and bioinformatics analysis and molecular cloning to examine the mechanism of splicing of PD1 and its consequence. RESULTS The soluble form of PD-1, generated by skipping exon 3 (∆Ex3PD1), was endogenously expressed in PBMCs and T cells and prevents cancer cell-mediated T cell repression. Multiple binding sites of SRSF1 are adjacent to PD-1 exon 3 splicing sites. Overexpression of phosphomimic SRSF1 resulted in preferential expression of flPD1. Inhibition of SRSF1 phosphorylation both by SRPK1 shRNA knockdown and by a selective inhibitor, SPHINX31, resulted in a switch in splicing to ∆Ex3PD1. Cholangiocarcinoma cell-mediated repression of T cell IL-2 expression was reversed by SPHINX31 (equivalent to pembrolizumab). CONCLUSIONS These results indicate that switching of the splicing decision from flPD1 to ∆Ex3PD1 by targeting SRPK1 could represent a potential novel mechanism of immune checkpoint inhibition in cancer.
Collapse
Affiliation(s)
- Mussarat Wahid
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Benjamart Pratoomthai
- Department of Basic Medical Science, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, 681 Samsen Road, Dusit, 10300, Bangkok, Thailand
| | - Isioma U Egbuniwe
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Hannah R Evans
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Roya Babaei-Jadidi
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Jason O Amartey
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Viola Erdelyi
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Kiren Yacqub-Usman
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Andrew M Jackson
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Jonathan C Morris
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Poulam M Patel
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - David O Bates
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK.
- COMPARE University of Birmingham and University of Nottingham, Midlands, UK.
| |
Collapse
|
45
|
Yandrapally S, Sarkar S, Banerjee S. HIV-1 Tat commandeers nuclear export of Rev-viral RNA complex by controlling hnRNPA2-mediated splicing. J Virol 2023; 97:e0104423. [PMID: 37905837 PMCID: PMC10688328 DOI: 10.1128/jvi.01044-23] [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: 07/13/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE HIV-infected host cells impose varied degrees of regulation on viral replication, from very high to abortive. Proliferation of HIV in astrocytes is limited when compared to immune cells, such as CD4+ T lymphocytes. Understanding such differential regulation is one of the key questions in the field as these cells permit HIV persistence and rebound viremia, challenging HIV treatment and clinical cure. This study focuses on understanding the molecular mechanism behind such cell-specific disparities. We show that one of the key mechanisms is the regulation of heterogenous nuclear ribonucleoprotein A2, a host factor involved in alternative splicing and RNA processing, by HIV-1 Tat in CD4+ T lymphocytes, not observed in astrocytes. This regulation causes an increase in the levels of unspliced/partially spliced viral RNA and nuclear export of Rev-RNA complexes which results in high viral propagation in CD4+ T lymphocytes. The study reveals a new mechanism imposed by HIV on host cells that determines the fate of infection.
Collapse
Affiliation(s)
- Sriram Yandrapally
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Satarupa Sarkar
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| |
Collapse
|
46
|
Feldner AC, Turner AK, Simpson JF, Estus S. Skipping of FCER1G Exon 2 Is Common in Human Brain But Not Associated with the Alzheimer's Disease Genetic Risk Factor rs2070902. J Alzheimers Dis Rep 2023; 7:1313-1322. [PMID: 38143775 PMCID: PMC10741965 DOI: 10.3233/adr-230076] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/30/2023] [Indexed: 12/26/2023] Open
Abstract
Background Understanding the mechanisms whereby genetic variants influence the risk of Alzheimer's disease (AD) may provide insights into treatments that could reduce AD risk. Objective Here, we sought to test the hypothesis that a single nucleotide polymorphism (SNP) associated with AD risk, rs2070902, influences splicing of FCER1G exon 2. Methods AD and non-AD brain samples were analyzed for FCER1G expression by genotyping, immunohistochemistry, immunofluorescence, and qPCR. Results The protein encoded by FCER1G, FcRγ, is robustly expressed in microglia in both AD and non-AD brain. The FCER1G isoform lacking exon 2 (D2-FCER1G) was readily detectable. Moreover, the proportion of FCER1G expressed as this isoform was increased in brains with high AD neuropathology. However, the proportion of FCER1G expressed as the D2-FCER1G isoform was not associated with rs2070902 genotype. Conclusions In summary, the proportion of FCER1G expressed as the D2-FCER1G isoform is increased with AD neuropathology but is not associated with rs2070902.
