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Dillingham CM, Cormaty H, Morgan EC, Tak AI, Esgdaille DE, Boutz PL, Sridharan R. KDM3A and KDM3B Maintain Naïve Pluripotency Through the Regulation of Alternative Splicing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.31.543088. [PMID: 37398291 PMCID: PMC10312572 DOI: 10.1101/2023.05.31.543088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Histone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cell (ESC) identity is characterized by a lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 family of histone demethylases removes the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find that KDM3A and KDM3B interact with RNA processing factors such as EFTUD2 and PRMT5. Acute selective degradation of the endogenous KDM3A and KDM3B proteins resulted in altered splicing independent of H3K9me2 status or catalytic activity. These splicing changes partially resemble the splicing pattern of the more blastocyst-like ground state of pluripotency and occurred in important chromatin and transcription factors such as Dnmt3b, Tbx3 and Tcf12. Our findings reveal non-canonical roles of histone demethylating enzymes in splicing to regulate cell identity.
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Affiliation(s)
- Caleb M Dillingham
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Harshini Cormaty
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ellen C Morgan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Andrew I Tak
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Dakarai E Esgdaille
- Department of Biochemistry and Biophysics, Center for RNA Biology, Wilmot Cancer Center, University of Rochester School of Medicine and Dentistry
| | - Paul L Boutz
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry
| | - Rupa Sridharan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53792, USA
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2
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Lee SJ, Emery D, Vukmanic E, Wang Y, Lu X, Wang W, Fortuny E, James R, Kaplan HJ, Liu Y, Du J, Dean DC. Metabolic transcriptomics dictate responses of cone photoreceptors to retinitis pigmentosa. Cell Rep 2023; 42:113054. [PMID: 37656622 PMCID: PMC10591869 DOI: 10.1016/j.celrep.2023.113054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/21/2023] [Accepted: 08/15/2023] [Indexed: 09/03/2023] Open
Abstract
Most mutations in retinitis pigmentosa (RP) arise in rod photoreceptors, but cone photoreceptors, responsible for high-resolution daylight and color vision, are subsequently affected, causing the most debilitating features of the disease. We used mass spectroscopy to follow 13C metabolites delivered to the outer retina and single-cell RNA sequencing to assess photoreceptor transcriptomes. The S cone metabolic transcriptome suggests engagement of the TCA cycle and ongoing response to ROS characteristic of oxidative phosphorylation, which we link to their histone modification transcriptome. Tumor necrosis factor (TNF) and its downstream effector RIP3, which drive ROS generation via mitochondrial dysfunction, are induced and activated as S cones undergo early apoptosis in RP. The long/medium-wavelength (L/M) cone transcriptome shows enhanced glycolytic capacity, which maintains their function as RP progresses. Then, as extracellular glucose eventually diminishes, L/M cones are sustained in long-term dormancy by lactate metabolism.
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Affiliation(s)
- Sang Joon Lee
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA; Department of Ophthalmology, Kosin University College of Medicine, #262 Gamcheon-ro, Seo-gu, Busan 49267, Korea
| | - Douglas Emery
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Eric Vukmanic
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Yekai Wang
- Departments of Ophthalmology and Visual Sciences and Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Xiaoqin Lu
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Wei Wang
- Department of Ophthalmology and Visual Sciences, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Enzo Fortuny
- Department of Neurosurgery, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Robert James
- Department of Neurosurgery, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Henry J Kaplan
- Department of Ophthalmology, St. Louis University School of Medicine, St. Louis MO 63110, USA
| | - Yongqing Liu
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA
| | - Jianhai Du
- Departments of Ophthalmology and Visual Sciences and Biochemistry and Molecular Medicine, West Virginia University, Morgantown, WV 26506, USA.
| | - Douglas C Dean
- Department of Medicine, Brown Cancer Center, University of Louisville Health Sciences Center, Louisville, KY 40202, USA.
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3
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Qiu Y, Wang H, Fan M, Pan H, Guan J, Jiang Y, Jia Z, Wu K, Zhou H, Zhuang Q, Lei Z, Ding X, Cai H, Dong Y, Yan L, Lin A, Fu Y, Zhang D, Yan Q, Wang Q. Impaired AIF-CHCHD4 interaction and mitochondrial calcium overload contribute to auditory neuropathy spectrum disorder in patient-iPSC-derived neurons with AIFM1 variant. Cell Death Dis 2023; 14:375. [PMID: 37365177 DOI: 10.1038/s41419-023-05899-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023]
Abstract
Auditory neuropathy spectrum disorder (ANSD) is a hearing impairment caused by dysfunction of inner hair cells, ribbon synapses, spiral ganglion neurons and/or the auditory nerve itself. Approximately 1/7000 newborns have abnormal auditory nerve function, accounting for 10%-14% of cases of permanent hearing loss in children. Although we previously identified the AIFM1 c.1265 G > A variant to be associated with ANSD, the mechanism by which ANSD is associated with AIFM1 is poorly understood. We generated induced pluripotent stem cells (iPSCs) from peripheral blood mononuclear cells (PBMCs) via nucleofection with episomal plasmids. The patient-specific iPSCs were edited via CRISPR/Cas9 technology to generate gene-corrected isogenic iPSCs. These iPSCs were further differentiated into neurons via neural stem cells (NSCs). The pathogenic mechanism was explored in these neurons. In patient cells (PBMCs, iPSCs, and neurons), the AIFM1 c.1265 G > A variant caused a novel splicing variant (c.1267-1305del), resulting in AIF p.R422Q and p.423-435del proteins, which impaired AIF dimerization. Such impaired AIF dimerization then weakened the interaction between AIF and coiled-coil-helix-coiled-coil-helix domain-containing protein 4 (CHCHD4). On the one hand, the mitochondrial import of ETC complex subunits was inhibited, subsequently leading to an increased ADP/ATP ratio and elevated ROS levels. On the other hand, MICU1-MICU2 heterodimerization was impaired, leading to mCa2+ overload. Calpain was activated by mCa2+ and subsequently cleaved AIF for its translocation into the nucleus, ultimately resulting in caspase-independent apoptosis. Interestingly, correction of the AIFM1 variant significantly restored the structure and function of AIF, further improving the physiological state of patient-specific iPSC-derived neurons. This study demonstrates that the AIFM1 variant is one of the molecular bases of ANSD. Mitochondrial dysfunction, especially mCa2+ overload, plays a prominent role in ANSD associated with AIFM1. Our findings help elucidate the mechanism of ANSD and may lead to the provision of novel therapies.
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Affiliation(s)
- Yue Qiu
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Hongyang Wang
- Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Mingjie Fan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
- Department of Pediatrics, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China
| | - Huaye Pan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jing Guan
- Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yangwei Jiang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Zexiao Jia
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Kaiwen Wu
- Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Hui Zhou
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Qianqian Zhuang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Zhaoying Lei
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xue Ding
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Huajian Cai
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yufei Dong
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lei Yan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Aifu Lin
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Yong Fu
- The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310052, China
| | - Dong Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Qingfeng Yan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
- Department of Pediatrics, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310003, China.
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou, Zhejiang, 310058, China.
| | - Qiuju Wang
- Senior Department of Otolaryngology, Head and Neck Surgery, Chinese PLA Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, 100853, China.
