1
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Hemphill WO, Steiner HR, Kominsky JR, Wuttke DS, Cech TR. Transcription factors ERα and Sox2 have differing multiphasic DNA- and RNA-binding mechanisms. RNA (NEW YORK, N.Y.) 2024; 30:1089-1105. [PMID: 38760076 PMCID: PMC11251522 DOI: 10.1261/rna.080027.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/01/2024] [Indexed: 05/19/2024]
Abstract
Many transcription factors (TFs) have been shown to bind RNA, leading to open questions regarding the mechanism(s) of this RNA binding and its role in regulating TF activities. Here, we use biophysical assays to interrogate the k on, k off, and K d for DNA and RNA binding of two model human TFs, ERα and Sox2. Unexpectedly, we found that both proteins exhibit multiphasic nucleic acid-binding kinetics. We propose that Sox2 RNA and DNA multiphasic binding kinetics can be explained by a conventional model for sequential Sox2 monomer association and dissociation. In contrast, ERα nucleic acid binding exhibited biphasic dissociation paired with novel triphasic association behavior, in which two apparent binding transitions are separated by a 10-20 min "lag" phase depending on protein concentration. We considered several conventional models for the observed kinetic behavior, none of which adequately explained all the ERα nucleic acid-binding data. Instead, simulations with a model incorporating sequential ERα monomer association, ERα nucleic acid complex isomerization, and product "feedback" on isomerization rate recapitulated the general kinetic trends for both ERα DNA and RNA binding. Collectively, our findings reveal that Sox2 and ERα bind RNA and DNA with previously unappreciated multiphasic binding kinetics, and that their reaction mechanisms differ with ERα binding nucleic acids via a novel reaction mechanism.
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Affiliation(s)
- Wayne O Hemphill
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Halley R Steiner
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Jackson R Kominsky
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
| | - Thomas R Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303, USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303, USA
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2
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Xiang JS, Schafer DM, Rothamel KL, Yeo GW. Decoding protein-RNA interactions using CLIP-based methodologies. Nat Rev Genet 2024:10.1038/s41576-024-00749-3. [PMID: 38982239 DOI: 10.1038/s41576-024-00749-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 07/11/2024]
Abstract
Protein-RNA interactions are central to all RNA processing events, with pivotal roles in the regulation of gene expression and cellular functions. Dysregulation of these interactions has been increasingly linked to the pathogenesis of human diseases. High-throughput approaches to identify RNA-binding proteins and their binding sites on RNA - in particular, ultraviolet crosslinking followed by immunoprecipitation (CLIP) - have helped to map the RNA interactome, yielding transcriptome-wide protein-RNA atlases that have contributed to key mechanistic insights into gene expression and gene-regulatory networks. Here, we review these recent advances, explore the effects of cellular context on RNA binding, and discuss how these insights are shaping our understanding of cellular biology. We also review the potential therapeutic applications arising from new knowledge of protein-RNA interactions.
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Affiliation(s)
- Joy S Xiang
- Division of Biomedical Sciences, UC Riverside, Riverside, CA, USA
| | - Danielle M Schafer
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA
| | - Katherine L Rothamel
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA.
- Sanford Laboratories for Innovative Medicines, La Jolla, CA, USA.
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3
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Tants JN, Oberstrass L, Weigand JE, Schlundt A. Structure and RNA-binding of the helically extended Roquin CCCH-type zinc finger. Nucleic Acids Res 2024:gkae555. [PMID: 38953172 DOI: 10.1093/nar/gkae555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 07/03/2024] Open
Abstract
Zinc finger (ZnF) domains appear in a pool of structural contexts and despite their small size achieve varying target specificities, covering single-stranded and double-stranded DNA and RNA as well as proteins. Combined with other RNA-binding domains, ZnFs enhance affinity and specificity of RNA-binding proteins (RBPs). The ZnF-containing immunoregulatory RBP Roquin initiates mRNA decay, thereby controlling the adaptive immune system. Its unique ROQ domain shape-specifically recognizes stem-looped cis-elements in mRNA 3'-untranslated regions (UTR). The N-terminus of Roquin contains a RING domain for protein-protein interactions and a ZnF, which was suggested to play an essential role in RNA decay by Roquin. The ZnF domain boundaries, its RNA motif preference and its interplay with the ROQ domain have remained elusive, also driven by the lack of high-resolution data of the challenging protein. We provide the solution structure of the Roquin-1 ZnF and use an RBNS-NMR pipeline to show that the ZnF recognizes AU-rich RNAs. We systematically refine the contributions of adenines in a poly(U)-background to specific complex formation. With the simultaneous binding of ROQ and ZnF to a natural target transcript of Roquin, our study for the first time suggests how Roquin integrates RNA shape and sequence features through the ROQ-ZnF tandem.