Collapse
Affiliation(s)
- Alyssa C. Feldner
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Andrew K. Turner
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - James F. Simpson
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Steven Estus
- Department of Physiology and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| |
Collapse
|
47
|
Xu X, Zhang L, Ye G, Shi J, Peng Y, Xin F, Lin Y, Wu Q, Lin X, Chen W. Hepatitis B doubly spliced protein (HBDSP) promotes hepatocellular carcinoma cell apoptosis via ETS1/GATA2/YY1-mediated p53 transcription. J Virol 2023; 97:e0108723. [PMID: 37929990 PMCID: PMC10688342 DOI: 10.1128/jvi.01087-23] [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: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023] Open
Abstract
IMPORTANCE Hepatitis B virus (HBV) spliced variants are associated with viral persistence or pathogenicity. Hepatitis B doubly spliced protein (HBDSP), which has been previously reported as a pleiotropic transactivator protein, can potentially serve as an HBV virulence factor. However, the underlying mechanisms of HBDSP in HBV-associated liver diseases remain to be elucidated. In this study, we revealed that HBDSP promotes cellular apoptosis and induces wt-p53-dependent apoptotic signaling pathway in wt-p53 hepatocellular cells by transactivating p53 transcription, and increases the release of HBV progeny. Therefore, HBDSP may promote the HBV particles release through wt-p53-dependent hepatocellular apoptosis. Our findings suggest that blocking HBDSP-induced wt-p53-dependent apoptosis might have therapeutic values for chronic hepatitis B.
Collapse
Affiliation(s)
- Xiazhen Xu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Lu Zhang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Guiying Ye
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jiajian Shi
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yibin Peng
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Fan Xin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yi Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qiong Wu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Xu Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wannan Chen
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| |
Collapse
|
48
|
Zhu B, Fisher E, Li L, Zhong P, Yan Z, Feng J. PTBP2 attenuation facilitates fibroblast to neuron conversion by promoting alternative splicing of neuronal genes. Stem Cell Reports 2023; 18:2268-2282. [PMID: 37832540 PMCID: PMC10679656 DOI: 10.1016/j.stemcr.2023.09.012] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
The direct conversion of human skin fibroblasts to neurons has a low efficiency and unclear mechanism. Here, we show that the knockdown of PTBP2 significantly enhanced the transdifferentiation induced by ASCL1, MIR9/9∗-124, and p53 shRNA (AMp) to generate mostly GABAergic neurons. Longitudinal RNA sequencing analyses identified the continuous induction of many RNA splicing regulators. Among these, the knockdown of RBFOX3 (NeuN), significantly abrogated the transdifferentiation. Overexpression of RBFOX3 significantly enhanced the conversion induced by AMp; the enhancement was occluded by PTBP2 knockdown. We found that PTBP2 attenuation significantly favored neuron-specific alternative splicing (AS) of many genes involved in synaptic transmission, signal transduction, and axon formation. RBFOX3 knockdown significantly reversed the effect, while RBFOX3 overexpression occluded the enhancement. The study reveals the critical role of neuron-specific AS in the direct conversion of human skin fibroblasts to neurons by showing that PTBP2 attenuation enhances this mechanism in concert with RBFOX3.
Collapse
Affiliation(s)
- Binglin Zhu
- Veterans Affairs Western New York Healthcare System, Buffalo, NY 14215, USA; Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Emily Fisher
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Li Li
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Ping Zhong
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Zhen Yan
- Veterans Affairs Western New York Healthcare System, Buffalo, NY 14215, USA; Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jian Feng
- Veterans Affairs Western New York Healthcare System, Buffalo, NY 14215, USA; Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY 14203, USA.