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4
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Kumar K, Sinha SK, Maity U, Kirti PB, Kumar KRR. Insights into established and emerging roles of SR protein family in plants and animals. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1763. [PMID: 36131558 DOI: 10.1002/wrna.1763] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 05/13/2023]
Abstract
Splicing of pre-mRNA is an essential part of eukaryotic gene expression. Serine-/arginine-rich (SR) proteins are highly conserved RNA-binding proteins present in all metazoans and plants. SR proteins are involved in constitutive and alternative splicing, thereby regulating the transcriptome and proteome diversity in the organism. In addition to their role in splicing, SR proteins are also involved in mRNA export, nonsense-mediated mRNA decay, mRNA stability, and translation. Due to their pivotal roles in mRNA metabolism, SR proteins play essential roles in normal growth and development. Hence, any misregulation of this set of proteins causes developmental defects in both plants and animals. SR proteins from the animal kingdom are extensively studied for their canonical and noncanonical functions. Compared with the animal kingdom, plant genomes harbor more SR protein-encoding genes and greater diversity of SR proteins, which are probably evolved for plant-specific functions. Evidence from both plants and animals confirms the essential role of SR proteins as regulators of gene expression influencing cellular processes, developmental stages, and disease conditions. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Kundan Kumar
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Shubham Kumar Sinha
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Upasana Maity
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
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5
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Multi-omics approach reveals posttranscriptionally regulated genes are essential for human pluripotent stem cells. iScience 2022; 25:104289. [PMID: 35573189 PMCID: PMC9097716 DOI: 10.1016/j.isci.2022.104289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 04/01/2022] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
The effects of transcription factors on the maintenance and differentiation of human-induced or embryonic pluripotent stem cells (iPSCs/ESCs) have been well studied. However, the importance of posttranscriptional regulatory mechanisms, which cause the quantitative dissociation of mRNA and protein expression, has not been explored in detail. Here, by combining transcriptome and proteome profiling, we identified 228 posttranscriptionally regulated genes with strict upregulation of the protein level in iPSCs/ESCs. Among them, we found 84 genes were vital for the survival of iPSCs and HDFs, including 20 genes that were specifically necessary for iPSC survival. These 20 proteins were upregulated only in iPSCs/ESCs and not in differentiated cells derived from the three germ layers. Although there are still unknown mechanisms that downregulate protein levels in HDFs, these results reveal that posttranscriptionally regulated genes have a crucial role in iPSC survival. The posttranscriptionally regulated 20 genes are necessary for iPSC survival The proteins of HSPA8, EIF3D, and NCBP2 are quickly degraded in HDFs mRNA localization affects the protein amounts in most of the 20 genes Translation is repressed in HDFs despite mRNA binding to ribosomes
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6
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Heazlewood SY, Ahmad T, Mohenska M, Guo BB, Gangatirkar P, Josefsson EC, Ellis SL, Ratnadiwakara M, Cao H, Cao B, Heazlewood CK, Williams B, Fulton M, White JF, Ramialison M, Nilsson SK, Änkö ML. The RNA-binding protein SRSF3 has an essential role in megakaryocyte maturation and platelet production. Blood 2022; 139:1359-1373. [PMID: 34852174 PMCID: PMC8900270 DOI: 10.1182/blood.2021013826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/06/2021] [Indexed: 11/20/2022] Open
Abstract
RNA processing is increasingly recognized as a critical control point in the regulation of different hematopoietic lineages including megakaryocytes responsible for the production of platelets. Platelets are anucleate cytoplasts that contain a rich repertoire of RNAs encoding proteins with essential platelet functions derived from the parent megakaryocyte. It is largely unknown how RNA binding proteins contribute to the development and functions of megakaryocytes and platelets. We show that serine-arginine-rich splicing factor 3 (SRSF3) is essential for megakaryocyte maturation and generation of functional platelets. Megakaryocyte-specific deletion of Srsf3 in mice led to macrothrombocytopenia characterized by megakaryocyte maturation arrest, dramatically reduced platelet counts, and abnormally large functionally compromised platelets. SRSF3 deficient megakaryocytes failed to reprogram their transcriptome during maturation and to load platelets with RNAs required for normal platelet function. SRSF3 depletion led to nuclear accumulation of megakaryocyte mRNAs, demonstrating that SRSF3 deploys similar RNA regulatory mechanisms in megakaryocytes as in other cell types. Our study further suggests that SRSF3 plays a role in sorting cytoplasmic megakaryocyte RNAs into platelets and demonstrates how SRSF3-mediated RNA processing forms a central part of megakaryocyte gene regulation. Understanding SRSF3 functions in megakaryocytes and platelets provides key insights into normal thrombopoiesis and platelet pathologies as SRSF3 RNA targets in megakaryocytes are associated with platelet diseases.
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Affiliation(s)
- Shen Y Heazlewood
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Tanveer Ahmad
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Monika Mohenska
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Belinda B Guo
- School of Biomedical Sciences, Pathology and Laboratory Science, University of Western Australia, WA, Australia
| | | | - Emma C Josefsson
- Walter and Eliza Hall Institute of Medical Research, VIC, Australia
- Department of Medical Biology, The University of Melbourne, VIC, Australia
| | - Sarah L Ellis
- Peter MacCallum Cancer Centre, and Sir Peter MacCallum Department of Oncology, University of Melbourne, VIC, Australia
- Olivia Newton-John Cancer Research Institute, Microscopy Facility and School of Cancer Medicine, La Trobe University, VIC, Australia
| | - Madara Ratnadiwakara
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
- Hudson Institute of Medical Research, VIC, Australia; and
- Department of Molecular and Translational Sciences, Monash University, VIC, Australia
| | - Huimin Cao
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Benjamin Cao
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Chad K Heazlewood
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Brenda Williams
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Madeline Fulton
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | | | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Susan K Nilsson
- Biomedical Manufacturing CSIRO, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
| | - Minna-Liisa Änkö
- Australian Regenerative Medicine Institute, Monash University, VIC, Australia
- Hudson Institute of Medical Research, VIC, Australia; and
- Department of Molecular and Translational Sciences, Monash University, VIC, Australia
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7
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MYCL promotes iPSC-like colony formation via MYC Box 0 and 2 domains. Sci Rep 2021; 11:24254. [PMID: 34930932 PMCID: PMC8688507 DOI: 10.1038/s41598-021-03260-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/01/2021] [Indexed: 11/08/2022] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) can differentiate into cells of the three germ layers and are promising cell sources for regenerative medicine therapies. However, current protocols generate hiPSCs with low efficiency, and the generated iPSCs have variable differentiation capacity among different clones. Our previous study reported that MYC proteins (c-MYC and MYCL) are essential for reprogramming and germline transmission but that MYCL can generate hiPSC colonies more efficiently than c-MYC. The molecular underpinnings for the different reprogramming efficiencies between c-MYC and MYCL, however, are unknown. In this study, we found that MYC Box 0 (MB0) and MB2, two functional domains conserved in the MYC protein family, contribute to the phenotypic differences and promote hiPSC generation in MYCL-induced reprogramming. Proteome analyses suggested that in MYCL-induced reprogramming, cell adhesion-related cytoskeletal proteins are regulated by the MB0 domain, while the MB2 domain regulates RNA processes. These findings provide a molecular explanation for why MYCL has higher reprogramming efficiency than c-MYC.
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8
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Vivori C, Papasaikas P, Stadhouders R, Di Stefano B, Rubio AR, Balaguer CB, Generoso S, Mallol A, Sardina JL, Payer B, Graf T, Valcárcel J. Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1. Genome Biol 2021; 22:171. [PMID: 34082786 PMCID: PMC8173870 DOI: 10.1186/s13059-021-02372-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/05/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Somatic cell reprogramming is the process that allows differentiated cells to revert to a pluripotent state. In contrast to the extensively studied rewiring of epigenetic and transcriptional programs required for reprogramming, the dynamics of post-transcriptional changes and their associated regulatory mechanisms remain poorly understood. Here we study the dynamics of alternative splicing changes occurring during efficient reprogramming of mouse B cells into induced pluripotent stem (iPS) cells and compare them to those occurring during reprogramming of mouse embryonic fibroblasts. RESULTS We observe a significant overlap between alternative splicing changes detected in the two reprogramming systems, which are generally uncoupled from changes in transcriptional levels. Correlation between gene expression of potential regulators and specific clusters of alternative splicing changes enables the identification and subsequent validation of CPSF3 and hnRNP UL1 as facilitators, and TIA1 as repressor of mouse embryonic fibroblasts reprogramming. We further find that these RNA-binding proteins control partially overlapping programs of splicing regulation, involving genes relevant for developmental and morphogenetic processes. CONCLUSIONS Our results reveal common programs of splicing regulation during reprogramming of different cell types and identify three novel regulators of this process and their targets.
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Affiliation(s)
- Claudia Vivori
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: The Francis Crick Institute, 1 Midland Road, London, NW1 1AT UK
| | - Panagiotis Papasaikas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66/Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Ralph Stadhouders
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Departments of Pulmonary Medicine and Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Bruno Di Stefano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Alkek Bldg Room N1020, Houston, TX 77030 USA
| | - Anna Ribó Rubio
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Clara Berenguer Balaguer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Josep Carreras Leukaemia Research Institute, Carretera de Can Ruti, Camí de les Escoles, s/n, 08916 Badalona, Spain
| | - Serena Generoso
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Anna Mallol
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - José Luis Sardina
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Present address: Josep Carreras Leukaemia Research Institute, Carretera de Can Ruti, Camí de les Escoles, s/n, 08916 Badalona, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Thomas Graf
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Carrer del Dr. Aiguader 88, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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9
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Wagner RE, Frye M. Noncanonical functions of the serine-arginine-rich splicing factor (SR) family of proteins in development and disease. Bioessays 2021; 43:e2000242. [PMID: 33554347 DOI: 10.1002/bies.202000242] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/19/2022]
Abstract
Members of the serine/arginine (SR)-rich protein family of splicing factors play versatile roles in RNA processing steps and are often essential for normal development. Dynamic changes in RNA processing and turnover allow fast cellular adaptions to a changing microenvironment and thereby closely cooperate with transcription factor networks that establish cell identity within tissues. SR proteins play fundamental roles in the processing of pre-mRNAs by regulating constitutive and alternative splicing. More recently, SR proteins have also been implicated in other aspects of RNA metabolism such as mRNA stability, transport and translation. The- emerging noncanonical functions highlight the multifaceted functions of these SR proteins and identify them as important coordinators of gene expression programmes. Accordingly, most SR proteins are essential for normal cell function and their misregulation contributes to human diseases such as cancer.
