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Vukadin L, Park B, Mohamed M, Li H, Elkholy A, Torrelli-Diljohn A, Kim JH, Jeong K, Murphy JM, Harvey CA, Dunlap S, Gehrs L, Lee H, Kim HG, Lee SN, Stanford D, Barrington RA, Foote JB, Sorace AG, Welner RS, Hildreth BE, Lim STS, Ahn EYE. A mouse model of ZTTK syndrome reveals indispensable SON functions in organ development and hematopoiesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.19.567732. [PMID: 38014320 PMCID: PMC10680872 DOI: 10.1101/2023.11.19.567732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Rare diseases are underrepresented in biomedical research, leading to insufficient awareness. Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome is a rare disease caused by genetic alterations that result in heterozygous loss-of-function of SON. While ZTTK syndrome patients suffer from numerous symptoms, the lack of model organisms hamper our understanding of both SON and this complex syndrome. Here, we developed Son haploinsufficiency (Son+/-) mice as a model of ZTTK syndrome and identified the indispensable roles of Son in organ development and hematopoiesis. Son+/- mice recapitulated clinical symptoms of ZTTK syndrome, including growth retardation, cognitive impairment, skeletal abnormalities, and kidney agenesis. Furthermore, we identified hematopoietic abnormalities in Son+/- mice, similar to those observed in human patients. Surface marker analyses and single-cell transcriptome profiling of hematopoietic stem and progenitor cells revealed that Son haploinsufficiency inclines cell fate toward the myeloid lineage but compromises lymphoid lineage development by reducing key genes required for lymphoid and B cell lineage specification. Additionally, Son haploinsufficiency causes inappropriate activation of erythroid genes and impaired erythroid maturation. These findings highlight the importance of the full gene dosage of Son in organ development and hematopoiesis. Our model serves as an invaluable research tool for this rare disease and related disorders associated with SON dysfunction.
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Affiliation(s)
- Lana Vukadin
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Bohye Park
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mostafa Mohamed
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Huashi Li
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Amr Elkholy
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alex Torrelli-Diljohn
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jung-Hyun Kim
- Metastasis Branch, Division of Cancer Biology, National Cancer Center, Goyang, Gyeonggi-do, Korea
| | - Kyuho Jeong
- Department of Medicine, College of Medicine, Dongguk University, Gyeongju, Korea
| | - James M Murphy
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Caitlin A. Harvey
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sophia Dunlap
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leah Gehrs
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hanna Lee
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hyung-Gyoon Kim
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Seth N. Lee
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Denise Stanford
- Department of Medicine, Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert A. Barrington
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Jeremy B. Foote
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anna G. Sorace
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert S. Welner
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Medicine, Division of Hematology and Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Blake E. Hildreth
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ssang-Taek Steve Lim
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Eun-Young Erin Ahn
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
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Tang S, You J, Liu L, Ouyang H, Jiang N, Duan J, Li C, Luo Y, Zhang W, Zhan M, Liu C, Lyu G, Zhang VW, Zhao H. Expanding the mutational spectrum of ZTTK syndrome: A de novo variant with global developmental delay and malnutrition in a Chinese patient. Mol Genet Genomic Med 2023; 11:e2188. [PMID: 37488749 PMCID: PMC10422072 DOI: 10.1002/mgg3.2188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/23/2022] [Accepted: 02/22/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Zhu-Tokita-Takenouchi-Kim (ZTTK, OMIM 617140) syndrome is a severe multisystem developmental disorder characterized by intellectual disability, developmental delay, cortical malformations, epilepsy, visual problems, musculoskeletal abnormalities, and congenital malformations. ZTTK syndrome is caused by a heterozygous pathogenic variant of the SON gene (NM_138927) at chromosome 21q22.1. The purpose of this study was to investigate the pathogenesis of a 6-month-old Chinese child who exhibited global developmental delay, muscle weakness, malnutrition, weight loss, and strabismus, brain abnormality, immunological system abnormalities. METHODS The little girl was tested for medical exome sequencing (MES) and mtDNA sequencing in trio. And, the mutation was validated by Sanger sequencing. RESULTS A novel de novo frameshift variant, c.1845_1870del26 (p.G616Sfs*61), in the SON gene was found in the proband. CONCLUSION We described a 6-month-old Chinese child with global developmental delay caused by pathogenic de novo mutation c.1845_1870del26 (p.G616Sfs*61) in the SON. Apart from a founder mutation, we reviewed the phenotypic abnormalities and genotypes in 79 individuals. The data showed that global developmental delay is accompanied by other system disorders. Our findings expanded the mutational spectrum of ZTTK syndrome and provide genetic counseling of baby with global developmental delay.
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Affiliation(s)
- Shuo Tang
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Jieyu You
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Li Liu
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Hongjuan Ouyang
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Na Jiang
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Jiaqi Duan
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Canlin Li
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Yanhong Luo
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Wenting Zhang
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Meizheng Zhan
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | - Chenxi Liu
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
| | | | | | - Hongmei Zhao
- Department of Digestive System DiseasesHunan Children's HospitalChangshaChina
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Busselez J, Uzbekov RE, Franco B, Pancione M. New insights into the centrosome-associated spliceosome components as regulators of ciliogenesis and tissue identity. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1776. [PMID: 36717357 DOI: 10.1002/wrna.1776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 02/01/2023]
Abstract
Biomolecular condensates are membrane-less assemblies of proteins and nucleic acids. Centrosomes are biomolecular condensates that play a crucial role in nuclear division, cytoskeletal remodeling, and cilia formation in animal cells. Spatial omics technology is providing new insights into the dynamic exchange of spliceosome components between the nucleus and the centrosome/cilium. Intriguingly, centrosomes are emerging as cytoplasmic sites for information storage, enriched with RNA molecules and RNA-processing proteins. Furthermore, growing evidence supports the view that nuclear spliceosome components assembled at the centrosome function as potential coordinators of splicing subprograms, pluripotency, and cell differentiation. In this article, we first discuss the current understanding of the centrosome/cilium complex, which controls both stem cell differentiation and pluripotency. We next explore the molecular mechanisms that govern splicing factor assembly and disassembly around the centrosome and examine how RNA processing pathways contribute to ciliogenesis. Finally, we discuss numerous unresolved compelling questions regarding the centrosome-associated spliceosome components and transcript variants within the cytoplasm as sources of RNA-based secondary messages in the regulation of cell identity and cell fate determination. This article is categorized under: RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > RNA Processing.
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Affiliation(s)
- Johan Busselez
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch-Graffenstaden, France
| | - Rustem E Uzbekov
- Faculté de Médecine, Université de Tours, Tours, France
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medicine, Medical Genetics, University of Naples "Federico II", Naples, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine program, University of Naples Federico II, Naples, Italy
| | - Massimo Pancione
- Department of Sciences and Technologies, University of Sannio, Benevento, Italy
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Complutense University Madrid, Madrid, Spain
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Halliday BJ, Baynam G, Ewans L, Greenhalgh L, Leventer RJ, Pilz DT, Sachdev R, Scheffer IE, Markie DM, McGillivray G, Robertson SP, Mandelstam S. Distinctive Brain Malformations in Zhu-Tokita-Takenouchi-Kim Syndrome. AJNR Am J Neuroradiol 2022; 43:1660-1666. [PMID: 36229163 PMCID: PMC9731255 DOI: 10.3174/ajnr.a7663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/08/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND AND PURPOSE Zhu-Tokita-Takenouchi-Kim syndrome is a severe multisystem malformation disorder characterized by developmental delay and a diverse array of congenital abnormalities. However, these currently identified phenotypic components provide limited guidance in diagnostic situations, due to both the nonspecificity and variability of these features. Here we report a case series of 7 individuals with a molecular diagnosis of Zhu-Tokita-Takenouchi-Kim syndrome, 5 ascertained by their presentation with the neuronal migration disorder, periventricular nodular heterotopia. MATERIALS AND METHODS Individuals with a molecular diagnosis of Zhu-Tokita-Takenouchi-Kim syndrome were recruited from 2 sources, a high-throughput sequencing study of individuals with periventricular nodular heterotopia or from clinical diagnostic sequencing studies. We analyzed available brain MR images of recruited individuals to characterize periventricular nodular heterotopia distribution and to identify the presence of any additional brain abnormalities. RESULTS Pathogenic variants in SON, causative of Zhu-Tokita-Takenouchi-Kim syndrome, were identified in 7 individuals. Brain MR images from these individuals were re-analyzed. A characteristic set of imaging anomalies in addition to periventricular nodular heterotopia was identified, including the elongation of the pituitary stalk, cerebellar enlargement with an abnormally shaped posterior fossa, rounding of the caudate nuclei, hippocampal malformations, and cortical anomalies including polymicrogyria or dysgyria. CONCLUSIONS The recurrent neuroradiologic changes identified here represent an opportunity to guide diagnostic formulation of Zhu-Tokita-Takenouchi-Kim syndrome on the basis of brain MR imaging evaluation.