| |
Collapse
|
49
|
Pino MG, Rich KA, Hall NJ, Jones ML, Fox A, Musier-Forsyth K, Kolb SJ. Heterogeneous splicing patterns resulting from KIF5A variants associated with amyotrophic lateral sclerosis. Hum Mol Genet 2023; 32:3166-3180. [PMID: 37593923 DOI: 10.1093/hmg/ddad134] [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: 04/24/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/19/2023] Open
Abstract
Single-nucleotide variants (SNVs) in the gene encoding Kinesin Family Member 5A (KIF5A), a neuronal motor protein involved in anterograde transport along microtubules, have been associated with amyotrophic lateral sclerosis (ALS). ALS is a rapidly progressive and fatal neurodegenerative disease that primarily affects the motor neurons. Numerous ALS-associated KIF5A SNVs are clustered near the splice-site junctions of the penultimate exon 27 and are predicted to alter the carboxy-terminal (C-term) cargo-binding domain of KIF5A. Mis-splicing of exon 27, resulting in exon exclusion, is proposed to be the mechanism by which these SNVs cause ALS. Whether all SNVs proximal to exon 27 result in exon exclusion is unclear. To address this question, we designed an in vitro minigene splicing assay in human embryonic kidney 293 cells, which revealed heterogeneous site-specific effects on splicing: only 5' splice-site (5'ss) SNVs resulted in exon skipping. We also quantified splicing in select clustered, regularly interspaced, short palindromic repeats-edited human stem cells, differentiated to motor neurons, and in neuronal tissues from a 5'ss SNV knock-in mouse, which showed the same result. Moreover, the survival of representative 3' splice site, 5'ss, and truncated C-term variant KIF5A (v-KIF5A) motor neurons was severely reduced compared with wild-type motor neurons, and overt morphological changes were apparent. While the total KIF5A mRNA levels were comparable across the cell lines, the total KIF5A protein levels were decreased for v-KIF5A lines, suggesting an impairment of protein synthesis or stability. Thus, despite the heterogeneous effect on ribonucleic acid splicing, KIF5A SNVs similarly reduce the availability of the KIF5A protein, leading to axonal transport defects and motor neuron pathology.
Collapse
Affiliation(s)
- Megan G Pino
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
- Department of Biological Chemistry & Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Kelly A Rich
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Nicholas J Hall
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
| | - Meredith L Jones
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Ashley Fox
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Karin Musier-Forsyth
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
- Department of Chemistry & Biochemistry, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| | - Stephen J Kolb
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
- Department of Biological Chemistry & Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, United States
| |
Collapse
|
50
|
Lipinski KA, Senn KA, Zeps NJ, Hoskins AA. Biochemical and genetic evidence supports Fyv6 as a second-step splicing factor in Saccharomyces cerevisiae. RNA 2023; 29:1792-1802. [PMID: 37625852 PMCID: PMC10578475 DOI: 10.1261/rna.079607.123] [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: 01/30/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023]
Abstract
Precursor mRNA (pre-mRNA) splicing is an essential process for gene expression in eukaryotes catalyzed by the spliceosome in two transesterification steps. The spliceosome is a large, highly dynamic complex composed of five small nuclear RNAs and dozens of proteins, some of which are needed throughout the splicing reaction while others only act during specific stages. The human protein FAM192A was recently proposed to be a splicing factor that functions during the second transesterification step, exon ligation, based on analysis of cryo-electron microscopy (cryo-EM) density. It was also proposed that Fyv6 might be the Saccharomyces cerevisiae functional and structural homolog of FAM192A; however, no biochemical or genetic data has been reported to support this hypothesis. Herein, we show that Fyv6 is a splicing factor and acts during exon ligation. Deletion of FYV6 results in genetic interactions with the essential splicing factors Prp8, Prp16, and Prp22 and decreases splicing in vivo of reporter genes harboring intron substitutions that limit the rate of exon ligation. When splicing is assayed in vitro, whole-cell extracts lacking Fyv6 accumulate first-step products and exhibit a defect in exon ligation. Moreover, loss of Fyv6 causes a change in 3' splice site (SS) selection in both a reporter gene and the endogenous SUS1 transcript in vivo. Together, these data suggest that Fyv6 is a component of the yeast spliceosome that influences 3' SS usage and the potential homolog of human FAM192A.
Collapse
Affiliation(s)
- Karli A Lipinski
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Katherine A Senn
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Natalie J Zeps
- 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
| |
Collapse
|