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Affiliation(s)
- Rebecca E Wagner
- German Cancer Research Center - Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Michaela Frye
- German Cancer Research Center - Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
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10
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Senoo M, Hozoji H, Ishikawa-Yamauchi Y, Takijiri T, Ohta S, Ukai T, Kabata M, Yamamoto T, Yamada Y, Ikawa M, Ozawa M. RNA-binding protein Ptbp1 regulates alternative splicing and transcriptome in spermatogonia and maintains spermatogenesis in concert with Nanos3. J Reprod Dev 2020; 66:459-467. [PMID: 32624547 PMCID: PMC7593632 DOI: 10.1262/jrd.2020-060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
PTBP1, a well-conserved RNA-binding protein, regulates cellular development by tuning posttranscriptional mRNA modification such as alternative splicing (AS)
or mRNA stabilization. We previously revealed that the loss of Ptbp1 in spermatogonia causes the dysregulation of spermatogenesis, but the
molecular mechanisms by which PTBP1 regulates spermatogonium homeostasis are unclear. In this study, changes of AS or transcriptome in
Ptbp1-knockout (KO) germline stem cells (GSC), an in vitro model of proliferating spermatogonia, was determined by next
generation sequencing. We identified more than 200 differentially expressed genes, as well as 85 genes with altered AS due to the loss of PTBP1. Surprisingly,
no differentially expressed genes overlapped with different AS genes in Ptbp1-KO GSC. In addition, we observed that the mRNA expression of
Nanos3, an essential gene for normal spermatogenesis, was significantly decreased in Ptbp1-KO spermatogonia. We also
revealed that PTBP1 protein binds to Nanos3 mRNA in spermatogonia. Furthermore,
Nanos3+/−;Ptbp1+/− mice exhibited abnormal spermatogenesis, which resembled the effects of germ
cell-specific Ptbp1 KO, whereas no significant abnormality was observed in mice heterozygous for either gene alone. These data implied that
PTBP1 regulates alternative splicing and transcriptome in spermatogonia under different molecular pathways, and contributes spermatogenesis, at least in part,
in concert with NANOS3.
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Affiliation(s)
- Manami Senoo
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Hiroshi Hozoji
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yu Ishikawa-Yamauchi
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takashi Takijiri
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Sho Ohta
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Tomoyo Ukai
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Mio Kabata
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.,Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto 606-8501, Japan.,AMED-CREST, Tokyo 100-0004, Japan.,Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Yasuhiro Yamada
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Masahito Ikawa
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.,Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Manabu Ozawa
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
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11
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Laaref AM, Manchon L, Bareche Y, Lapasset L, Tazi J. The core spliceosomal factor U2AF1 controls cell-fate determination via the modulation of transcriptional networks. RNA Biol 2020; 17:857-871. [PMID: 32150510 PMCID: PMC7549707 DOI: 10.1080/15476286.2020.1733800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
Alternative splicing (AS) plays a central role during cell-fate determination. However, how the core spliceosomal factors (CSFs) are involved in this process is poorly understood. Here, we report the down-regulation of the U2AF1 CSF during stem cell differentiation. To investigate its function in stemness and differentiation, we downregulated U2AF1 in human induced pluripotent stem cells (hiPSCs), using an inducible-shRNA system, to the level found in differentiated ectodermal, mesodermal and endodermal cells. RNA sequencing and computational analysis reveal that U2AF1 down-regulation modulates the expression of development-regulating genes and regulates transcriptional networks involved in cell-fate determination. Furthermore, U2AF1 down-regulation induces a switch in the AS of transcription factors (TFs) required to establish specific cell lineages, and favours the splicing of a differentiated cell-specific isoform of DNMT3B. Our results showed that the differential expression of the core spliceosomal factor U2AF1, between stem cells and the precursors of the three germ layers regulates a cell-type-specific alternative splicing programme and a transcriptional network involved in cell-fate determination via the modulation of gene expression and alternative splicing of transcription regulators.
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Affiliation(s)
| | | | - Yacine Bareche
- IGMM, CNRS, University of Montpellier, Montpellier, France
- Breast Cancer Translational Research Laboratory, J. C. Heuson, Institut Jules Bordet, Université Libre De Bruxelles, Brussels, Belgium
| | - Laure Lapasset
- IGMM, CNRS, University of Montpellier, Montpellier, France
- VP research, CNRS, University of Montpellier, Montpellier, France
| | - Jamal Tazi
- IGMM, CNRS, University of Montpellier, Montpellier, France
- Lead Contact
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12
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Chua BA, Van Der Werf I, Jamieson C, Signer RAJ. Post-Transcriptional Regulation of Homeostatic, Stressed, and Malignant Stem Cells. Cell Stem Cell 2020; 26:138-159. [PMID: 32032524 PMCID: PMC7158223 DOI: 10.1016/j.stem.2020.01.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cellular identity is not driven by differences in genomic content but rather by epigenomic, transcriptomic, and proteomic heterogeneity. Although regulation of the epigenome plays a key role in shaping stem cell hierarchies, differential expression of transcripts only partially explains protein abundance. The epitranscriptome, translational control, and protein degradation have emerged as fundamental regulators of proteome complexity that regulate stem cell identity and function. Here, we discuss how post-transcriptional mechanisms enable stem cell homeostasis and responsiveness to developmental cues and environmental stressors by rapidly shaping the content of their proteome and how these processes are disrupted in pre-malignant and malignant states.
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Affiliation(s)
- Bernadette A Chua
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093 USA
| | - Inge Van Der Werf
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093 USA; Sanford Stem Cell Clinical Center, La Jolla, CA 92037, USA
| | - Catriona Jamieson
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093 USA; Sanford Stem Cell Clinical Center, La Jolla, CA 92037, USA.
| | - Robert A J Signer
- Division of Regenerative Medicine, Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093 USA.
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13
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Brumbaugh J, Di Stefano B, Hochedlinger K. Reprogramming: identifying the mechanisms that safeguard cell identity. Development 2019; 146:146/23/dev182170. [PMID: 31792064 DOI: 10.1242/dev.182170] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Development and homeostasis rely upon concerted regulatory pathways to establish the specialized cell types needed for tissue function. Once a cell type is specified, the processes that restrict and maintain cell fate are equally important in ensuring tissue integrity. Over the past decade, several approaches to experimentally reprogram cell fate have emerged. Importantly, efforts to improve and understand these approaches have uncovered novel molecular determinants that reinforce lineage commitment and help resist cell fate changes. In this Review, we summarize recent studies that have provided insights into the various chromatin factors, post-transcriptional processes and features of genomic organization that safeguard cell identity in the context of reprogramming to pluripotency. We also highlight how these factors function in other experimental, physiological and pathological cell fate transitions, including direct lineage conversion, pluripotency-to-totipotency reversion and cancer.
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Affiliation(s)
- Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.,Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA .,Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.,Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
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14
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Kanitz A, Syed AP, Kaji K, Zavolan M. Conserved regulation of RNA processing in somatic cell reprogramming. BMC Genomics 2019; 20:100. [PMID: 30704403 PMCID: PMC6357513 DOI: 10.1186/s12864-019-5438-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at the level of RNA processing. These include the expression of specific transcript isoforms and 3' untranslated regions. A number of studies have uncovered RNA processing factors that modulate the efficiency of the reprogramming process. However, a comprehensive evaluation of the involvement of RNA processing factors in the reprogramming of somatic mammalian cells is lacking. RESULTS Here, we used data from a large number of studies carried out in three mammalian species, mouse, chimpanzee and human, to uncover consistent changes in gene expression upon reprogramming of somatic cells. We found that a core set of nine splicing factors have consistent changes across the majority of data sets in all three species. Most striking among these are ESRP1 and ESRP2, which accelerate and enhance the efficiency of somatic cell reprogramming by promoting isoform expression changes associated with mesenchymal-to-epithelial transition. We further identify genes and processes in which splicing changes are observed in both human and mouse. CONCLUSIONS Our results provide a general resource for gene expression and splicing changes that take place during somatic cell reprogramming. Furthermore, they support the concept that splicing factors with evolutionarily conserved, cell type-specific expression can modulate the efficiency of the process by reinforcing intermediate states resembling the cell types in which these factors are normally expressed.
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Affiliation(s)
- Alexander Kanitz
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Afzal Pasha Syed
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Keisuke Kaji
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
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15
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Senoo M, Takijiri T, Yoshida N, Ozawa M, Ikawa M. PTBP1 contributes to spermatogenesis through regulation of proliferation in spermatogonia. J Reprod Dev 2018; 65:37-46. [PMID: 30416150 PMCID: PMC6379764 DOI: 10.1262/jrd.2018-109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) is a highly conserved RNA-binding protein that is a well-known regulator of alternative splicing. Testicular tissue is one of the richest
tissues with respect to the number of alternative splicing mRNA isoforms, but the molecular role(s) of PTBP1 in the regulation of these isoforms during spermatogenesis is still unclear.
Here, we developed a germ cell–specific Ptbp1 conditional knockout (cKO) mouse model by using the Cre-loxP system to investigate the role of PTBP1 in spermatogenesis. Testis
weight in Ptbp1 cKO mice was comparable to that in age-matched controls until 3 weeks of age; at ≥ 2 months old, testis weight was significantly lighter in cKO mice than in
age-matched controls. Sperm count in Ptbp1 cKO mice at 2 months old was comparable to that in controls, whereas sperm count significantly decreased at 6 months old.
Seminiferous tubules that exhibited degeneration in spermatogenic function were more evident in the 2-month-old Ptbp1 cKO mice than in controls. In addition, the early
neonatal proliferation of spermatogonia, during postnatal days 1–5, was significantly retarded in Ptbp1 cKO mice compared with that in controls. An in vitro
spermatogonia culture model (germline stem cells) revealed that hydroxytamoxifen-induced deletion of PTBP1 from germline stem cells caused severe proliferation arrest accompanied by an
increase of apoptotic cell death. These data suggest that PTBP1 contributes to spermatogenesis through regulation of spermatogonia proliferation.