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Affiliation(s)
- B J Halliday
- From the Departments of Women's and Children's Health (B.J.H., S.P.R.)
| | - G Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia (G.B.), Undiagnosed Diseases Program, King Edward Memorial Hospital, Perth, Australia
| | - L Ewans
- Centre for Population Genomics (L.E.), Garvan Institute of Medical Research, Sydney, Australia
- Centre for Clinical Genetics (L.E., R.S.), Sydney Children's Hospital, Sydney, Australia
| | - L Greenhalgh
- Liverpool Centre for Genomic Medicine (L.G.), Liverpool Women's Hospital, Liverpool, England
| | - R J Leventer
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Department of Paediatrics (R.J.L., I.E.S., S.M.), Epilepsy Research Centre
- Departments of Neurology (R.J.L., I.E.S.)
| | - D T Pilz
- West of Scotland Genetics Service (D.T.P.), Queen Elizabeth University Hospital, Glasgow, UK
| | - R Sachdev
- Centre for Clinical Genetics (L.E., R.S.), Sydney Children's Hospital, Sydney, Australia
| | - I E Scheffer
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Department of Paediatrics (R.J.L., I.E.S., S.M.), Epilepsy Research Centre
- Austin Health (I.E.S.)
- Florey Institute (I.E.S.), University of Melbourne, Melbourne, Australia
- Departments of Neurology (R.J.L., I.E.S.)
| | - D M Markie
- Pathology (D.M.M.), OtagoMedical School, University of Otago, Dunedin, New Zealand
| | - G McGillivray
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Victorian Clinical Genetics Services (G.M.), Murdoch Children's Research Institute, Melbourne, Australia
| | - S P Robertson
- From the Departments of Women's and Children's Health (B.J.H., S.P.R.)
| | - S Mandelstam
- Murdoch Children's Research Institute (R.J.L., I.E.S., G.M., S.M.), Melbourne, Australia
- Department of Paediatrics (R.J.L., I.E.S., S.M.), Epilepsy Research Centre
- Radiology (S.M.), Royal Children's Hospital, Melbourne, Australia
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Cacioppo R, Lindon C. Regulating the regulator: a survey of mechanisms from transcription to translation controlling expression of mammalian cell cycle kinase Aurora A. Open Biol 2022; 12:220134. [PMID: 36067794 PMCID: PMC9448500 DOI: 10.1098/rsob.220134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Aurora Kinase A (AURKA) is a positive regulator of mitosis with a strict cell cycle-dependent expression pattern. Recently, novel oncogenic roles of AURKA have been uncovered that are independent of the kinase activity and act within multiple signalling pathways, including cell proliferation, survival and cancer stem cell phenotypes. For this, cellular abundance of AURKA protein is per se crucial and must be tightly fine-tuned. Indeed, AURKA is found overexpressed in different cancers, typically as a result of gene amplification or enhanced transcription. It has however become clear that impaired processing, decay and translation of AURKA mRNA can also offer the basis for altered AURKA levels. Accordingly, the involvement of gene expression mechanisms controlling AURKA expression in human diseases is increasingly recognized and calls for much more research. Here, we explore and create an integrated view of the molecular processes regulating AURKA expression at the level of transcription, post-transcription and translation, intercalating discussion on how impaired regulation underlies disease. Given that targeting AURKA levels might affect more functions compared to inhibiting the kinase activity, deeper understanding of its gene expression may aid the design of alternative and therapeutically more successful ways of suppressing the AURKA oncogene.
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Affiliation(s)
- Roberta Cacioppo
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Catherine Lindon
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
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Establishing the phenotypic spectrum of ZTTK syndrome by analysis of 52 individuals with variants in SON. Eur J Hum Genet 2022; 30:271-281. [PMID: 34521999 PMCID: PMC8904542 DOI: 10.1038/s41431-021-00960-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/16/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome, an intellectual disability syndrome first described in 2016, is caused by heterozygous loss-of-function variants in SON. Its encoded protein promotes pre-mRNA splicing of many genes essential for development. Whereas individual phenotypic traits have previously been linked to erroneous splicing of SON target genes, the phenotypic spectrum and the pathogenicity of missense variants have not been further evaluated. We present the phenotypic abnormalities in 52 individuals, including 17 individuals who have not been reported before. In total, loss-of-function variants were detected in 49 individuals (de novo in 47, inheritance unknown in 2), and in 3, a missense variant was observed (2 de novo, 1 inheritance unknown). Phenotypic abnormalities, systematically collected and analyzed in Human Phenotype Ontology, were found in all organ systems. Significant inter-individual phenotypic variability was observed, even in individuals with the same recurrent variant (n = 13). SON haploinsufficiency was previously shown to lead to downregulation of downstream genes, contributing to specific phenotypic features. Similar functional analysis for one missense variant, however, suggests a different mechanism than for heterozygous loss-of-function. Although small in numbers and while pathogenicity of these variants is not certain, these data allow for speculation whether de novo missense variants cause ZTTK syndrome via another mechanism, or a separate overlapping syndrome. In conclusion, heterozygous loss-of-function variants in SON define a recognizable syndrome, ZTTK, associated with a broad, severe phenotypic spectrum, characterized by a large inter-individual variability. These observations provide essential information for affected individuals, parents, and healthcare professionals to ensure appropriate clinical management.
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Stemm-Wolf AJ, O’Toole ET, Sheridan RM, Morgan JT, Pearson CG. The SON RNA splicing factor is required for intracellular trafficking structures that promote centriole assembly and ciliogenesis. Mol Biol Cell 2021; 32:ar4. [PMID: 34406792 PMCID: PMC8684746 DOI: 10.1091/mbc.e21-06-0305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/16/2021] [Accepted: 07/23/2021] [Indexed: 11/11/2022] Open
Abstract
Control of centrosome assembly is critical for cell division, intracellular trafficking, and cilia. Regulation of centrosome number occurs through the precise duplication of centrioles that reside in centrosomes. Here we explored transcriptional control of centriole assembly and find that the RNA splicing factor SON is specifically required for completing procentriole assembly. Whole genome mRNA sequencing identified genes whose splicing and expression are affected by the reduction of SON, with an enrichment in genes involved in the microtubule (MT) cytoskeleton, centrosome, and centriolar satellites. SON is required for the proper splicing and expression of CEP131, which encodes a major centriolar satellite protein and is required to organize the trafficking and MT network around the centrosomes. This study highlights the importance of the distinct MT trafficking network that is intimately associated with nascent centrioles and is responsible for procentriole development and efficient ciliogenesis.
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Affiliation(s)
- Alexander J. Stemm-Wolf
- Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
| | | | - Ryan M. Sheridan
- RNA Biosciences Initiative (RBI), University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
| | - Jacob T. Morgan
- Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
| | - Chad G. Pearson
- Department of Cell and Developmental Biology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045
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Kim JH, Jeong K, Li J, Murphy JM, Vukadin L, Stone JK, Richard A, Tran J, Gillespie GY, Flemington EK, Sobol RW, Lim STS, Ahn EYE. SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity. Nat Commun 2021; 12:5551. [PMID: 34548489 PMCID: PMC8455679 DOI: 10.1038/s41467-021-25892-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/01/2021] [Indexed: 12/15/2022] Open
Abstract
While dysregulation of RNA splicing has been recognized as an emerging target for cancer therapy, the functional significance of RNA splicing and individual splicing factors in brain tumors is poorly understood. Here, we identify SON as a master regulator that activates PTBP1-mediated oncogenic splicing while suppressing RBFOX2-mediated non-oncogenic neuronal splicing in glioblastoma multiforme (GBM). SON is overexpressed in GBM patients and SON knockdown causes failure in intron removal from the PTBP1 transcript, resulting in PTBP1 downregulation and inhibition of its downstream oncogenic splicing. Furthermore, SON forms a complex with hnRNP A2B1 and antagonizes RBFOX2, which leads to skipping of RBFOX2-targeted cassette exons, including the PTBP2 neuronal exon. SON knockdown inhibits proliferation and clonogenicity of GBM cells in vitro and significantly suppresses tumor growth in orthotopic xenografts in vivo. Collectively, our study reveals that SON-mediated RNA splicing is a GBM vulnerability, implicating SON as a potential therapeutic target in brain tumors.
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Affiliation(s)
- Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Kyuho Jeong
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - James M Murphy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Lana Vukadin
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joshua K Stone
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Alexander Richard
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Johnny Tran
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA.
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA.
| | - Ssang-Teak Steve Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.
| | - Eun-Young Erin Ahn
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
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9
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SON inhibits megakaryocytic differentiation via repressing RUNX1 and the megakaryocytic gene expression program in acute megakaryoblastic leukemia. Cancer Gene Ther 2021; 28:1000-1015. [PMID: 33247227 PMCID: PMC8155101 DOI: 10.1038/s41417-020-00262-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/07/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
A high incidence of acute megakaryoblastic leukemia (AMKL) in Down syndrome patients implies that chromosome 21 genes have a pivotal role in AMKL development, but the functional contribution of individual genes remains elusive. Here, we report that SON, a chromosome 21-encoded DNA- and RNA-binding protein, inhibits megakaryocytic differentiation by suppressing RUNX1 and the megakaryocytic gene expression program. As megakaryocytic progenitors differentiate, SON expression is drastically reduced, with mature megakaryocytes having the lowest levels. In contrast, AMKL cells express an aberrantly high level of SON, and knockdown of SON induced the onset of megakaryocytic differentiation in AMKL cell lines. Genome-wide transcriptome analyses revealed that SON knockdown turns on the expression of pro-megakaryocytic genes while reducing erythroid gene expression. Mechanistically, SON represses RUNX1 expression by directly binding to the proximal promoter and two enhancer regions, the known +23 kb enhancer and the novel +139 kb enhancer, at the RUNX1 locus to suppress H3K4 methylation. In addition, SON represses the expression of the AP-1 complex subunits JUN, JUNB, and FOSB which are required for late megakaryocytic gene expression. Our findings define SON as a negative regulator of RUNX1 and megakaryocytic differentiation, implicating SON overexpression in impaired differentiation during AMKL development.
