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Cheng LC, Zheng D, Baljinnyam E, Sun F, Ogami K, Yeung PL, Hoque M, Lu CW, Manley JL, Tian B. Widespread transcript shortening through alternative polyadenylation in secretory cell differentiation. Nat Commun 2020; 11:3182. [PMID: 32576858 PMCID: PMC7311474 DOI: 10.1038/s41467-020-16959-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/29/2020] [Indexed: 11/29/2022] Open
Abstract
Most eukaryotic genes produce alternative polyadenylation (APA) isoforms. Here we report that, unlike previously characterized cell lineages, differentiation of syncytiotrophoblast (SCT), a cell type critical for hormone production and secretion during pregnancy, elicits widespread transcript shortening through APA in 3'UTRs and in introns. This global APA change is observed in multiple in vitro trophoblast differentiation models, and in single cells from placentas at different stages of pregnancy. Strikingly, the transcript shortening is unrelated to cell proliferation, a feature previously associated with APA control, but instead accompanies increased secretory functions. We show that 3'UTR shortening leads to transcripts with higher mRNA stability, which augments transcriptional activation, especially for genes involved in secretion. Moreover, this mechanism, named secretion-coupled APA (SCAP), is also executed in B cell differentiation to plasma cells. Together, our data indicate that SCAP tailors the transcriptome during formation of secretory cells, boosting their protein production and secretion capacity.
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Affiliation(s)
- Larry C Cheng
- Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
- Program in Gene Expression and Regulation, and Center for Systems and Computational Biology, Wistar Institute, Philadelphia, PA 19104, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Erdene Baljinnyam
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Fangzheng Sun
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Koichi Ogami
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
- Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Percy Luk Yeung
- Robert Wood Johnson Medical School and Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Mainul Hoque
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Chi-Wei Lu
- Robert Wood Johnson Medical School and Child Health Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Bin Tian
- Graduate Program in Quantitative Biomedicine, School of Graduate Studies, Rutgers University, New Brunswick, NJ 08901, USA.
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.
- Program in Gene Expression and Regulation, and Center for Systems and Computational Biology, Wistar Institute, Philadelphia, PA 19104, USA.
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Yamazaki T, Liu L, Lazarev D, Al-Zain A, Fomin V, Yeung PL, Chambers SM, Lu CW, Studer L, Manley JL. Corrigendum: TCF3 alternative splicing controlled by hnRNP H/F regulates E-cadherin expression and hESC pluripotency. Genes Dev 2019; 33:733-736. [DOI: 10.1101/gad.326983.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Yamazaki T, Liu L, Lazarev D, Al-Zain A, Fomin V, Yeung PL, Chambers SM, Lu CW, Studer L, Manley JL. TCF3 alternative splicing controlled by hnRNP H/F regulates E-cadherin expression and hESC pluripotency. Genes Dev 2018; 32:1161-1174. [PMID: 30115631 PMCID: PMC6120717 DOI: 10.1101/gad.316984.118] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 06/22/2018] [Indexed: 12/13/2022]
Abstract
Yamazaki et al. show that alternative splicing creates two TCF3 isoforms (E12 and E47) and identified two related splicing factors, hnRNPs H1 and F (hnRNP H/F), that regulate TCF3 splicing. Expression of known TCF3 target E-cadherin, critical for maintaining ESC pluripotency, is repressed by E47 but not by E12. Alternative splicing (AS) plays important roles in embryonic stem cell (ESC) differentiation. In this study, we first identified transcripts that display specific AS patterns in pluripotent human ESCs (hESCs) relative to differentiated cells. One of these encodes T-cell factor 3 (TCF3), a transcription factor that plays important roles in ESC differentiation. AS creates two TCF3 isoforms, E12 and E47, and we identified two related splicing factors, heterogeneous nuclear ribonucleoproteins (hnRNPs) H1 and F (hnRNP H/F), that regulate TCF3 splicing. We found that hnRNP H/F levels are high in hESCs, leading to high E12 expression, but decrease during differentiation, switching splicing to produce elevated E47 levels. Importantly, hnRNP H/F knockdown not only recapitulated the switch in TCF3 AS but also destabilized hESC colonies and induced differentiation. Providing an explanation for this, we show that expression of known TCF3 target E-cadherin, critical for maintaining ESC pluripotency, is repressed by E47 but not by E12.