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Affiliation(s)
- Manami Senoo
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan.,Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Takashi Takijiri
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108-8639, Japan.,Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Nobuaki Yoshida
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Manabu Ozawa
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Masahito Ikawa
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.,Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
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16
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Culjkovic-Kraljacic B, Borden KLB. The Impact of Post-transcriptional Control: Better Living Through RNA Regulons. Front Genet 2018; 9:512. [PMID: 30455716 PMCID: PMC6230556 DOI: 10.3389/fgene.2018.00512] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022] Open
Abstract
Traditionally, cancer is viewed as a disease driven by genetic mutations and/or epigenetic and transcriptional dysregulation. While these are undoubtedly important drivers, many recent studies highlight the disconnect between the proteome and the genome or transcriptome. At least in part, this disconnect arises as a result of dysregulated RNA metabolism which underpins the altered proteomic landscape observed. Thus, it is important to understand the basic mechanisms governing post-transcriptional control and how these processes can be co-opted to drive cancer cell phenotypes. In some cases, groups of mRNAs that encode protein involved in specific oncogenic processes can be co-regulated at multiple processing levels in order to turn on entire biochemical pathways. Indeed, the RNA regulon model was postulated as a means to understand how cells coordinately regulate transcripts encoding proteins in the same biochemical pathways. In this review, we describe some of the basic mRNA processes that are dysregulated in cancer and the biological impact this has on the cell. This dysregulation can affect networks of RNAs simultaneously thereby underpinning the oncogenic phenotypes observed.
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Affiliation(s)
- Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer, Department of Pathology and Cell Biology, University of Montreal, Montreal, QC, Canada
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17
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Ito Y, Nakamura S, Sugimoto N, Shigemori T, Kato Y, Ohno M, Sakuma S, Ito K, Kumon H, Hirose H, Okamoto H, Nogawa M, Iwasaki M, Kihara S, Fujio K, Matsumoto T, Higashi N, Hashimoto K, Sawaguchi A, Harimoto KI, Nakagawa M, Yamamoto T, Handa M, Watanabe N, Nishi E, Arai F, Nishimura S, Eto K. Turbulence Activates Platelet Biogenesis to Enable Clinical Scale Ex Vivo Production. Cell 2018; 174:636-648.e18. [PMID: 30017246 DOI: 10.1016/j.cell.2018.06.011] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 03/30/2018] [Accepted: 05/23/2018] [Indexed: 12/14/2022]
Abstract
The ex vivo generation of platelets from human-induced pluripotent cells (hiPSCs) is expected to compensate donor-dependent transfusion systems. However, manufacturing the clinically required number of platelets remains unachieved due to the low platelet release from hiPSC-derived megakaryocytes (hiPSC-MKs). Here, we report turbulence as a physical regulator in thrombopoiesis in vivo and its application to turbulence-controllable bioreactors. The identification of turbulent energy as a determinant parameter allowed scale-up to 8 L for the generation of 100 billion-order platelets from hiPSC-MKs, which satisfies clinical requirements. Turbulent flow promoted the release from megakaryocytes of IGFBP2, MIF, and Nardilysin to facilitate platelet shedding. hiPSC-platelets showed properties of bona fide human platelets, including circulation and hemostasis capacities upon transfusion in two animal models. This study provides a concept in which a coordinated physico-chemical mechanism promotes platelet biogenesis and an innovative strategy for ex vivo platelet manufacturing.
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Affiliation(s)
- Yukitaka Ito
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Kyoto Development Center, Megakaryon Corporation, Kyoto, Japan
| | - Sou Nakamura
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Naoshi Sugimoto
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | | | - Yoshikazu Kato
- Mixing Technology Laboratory, SATAKE Chemical Equipment Manufacturing Ltd., Saitama, Japan
| | - Mikiko Ohno
- Department of Pharmacology, Shiga University of Medical Science, Otsu, Japan
| | - Shinya Sakuma
- Department of Micro-Nano Systems Engineering, Nagoya University, Nagoya, Japan
| | - Keitaro Ito
- Department of Micro-Nano Systems Engineering, Nagoya University, Nagoya, Japan
| | - Hiroki Kumon
- Department of Micro-Nano Systems Engineering, Nagoya University, Nagoya, Japan
| | - Hidenori Hirose
- Kyoto Development Center, Megakaryon Corporation, Kyoto, Japan
| | - Haruki Okamoto
- Kyoto Development Center, Megakaryon Corporation, Kyoto, Japan
| | - Masayuki Nogawa
- Center for Transfusion Medicine and Cell Therapy, Keio University School of Medicine, Tokyo, Japan
| | - Mio Iwasaki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shunsuke Kihara
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kosuke Fujio
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Takuya Matsumoto
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Natsumi Higashi
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kazuya Hashimoto
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Akira Sawaguchi
- Department of Anatomy, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Ken-Ichi Harimoto
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Masato Nakagawa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; AMED-CREST, AMED, Tokyo, Japan
| | - Makoto Handa
- Center for Transfusion Medicine and Cell Therapy, Keio University School of Medicine, Tokyo, Japan
| | - Naohide Watanabe
- Center for Transfusion Medicine and Cell Therapy, Keio University School of Medicine, Tokyo, Japan
| | - Eiichiro Nishi
- Department of Pharmacology, Shiga University of Medical Science, Otsu, Japan
| | - Fumihito Arai
- Department of Micro-Nano Systems Engineering, Nagoya University, Nagoya, Japan
| | - Satoshi Nishimura
- Center for Molecular Medicine, Jichi Medical University, Tochigi, Japan
| | - Koji Eto
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Department of Regenerative Medicine, Chiba University Graduate School of Medicine, Chiba, Japan.
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18
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Ratnadiwakara M, Archer SK, Dent CI, Ruiz De Los Mozos I, Beilharz TH, Knaupp AS, Nefzger CM, Polo JM, Anko ML. SRSF3 promotes pluripotency through Nanog mRNA export and coordination of the pluripotency gene expression program. eLife 2018; 7:37419. [PMID: 29741478 PMCID: PMC5963917 DOI: 10.7554/elife.37419] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 05/05/2018] [Indexed: 12/28/2022] Open
Abstract
The establishment and maintenance of pluripotency depend on precise coordination of gene expression. We establish serine-arginine-rich splicing factor 3 (SRSF3) as an essential regulator of RNAs encoding key components of the mouse pluripotency circuitry, SRSF3 ablation resulting in the loss of pluripotency and its overexpression enhancing reprogramming. Strikingly, SRSF3 binds to the core pluripotency transcription factor Nanog mRNA to facilitate its nucleo-cytoplasmic export independent of splicing. In the absence of SRSF3 binding, Nanog mRNA is sequestered in the nucleus and protein levels are severely downregulated. Moreover, SRSF3 controls the alternative splicing of the export factor Nxf1 and RNA regulators with established roles in pluripotency, and the steady-state levels of mRNAs encoding chromatin modifiers. Our investigation links molecular events to cellular functions by demonstrating how SRSF3 regulates the pluripotency genes and uncovers SRSF3-RNA interactions as a critical means to coordinate gene expression during reprogramming, stem cell self-renewal and early development.
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Affiliation(s)
- Madara Ratnadiwakara
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Stuart K Archer
- Bioinformatics Platform, Monash University, Clayton, Australia
| | - Craig I Dent
- School of Biological Sciences, Monash University, Melbourne, Australia
| | | | - Traude H Beilharz
- Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Anja S Knaupp
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
| | - Minna-Liisa Anko
- Department of Anatomy and Developmental Biology, Monash University, Melbourne, Australia.,Biomedicine Discovery Institute, Development and Stem Cells Program, Monash University, Melbourne, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Australia
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19
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A Loss of Function Screen of Epigenetic Modifiers and Splicing Factors during Early Stage of Cardiac Reprogramming. Stem Cells Int 2018; 2018:3814747. [PMID: 29743891 PMCID: PMC5878887 DOI: 10.1155/2018/3814747] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 12/04/2017] [Indexed: 02/07/2023] Open
Abstract
Direct reprogramming of cardiac fibroblasts (CFs) to induced cardiomyocytes (iCMs) is a newly emerged promising approach for cardiac regeneration, disease modeling, and drug discovery. However, its potential has been drastically limited due to the low reprogramming efficiency and largely unknown underlying molecular mechanisms. We have previously screened and identified epigenetic factors related to histone modification during iCM reprogramming. Here, we used shRNAs targeting an additional battery of epigenetic factors involved in chromatin remodeling and RNA splicing factors to further identify inhibitors and facilitators of direct cardiac reprogramming. Knockdown of RNA splicing factors Sf3a1 or Sf3b1 significantly reduced the percentage and total number of cardiac marker positive iCMs accompanied with generally repressed gene expression. Removal of another RNA splicing factor Zrsr2 promoted the acquisition of CM molecular features in CFs and mouse embryonic fibroblasts (MEFs) at both protein and mRNA levels. Moreover, a consistent increase of reprogramming efficiency was observed in CFs and MEFs treated with shRNAs targeting Bcor (component of BCOR complex superfamily) or Stag2 (component of cohesin complex). Our work thus reveals several additional epigenetic and splicing factors that are either inhibitory to or required for iCM reprogramming and highlights the importance of epigenetic regulation and RNA splicing process during cell fate conversion.