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Penev A, Bazley A, Shen M, Boeke JD, Savage SA, Sfeir A. Alternative splicing is a developmental switch for hTERT expression. Mol Cell 2021; 81:2349-2360.e6. [PMID: 33852895 PMCID: PMC8943697 DOI: 10.1016/j.molcel.2021.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 01/02/2023]
Abstract
Telomere length control is critical for cellular lifespan and tumor suppression. Telomerase is transiently activated in the inner cell mass of the developing blastocyst to reset telomere reserves. Its silencing upon differentiation leads to gradual telomere shortening in somatic cells. Here, we report that transcriptional regulation through cis-regulatory elements only partially accounts for telomerase activation in pluripotent cells. Instead, developmental control of telomerase is primarily driven by an alternative splicing event, centered around hTERT exon 2. Skipping of exon 2 triggers hTERT mRNA decay in differentiated cells, and conversely, its retention promotes telomerase accumulation in pluripotent cells. We identify SON as a regulator of exon 2 alternative splicing and report a patient carrying a SON mutation and suffering from insufficient telomerase and short telomeres. In summary, our study highlights a critical role for hTERT alternative splicing in the developmental regulation of telomerase and implicates defective splicing in telomere biology disorders.
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Affiliation(s)
- Alex Penev
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Andrew Bazley
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Michael Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Agnel Sfeir
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA.
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11
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Belmonte RL, Engbretson IL, Kim JH, Cajias I, Ahn EYE, Stachura DL. son is necessary for proper vertebrate blood development. PLoS One 2021; 16:e0247489. [PMID: 33630943 PMCID: PMC7906411 DOI: 10.1371/journal.pone.0247489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
The gene SON is on human chromosome 21 (21q22.11) and is thought to be associated with hematopoietic disorders that accompany Down syndrome. Additionally, SON is an RNA splicing factor that plays a role in the transcription of leukemia-associated genes. Previously, we showed that mutations in SON cause malformations in human and zebrafish spines and brains during early embryonic development. To examine the role of SON in normal hematopoiesis, we reduced expression of the zebrafish homolog of SON in zebrafish at the single-cell developmental stage with specific morpholinos. In addition to the brain and spinal malformations we also observed abnormal blood cell levels upon son knockdown. We then investigated how blood production was altered when levels of son were reduced. Decreased levels of son resulted in lower amounts of red blood cells when visualized with lcr:GFP transgenic fish. There were also reduced thrombocytes seen with cd41:GFP fish, and myeloid cells when mpx:GFP fish were examined. We also observed a significant decrease in the quantity of T cells, visualized with lck:GFP fish. However, when we examined their hematopoietic stem and progenitor cells (HSPCs), we saw no difference in colony-forming capability. These studies indicate that son is essential for the proper differentiation of the innate and adaptive immune system, and further investigation determining the molecular pathways involved during blood development should elucidate important information about vertebrate HSPC generation, proliferation, and differentiation.
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Affiliation(s)
- Rebecca L. Belmonte
- Department of Biological Sciences, California State University Chico, Chico, California, United States of America
| | - Isabella L. Engbretson
- Department of Biological Sciences, California State University Chico, Chico, California, United States of America
| | - Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, United States of America
| | - Illiana Cajias
- Department of Biological Sciences, California State University Chico, Chico, California, United States of America
| | - Eun-Young Erin Ahn
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - David L. Stachura
- Department of Biological Sciences, California State University Chico, Chico, California, United States of America
- * E-mail:
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12
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Bohnsack KE, Ficner R, Bohnsack MT, Jonas S. Regulation of DEAH-box RNA helicases by G-patch proteins. Biol Chem 2021; 402:561-579. [PMID: 33857358 DOI: 10.1515/hsz-2020-0338] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
RNA helicases of the DEAH/RHA family form a large and conserved class of enzymes that remodel RNA protein complexes (RNPs) by translocating along the RNA. Driven by ATP hydrolysis, they exert force to dissociate hybridized RNAs, dislocate bound proteins or unwind secondary structure elements in RNAs. The sub-cellular localization of DEAH-helicases and their concomitant association with different pathways in RNA metabolism, such as pre-mRNA splicing or ribosome biogenesis, can be guided by cofactor proteins that specifically recruit and simultaneously activate them. Here we review the mode of action of a large class of DEAH-specific adaptor proteins of the G-patch family. Defined only by their eponymous short glycine-rich motif, which is sufficient for helicase binding and stimulation, this family encompasses an immensely varied array of domain compositions and is linked to an equally diverse set of functions. G-patch proteins are conserved throughout eukaryotes and are even encoded within retroviruses. They are involved in mRNA, rRNA and snoRNA maturation, telomere maintenance and the innate immune response. Only recently was the structural and mechanistic basis for their helicase enhancing activity determined. We summarize the molecular and functional details of G-patch-mediated helicase regulation in their associated pathways and their involvement in human diseases.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany.,Göttingen Centre for Molecular Biosciences, Georg-August University, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany.,Göttingen Centre for Molecular Biosciences, Georg-August University, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Stefanie Jonas
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, CH-8093 Zurich, Switzerland
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13
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Hachim MY, Al Heialy S, Senok A, Hamid Q, Alsheikh-Ali A. Molecular Basis of Cardiac and Vascular Injuries Associated With COVID-19. Front Cardiovasc Med 2020; 7:582399. [PMID: 33240937 PMCID: PMC7669624 DOI: 10.3389/fcvm.2020.582399] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 09/18/2020] [Indexed: 12/28/2022] Open
Abstract
Background: Coronavirus disease 2019 (COVID-19) is a viral respiratory illness caused by the novel coronavirus SARS-CoV-2. The presence of the pre-existing cardiac disease is associated with an increased likelihood of severe clinical course and mortality in patients with COVID-19. Besides, current evidence indicates that a significant number of patients with COVID-19 also exhibit cardiovascular involvement even in the absence of known cardiac risk factors. Therefore, there is a need to understand the underlying mechanisms and genetic predispositions that explain cardiovascular involvement in COVID-19. Objectives:In silico analysis of publicly available datasets to decipher the molecular basis, potential pathways, and the role of the endothelium in the pathogenesis of cardiac and vascular injuries in COVID-19. Materials and Methods: Consistent significant differentially expressed genes (DEGs) shared by endothelium and peripheral immune cells were identified in five microarray transcriptomic profiling datasets in patients with venous thromboembolism “VTE,” acute coronary syndrome, heart failure and/or cardiogenic shock (main cardiovascular injuries related to COVID-19) compared to healthy controls. The identified genes were further examined in the publicly available transcriptomic dataset for cell/tissue specificity in lung tissue, in different ethnicities and in SARS-CoV-2 infected vs. mock-infected lung tissues and cardiomyocytes. Results: We identified 36 DEGs in blood and endothelium known to play key roles in endothelium and vascular biology, regulation of cellular response to stress as well as endothelial cell migration. Some of these genes were upregulated significantly in SARS-CoV-2 infected lung tissues. On the other hand, some genes with cardioprotective functions were downregulated in SARS-CoV-2 infected cardiomyocytes. Conclusion: In conclusion, our findings from the analysis of publicly available transcriptomic datasets identified shared core genes pertinent to cardiac and vascular-related injuries and their probable role in genetic susceptibility to cardiovascular injury in patients with COVID-19.
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Affiliation(s)
- Mahmood Yaseen Hachim
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Saba Al Heialy
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Abiola Senok
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Qutayba Hamid
- Meakins-Christie Laboratories, Research Institute of the McGill University Health Center, Montreal, QC, Canada.,College of Medicine, Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Alawi Alsheikh-Ali
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
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14
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Gregory DJ, DeLoid GM, Salmon SL, Metzger DW, Kramnik I, Kobzik L. SON DNA-binding protein mediates macrophage autophagy and responses to intracellular infection. FEBS Lett 2020; 594:2782-2799. [PMID: 32484234 DOI: 10.1002/1873-3468.13851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 05/11/2020] [Indexed: 12/09/2022]
Abstract
Intracellular pathogens affect diverse host cellular defence and metabolic pathways. Here, we used infection with Francisella tularensis to identify SON DNA-binding protein as a central determinant of macrophage activities. RNAi knockdown of SON increases survival of human macrophages following F. tularensis infection or inflammasome stimulation. SON is required for macrophage autophagy, interferon response factor 3 expression, type I interferon response and inflammasome-associated readouts. SON knockdown has gene- and stimulus-specific effects on inflammatory gene expression. SON is required for accurate splicing and expression of GBF1, a key mediator of cis-Golgi structure and function. Chemical GBF1 inhibition has similar effects to SON knockdown, suggesting that SON controls macrophage functions at least in part by controlling Golgi-associated processes.