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Affiliation(s)
- Takashi Yamazaki
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Lizhi Liu
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Denis Lazarev
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Amr Al-Zain
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Vitalay Fomin
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Percy Luk Yeung
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Child Health Institute of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Stuart M Chambers
- The Center for Stem Cell Biology, Sloan Kettering Institute, New York, New York 10065, USA.,Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Chi-Wei Lu
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Child Health Institute of New Jersey, New Brunswick, New Jersey 08901, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan Kettering Institute, New York, New York 10065, USA.,Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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Williams M, Prem S, Zhou X, Matteson P, Yeung PL, Lu CW, Pang Z, Brzustowicz L, Millonig JH, Dicicco-Bloom E. Rapid Detection of Neurodevelopmental Phenotypes in Human Neural Precursor Cells (NPCs). J Vis Exp 2018. [PMID: 29553565 DOI: 10.3791/56628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human brain development proceeds through a series of precisely orchestrated processes, with earlier stages distinguished by proliferation, migration, and neurite outgrowth; and later stages characterized by axon/dendrite outgrowth and synapse formation. In neurodevelopmental disorders, often one or more of these processes are disrupted, leading to abnormalities in brain formation and function. With the advent of human induced pluripotent stem cell (hiPSC) technology, researchers now have an abundant supply of human cells that can be differentiated into virtually any cell type, including neurons. These cells can be used to study both normal brain development and disease pathogenesis. A number of protocols using hiPSCs to model neuropsychiatric disease use terminally differentiated neurons or use 3D culture systems termed organoids. While these methods have proven invaluable in studying human disease pathogenesis, there are some drawbacks. Differentiation of hiPSCs into neurons and generation of organoids are lengthy and costly processes that can impact the number of experiments and variables that can be assessed. In addition, while post-mitotic neurons and organoids allow the study of disease-related processes, including dendrite outgrowth and synaptogenesis, they preclude the study of earlier processes like proliferation and migration. In neurodevelopmental disorders, such as autism, abundant genetic and post-mortem evidence indicates defects in early developmental processes. Neural precursor cells (NPCs), a highly proliferative cell population, may be a suitable model in which to ask questions about ontogenetic processes and disease initiation. We now extend methodologies learned from studying development in mouse and rat cortical cultures to human NPCs. The use of NPCs allows us to investigate disease-related phenotypes and define how different variables (e.g., growth factors, drugs) impact developmental processes including proliferation, migration, and differentiation in only a few days. Ultimately, this toolset can be used in a reproducible and high-throughput manner to identify disease-specific mechanisms and phenotypes in neurodevelopmental disorders.
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Affiliation(s)
- Madeline Williams
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School
| | - Smrithi Prem
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School
| | - Xiaofeng Zhou
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School
| | - Paul Matteson
- Center for Advanced Biotechnology and Medicine, Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School
| | - Percy Luk Yeung
- The Child Health Institute of NJ, Department of Obstetrics, Gynecology, and Reproductive Services, Rutgers Robert Wood Johnson Medical School
| | - Chi-Wei Lu
- The Child Health Institute of NJ, Department of Obstetrics, Gynecology, and Reproductive Services, Rutgers Robert Wood Johnson Medical School
| | - Zhiping Pang
- The Child Health Institute of NJ, Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School
| | | | - James H Millonig
- Center for Advanced Biotechnology and Medicine, Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School
| | - Emanuel Dicicco-Bloom
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School;
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Yeung PL, Denissova NG, Nasello C, Hakhverdyan Z, Chen JD, Brenneman MA. Promyelocytic leukemia nuclear bodies support a late step in DNA double-strand break repair by homologous recombination. J Cell Biochem 2012; 113:1787-99. [PMID: 22213200 DOI: 10.1002/jcb.24050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The PML protein and PML nuclear bodies (PML-NB) are implicated in multiple cellular functions relevant to tumor suppression, including DNA damage response. In most cases of acute promyelocytic leukemia, the PML and retinoic acid receptor alpha (RARA) genes are translocated, resulting in expression of oncogenic PML-RARα fusion proteins. PML-NB fail to form normally, and promyelocytes remain in an undifferentiated, abnormally proliferative state. We examined the involvement of PML protein and PML-NB in homologous recombinational repair (HRR) of chromosomal DNA double-strand breaks. Transient overexpression of wild-type PML protein isoforms produced hugely enlarged or aggregated PML-NB and reduced HRR by ~2-fold, suggesting that HRR depends to some extent upon normal PML-NB structure. Knockdown of PML by RNA interference sharply attenuated formation of PML-NB and reduced HRR by up to 20-fold. However, PML-knockdown cells showed apparently normal induction of H2AX phosphorylation and RAD51 foci after DNA damage by ionizing radiation. These findings indicate that early steps in HRR, including recognition of DNA double-strand breaks, initial processing of ends, and assembly of single-stranded DNA/RAD51 nucleoprotein filaments, do not depend upon PML-NB. The HRR deficit in PML-depleted cells thus reflects inhibition of later steps in the repair pathway. Expression of PML-RARα fusion proteins disrupted PML-NB structure and reduced HRR by up to 10-fold, raising the possibility that defective HRR and resulting genomic instability may figure in the pathogenesis, progression and relapse of acute promyelocytic leukemia.