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Affiliation(s)
- Jan-Niklas Tants
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
| | - Lasse Oberstrass
- University of Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany
| | - Julia E Weigand
- University of Marburg, Department of Pharmacy, Institute of Pharmaceutical Chemistry, Marbacher Weg 6, 35037 Marburg, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences and Biomolecular Resonance Center (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7-9, 60438 Frankfurt, Germany
- University of Greifswald, Institute of Biochemistry, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
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4
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Hou X, Xu Q, Liu R. CREB3 facilitates Donafenib resistance in hepatocellular carcinoma cells via the LSD1/CoREST/p65 axis by transcriptionally activating long noncoding RNA ZFAS1. Transl Oncol 2024; 44:101684. [PMID: 38641372 DOI: 10.1016/j.tranon.2023.101684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/11/2023] [Accepted: 04/27/2023] [Indexed: 04/21/2024] Open
Abstract
OBJECTIVE Drug resistance greatly limits the therapeutic effect of a drug. This study aimed to explore the role of long noncoding RNA ZFAS1 in Donafenib resistance of hepatocellular carcinoma (HCC) cells. METHODS The expression of CREB3, ZFAS1, and p65 in HCC cell lines was measured by RT-qPCR and western blotting. After transfection with sh-ZFAS1, sh-CREB3, or sh-CREB3 + oe-p65 in Donafenib-resistent (DR) HCC cell lines, the transfection efficiency was evaluated by RT-qPCR and western blotting. The proliferation and IC50 to Donafenib of HCC cell lines was examined by MTT assay. Cell proliferation and apoptosis were examined by colony formation and flow cytometry assays. Then, the correlation amongst CREB3, ZFAS1, LSD1/CoREST, and p65 was analysed by ChIP, dual-luciferase reporter gene, and RIP assays. RESULTS ZFAS1, CREB3, and p65 were upregulated in HepG2-DR and Huh7-DR cells. Silencing of ZFAS1 or CREB3 enhanced the sensitivity of HCC cells to Donafenib, inhibited cell proliferation and IC50, and increased cell apoptosis, which were reversed by p65 overexpression. Mechanistically, CREB3 bound to ZFAS1 promoter to augment ZFAS1 transcriptional expression, and ZFAS1 recruited LSD1/CoREST to the p65 promoter region to decrease H3K4 methylation and elevate p65 transcriptional expression. CONCLUSION CREB3 overexpression contributed to Donafenib resistance in HCC cells by activating the ZFAS1/p65 axis.
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Affiliation(s)
- Xunbo Hou
- Department of Interventional, Harbin Medical University Cancer Hospital, No. 150, Haping Rd, Nangang District, Harbin, Heilongjiang 150081, PR China
| | - Qiannan Xu
- Department of Anesthesiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, PR China
| | - Ruibao Liu
- Department of Interventional, Harbin Medical University Cancer Hospital, No. 150, Haping Rd, Nangang District, Harbin, Heilongjiang 150081, PR China.
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5
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Guo JK, Blanco MR, Walkup WG, Bonesteele G, Urbinati CR, Banerjee AK, Chow A, Ettlin O, Strehle M, Peyda P, Amaya E, Trinh V, Guttman M. Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. Mol Cell 2024; 84:1271-1289.e12. [PMID: 38387462 PMCID: PMC10997485 DOI: 10.1016/j.molcel.2024.01.026] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Polycomb repressive complex 2 (PRC2) is reported to bind to many RNAs and has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate gene expression. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here, we revisit the evidence supporting RNA binding by PRC2 and show that many reported interactions may not occur in vivo. Using denaturing purification of in vivo crosslinked RNA-protein complexes in human and mouse cell lines, we observe a loss of detectable RNA binding to PRC2 and chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, and others), despite accurately mapping bona fide RNA-binding sites across others (SPEN, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.