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20
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Zhou J, Ma S, Wang D, Zeng J, Jiang T. FreePSI: an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome. Nucleic Acids Res 2018; 46:e11. [PMID: 29136203 PMCID: PMC5778508 DOI: 10.1093/nar/gkx1059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 10/19/2017] [Indexed: 11/19/2022] Open
Abstract
Alternative splicing plays an important role in many cellular processes of eukaryotic organisms. The exon-inclusion ratio, also known as percent spliced in, is often regarded as one of the most effective measures of alternative splicing events. The existing methods for estimating exon-inclusion ratios at the genome scale all require the existence of a reference transcriptome. In this paper, we propose an alignment-free method, FreePSI, to perform genome-wide estimation of exon-inclusion ratios from RNA-Seq data without relying on the guidance of a reference transcriptome. It uses a novel probabilistic generative model based on k-mer profiles to quantify the exon-inclusion ratios at the genome scale and an efficient expectation-maximization algorithm based on a divide-and-conquer strategy and ultrafast conjugate gradient projection descent method to solve the model. We compare FreePSI with the existing methods on simulated and real RNA-seq data in terms of both accuracy and efficiency and show that it is able to achieve very good performance even though a reference transcriptome is not provided. Our results suggest that FreePSI may have important applications in performing alternative splicing analysis for organisms that do not have quality reference transcriptomes. FreePSI is implemented in C++ and freely available to the public on GitHub.
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Affiliation(s)
- Jianyu Zhou
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China.,Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China
| | - Shining Ma
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Dongfang Wang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, China
| | - Tao Jiang
- MOE Key Laboratory of Bioinformatics; Bioinformatics Division and Center for Synthetic & Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China.,Department of Computer Science and Technology, Tsinghua University, Beijing 100084, China.,Department of Computer Science and Engineering, University of California, Riverside, CA 92521, USA
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21
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Zavolan M, Kanitz A. RNA splicing and its connection with other regulatory layers in somatic cell reprogramming. Curr Opin Cell Biol 2017; 52:8-13. [PMID: 29275148 DOI: 10.1016/j.ceb.2017.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/05/2017] [Accepted: 12/11/2017] [Indexed: 01/30/2023]
Abstract
Understanding how cell identity is established and maintained is one of the most exciting challenges of molecular biology today. Recent work has added a conserved layer of RNA splicing and other post-transcriptional regulatory processes to the transcriptional and epigenetic networks already known to cooperate in the establishment and maintenance of cell identity. Here we summarize these findings, highlighting specifically the multitude of splicing factors that can modulate the efficiency of somatic cell reprogramming. Distinct patterns of gene expression dynamics of these factors during reprogramming suggest that further improvements in efficiency could be obtained through optimal timing of overexpression or knockdown of individual regulators.
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Affiliation(s)
- Mihaela Zavolan
- RNA Regulatory Networks, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland; Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.
| | - Alexander Kanitz
- RNA Regulatory Networks, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland; Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
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22
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Han H, Braunschweig U, Gonatopoulos-Pournatzis T, Weatheritt RJ, Hirsch CL, Ha KCH, Radovani E, Nabeel-Shah S, Sterne-Weiler T, Wang J, O'Hanlon D, Pan Q, Ray D, Zheng H, Vizeacoumar F, Datti A, Magomedova L, Cummins CL, Hughes TR, Greenblatt JF, Wrana JL, Moffat J, Blencowe BJ. Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors. Mol Cell 2017; 65:539-553.e7. [PMID: 28157508 DOI: 10.1016/j.molcel.2017.01.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 11/16/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022]
Abstract
Networks of coordinated alternative splicing (AS) events play critical roles in development and disease. However, a comprehensive knowledge of the factors that regulate these networks is lacking. We describe a high-throughput system for systematically linking trans-acting factors to endogenous RNA regulatory events. Using this system, we identify hundreds of factors associated with diverse regulatory layers that positively or negatively control AS events linked to cell fate. Remarkably, more than one-third of the regulators are transcription factors. Further analyses of the zinc finger protein Zfp871 and BTB/POZ domain transcription factor Nacc1, which regulate neural and stem cell AS programs, respectively, reveal roles in controlling the expression of specific splicing regulators. Surprisingly, these proteins also appear to regulate target AS programs via binding RNA. Our results thus uncover a large "missing cache" of splicing regulators among annotated transcription factors, some of which dually regulate AS through direct and indirect mechanisms.
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Affiliation(s)
- Hong Han
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | | | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Calley L Hirsch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Kevin C H Ha
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ernest Radovani
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Juli Wang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Dave O'Hanlon
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Qun Pan
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frederick Vizeacoumar
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Alessandro Datti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Lilia Magomedova
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Carolyn L Cummins
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jeffrey L Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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23
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Abstract
Alternative splicing (AS) greatly expands the coding capacities of genomes by allowing the generation of multiple mature mRNAs from a limited number of genes. Although the massive switch in AS profiles that often accompanies variations in gene expression patterns occurring during cell differentiation has been characterized for a variety of models, their causes and mechanisms remain largely unknown. Here, we integrate foundational and recent studies indicating the AS switches that govern the processes of cell fate determination. We include some distinct AS events in pluripotent cells and somatic reprogramming and discuss new progresses on alternative isoform expression in adipogenesis, myogenic differentiation and stimulation of immune cells. Finally, we cover novel insights on AS mechanisms during neuronal differentiation, paying special attention to the role of chromatin structure.
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Affiliation(s)
- Ana Fiszbein
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
| | - Alberto R Kornblihtt
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
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24
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EMT and stemness: flexible processes tuned by alternative splicing in development and cancer progression. Mol Cancer 2017; 16:8. [PMID: 28137272 PMCID: PMC5282733 DOI: 10.1186/s12943-016-0579-2] [Citation(s) in RCA: 198] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 12/25/2016] [Indexed: 12/17/2022] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is associated with metastasis formation as well as with generation and maintenance of cancer stem cells. In this way, EMT contributes to tumor invasion, heterogeneity and chemoresistance. Morphological and functional changes involved in these processes require robust reprogramming of gene expression, which is only partially accomplished at the transcriptional level. Alternative splicing is another essential layer of gene expression regulation that expands the cell proteome. This step in post-transcriptional regulation of gene expression tightly controls cell identity between epithelial and mesenchymal states and during stem cell differentiation. Importantly, dysregulation of splicing factor function and cancer-specific splicing isoform expression frequently occurs in human tumors, suggesting the importance of alternative splicing regulation for cancer biology. In this review, we briefly discuss the role of EMT programs in development, stem cell differentiation and cancer progression. Next, we focus on selected examples of key factors involved in EMT and stem cell differentiation that are regulated post-transcriptionally through alternative splicing mechanisms. Lastly, we describe relevant oncogenic splice-variants that directly orchestrate cancer stem cell biology and tumor EMT, which may be envisioned as novel targets for therapeutic intervention.
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25
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Vazquez-Arango P, Vowles J, Browne C, Hartfield E, Fernandes H, Mandefro B, Sareen D, James W, Wade-Martins R, Cowley SA, Murphy S, O'Reilly D. Variant U1 snRNAs are implicated in human pluripotent stem cell maintenance and neuromuscular disease. Nucleic Acids Res 2016; 44:10960-10973. [PMID: 27536002 PMCID: PMC5159530 DOI: 10.1093/nar/gkw711] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 02/06/2023] Open
Abstract
The U1 small nuclear (sn)RNA (U1) is a multifunctional ncRNA, known for its pivotal role in pre-mRNA splicing and regulation of RNA 3' end processing events. We recently demonstrated that a new class of human U1-like snRNAs, the variant (v)U1 snRNAs (vU1s), also participate in pre-mRNA processing events. In this study, we show that several human vU1 genes are specifically upregulated in stem cells and participate in the regulation of cell fate decisions. Significantly, ectopic expression of vU1 genes in human skin fibroblasts leads to increases in levels of key pluripotent stem cell mRNA markers, including NANOG and SOX2. These results reveal an important role for vU1s in the control of key regulatory networks orchestrating the transitions between stem cell maintenance and differentiation. Moreover, vU1 expression varies inversely with U1 expression during differentiation and cell re-programming and this pattern of expression is specifically de-regulated in iPSC-derived motor neurons from Spinal Muscular Atrophy (SMA) type 1 patient's. Accordingly, we suggest that an imbalance in the vU1/U1 ratio, rather than an overall reduction in Uridyl-rich (U)-snRNAs, may contribute to the specific neuromuscular disease phenotype associated with SMA.