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Affiliation(s)
- Percy Luk Yeung
- The Human Genetics Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA
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Abstract
Daxx plays a major role in several important signaling pathways including transcription and cell death. It has been postulated that Daxx regulates both events from the nucleus; however, the mechanism by which Daxx is localized in the nucleus remains obscure. Here we show that nuclear localization of Daxx is controlled by two independent signals and importin 3. Domain analysis reveals that Daxx contains two separate nuclear localizing domains. Site-directed mutagenesis reveals that the basic aa sequence RLKRK at residues 227-231 (NLS1) is responsible for nuclear localization of N-terminal domain, while aa sequence KKSRKEKK at residues 630-637 (NLS2) is responsible for nuclear localization of the C-terminal domain. Mutations of a NLS consensus sequence RKKRR at residues 391-395 and several other basic aa clusters have no effect on Daxx nuclear localization. In full-length Daxx, NLS1 contributes partially to nuclear localization, while NLS2 plays a major role. Markedly, it is essential to disrupt both NLS1 and NLS2 in order to completely block nuclear localization of the full-length protein and to prevent its association with PML nuclear bodies. Furthermore, Daxx interacts selectively with importin alpha3 through its NLS1 and NLS2 sequences. Conversely, importin alpha3 utilizes two NLS-binding sites for Daxx interaction, suggesting that the importin/mediates nuclear import of Daxx. Finally, we show that nuclear localization of Daxx is essential for its transcriptional effects on GR and p53. Together, these data unveil a molecular mechanism that controls nuclear localization of Daxx and support a nuclear role of Daxx in transcriptional regulation.
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Affiliation(s)
- Percy Luk Yeung
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
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Yeung PL, Zhang A, Chen JD. Nuclear localization of coactivator RAC3 is mediated by a bipartite NLS and importin alpha3. Biochem Biophys Res Commun 2006; 348:13-24. [PMID: 16875678 DOI: 10.1016/j.bbrc.2006.06.163] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2006] [Accepted: 06/26/2006] [Indexed: 10/24/2022]
Abstract
The nuclear receptor coactivator RAC3 (also known as SRC-3/ACTR/AIB1/p/CIP/TRAM-1) belongs to the p160 coactivator family, which are involved in several physiological processes and diseases. Here we have investigated how RAC3 is translocated into the nucleus and show that it is mediated through a bipartite NLS and importin alpha3. This bipartite NLS is located within the conserved bHLH domain, and its mutation abolished nuclear localization. The NLS is also sufficient to cause nuclear import of EGFP, and the activity requires basic amino acids within the NLS. RAC3 binds strongly to importin alpha3, which also depends on the basic amino acids. Functionally, RAC3 cytoplasmic mutant loses its ability to enhance transcription, suggesting that nuclear localization is essential for coactivator function. Together, these results reveal a previous unknown mechanism for nuclear translocation of p160 coactivators and a critical function of the conserved bHLH within the coactivator.
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Affiliation(s)
- Percy Luk Yeung
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, NJ, USA
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Zhang A, Yeung PL, Li CW, Tsai SC, Dinh GK, Wu X, Li H, Chen JD. Identification of a novel family of ankyrin repeats containing cofactors for p160 nuclear receptor coactivators. J Biol Chem 2004; 279:33799-805. [PMID: 15184363 DOI: 10.1074/jbc.m403997200] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the p160 nuclear receptor coactivators interact with liganded nuclear receptors to enhance transcription of target genes. Here we identify a novel family of ankyrin repeats containing cofactors (ANCOs) that interact with the p160 coactivators. ANCO-1 binds to the conserved Per-Arnt-Sim (PAS) region of the p160 coactivators. It encodes a large nuclear protein with five ankyrin repeats, and parts of its sequences have been reported as nasopharyngeal carcinoma susceptibility protein and medulloblastoma antigen. Immunofluorescence staining reveals discrete nuclear foci of ANCO-1 that are distinct from known nuclear structures. Intriguingly, ANCO-1 also colocalizes and interacts with histone deacetylases. Transient reporter gene assay shows that ANCO-1 expression inhibits ligand-dependent transactivation by both steroid and nonsteroid nuclear receptors. Taken together, we have identified a novel family of ankyrin repeats containing cofactors that may recruit histone deacetylases to the p160 coactivators/nuclear receptor complex to inhibit ligand-dependent transactivation.
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Affiliation(s)
- Aihua Zhang
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854-5635, USA
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