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Affiliation(s)
- Jimmy K Guo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ward G Walkup
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant Bonesteele
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carl R Urbinati
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Olivia Ettlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Parham Peyda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Enrique Amaya
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vickie Trinh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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6
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Hemphill WO, Steiner HR, Kominsky JR, Wuttke DS, Cech TR. Transcription factors ERα and Sox2 have differing multiphasic DNA and RNA binding mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585577. [PMID: 38562825 PMCID: PMC10983890 DOI: 10.1101/2024.03.18.585577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Many transcription factors (TFs) have been shown to bind RNA, leading to open questions regarding the mechanism(s) of this RNA binding and its role in regulating TF activities. Here we use biophysical assays to interrogate the k o n , k o f f , and K d for DNA and RNA binding of two model human transcription factors, ERα and Sox2. Unexpectedly, we found that both proteins exhibited multiphasic nucleic acid binding kinetics. We propose that Sox2 RNA and DNA multiphasic binding kinetics could be explained by a conventional model for sequential Sox2 monomer association and dissociation. In contrast, ERα nucleic acid binding exhibited biphasic dissociation paired with novel triphasic association behavior, where two apparent binding transitions are separated by a 10-20 min "lag" phase depending on protein concentration. We considered several conventional models for the observed kinetic behavior, none of which adequately explained all the ERα nucleic acid binding data. Instead, simulations with a model incorporating sequential ERα monomer association, ERα nucleic acid complex isomerization, and product "feedback" on isomerization rate recapitulated the general kinetic trends for both ERα DNA and RNA binding. Collectively, our findings reveal that Sox2 and ERα bind RNA and DNA with previously unappreciated multiphasic binding kinetics, and that their reaction mechanisms differ with ERα binding nucleic acids via a novel reaction mechanism.
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Affiliation(s)
- Wayne O. Hemphill
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303 USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303 USA
| | - Halley R. Steiner
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303 USA
| | - Jackson R. Kominsky
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303 USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303 USA
| | - Deborah S. Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303 USA
| | - Thomas R. Cech
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80303 USA
- Howard Hughes Medical Institute and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado 80303 USA
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7
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Bjarnason S, McIvor JAP, Prestel A, Demény KS, Bullerjahn JT, Kragelund BB, Mercadante D, Heidarsson PO. DNA binding redistributes activation domain ensemble and accessibility in pioneer factor Sox2. Nat Commun 2024; 15:1445. [PMID: 38365983 PMCID: PMC10873366 DOI: 10.1038/s41467-024-45847-2] [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: 07/13/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024] Open
Abstract
More than 1600 human transcription factors orchestrate the transcriptional machinery to control gene expression and cell fate. Their function is conveyed through intrinsically disordered regions (IDRs) containing activation or repression domains but lacking quantitative structural ensemble models prevents their mechanistic decoding. Here we integrate single-molecule FRET and NMR spectroscopy with molecular simulations showing that DNA binding can lead to complex changes in the IDR ensemble and accessibility. The C-terminal IDR of pioneer factor Sox2 is highly disordered but its conformational dynamics are guided by weak and dynamic charge interactions with the folded DNA binding domain. Both DNA and nucleosome binding induce major rearrangements in the IDR ensemble without affecting DNA binding affinity. Remarkably, interdomain interactions are redistributed in complex with DNA leading to variable exposure of two activation domains critical for transcription. Charged intramolecular interactions allowing for dynamic redistributions may be common in transcription factors and necessary for sensitive tuning of structural ensembles.
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Affiliation(s)
- Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Jordan A P McIvor
- School of Chemical Science, University of Auckland, Auckland, New Zealand
| | - Andreas Prestel
- Department of Biology, REPIN and Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Kinga S Demény
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland
| | - Jakob T Bullerjahn
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue-Straße 3, 60438, Frankfurt am Main, Germany
| | - Birthe B Kragelund
- Department of Biology, REPIN and Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
| | - Davide Mercadante
- School of Chemical Science, University of Auckland, Auckland, New Zealand.
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Sturlugata 7, 102, Reykjavík, Iceland.