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Affiliation(s)
- David J Gregory
- Molecular and Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Pediatric Infectious Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Glen M DeLoid
- Molecular and Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sharon L Salmon
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Dennis W Metzger
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Igor Kramnik
- Pulmonary Center, Department of Medicine, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, MA, USA
| | - Lester Kobzik
- Molecular and Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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15
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Schroeder AM, Allahyari M, Vogler G, Missinato MA, Nielsen T, Yu MS, Theis JL, Larsen LA, Goyal P, Rosenfeld JA, Nelson TJ, Olson TM, Colas AR, Grossfeld P, Bodmer R. Model system identification of novel congenital heart disease gene candidates: focus on RPL13. Hum Mol Genet 2020; 28:3954-3969. [PMID: 31625562 DOI: 10.1093/hmg/ddz213] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/28/2019] [Accepted: 06/21/2019] [Indexed: 12/12/2022] Open
Abstract
Genetics is a significant factor contributing to congenital heart disease (CHD), but our understanding of the genetic players and networks involved in CHD pathogenesis is limited. Here, we searched for de novo copy number variations (CNVs) in a cohort of 167 CHD patients to identify DNA segments containing potential pathogenic genes. Our search focused on new candidate disease genes within 19 deleted de novo CNVs, which did not cover known CHD genes. For this study, we developed an integrated high-throughput phenotypical platform to probe for defects in cardiogenesis and cardiac output in human induced pluripotent stem cell (iPSC)-derived multipotent cardiac progenitor (MCPs) cells and, in parallel, in the Drosophila in vivo heart model. Notably, knockdown (KD) in MCPs of RPL13, a ribosomal gene and SON, an RNA splicing cofactor, reduced proliferation and differentiation of cardiomyocytes, while increasing fibroblasts. In the fly, heart-specific RpL13 KD, predominantly at embryonic stages, resulted in a striking 'no heart' phenotype. KD of Son and Pdss2, among others, caused structural and functional defects, including reduced or abolished contractility, respectively. In summary, using a combination of human genetics and cardiac model systems, we identified new genes as candidates for causing human CHD, with particular emphasis on ribosomal genes, such as RPL13. This powerful, novel approach of combining cardiac phenotyping in human MCPs and in the in vivo Drosophila heart at high throughput will allow for testing large numbers of CHD candidates, based on patient genomic data, and for building upon existing genetic networks involved in heart development and disease.
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Affiliation(s)
- Analyne M Schroeder
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Massoud Allahyari
- Department of Pediatrics, UCSD School of Medicine, La Jolla, CA, USA
| | - Georg Vogler
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Maria A Missinato
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Tanja Nielsen
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael S Yu
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jeanne L Theis
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Lars A Larsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Preeya Goyal
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Timothy J Nelson
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Timothy M Olson
- Division of Pediatric Cardiology, Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Alexandre R Colas
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Paul Grossfeld
- Department of Pediatrics, UCSD School of Medicine, La Jolla, CA, USA
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
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16
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Ueda M, Matsuki T, Fukada M, Eda S, Toya A, Iio A, Tabata H, Nakayama A. Knockdown of Son, a mouse homologue of the ZTTK syndrome gene, causes neuronal migration defects and dendritic spine abnormalities. Mol Brain 2020; 13:80. [PMID: 32448361 PMCID: PMC7245844 DOI: 10.1186/s13041-020-00622-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/12/2020] [Indexed: 01/08/2023] Open
Abstract
Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome, a rare congenital anomaly syndrome characterized by intellectual disability, brain malformation, facial dysmorphism, musculoskeletal abnormalities, and some visceral malformations is caused by de novo heterozygous mutations of the SON gene. The nuclear protein SON is involved in gene transcription and RNA splicing; however, the roles of SON in neural development remain undetermined. We investigated the effects of Son knockdown on neural development in mice and found that Son knockdown in neural progenitors resulted in defective migration during corticogenesis and reduced spine density on mature cortical neurons. The induction of human wild-type SON expression rescued these neural abnormalities, confirming that the abnormalities were caused by SON insufficiency. We also applied truncated SON proteins encoded by disease-associated mutant SON genes for rescue experiments and found that a truncated SON protein encoded by the most prevalent SON mutant found in ZTTK syndrome rescued the neural abnormalities while another much shorter mutant SON protein did not. These data indicate that SON insufficiency causes neuronal migration defects and dendritic spine abnormalities, which seem neuropathological bases of the neural symptoms of ZTTK syndrome. In addition, the results support that the neural abnormalities in ZTTK syndrome are caused by SON haploinsufficiency independent of the types of mutation that results in functional or dysfunctional proteins.
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Affiliation(s)
- Masashi Ueda
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, 4800392, Japan
| | - Tohru Matsuki
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, 4800392, Japan
| | - Masahide Fukada
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, 4800392, Japan
| | - Shima Eda
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, 4800392, Japan
| | - Akie Toya
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, 4800392, Japan.,Department of Neurobiochemistry, Nagoya University School of Medicine, Nagoya, Aichi, 4668560, Japan
| | - Akio Iio
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, 4800392, Japan.,Biogate Co. Ltd., 331-1 Ohmori, Yamagata, Gifu, 5012123, Japan
| | - Hidenori Tabata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, 4800392, Japan
| | - Atsuo Nakayama
- Department of Cellular Pathology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, 4800392, Japan. .,Department of Neurobiochemistry, Nagoya University School of Medicine, Nagoya, Aichi, 4668560, Japan.
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17
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Tan Y, Duan L, Yang K, Liu Q, Wang J, Dong Z, Li Z, He Y, Yan Y, Lin L. A novel frameshift variant in SON causes Zhu-Tokita-Takenouchi-Kim Syndrome. J Clin Lab Anal 2020; 34:e23326. [PMID: 32291808 PMCID: PMC7439338 DOI: 10.1002/jcla.23326] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/08/2020] [Accepted: 03/14/2020] [Indexed: 12/16/2022] Open
Abstract
Background Zhu‐Tokita‐Takenouchi‐Kim syndrome is a severe multisystem developmental disorder characterized by intellectual disability, developmental delay, malformations of the cerebral cortex, epilepsy, vision problems, musculoskeletal abnormalities, and congenital malformations. This syndrome is caused by heterozygous pathogenic variants in the SON gene at chromosome 21q22.1. Objectives The aim of this study was to investigate the pathogenesis of a 4‐year‐old Chinese child who displayed severe intellectual disability, delayed psychomotor development, and facial dysmorphism. Methods A sequential detection including chromosome karyotyping, chromosome microarray analysis (CMA), and whole‐exome sequencing (WES) was performed on this child. The familial verification of WES result was conducted by Sanger sequencing. Results A de novo frameshift variant SON: c.5230delC (p.Arg1744ValfsTer29) was identified in the proband. The identical variant was not found in his family members. The frequencies of this variant in gnomAD/gnomAD_EAS databases were both none. Conclusions This study substantiates that SON: c.5230delC (p.Arg1744ValfsTer29) is a pathogenic variant of Zhu‐Tokita‐Takenouchi‐Kim syndrome and it is the first time to report Zhu‐Tokita‐Takenouchi‐Kim syndrome in China.
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Affiliation(s)
- Ya Tan
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, China
| | - Ling Duan
- Mianyang Maternity and Child Health Care Hospital, Sichuan, China
| | - Kai Yang
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, China
| | - Qian Liu
- Department of Neurological Rehabilitation, Gansu Provincial Hospital, Gansu, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, China
| | - Zhe Dong
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, China
| | - Zhi Li
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, China
| | - Yiwen He
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, China
| | - Yousheng Yan
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, China.,National Research Institute for Family Planning, Beijing, China
| | - Li Lin
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, China
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18
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Hochberg-Laufer H, Neufeld N, Brody Y, Nadav-Eliyahu S, Ben-Yishay R, Shav-Tal Y. Availability of splicing factors in the nucleoplasm can regulate the release of mRNA from the gene after transcription. PLoS Genet 2019; 15:e1008459. [PMID: 31765392 PMCID: PMC6901260 DOI: 10.1371/journal.pgen.1008459] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 12/09/2019] [Accepted: 10/04/2019] [Indexed: 11/18/2022] Open
Abstract
Gene expression dynamics can be measured in single living cells. Using a detectable transcriptionally active gene in living cells, we previously found that an mRNA undergoing several splicing events was retained at this gene after transcription until completion of mRNA processing. To determine the reason for this delay in release and whether mRNA retention on the gene might depend on splicing factor availability, we modulated the levels of splicing factors in the nucleus. Increasing the abundance of the diffusing fraction of splicing factors by their overexpression or by Clk1 kinase overexpression to disassemble nuclear speckles, led to a reduction in splicing factor residence times on the active gene, and the retained mRNA was rapidly released from the gene. Other treatments such as overexpression of a mutant inactive Clk1, the downregulation of MALAT1 lncRNA or of the Son protein, or the overexpression of the splicing factor import factor TNPO3, did not affect the dynamics of mRNA release from the gene. We found that the faster release of the mRNA from the gene mediated by increased availability of splicing factors, was dependent on the RS domain of the splicing factors and its phosphorylation state. We propose that the relative abundancies of splicing factors in the nucleoplasm can affect their availability for the splicing events taking place, and regulate the kinetics of mRNA release from the gene after processing. Genetic information is contained in the cell nucleus and encodes proteins. However, protein production takes place in the cytoplasm, and so a molecule is needed to connect between the nucleus and cytoplasm. This messenger molecule is called messenger RNA (mRNA). It is produced and copied from the DNA, and after some processing will travel to the cytoplasm to encode proteins. This study focuses on the timing of mRNA release from the gene after it is copied from the DNA. Processing of mRNA includes the removal of some of its pieces and the stitching back of the remaining parts. This is called splicing. We found that mRNAs undergoing many splicing events are retained on the gene until splicing has completed, and examined what is the cause for this delay. We found that the factors performing the splicing might be limiting the process if their levels are not high enough at the gene locus. By increasing splicing factor levels in the nucleus we show that their abundance increases the rate at which mRNA is released. This means that the cell can regulate gene expression rates by limiting the availability of splicing factors that are free to take part in the processing of mRNA.