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Affiliation(s)
- Pilar Vazquez-Arango
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
| | - Jane Vowles
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK,Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Cathy Browne
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
| | - Elizabeth Hartfield
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK,Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Hugo J. R. Fernandes
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK,Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Berhan Mandefro
- Cedars-Sinai Medical Center, Board of Governors-Regenerative Medicine Institute and Department of Biomedical Sciences, 8700 Beverly Blvd, AHSP A8418, Los Angeles, CA 90048, USA,iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Dhruv Sareen
- Cedars-Sinai Medical Center, Board of Governors-Regenerative Medicine Institute and Department of Biomedical Sciences, 8700 Beverly Blvd, AHSP A8418, Los Angeles, CA 90048, USA,iPSC Core, The David and Janet Polak Foundation Stem Cell Core Laboratory, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - William James
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK,Oxford Parkinson's Disease Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Sally A. Cowley
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK,Oxford Parkinson's Disease Centre, University of Oxford, Oxford, UK
| | - Shona Murphy
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
| | - Dawn O'Reilly
- University of Oxford, Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK
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26
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Hirsch CL, Wrana JL, Dent SYR. KATapulting toward Pluripotency and Cancer. J Mol Biol 2016; 429:1958-1977. [PMID: 27720985 DOI: 10.1016/j.jmb.2016.09.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/30/2016] [Indexed: 12/20/2022]
Abstract
Development is generally regarded as a unidirectional process that results in the acquisition of specialized cell fates. During this process, cellular identity is precisely defined by signaling cues that tailor the chromatin landscape for cell-specific gene expression programs. Once established, these pathways and cell states are typically resistant to disruption. However, loss of cell identity occurs during tumor initiation and upon injury response. Moreover, terminally differentiated cells can be experimentally provoked to become pluripotent. Chromatin reorganization is key to the establishment of new gene expression signatures and thus new cell identity. Here, we explore an emerging concept that lysine acetyltransferase (KAT) enzymes drive cellular plasticity in the context of somatic cell reprogramming and tumorigenesis.
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Affiliation(s)
- Calley L Hirsch
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada.
| | - Jeffrey L Wrana
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Sharon Y R Dent
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, USA.
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27
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Cellular Functions and Gene and Protein Expression Profiles in Endothelial Cells Derived from Moyamoya Disease-Specific iPS Cells. PLoS One 2016; 11:e0163561. [PMID: 27662211 PMCID: PMC5035048 DOI: 10.1371/journal.pone.0163561] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 09/11/2016] [Indexed: 01/16/2023] Open
Abstract
Background and purpose Moyamoya disease (MMD) is a slow, progressive steno-occlusive disease, arising in the terminal portions of the cerebral internal carotid artery. However, the functions and characteristics of the endothelial cells (ECs) in MMD are unknown. We analyzed these features using induced pluripotent stem cell (iPSC)-derived ECs. Methods iPSC lines were established from the peripheral blood of three patients with MMD carrying the variant RNF213 R4810K, and three healthy persons used as controls. After the endothelial differentiation of iPSCs, CD31+CD144+ cells were purified as ECs using a cell sorter. We analyzed their proliferation, angiogenesis, and responses to some angiogenic factors, namely VEGF, bFGF, TGF-β, and BMP4. The ECs were also analyzed using DNA microarray and proteomics to perform comprehensive gene and protein expression analysis. Results Angiogenesis was significantly impaired in MMD regardless of the presence of any angiogenic factor. On the contrary, endothelial proliferation was not significant between control- and MMD-derived cells. Regarding DNA microarray, pathway analysis illustrated that extracellular matrix (ECM) receptor-related genes, including integrin β3, were significantly downregulated in MMD. Proteomic analysis revealed that cytoskeleton-related proteins were downregulated and splicing regulation-related proteins were upregulated in MMD. Conclusions Downregulation of ECM receptor-related genes may be associated with impaired angiogenic activity in ECs derived from iPSCs from patients with MMD. Upregulation of splicing regulation-related proteins implied differences in splicing patterns between control and MMD ECs.
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28
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A developmental coordinate of pluripotency among mice, monkeys and humans. Nature 2016; 537:57-62. [DOI: 10.1038/nature19096] [Citation(s) in RCA: 312] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 07/12/2016] [Indexed: 12/22/2022]
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29
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Solana J, Irimia M, Ayoub S, Orejuela MR, Zywitza V, Jens M, Tapial J, Ray D, Morris Q, Hughes TR, Blencowe BJ, Rajewsky N. Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians. eLife 2016; 5. [PMID: 27502555 PMCID: PMC4978528 DOI: 10.7554/elife.16797] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/07/2016] [Indexed: 12/11/2022] Open
Abstract
In contrast to transcriptional regulation, the function of alternative splicing (AS) in stem cells is poorly understood. In mammals, MBNL proteins negatively regulate an exon program specific of embryonic stem cells; however, little is known about the in vivo significance of this regulation. We studied AS in a powerful in vivo model for stem cell biology, the planarian Schmidtea mediterranea. We discover a conserved AS program comprising hundreds of alternative exons, microexons and introns that is differentially regulated in planarian stem cells, and comprehensively identify its regulators. We show that functional antagonism between CELF and MBNL factors directly controls stem cell-specific AS in planarians, placing the origin of this regulatory mechanism at the base of Bilaterians. Knockdown of CELF or MBNL factors lead to abnormal regenerative capacities by affecting self-renewal and differentiation sets of genes, respectively. These results highlight the importance of AS interactions in stem cell regulation across metazoans. DOI:http://dx.doi.org/10.7554/eLife.16797.001 Stem cells are specialized cells found in all animals that can develop into several different types of mature cells. Stem cells are therefore well suited for maintaining organs that are in heavy use, such as the intestine, and for regenerating tissues that are prone to injury, like the skin. One reason why stem cells differ from mature cell types is because they activate, or “express”, different sets of genes. In addition, many genes can be expressed as one of several versions. These variants, also known as isoforms, are generated by a process called alternative splicing. In mature cells in mammals, a group of proteins called the MBNL proteins help to prevent the expression of gene isoforms that are characteristic to stem cells. The adult flatworm Schmidtea mediterranea contains stem cells that can regenerate any part of the body. Solana, Irimia et al. have now investigated whether alternative splicing is important for controlling how the worm’s stem cells behave. After establishing which gene isoforms are expressed in the stem cells and the mature cells, the levels of different sets of proteins that control alternative splicing were experimentally reduced. The results indicate that just as seen in mammals, the MBNL proteins reduce the expression of stem cell-related gene isoforms in the flatworms. Furthermore, Solana, Irimia et al. found that another protein called CELF counteracts MBNL proteins by helping to express gene isoforms that are active in stem cells. The interplay between the MBNL and CELF proteins has also been observed in human cells. Thus, it appears that this way of controlling alternative splicing is common to flatworms and mammals and is therefore evolutionarily ancient. This suggests that other similar ways of controlling stem cells by interactions between regulatory proteins might be working in all animal stem cells. Further studies are now needed to investigate these control proteins. DOI:http://dx.doi.org/10.7554/eLife.16797.002
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Affiliation(s)
- Jordi Solana
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Salah Ayoub
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marta Rodriguez Orejuela
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Vera Zywitza
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Marvin Jens
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Javier Tapial
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Quaid Morris
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
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30
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Lin J, Hu Y, Nunez S, Foulkes AS, Cieply B, Xue C, Gerelus M, Li W, Zhang H, Rader DJ, Musunuru K, Li M, Reilly MP. Transcriptome-Wide Analysis Reveals Modulation of Human Macrophage Inflammatory Phenotype Through Alternative Splicing. Arterioscler Thromb Vasc Biol 2016; 36:1434-47. [PMID: 27230130 PMCID: PMC4919157 DOI: 10.1161/atvbaha.116.307573] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/17/2016] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Human macrophages can shift phenotype across the inflammatory M1 and reparative M2 spectrum in response to environmental challenges, but the mechanisms promoting inflammatory and cardiometabolic disease-associated M1 phenotypes remain incompletely understood. Alternative splicing (AS) is emerging as an important regulator of cellular function, yet its role in macrophage activation is largely unknown. We investigated the extent to which AS occurs in M1 activation within the cardiometabolic disease context and validated a functional genomic cell model for studying human macrophage-related AS events. APPROACH AND RESULTS From deep RNA-sequencing of resting, M1, and M2 primary human monocyte-derived macrophages, we found 3860 differentially expressed genes in M1 activation and detected 233 M1-induced AS events; the majority of AS events were cell- and M1-specific with enrichment for pathways relevant to macrophage inflammation. Using genetic variant data for 10 cardiometabolic traits, we identified 28 trait-associated variants within the genomic loci of 21 alternatively spliced genes and 15 variants within 7 differentially expressed regulatory splicing factors in M1 activation. Knockdown of 1 such splicing factor, CELF1, in primary human macrophages led to increased inflammatory response to M1 stimulation, demonstrating CELF1's potential modulation of the M1 phenotype. Finally, we demonstrated that an induced pluripotent stem cell-derived macrophage system recapitulates M1-associated AS events and provides a high-fidelity macrophage AS model. CONCLUSIONS AS plays a role in defining macrophage phenotype in a cell- and stimulus-specific fashion. Alternatively spliced genes and splicing factors with trait-associated variants may reveal novel pathways and targets in cardiometabolic diseases.
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Affiliation(s)
- Jennie Lin
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.).
| | - Yu Hu
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Sara Nunez
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Andrea S Foulkes
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Benjamin Cieply
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Chenyi Xue
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Mark Gerelus
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Wenjun Li
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Hanrui Zhang
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Daniel J Rader
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Kiran Musunuru
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Mingyao Li
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Muredach P Reilly
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.).