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8
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Ghosh T, Almeida RG, Zhao C, Mannioui A, Martin E, Fleet A, Chen CZ, Assinck P, Ellams S, Gonzalez GA, Graham SC, Rowitch DH, Stott K, Adams I, Zalc B, Goldman N, Lyons DA, Franklin RJM. A retroviral link to vertebrate myelination through retrotransposon-RNA-mediated control of myelin gene expression. Cell 2024; 187:814-830.e23. [PMID: 38364788 DOI: 10.1016/j.cell.2024.01.011] [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: 12/12/2022] [Revised: 10/12/2023] [Accepted: 01/07/2024] [Indexed: 02/18/2024]
Abstract
Myelin, the insulating sheath that surrounds neuronal axons, is produced by oligodendrocytes in the central nervous system (CNS). This evolutionary innovation, which first appears in jawed vertebrates, enabled rapid transmission of nerve impulses, more complex brains, and greater morphological diversity. Here, we report that RNA-level expression of RNLTR12-int, a retrotransposon of retroviral origin, is essential for myelination. We show that RNLTR12-int-encoded RNA binds to the transcription factor SOX10 to regulate transcription of myelin basic protein (Mbp, the major constituent of myelin) in rodents. RNLTR12-int-like sequences (which we name RetroMyelin) are found in all jawed vertebrates, and we further demonstrate their function in regulating myelination in two different vertebrate classes (zebrafish and frogs). Our study therefore suggests that retroviral endogenization played a prominent role in the emergence of vertebrate myelin.
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Affiliation(s)
- Tanay Ghosh
- Altos Labs-Cambridge Institute of Science, Cambridge CB21 6GP, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AW, UK.
| | - Rafael G Almeida
- Centre for Discovery Brain Sciences, MS society Edinburgh Centre for MS Research, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Chao Zhao
- Altos Labs-Cambridge Institute of Science, Cambridge CB21 6GP, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AW, UK
| | - Abdelkrim Mannioui
- Sorbonne Université, Institut de Biologie Paris-Seine (IBPS), Aquatic Facility, 75005 Paris, France
| | - Elodie Martin
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Alex Fleet
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AW, UK
| | - Civia Z Chen
- Altos Labs-Cambridge Institute of Science, Cambridge CB21 6GP, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AW, UK
| | - Peggy Assinck
- Altos Labs-Cambridge Institute of Science, Cambridge CB21 6GP, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AW, UK
| | - Sophie Ellams
- Altos Labs-Cambridge Institute of Science, Cambridge CB21 6GP, UK
| | - Ginez A Gonzalez
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AW, UK
| | - Stephen C Graham
- Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - David H Rowitch
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Ian Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Bernard Zalc
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, 75013 Paris, France
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome, Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David A Lyons
- Centre for Discovery Brain Sciences, MS society Edinburgh Centre for MS Research, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh EH16 4SB, UK
| | - Robin J M Franklin
- Altos Labs-Cambridge Institute of Science, Cambridge CB21 6GP, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0AW, UK.
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9
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Sato J, Satoh Y, Yamamoto T, Watanabe T, Matsubara S, Satake H, Kimura AP. PTBP2 binds to a testis-specific long noncoding RNA, Tesra, and activates transcription of the Prss42/Tessp-2 gene. Gene 2024; 893:147907. [PMID: 37858745 DOI: 10.1016/j.gene.2023.147907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/22/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
Long noncoding RNAs (lncRNAs) have recently been proved to be functional in the testis. Tesra, a testis-specific lncRNA, was suggested to activate the transcription of Prss42/Tessp-2, a gene that is involved in meiotic progression, in mouse spermatocytes. To reveal the molecular mechanism underlying the activation, we searched for Tesra-binding proteins by a Ribotrap assay followed by LC-MS/MS analysis and identified polypyrimidine tract binding protein 2 (PTBP2) as a candidate. Analysis of public RNA-seq data and our qRT-PCR results indicated that Ptbp2 mRNA showed an expression pattern similar to the expression patterns of Tesra and Prss42/Tessp-2 during testis development. Moreover, PTBP2 was found to be associated with Tesra in testicular germ cells by RNA immunoprecipitation. To evaluate the effect of PTBP2 on the Prss42/Tessp-2 promoter, we established an in vitro reporter gene assay system in which Tesra expression could be induced by the Tet-on system and thereby Prss42/Tessp-2 promoter activity could be increased. In this system, the Prss42/Tessp-2 promoter activity was significantly decreased by the knockdown of PTBP2. These results suggest that PTBP2 contributes to Prss42/Tessp-2 transcriptional activation by Tesra in spermatocytes. The finding provides a precious example of a molecular mechanism of testis lncRNA functioning in spermatogenesis.