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Affiliation(s)
- Hodaya Hochberg-Laufer
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Neufeld
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Yehuda Brody
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Shani Nadav-Eliyahu
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Rakefet Ben-Yishay
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
- * E-mail:
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19
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Tay MLI, Pek JW. SON protects nascent transcripts from unproductive degradation by counteracting DIP1. PLoS Genet 2019; 15:e1008498. [PMID: 31730657 PMCID: PMC6881055 DOI: 10.1371/journal.pgen.1008498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/27/2019] [Accepted: 10/28/2019] [Indexed: 11/18/2022] Open
Abstract
Gene expression involves the transcription and splicing of nascent transcripts through the removal of introns. In Drosophila, a double-stranded RNA binding protein Disco-interacting protein 1 (DIP1) targets INE-1 stable intronic sequence RNAs (sisRNAs) for degradation after splicing. How nascent transcripts that also contain INE-1 sequences escape degradation remains unknown. Here we observe that these nascent transcripts can also be bound by DIP1 but the Drosophila homolog of SON (Dsn) protects them from unproductive degradation in ovaries. Dsn localizes to the satellite body where active decay of INE-1 sisRNAs by DIP1 occurs. Dsn is a repressor of DIP1 posttranslational modifications (primarily sumoylation) that are assumed to be required for efficient DIP1 activity. Moreover, the pre-mRNA destabilization caused by Dsn depletion is rescued in DIP1 or Sumo heterozygous mutants, suggesting that Dsn is a negative regulator of DIP1. Our results reveal that under normal circumstances nascent transcripts are susceptible to DIP1-mediated degradation, however intronic sequences are protected by Dsn until intron excision has taken place.
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Affiliation(s)
| | - Jun Wei Pek
- Temasek Life Sciences Laboratory, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
- * E-mail:
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20
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Chapman RM, Tinsley CL, Hill MJ, Forrest MP, Tansey KE, Pardiñas AF, Rees E, Doyle AM, Wilkinson LS, Owen MJ, O’Donovan MC, Blake DJ. Convergent Evidence That ZNF804A Is a Regulator of Pre-messenger RNA Processing and Gene Expression. Schizophr Bull 2019; 45:1267-1278. [PMID: 30597088 PMCID: PMC6811834 DOI: 10.1093/schbul/sby183] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies have linked common variation in ZNF804A with an increased risk of schizophrenia. However, little is known about the biology of ZNF804A and its role in schizophrenia. Here, we investigate the function of ZNF804A using a variety of complementary molecular techniques. We show that ZNF804A is a nuclear protein that interacts with neuronal RNA splicing factors and RNA-binding proteins including RBFOX1, which is also associated with schizophrenia, CELF3/4, components of the ubiquitin-proteasome system and the ZNF804A paralog, GPATCH8. GPATCH8 also interacts with splicing factors and is localized to nuclear speckles indicative of a role in pre-messenger RNA (mRNA) processing. Sequence analysis showed that GPATCH8 contains ultraconserved, alternatively spliced poison exons that are also regulated by RBFOX proteins. ZNF804A knockdown in SH-SY5Y cells resulted in robust changes in gene expression and pre-mRNA splicing converging on pathways associated with nervous system development, synaptic contact, and cell adhesion. We observed enrichment (P = 1.66 × 10-9) for differentially spliced genes in ZNF804A-depleted cells among genes that contain RBFOX-dependent alternatively spliced exons. Differentially spliced genes in ZNF804A-depleted cells were also enriched for genes harboring de novo loss of function mutations in autism spectrum disorder (P = 6.25 × 10-7, enrichment 2.16) and common variant alleles associated with schizophrenia (P = .014), bipolar disorder and schizophrenia (P = .003), and autism spectrum disorder (P = .005). These data suggest that ZNF804A and its paralogs may interact with neuronal-splicing factors and RNA-binding proteins to regulate the expression of a subset of synaptic and neurodevelopmental genes.
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Affiliation(s)
- Ria M Chapman
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Caroline L Tinsley
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Matthew J Hill
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Marc P Forrest
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK,Present address: Department of Physiology, Feinberg School of Medicine, Northwestern University, Ward, Chicago, IL 60611
| | - Katherine E Tansey
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK,College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK
| | - Antonio F Pardiñas
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Elliott Rees
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - A Michelle Doyle
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Lawrence S Wilkinson
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK,School of Psychology, Cardiff University, Cardiff, UK
| | - Michael J Owen
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael C O’Donovan
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | - Derek J Blake
- Division of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK,To whom correspondence should be addressed; tel: 44(0)2920 688468, fax: +44(0)29 2068 7068, e-mail:
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21
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Kim JH, Park EY, Chitayat D, Stachura DL, Schaper J, Lindstrom K, Jewett T, Wieczorek D, Draaisma JM, Sinnema M, Hoeberigs C, Hempel M, Bachman KK, Seeley AH, Stone JK, Kong HK, Vukadin L, Richard A, Shinde DN, McWalter K, Si YC, Douglas G, Lim ST, Vissers LELM, Lemaire M, Ahn EYE. SON haploinsufficiency causes impaired pre-mRNA splicing of CAKUT genes and heterogeneous renal phenotypes. Kidney Int 2019; 95:1494-1504. [PMID: 31005274 DOI: 10.1016/j.kint.2019.01.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 12/10/2018] [Accepted: 01/04/2019] [Indexed: 10/27/2022]
Abstract
Although genetic testing is increasingly used in clinical nephrology, a large number of patients with congenital abnormalities of the kidney and urinary tract (CAKUT) remain undiagnosed with current gene panels. Therefore, careful curation of novel genetic findings is key to improving diagnostic yields. We recently described a novel intellectual disability syndrome caused by de novo heterozygous loss-of-function mutations in the gene encoding the splicing factor SON. Here, we show that many of these patients, including two previously unreported, exhibit a wide array of kidney abnormalities. Detailed phenotyping of 14 patients with SON haploinsufficiency identified kidney anomalies in 8 patients, including horseshoe kidney, unilateral renal hypoplasia, and renal cysts. Recurrent urinary tract infections, electrolyte disturbances, and hypertension were also observed in some patients. SON knockdown in kidney cell lines leads to abnormal pre-mRNA splicing, resulting in decreased expression of several established CAKUT genes. Furthermore, these molecular events were observed in patient-derived cells with SON haploinsufficiency. Taken together, our data suggest that the wide spectrum of phenotypes in patients with a pathogenic SON mutation is a consequence of impaired pre-mRNA splicing of several CAKUT genes. We propose that genetic testing panels designed to diagnose children with a kidney phenotype should include the SON gene.
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Affiliation(s)
- Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Eun Young Park
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada; The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - David L Stachura
- Department of Biological Sciences, California State University Chico, Chico, California, USA
| | - Jörg Schaper
- Institute of Diagnostic and Interventional Radiology, University of Düsseldorf, Düsseldorf, Germany
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Tamison Jewett
- Department of Pediatrics, Section on Medical Genetics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Dagmar Wieczorek
- Institute of Human Genetics, University Clinic Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany; Institute of Human Genetics, University Clinic Essen, University Duisburg-Essen, Essen, Germany
| | - Jos M Draaisma
- Department of Pediatrics, Radboudumc Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Margje Sinnema
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Christianne Hoeberigs
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Joshua K Stone
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Hyun Kyung Kong
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Lana Vukadin
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Alexander Richard
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | | | | | | | | | - Ssang-Taek Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mathieu Lemaire
- Division of Nephrology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada; Cell Biology Program, SickKids Research Institute, University of Toronto, Toronto, Ontario, Canada.
| | - Eun-Young Erin Ahn
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.
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22
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Planells B, Gómez-Redondo I, Pericuesta E, Lonergan P, Gutiérrez-Adán A. Differential isoform expression and alternative splicing in sex determination in mice. BMC Genomics 2019; 20:202. [PMID: 30871468 PMCID: PMC6419433 DOI: 10.1186/s12864-019-5572-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/27/2019] [Indexed: 02/06/2023] Open
Abstract
Background Alternative splicing (AS) may play an important role in gonadal sex determination (GSD) in mammals. The present study was designed to identify differentially expressed isoforms and AS modifications accompanying GSD in mice. Results Using deep RNA-sequencing, we performed a transcriptional analysis of XX and XY gonads during sex determination on embryonic days 11 (E11) and 12 (E12). Analysis of differentially expressed genes (DEG) identified hundreds of genes related to GSD and early sex differentiation that may represent good candidates for sex reversal. Expression at time point E11 in males was significantly enriched in RNA splicing and mRNA processing Gene Ontology terms. Differentially expressed isoform analysis identified hundreds of specific isoforms related to GSD, many of which showed no differences in the DEG analysis. Hundreds of AS events were identified as modified at E11 and E12. Female E11 gonads featured sex-biased upregulation of intron retention (in genes related to regulation of transcription, protein phosphorylation, protein transport and mRNA splicing) and exon skipping (in genes related to chromatin repression) suggesting AS as a post-transcription mechanism that controls sex determination of the bipotential fetal gonad. Conclusion Our data suggests an important role of splicing regulatory mechanisms for sex determination in mice. Electronic supplementary material The online version of this article (10.1186/s12864-019-5572-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamín Planells
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain.,School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Isabel Gómez-Redondo
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Eva Pericuesta
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Alfonso Gutiérrez-Adán
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain.