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Toh CX, Chan JW, Chong ZS, Wang H, Guo H, Satapathy S, Ma D, Goh G, Khattar E, Yang L, Tergaonkar V, Chang YT, Collins J, Daley G, Wee K, Farran CEL, Li H, Lim YP, Bard F, Loh YH. RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming. Cell Rep 2016; 15:2597-607. [DOI: 10.1016/j.celrep.2016.05.049] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/03/2016] [Accepted: 05/11/2016] [Indexed: 01/02/2023] Open
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Xu Y, Zhang M, Li W, Zhu X, Bao X, Qin B, Hutchins AP, Esteban MA. Transcriptional Control of Somatic Cell Reprogramming. Trends Cell Biol 2016; 26:272-288. [DOI: 10.1016/j.tcb.2015.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 12/07/2015] [Accepted: 12/16/2015] [Indexed: 01/26/2023]
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Cieply B, Park JW, Nakauka-Ddamba A, Bebee TW, Guo Y, Shang X, Lengner CJ, Xing Y, Carstens RP. Multiphasic and Dynamic Changes in Alternative Splicing during Induction of Pluripotency Are Coordinated by Numerous RNA-Binding Proteins. Cell Rep 2016; 15:247-55. [PMID: 27050523 DOI: 10.1016/j.celrep.2016.03.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 12/17/2015] [Accepted: 03/04/2016] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing (AS) plays a critical role in cell fate transitions, development, and disease. Recent studies have shown that AS also influences pluripotency and somatic cell reprogramming. We profiled transcriptome-wide AS changes that occur during reprogramming of fibroblasts to pluripotency. This analysis revealed distinct phases of AS, including a splicing program that is unique to transgene-independent induced pluripotent stem cells (iPSCs). Changes in the expression of AS factors Zcchc24, Esrp1, Mbnl1/2, and Rbm47 were demonstrated to contribute to phase-specific AS. RNA-binding motif enrichment analysis near alternatively spliced exons provided further insight into the combinatorial regulation of AS during reprogramming by different RNA-binding proteins. Ectopic expression of Esrp1 enhanced reprogramming, in part by modulating the AS of the epithelial specific transcription factor Grhl1. These data represent a comprehensive temporal analysis of the dynamic regulation of AS during the acquisition of pluripotency.
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Affiliation(s)
- Benjamin Cieply
- Department of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Juw Won Park
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40292, USA; KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
| | - Angela Nakauka-Ddamba
- Department of Biomedical Sciences and Institute for Regenerative Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas W Bebee
- Department of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yang Guo
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; School of Computer Science, Northwestern Polytechnical University, Xian 710072, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xian 710072, China
| | - Christopher J Lengner
- Department of Biomedical Sciences and Institute for Regenerative Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Russ P Carstens
- Department of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Ajiro M, Jia R, Yang Y, Zhu J, Zheng ZM. A genome landscape of SRSF3-regulated splicing events and gene expression in human osteosarcoma U2OS cells. Nucleic Acids Res 2015; 44:1854-70. [PMID: 26704980 PMCID: PMC4770227 DOI: 10.1093/nar/gkv1500] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 12/11/2015] [Indexed: 02/07/2023] Open
Abstract
Alternative RNA splicing is an essential process to yield proteomic diversity in eukaryotic cells, and aberrant splicing is often associated with numerous human diseases and cancers. We recently described serine/arginine-rich splicing factor 3 (SRSF3 or SRp20) being a proto-oncogene. However, the SRSF3-regulated splicing events responsible for its oncogenic activities remain largely unknown. By global profiling of the SRSF3-regulated splicing events in human osteosarcoma U2OS cells, we found that SRSF3 regulates the expression of 60 genes including ERRFI1, ANXA1 and TGFB2, and 182 splicing events in 164 genes, including EP300, PUS3, CLINT1, PKP4, KIF23, CHK1, SMC2, CKLF, MAP4, MBNL1, MELK, DDX5, PABPC1, MAP4K4, Sp1 and SRSF1, which are primarily associated with cell proliferation or cell cycle. Two SRSF3-binding motifs, CCAGC(G)C and A(G)CAGCA, are enriched to the alternative exons. An SRSF3-binding site in the EP300 exon 14 is essential for exon 14 inclusion. We found that the expression of SRSF1 and SRSF3 are mutually dependent and coexpressed in normal and tumor tissues/cells. SRSF3 also significantly regulates the expression of at least 20 miRNAs, including a subset of oncogenic or tumor suppressive miRNAs. These data indicate that SRSF3 affects a global change of gene expression to maintain cell homeostasis.
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Affiliation(s)
- Masahiko Ajiro
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Rong Jia
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yanqin Yang
- DNA Sequencing and Genomics Core, System Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jun Zhu
- DNA Sequencing and Genomics Core, System Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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35
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Naftelberg S, Schor IE, Ast G, Kornblihtt AR. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem 2015; 84:165-98. [PMID: 26034889 DOI: 10.1146/annurev-biochem-060614-034242] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative precursor messenger RNA (pre-mRNA) splicing plays a pivotal role in the flow of genetic information from DNA to proteins by expanding the coding capacity of genomes. Regulation of alternative splicing is as important as regulation of transcription to determine cell- and tissue-specific features, normal cell functioning, and responses of eukaryotic cells to external cues. Its importance is confirmed by the evolutionary conservation and diversification of alternative splicing and the fact that its deregulation causes hereditary disease and cancer. This review discusses the multiple layers of cotranscriptional regulation of alternative splicing in which chromatin structure, DNA methylation, histone marks, and nucleosome positioning play a fundamental role in providing a dynamic scaffold for interactions between the splicing and transcription machineries. We focus on evidence for how the kinetics of RNA polymerase II (RNAPII) elongation and the recruitment of splicing factors and adaptor proteins to chromatin components act in coordination to regulate alternative splicing.
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Affiliation(s)
- Shiran Naftelberg
- Sackler Medical School, Tel Aviv University, Tel Aviv 69978, Israel;
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36
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Yang Bai, Shufan Ji, Qinghua Jiang, Yadong Wang. Identification Exon Skipping Events From High-Throughput RNA Sequencing Data. IEEE Trans Nanobioscience 2015; 14:562-9. [DOI: 10.1109/tnb.2015.2419812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Hirsch CL, Coban Akdemir Z, Wang L, Jayakumaran G, Trcka D, Weiss A, Hernandez JJ, Pan Q, Han H, Xu X, Xia Z, Salinger AP, Wilson M, Vizeacoumar F, Datti A, Li W, Cooney AJ, Barton MC, Blencowe BJ, Wrana JL, Dent SYR. Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming. Genes Dev 2015; 29:803-16. [PMID: 25877919 PMCID: PMC4403257 DOI: 10.1101/gad.255109.114] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/20/2015] [Indexed: 11/29/2022]
Abstract
Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Hirsch et al. performed a functional RNAi screen and identified components of the SAGA histone acetyltransferase complex, in particular Gcn5, as critical regulators of reprogramming initiation. In mouse pluripotent stem cells, Gcn5 strongly associates with Myc, and, upon initiation of somatic reprogramming, Gcn5 and Myc form a positive feed-forward loop that activates a distinct alternative splicing network and the early acquisition of pluripotency-associated splicing events. Embryonic stem cells are maintained in a self-renewing and pluripotent state by multiple regulatory pathways. Pluripotent-specific transcriptional networks are sequentially reactivated as somatic cells reprogram to achieve pluripotency. How epigenetic regulators modulate this process and contribute to somatic cell reprogramming is not clear. Here we performed a functional RNAi screen to identify the earliest epigenetic regulators required for reprogramming. We identified components of the SAGA histone acetyltransferase complex, in particular Gcn5, as critical regulators of reprogramming initiation. Furthermore, we showed in mouse pluripotent stem cells that Gcn5 strongly associates with Myc and that, upon initiation of somatic reprogramming, Gcn5 and Myc form a positive feed-forward loop that activates a distinct alternative splicing network and the early acquisition of pluripotency-associated splicing events. These studies expose a Myc–SAGA pathway that drives expression of an essential alternative splicing regulatory network during somatic cell reprogramming.
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Affiliation(s)
- Calley L Hirsch
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Zeynep Coban Akdemir
- Program in Genes and Development, Graduate School of Biomedical Sciences, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Li Wang
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA; Program in Molecular Carcinogenesis, Graduate School of Biomedical Sciences, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Gowtham Jayakumaran
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Dan Trcka
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Alexander Weiss
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - J Javier Hernandez
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Qun Pan
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Hong Han
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Xueping Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zheng Xia
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Andrew P Salinger
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Marenda Wilson
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA
| | - Frederick Vizeacoumar
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Alessandro Datti
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Wei Li
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA; Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Austin J Cooney
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Michelle C Barton
- Program in Genes and Development, Graduate School of Biomedical Sciences, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA
| | - Benjamin J Blencowe
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Jeffrey L Wrana
- Center for Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada;
| | - Sharon Y R Dent
- Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Smithville, Texas 78957, USA;
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Nakamura T, Yabuta Y, Okamoto I, Aramaki S, Yokobayashi S, Kurimoto K, Sekiguchi K, Nakagawa M, Yamamoto T, Saitou M. SC3-seq: a method for highly parallel and quantitative measurement of single-cell gene expression. Nucleic Acids Res 2015; 43:e60. [PMID: 25722368 PMCID: PMC4482058 DOI: 10.1093/nar/gkv134] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 02/09/2015] [Indexed: 12/18/2022] Open
Abstract
Single-cell mRNA sequencing (RNA-seq) methods have undergone rapid development in recent years, and transcriptome analysis of relevant cell populations at single-cell resolution has become a key research area of biomedical sciences. We here present single-cell mRNA 3-prime end sequencing (SC3-seq), a practical methodology based on PCR amplification followed by 3-prime-end enrichment for highly quantitative, parallel and cost-effective measurement of gene expression in single cells. The SC3-seq allows excellent quantitative measurement of mRNAs ranging from the 10,000-cell to 1-cell level, and accordingly, allows an accurate estimate of the transcript levels by a regression of the read counts of spike-in RNAs with defined copy numbers. The SC3-seq has clear advantages over other typical single-cell RNA-seq methodologies for the quantitative measurement of transcript levels and at a sequence depth required for the saturation of transcript detection. The SC3-seq distinguishes four distinct cell types in the peri-implantation mouse blastocysts. Furthermore, the SC3-seq reveals the heterogeneity in human-induced pluripotent stem cells (hiPSCs) cultured under on-feeder as well as feeder-free conditions, demonstrating a more homogeneous property of the feeder-free hiPSCs. We propose that SC3-seq might be used as a powerful strategy for single-cell transcriptome analysis in a broad range of investigations in biomedical sciences.