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23
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Alignment of Mitotic Chromosomes in Human Cells Involves SR-Like Splicing Factors Btf and TRAP150. Int J Mol Sci 2017; 18:ijms18091956. [PMID: 28895891 PMCID: PMC5618605 DOI: 10.3390/ijms18091956] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 09/07/2017] [Accepted: 09/09/2017] [Indexed: 11/25/2022] Open
Abstract
Serine-arginine-rich (SR) or SR-like splicing factors interact with exon junction complex proteins during pre-mRNA processing to promote mRNA packaging into mature messenger ribonucleoproteins (mRNPs) and to dictate mRNA stability, nuclear export, and translation. The SR protein family is complex, and while many classical SR proteins have well-defined mRNA processing functions, those of other SR-like proteins is unclear. Here, we show that depletion of the homologous non-classical serine-arginine-rich (SR) splicing factors Bcl2-associated transcription factor (Btf or BCLAF) and thyroid hormone receptor-associated protein of 150 kDa (TRAP150) causes mitotic defects. We hypothesized that the depletion of these SR-like factors affects mitosis indirectly through an altered expression of mitotic checkpoint regulator transcripts. We observed an altered abundance of transcripts that encode mitotic regulators and mitotic chromosome misalignment defects following Btf and/or TRAP150 depletion. We propose that, in addition to their previously reported roles in maintaining mRNA distribution, Btf and TRAP150 control the abundance of transcripts encoding mitotic regulators, thereby affecting mitotic progression in human cells.
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24
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Casein kinase 1 is recruited to nuclear speckles by FAM83H and SON. Sci Rep 2016; 6:34472. [PMID: 27681590 PMCID: PMC5041083 DOI: 10.1038/srep34472] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/14/2016] [Indexed: 11/29/2022] Open
Abstract
In some fibroblasts, casein kinase 1α (CK1α) is localized to nuclear speckles, which are sub-nuclear compartments supplying splicing factors, whereas it is recruited on keratin filaments in colorectal cancer cells such as DLD1 cells. In order to obtain a deeper understanding of why CK1α is localized to these different subcellular sites, we herein elucidated the mechanisms underlying its localization to nuclear speckles. CK1α and FAM83H were localized to nuclear speckles in RKO and WiDr colorectal cancer cells, which do not express simple epithelial keratins, and in DLD1 cells transfected with siRNAs for type I keratins. The localization of FAM83H to nuclear speckles was also detected in colorectal cancer cells with a poorly organized keratin cytoskeleton in colorectal cancer tissues. Using an interactome analysis of FAM83H, we identified SON, a protein present in nuclear speckles, as a scaffold protein to which FAM83H recruits CK1α. This result was supported by the knockdown of FAM83H or SON delocalizing CK1α from nuclear speckles. We also found that CK1δ and ε are localized to nuclear speckles in a FAM83H-dependent manner. These results suggest that CK1 is recruited to nuclear speckles by FAM83H and SON in the absence of an intact keratin cytoskeleton.
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25
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Kim JH, Shinde D, Reijnders M, Hauser N, Belmonte R, Wilson G, Bosch D, Bubulya P, Shashi V, Petrovski S, Stone J, Park E, Veltman J, Sinnema M, Stumpel C, Draaisma J, Nicolai J, Yntema H, Lindstrom K, de Vries B, Jewett T, Santoro S, Vogt J, Bachman K, Seeley A, Krokosky A, Turner C, Rohena L, Hempel M, Kortüm F, Lessel D, Neu A, Strom T, Wieczorek D, Bramswig N, Laccone F, Behunova J, Rehder H, Gordon C, Rio M, Romana S, Tang S, El-Khechen D, Cho M, McWalter K, Douglas G, Baskin B, Begtrup A, Funari T, Schoch K, Stegmann A, Stevens S, Zhang DE, Traver D, Yao X, MacArthur D, Brunner H, Mancini G, Myers R, Owen L, Lim ST, Stachura D, Vissers L, Ahn EY, Vissers LELM, Ahn EYE. De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome. Am J Hum Genet 2016; 99:711-719. [PMID: 27545680 PMCID: PMC5011044 DOI: 10.1016/j.ajhg.2016.06.029] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/24/2016] [Indexed: 12/01/2022] Open
Abstract
The overall understanding of the molecular etiologies of intellectual disability (ID) and developmental delay (DD) is increasing as next-generation sequencing technologies identify genetic variants in individuals with such disorders. However, detailed analyses conclusively confirming these variants, as well as the underlying molecular mechanisms explaining the diseases, are often lacking. Here, we report on an ID syndrome caused by de novo heterozygous loss-of-function (LoF) mutations in SON. The syndrome is characterized by ID and/or DD, malformations of the cerebral cortex, epilepsy, vision problems, musculoskeletal abnormalities, and congenital malformations. Knockdown of son in zebrafish resulted in severe malformation of the spine, brain, and eyes. Importantly, analyses of RNA from affected individuals revealed that genes critical for neuronal migration and cortex organization (TUBG1, FLNA, PNKP, WDR62, PSMD3, and HDAC6) and metabolism (PCK2, PFKL, IDH2, ACY1, and ADA) are significantly downregulated because of the accumulation of mis-spliced transcripts resulting from erroneous SON-mediated RNA splicing. Our data highlight SON as a master regulator governing neurodevelopment and demonstrate the importance of SON-mediated RNA splicing in human development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
| | - Eun-Young Erin Ahn
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA.
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26
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Tokita M, Braxton A, Shao Y, Lewis A, Vincent M, Küry S, Besnard T, Isidor B, Latypova X, Bézieau S, Liu P, Motter C, Melver C, Robin N, Infante E, McGuire M, El-Gharbawy A, Littlejohn R, McLean S, Bi W, Bacino C, Lalani S, Scott D, Eng C, Yang Y, Schaaf C, Walkiewicz M. De Novo Truncating Variants in SON Cause Intellectual Disability, Congenital Malformations, and Failure to Thrive. Am J Hum Genet 2016; 99:720-727. [PMID: 27545676 DOI: 10.1016/j.ajhg.2016.06.035] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/24/2016] [Indexed: 10/21/2022] Open
Abstract
SON is a key component of the spliceosomal complex and a critical mediator of constitutive and alternative splicing. Additionally, SON has been shown to influence cell-cycle progression, genomic integrity, and maintenance of pluripotency in stem cell populations. The clear functional relevance of SON in coordinating essential cellular processes and its presence in diverse human tissues suggests that intact SON might be crucial for normal growth and development. However, the phenotypic effects of deleterious germline variants in SON have not been clearly defined. Herein, we describe seven unrelated individuals with de novo variants in SON and propose that deleterious variants in SON are associated with a severe multisystem disorder characterized by developmental delay, persistent feeding difficulties, and congenital malformations, including brain anomalies.
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27
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Kim JH, Baddoo MC, Park EY, Stone JK, Park H, Butler TW, Huang G, Yan X, Pauli-Behn F, Myers RM, Tan M, Flemington EK, Lim ST, Ahn EYE. SON and Its Alternatively Spliced Isoforms Control MLL Complex-Mediated H3K4me3 and Transcription of Leukemia-Associated Genes. Mol Cell 2016; 61:859-73. [PMID: 26990989 DOI: 10.1016/j.molcel.2016.02.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 12/16/2015] [Accepted: 02/17/2016] [Indexed: 10/22/2022]
Abstract
Dysregulation of MLL complex-mediated histone methylation plays a pivotal role in gene expression associated with diseases, but little is known about cellular factors modulating MLL complex activity. Here, we report that SON, previously known as an RNA splicing factor, controls MLL complex-mediated transcriptional initiation. SON binds to DNA near transcription start sites, interacts with menin, and inhibits MLL complex assembly, resulting in decreased H3K4me3 and transcriptional repression. Importantly, alternatively spliced short isoforms of SON are markedly upregulated in acute myeloid leukemia. The short isoforms compete with full-length SON for chromatin occupancy but lack the menin-binding ability, thereby antagonizing full-length SON function in transcriptional repression while not impairing full-length SON-mediated RNA splicing. Furthermore, overexpression of a short isoform of SON enhances replating potential of hematopoietic progenitors. Our findings define SON as a fine-tuner of the MLL-menin interaction and reveal short SON overexpression as a marker indicating aberrant transcriptional initiation in leukemia.
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Affiliation(s)
- Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Melody C Baddoo
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA
| | - Eun Young Park
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Joshua K Stone
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Hyeonsoo Park
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Thomas W Butler
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Gang Huang
- Division of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaomei Yan
- Division of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | | | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Ming Tan
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | | | - Ssang-Taek Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Eun-Young Erin Ahn
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA.
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28
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Liu Y, Liu J, Wang Z, He JJ. Tip110 binding to U6 small nuclear RNA and its participation in pre-mRNA splicing. Cell Biosci 2015. [PMID: 26203351 PMCID: PMC4511435 DOI: 10.1186/s13578-015-0032-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background RNA–protein interactions play important roles in gene expression control. These interactions are mediated by several recurring RNA-binding motifs including a well-known and characterized ribonucleoprotein motif or so-called RNA recognition motif (RRM). Results In the current study, we set out to identify the RNA ligand(s) of a RRM-containing protein Tip110, also known as p110nrb, SART3, or p110, using a RNA-based yeast three-hybrid cloning strategy. Six putative RNA targets were isolated and found to contain a consensus sequence that was identical to nucleotides 34–46 of U6 small nuclear RNA. Tip110 binding to U6 was confirmed to be specific and RRM-dependent in an electrophoretic mobility shift assay. Both in vitro pre-mRNA splicing assay and in vivo splicing-dependent reporter gene assay showed that the pre-mRNA splicing was correlated with Tip110 expression. Moreover, Tip110 was found in the spliceosomes containing pre-spliced pre-mRNA and spliced mRNA products. Nonetheless, the RRM-deleted mutant (ΔRRM) that did not bind to U6 showed promotion in vitro pre-mRNA splicing, whereas the nuclear localization signal (NLS)-deleted mutant ΔNLS that bound to U6 promoted the pre-mRNA splicing both in vitro and in vivo. Lastly, RNA-Seq analysis confirmed that Tip110 regulated a number of gene pre-mRNA splicing including several splicing factors. Conclusions Taken together, these results demonstrate that Tip110 is directly involved in constitutive eukaryotic pre-mRNA splicing, likely through its binding to U6 and regulation of other splicing factors, and provide further evidence to support the global roles of Tip110 in regulation of host gene expression.
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Affiliation(s)
- Ying Liu
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 USA
| | - Jinfeng Liu
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 USA ; Department of Infectious Diseases, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi China
| | - Zenyuan Wang
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 USA ; Department of Forensic Science, College of Medicine, Xi'an Jiaotong University, Xi'an, 710061 Shaanxi China
| | - Johnny J He
- Department of Cell Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX 76107 USA
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29
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Battini VP, Bubulya A, Bubulya PA. Accurate splicing of HDAC6 pre-mRNA requires SON. Int J Mol Sci 2015; 16:5886-99. [PMID: 25782155 PMCID: PMC4394511 DOI: 10.3390/ijms16035886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/19/2015] [Accepted: 03/03/2015] [Indexed: 11/26/2022] Open
Abstract
Pre-mRNA splicing requires proper splice site selection mediated by many factors including snRNPs and serine-arginine rich (SR) splicing factors. Our lab previously reported that the SR-like protein SON maintains organization of pre-mRNA splicing factors in nuclear speckles as well as splicing of many human transcripts including mRNAs coding for the chromatin-modifying enzymes HDAC6, ADA and SETD8. However, the mechanism by which SON maintains accurate splicing is unknown. To build tools for understanding SON-dependent pre-mRNA splicing, we constructed a minigene reporter plasmid driving expression of the genomic sequence spanning exons 26 through 29 of HDAC6. Following SON depletion, we observed altered splicing of HDAC6 reporter transcripts that showed exclusion of exons 27 and 28, reflecting the splicing patterns of endogenous HDAC6 mRNA. Importantly, loss of HDAC6 biological function was also observed, as indicated by truncated HDAC6 protein and corresponding absence of aggresome assembly activities of HDAC6 binding-of-ubiquitin zinc finger (BUZ) domain. We therefore propose that SON-mediated splicing regulation of HDAC6 is essential for supporting protein degradation pathways that prevent human disease.
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Affiliation(s)
- Vishnu Priya Battini
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA.
| | - Athanasios Bubulya
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA.
| | - Paula A Bubulya
- Department of Biological Sciences, Wright State University, Dayton, OH 45435, USA.
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30
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van der Lelij P, Stocsits RR, Ladurner R, Petzold G, Kreidl E, Koch B, Schmitz J, Neumann B, Ellenberg J, Peters JM. SNW1 enables sister chromatid cohesion by mediating the splicing of sororin and APC2 pre-mRNAs. EMBO J 2014; 33:2643-58. [PMID: 25257309 DOI: 10.15252/embj.201488202] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Although splicing is essential for the expression of most eukaryotic genes, inactivation of splicing factors causes specific defects in mitosis. The molecular cause of this defect is unknown. Here, we show that the spliceosome subunits SNW1 and PRPF8 are essential for sister chromatid cohesion in human cells. A transcriptome-wide analysis revealed that SNW1 or PRPF8 depletion affects the splicing of specific introns in a subset of pre-mRNAs, including pre-mRNAs encoding the cohesion protein sororin and the APC/C subunit APC2. SNW1 depletion causes cohesion defects predominantly by reducing sororin levels, which causes destabilisation of cohesin on DNA. SNW1 depletion also reduces APC/C activity and contributes to cohesion defects indirectly by delaying mitosis and causing "cohesion fatigue". Simultaneous expression of sororin and APC2 from intron-less cDNAs restores cohesion in SNW1-depleted cells. These results indicate that the spliceosome is required for mitosis because it enables expression of genes essential for cohesion. Our transcriptome-wide identification of retained introns in SNW1- and PRPF8-depleted cells may help to understand the aetiology of diseases associated with splicing defects, such as retinosa pigmentosum and cancer.
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Affiliation(s)
| | | | - Rene Ladurner
- IMP Research Institute of Molecular Pathology, Vienna, Austria
| | - Georg Petzold
- IMP Research Institute of Molecular Pathology, Vienna, Austria
| | - Emanuel Kreidl
- IMP Research Institute of Molecular Pathology, Vienna, Austria
| | - Birgit Koch
- IMP Research Institute of Molecular Pathology, Vienna, Austria EMBL Heidelberg, Heidelberg, Germany
| | - Julia Schmitz
- IMP Research Institute of Molecular Pathology, Vienna, Austria
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31
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Hickey CJ, Kim JH, Ahn EYE. New discoveries of old SON: a link between RNA splicing and cancer. J Cell Biochem 2014; 115:224-31. [PMID: 24030980 DOI: 10.1002/jcb.24672] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/06/2013] [Indexed: 12/11/2022]
Abstract
The SON protein is a ubiquitously expressed DNA- and RNA-binding protein primarily localized to nuclear speckles. Although several early studies implicated SON in DNA-binding, tumorigenesis and apoptosis, functional significance of this protein had not been recognized until recent studies discovered SON as a novel RNA splicing co-factor. During constitutive RNA splicing, SON ensures efficient intron removal from the transcripts containing suboptimal splice sites. Importantly, SON-mediated splicing is required for proper processing of selective transcripts related to cell cycle, microtubules, centrosome maintenance, and genome stability. Moreover, SON regulates alternative splicing of RNAs from the genes involved in apoptosis and epigenetic modification. In addition to the role in RNA splicing, SON has an ability to suppress transcriptional activation at certain promoter/enhancer DNA sequences. Considering the multiple SON target genes which are directly involved in cell proliferation, genome stability and chromatin modifications, SON is an emerging player in gene regulation during cancer development and progression. Here, we summarize available information from several early studies on SON, and highlight recent discoveries describing molecular mechanisms of SON-mediated gene regulation. We propose that our future effort on better understanding of diverse SON functions would reveal novel targets for cancer therapy.
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32
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Ammon T, Mishra SK, Kowalska K, Popowicz GM, Holak TA, Jentsch S. The conserved ubiquitin-like protein Hub1 plays a critical role in splicing in human cells. J Mol Cell Biol 2014; 6:312-23. [PMID: 24872507 PMCID: PMC4141198 DOI: 10.1093/jmcb/mju026] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Different from canonical ubiquitin-like proteins, Hub1 does not form covalent conjugates with substrates but binds proteins non-covalently. In Saccharomyces cerevisiae, Hub1 associates with spliceosomes and mediates alternative splicing of SRC1, without affecting pre-mRNA splicing generally. Human Hub1 is highly similar to its yeast homolog, but its cellular function remains largely unexplored. Here, we show that human Hub1 binds to the spliceosomal protein Snu66 as in yeast; however, unlike its S. cerevisiae homolog, human Hub1 is essential for viability. Prolonged in vivo depletion of human Hub1 leads to various cellular defects, including splicing speckle abnormalities, partial nuclear retention of mRNAs, mitotic catastrophe, and consequently cell death by apoptosis. Early consequences of Hub1 depletion are severe splicing defects, however, only for specific splice sites leading to exon skipping and intron retention. Thus, the ubiquitin-like protein Hub1 is not a canonical spliceosomal factor needed generally for splicing, but rather a modulator of spliceosome performance and facilitator of alternative splicing.
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Affiliation(s)
- Tim Ammon
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Shravan Kumar Mishra
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Present address: Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector 81, SAS Nagar, 140306 Punjab, India
| | - Kaja Kowalska
- NMR Spectroscopy, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Grzegorz M Popowicz
- NMR Spectroscopy, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Present address: Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Tad A Holak
- NMR Spectroscopy, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Present address: Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Cracow, Poland
| | - Stefan Jentsch
- Department of Molecular Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Lu X, Ng HH, Bubulya PA. The role of SON in splicing, development, and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:637-46. [PMID: 24789761 DOI: 10.1002/wrna.1235] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/07/2014] [Accepted: 03/09/2014] [Indexed: 12/22/2022]
Abstract
SON is a nuclear protein involved in multiple cellular processes including transcription, pre-messenger RNA (mRNA) splicing, and cell cycle regulation. Although SON was discovered 25 years ago, the importance of SON's function was only realized recently when its roles in nuclear organization and pre-mRNA splicing as well as the influence of these activities in maintaining cellular health were unveiled. Furthermore, SON was implicated to have a key role in stem cells as well as during the onset of various diseases such as cancer, influenza, and hepatitis. Here we review the progress that has been made in studying this multifunctional protein and discuss questions that remain to be answered about SON.