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Affiliation(s)
- Tomonori Nakamura
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yukihiro Yabuta
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ikuhiro Okamoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinya Aramaki
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shihori Yokobayashi
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin Yoshida, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kazuki Kurimoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | | | - Masato Nakagawa
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin Yoshida, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takuya Yamamoto
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin Yoshida, Sakyo-ku, Kyoto 606-8507, Japan Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin Yoshida, Sakyo-ku, Kyoto 606-8507, Japan Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
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The L1TD1 protein interactome reveals the importance of post-transcriptional regulation in human pluripotency. Stem Cell Reports 2015; 4:519-28. [PMID: 25702638 PMCID: PMC4376047 DOI: 10.1016/j.stemcr.2015.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 01/16/2015] [Accepted: 01/16/2015] [Indexed: 11/24/2022] Open
Abstract
The RNA-binding protein L1TD1 is one of the most specific and abundant proteins in pluripotent stem cells and is essential for the maintenance of pluripotency in human cells. Here, we identify the protein interaction network of L1TD1 in human embryonic stem cells (hESCs) and provide insights into the interactome network constructed in human pluripotent cells. Our data reveal that L1TD1 has an important role in RNA splicing, translation, protein traffic, and degradation. L1TD1 interacts with multiple stem-cell-specific proteins, many of which are still uncharacterized in the context of development. Further, we show that L1TD1 is a part of the pluripotency interactome network of OCT4, SOX2, and NANOG, bridging nuclear and cytoplasmic regulation and highlighting the importance of RNA biology in pluripotency. A protein interactome is constructed in human embryonic stem cells L1TD1 interacts with U2af1 and Srsf3, which are vital for somatic cell reprogramming L1TD1 is involved in the high proteasome activity of pluripotent cells L1TD1 connects uncharacterized factors to the OCT4, SOX2, and NANOG network
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40
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Chen K, Dai X, Wu J. Alternative splicing: An important mechanism in stem cell biology. World J Stem Cells 2015; 7:1-10. [PMID: 25621101 PMCID: PMC4300919 DOI: 10.4252/wjsc.v7.i1.1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 09/22/2014] [Accepted: 10/27/2014] [Indexed: 02/06/2023] Open
Abstract
Alternative splicing (AS) is an essential mechanism in post-transcriptional regulation and leads to protein diversity. It has been shown that AS is prevalent in metazoan genomes, and the splicing pattern is dynamically regulated in different tissues and cell types, including embryonic stem cells. These observations suggest that AS may play critical roles in stem cell biology. Since embryonic stem cells and induced pluripotent stem cells have the ability to give rise to all types of cells and tissues, they hold the promise of future cell-based therapy. Many efforts have been devoted to understanding the mechanisms underlying stem cell self-renewal and differentiation. However, most of the studies focused on the expression of a core set of transcription factors and regulatory RNAs. The role of AS in stem cell differentiation was not clear. Recent advances in high-throughput technologies have allowed the profiling of dynamic splicing patterns and cis-motifs that are responsible for AS at a genome-wide scale, and provided novel insights in a number of studies. In this review, we discuss some recent findings involving AS and stem cells. An emerging picture from these findings is that AS is integrated in the transcriptional and post-transcriptional networks and together they control pluripotency maintenance and differentiation of stem cells.
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41
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Sen S, Langiewicz M, Jumaa H, Webster NJ. Deletion of serine/arginine-rich splicing factor 3 in hepatocytes predisposes to hepatocellular carcinoma in mice. Hepatology 2015; 61:171-83. [PMID: 25132062 PMCID: PMC4280350 DOI: 10.1002/hep.27380] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 08/13/2014] [Indexed: 12/17/2022]
Abstract
UNLABELLED Alterations in RNA splicing are associated with cancer, but it is not clear whether they result from malignant transformation or have a causative role. We show here that hepatocyte-specific deletion of serine/arginine-rich splicing factor 3 (SRSF3) impairs hepatocyte maturation and metabolism in early adult life, and mice develop spontaneous hepatocellular carcinoma (HCC) with aging. Tumor development is preceded by chronic liver disease with progressive steatosis and fibrosis. SRSF3 protects mice against CCl4 -induced fibrosis and carcinogenesis and suppresses inclusion of the profibrogenic EDA exon in fibronectin 1. Loss of SRSF3 increases expression of insulin-like growth factor 2 and the A-isoform of the insulin receptor, allowing aberrant activation of mitogenic signaling, promotes aberrant splicing and expression of epithelial to mesenchymal transition (EMT) genes, and activates Wnt/β-catenin signaling leading to c-Myc induction. Finally, SRSF3 expression is either decreased or the protein mislocalized in human HCC. CONCLUSION Our data suggest a potential role for SRSF3 in preventing hepatic carcinogenesis by regulating splicing to suppress fibrosis, mitogenic splicing, and EMT. Thus, these mice may provide an attractive model to discover the pathogenic mechanisms linking aberrant pre-messenger RNA splicing with liver damage, fibrosis, and HCC.
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Affiliation(s)
- Supriya Sen
- Medical Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, CA 92093, USA
| | - Magda Langiewicz
- Medical Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Hassan Jumaa
- Center for Biological Signaling Studies BIOSS, Albert-Ludwigs Universität, Freiburg 79098, Germany
| | - Nicholas J.G. Webster
- Medical Research Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA
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Abstract
Embryonic stem cell maintenance, differentiation, and somatic cell reprogramming require the interplay of multiple pluripotency factors, epigenetic remodelers, and extracellular signaling pathways. RNA-binding proteins (RBPs) are involved in a wide range of regulatory pathways, from RNA metabolism to epigenetic modifications. In recent years we have witnessed more and more studies on the discovery of new RBPs and the assessment of their functions in a variety of biological systems, including stem cells. We review the current studies on RBPs and focus on those that have functional implications in pluripotency, differentiation, and/or reprogramming in both the human and mouse systems.
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43
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Premature termination of reprogramming in vivo leads to cancer development through altered epigenetic regulation. Cell 2014; 156:663-77. [PMID: 24529372 DOI: 10.1016/j.cell.2014.01.005] [Citation(s) in RCA: 320] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 11/06/2013] [Accepted: 01/03/2014] [Indexed: 12/11/2022]
Abstract
Cancer is believed to arise primarily through accumulation of genetic mutations. Although induced pluripotent stem cell (iPSC) generation does not require changes in genomic sequence, iPSCs acquire unlimited growth potential, a characteristic shared with cancer cells. Here, we describe a murine system in which reprogramming factor expression in vivo can be controlled temporally with doxycycline (Dox). Notably, transient expression of reprogramming factors in vivo results in tumor development in various tissues consisting of undifferentiated dysplastic cells exhibiting global changes in DNA methylation patterns. The Dox-withdrawn tumors arising in the kidney share a number of characteristics with Wilms tumor, a common pediatric kidney cancer. We also demonstrate that iPSCs derived from Dox-withdrawn kidney tumor cells give rise to nonneoplastic kidney cells in mice, proving that they have not undergone irreversible genetic transformation. These findings suggest that epigenetic regulation associated with iPSC derivation may drive development of particular types of cancer.
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44
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Hooper JE. A survey of software for genome-wide discovery of differential splicing in RNA-Seq data. Hum Genomics 2014; 8:3. [PMID: 24447644 PMCID: PMC3903050 DOI: 10.1186/1479-7364-8-3] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/26/2013] [Indexed: 01/10/2023] Open
Abstract
Alternative splicing is a major contributor to cellular diversity. Therefore the identification and quantification of differentially spliced transcripts in genome-wide transcript analysis is an important consideration. Here, I review the software available for analysis of RNA-Seq data for differential splicing and discuss intrinsic challenges for differential splicing analyses. Three approaches to differential splicing analysis are described, along with their associated software implementations, their strengths, limitations, and caveats. Suggestions for future work include more extensive experimental validation to assess accuracy of the software predictions and consensus formats for outputs that would facilitate visualizations, data exchange, and downstream analyses.
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Affiliation(s)
- Joan E Hooper
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, 12801 17th Ave, rm 12103, MS 8108, PO Box 6511, Aurora, CO 80045, USA.
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45
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Affiliation(s)
- Chen Gao
- Departments of Anesthesiology, Physiology and Medicine, Molecular Biology Institute, David Geffen School of Medicine at University of California at Los Angeles
| | - Yibin Wang
- Departments of Anesthesiology, Physiology and Medicine, Molecular Biology Institute, David Geffen School of Medicine at University of California at Los Angeles
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