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Affiliation(s)
- Xinyi Lu
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore, Singapore
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Lu X, Göke J, Sachs F, Jacques PÉ, Liang H, Feng B, Bourque G, Bubulya PA, Ng HH. SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells. Nat Cell Biol 2013; 15:1141-1152. [PMID: 24013217 DOI: 10.1038/ncb2839] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 08/07/2013] [Indexed: 12/18/2022]
Abstract
Human embryonic stem cells (hESCs) harbour the ability to undergo lineage-specific differentiation into clinically relevant cell types. Transcription factors and epigenetic modifiers are known to play important roles in the maintenance of pluripotency of hESCs. However, little is known about regulation of pluripotency through splicing. In this study, we identify the spliceosome-associated factor SON as a factor essential for the maintenance of hESCs. Depletion of SON in hESCs results in the loss of pluripotency and cell death. Using genome-wide RNA profiling, we identified transcripts that are regulated by SON. Importantly, we confirmed that SON regulates the proper splicing of transcripts encoding for pluripotency regulators such as OCT4, PRDM14, E4F1 and MED24. Furthermore, we show that SON is bound to these transcripts in vivo. In summary, we connect a splicing-regulatory network for accurate transcript production to the maintenance of pluripotency and self-renewal of hESCs.
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Affiliation(s)
- Xinyi Lu
- Gene Regulation Laboratory, Genome Institute of Singapore, 138672, Singapore.,Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Jonathan Göke
- Gene Regulation Laboratory, Genome Institute of Singapore, 138672, Singapore
| | - Friedrich Sachs
- Gene Regulation Laboratory, Genome Institute of Singapore, 138672, Singapore.,Department of Biochemistry, National University of Singapore, 117597, Singapore
| | - Pierre-Étienne Jacques
- Department of Biology, Université de Sherbrooke, 2500 boulevard de l'Université Sherbrooke, Québec J1K 2R1, Canada
| | - Hongqing Liang
- Gene Regulation Laboratory, Genome Institute of Singapore, 138672, Singapore
| | - Bo Feng
- School of Biomedical Sciences, Lo Kwee Seong Integrated Biomedical Sciences Building, Chinese University of Hong Kong, Hong Kong 999077, China
| | - Guillaume Bourque
- McGill University & Genome Quebec Innovation Center, 740 Dr Penfield Avenue, Montréal, Québec H3A 1A4, Canada
| | - Paula A Bubulya
- Department of Biological Sciences, Wright State University, Dayton, Ohio 45435, USA
| | - Huck-Hui Ng
- Gene Regulation Laboratory, Genome Institute of Singapore, 138672, Singapore.,Department of Biological Sciences, National University of Singapore, 117543, Singapore.,Department of Biochemistry, National University of Singapore, 117597, Singapore.,Graduate School for Integrative Sciences & Engineering, National University of Singapore, 117456, Singapore.,School of Biological Sciences, Nanyang Technological University, 637551, Singapore
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Varia S, Potabathula D, Deng Z, Bubulya A, Bubulya PA. Btf and TRAP150 have distinct roles in regulating subcellular mRNA distribution. Nucleus 2013; 4:229-40. [PMID: 23778535 DOI: 10.4161/nucl.25187] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transcription of protein-coding genes in mammalian cells is coordinated with pre-mRNA processing as well as the assembly and nuclear export of mRNPs. Btf (BCLAF1) and TRAP150 (THRAP3) were previously reported to associate with in vitro spliced mRNPs and also as a part of the spliceosome, suggesting they are involved in pre-mRNA processing. Btf and TRAP150 are serine-arginine-rich (SR) proteins with significant sequence similarity, but the extent of their functional overlap is not yet clear. We show that both Btf and TRAP150 localize at a constitutively active β-tropomyosin (BTM) reporter minigene locus in mammalian cells. Both proteins also localize at a U2OS 2-6-3 reporter gene locus in a RNA polymerase II (RNAPII) transcription-dependent manner. While Btf and TRAP150 showed some overlap with reporter RNA and other pre-mRNA processing factors at transcription loci, they showed the most precise overlap with the exon junction complex (EJC) protein Magoh. Since EJC components have roles in nuclear export, we examined nuclear/cytoplasmic mRNA distribution after Btf or TRAP150 knockdown. Btf depletion caused an increase of β-tropomyosin minigene reporter transcripts in the cytoplasm as well as global increase of endogenous polyadenylated RNA in the cytoplasm, while TRAP150 depletion did not. We provide evidence that Btf has functions distinct from TRAP150 in regulating the subcellular distribution of mRNAs in human cells.
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Current world literature. Curr Opin Lipidol 2013; 24:178-81. [PMID: 23481230 DOI: 10.1097/mol.0b013e32835f8a8c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Regulation of splicing by SR proteins and SR protein-specific kinases. Chromosoma 2013; 122:191-207. [PMID: 23525660 DOI: 10.1007/s00412-013-0407-z] [Citation(s) in RCA: 312] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/04/2013] [Accepted: 03/06/2013] [Indexed: 12/21/2022]
Abstract
Genomic sequencing reveals similar but limited numbers of protein-coding genes in different genomes, which begs the question of how organismal diversities are generated. Alternative pre-mRNA splicing, a widespread phenomenon in higher eukaryotic genomes, is thought to provide a mechanism to increase the complexity of the proteome and introduce additional layers for regulating gene expression in different cell types and during development. Among a large number of factors implicated in the splicing regulation are the SR protein family of splicing factors and SR protein-specific kinases. Here, we summarize the rules for SR proteins to function as splicing regulators, which depend on where they bind in exons versus intronic regions, on alternative exons versus flanking competing exons, and on cooperative as well as competitive binding between different SR protein family members on many of those locations. We review the importance of cycles of SR protein phosphorylation/dephosphorylation in the splicing reaction with emphasis on the recent molecular insight into the role of SR protein phosphorylation in early steps of spliceosome assembly. Finally, we highlight recent discoveries of SR protein-specific kinases in transducing growth signals to regulate alternative splicing in the nucleus and the connection of both SR proteins and SR protein kinases to human diseases, particularly cancer.
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Ahn EEY, Higashi T, Yan M, Matsuura S, Hickey CJ, Lo MC, Shia WJ, DeKelver RC, Zhang DE. SON protein regulates GATA-2 through transcriptional control of the microRNA 23a~27a~24-2 cluster. J Biol Chem 2013; 288:5381-8. [PMID: 23322776 DOI: 10.1074/jbc.m112.447227] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
SON is a DNA- and RNA-binding protein localized in nuclear speckles. Although its function in RNA splicing for effective cell cycle progression and genome stability was recently unveiled, other mechanisms of SON functions remain unexplored. Here, we report that SON regulates GATA-2, a key transcription factor involved in hematopoietic stem cell maintenance and differentiation. SON is highly expressed in undifferentiated hematopoietic stem/progenitor cells and leukemic blasts. SON knockdown leads to significant depletion of GATA-2 protein with marginal down-regulation of GATA-2 mRNA. We show that miR-27a is up-regulated upon SON knockdown and targets the 3'-UTR of GATA-2 mRNA in hematopoietic cells. Up-regulation of miR-27a was due to activation of the promoter of the miR-23a∼27a∼24-2 cluster, suggesting that SON suppresses this promoter to lower the microRNAs from this cluster. Our data revealed a previously unidentified role of SON in microRNA production via regulating the transcription process, thereby modulating GATA-2 at the protein level during hematopoietic differentiation.
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Affiliation(s)
- Erin Eun-Young Ahn
- Moores UCSD Cancer Center, the University of California San Diego, La Jolla, California 92093, USA
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Four parameters increase the sensitivity and specificity of the exon array analysis and disclose 25 novel aberrantly spliced exons in myotonic dystrophy. J Hum Genet 2012; 57:368-74. [PMID: 22513715 DOI: 10.1038/jhg.2012.37] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is an RNA gain-of-function disorder in which abnormally expanded CTG repeats of DMPK sequestrate a splicing trans-factor MBNL1 and upregulate another splicing trans-factor CUGBP1. To identify a diverse array of aberrantly spliced genes, we performed the exon array analysis of DM1 muscles. We analyzed 72 exons by RT-PCR and found that 27 were aberrantly spliced, whereas 45 were not. Among these, 25 were novel and especially splicing aberrations of LDB3 exon 4 and TTN exon 45 were unique to DM1. Retrospective analysis revealed that four parameters efficiently detect aberrantly spliced exons: (i) the signal intensity is high; (ii) the ratio of probe sets with reliable signal intensities (that is, detection above background P-value=0.000) is high within a gene; (iii) the splice index (SI) is high; and (iv) SI is deviated from SIs of the other exons that can be estimated by calculating the deviation value (DV). Application of the four parameters gave rise to a sensitivity of 77.8% and a specificity of 95.6% in our data set. We propose that calculation of DV, which is unique to our analysis, is of particular importance in analyzing the exon array data.
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