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Affiliation(s)
- Josei Sato
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yui Satoh
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Takehiro Yamamoto
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
| | - Takehiro Watanabe
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Atsushi P Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan.
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10
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Yoo W, Song YW, Kim J, Ahn J, Kim J, Shin Y, Ryu JK, Kim KK. Molecular basis for SOX2-dependent regulation of super-enhancer activity. Nucleic Acids Res 2023; 51:11999-12019. [PMID: 37930832 PMCID: PMC10711550 DOI: 10.1093/nar/gkad908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/22/2023] [Accepted: 10/06/2023] [Indexed: 11/08/2023] Open
Abstract
Pioneer transcription factors (TFs) like SOX2 are vital for stemness and cancer through enhancing gene expression within transcriptional condensates formed with coactivators, RNAs and mediators on super-enhancers (SEs). Despite their importance, how these factors work together for transcriptional condensation and activation remains unclear. SOX2, a pioneer TF found in SEs of pluripotent and cancer stem cells, initiates SE-mediated transcription by binding to nucleosomes, though the mechanism isn't fully understood. To address SOX2's role in SEs, we identified mSE078 as a model SOX2-enriched SE and p300 as a coactivator through bioinformatic analysis. In vitro and cell assays showed SOX2 forms condensates with p300 and SOX2-binding motifs in mSE078. We further proved that SOX2 condensation is highly correlated with mSE078's enhancer activity in cells. Moreover, we successfully demonstrated that p300 not only elevated transcriptional activity but also triggered chromatin acetylation via its direct interaction with SOX2 within these transcriptional condensates. Finally, our validation of SOX2-enriched SEs showcased their contribution to target gene expression in both stem cells and cancer cells. In its entirety, this study imparts valuable mechanistic insights into the collaborative interplay of SOX2 and its coactivator p300, shedding light on the regulation of transcriptional condensation and activation within SOX2-enriched SEs.
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Affiliation(s)
- Wanki Yoo
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Yi Wei Song
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Jihyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jihye Ahn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Je-Kyung Ryu
- Department of Physics & Astronomy, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Graduate School of Basic Medical Science (GSBMS), Institute for Antimicrobial Resistance Research and Therapeutics, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
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11
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López L, Fernández-Vañes L, Cabal VN, García-Marín R, Suárez-Fernández L, Codina-Martínez H, Lorenzo-Guerra SL, Vivanco B, Blanco-Lorenzo V, Llorente JL, López F, Hermsen MA. Sox2 and βIII-Tubulin as Biomarkers of Drug Resistance in Poorly Differentiated Sinonasal Carcinomas. J Pers Med 2023; 13:1504. [PMID: 37888115 PMCID: PMC10608336 DOI: 10.3390/jpm13101504] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/10/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
Poorly differentiated sinonasal carcinomas (PDCs) are tumors that have a poor prognosis despite advances in classical treatment. Predictive and prognostic markers and new personalized treatments could improve the oncological outcomes of patients. In this study, we analyzed SOX2 and βIII-tubulin as biomarkers that could have prognostic and therapeutic impacts on these tumors. The cohort included 57 cases of PDCs: 36 sinonasal undifferentiated carcinoma (SNUC) cases, 13 olfactory neuroblastoma (ONB) cases, and 8 sinonasal neuroendocrine carcinoma (SNEC) cases. Clinical follow-up data were available for 26 of these cases. Sox2 expression was detected using immunohistochemistry in 6 (75%) SNEC cases, 19 (53%) SNUC cases, and 6 (46%) ONB cases. The absence of Sox2 staining correlated with a higher rate of recurrence (p = 0.015), especially distant recurrence. The majority of cases showed βIII-tubulin expression, with strong positivity in 85%, 75%, and 64% of SNEC, ONB, and SNUC cases, respectively. Tumors with stronger βIII-tubulin expression demonstrated longer disease-free survival than those with no expression or low expression (p = 0.049). Sox2 and βIII-tubulin expression is common in poorly differentiated sinonasal tumors and has prognostic and therapeutic utility.
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Affiliation(s)
- Luis López
- Department of Otolaryngology, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (L.L.); (L.F.-V.); (J.L.L.)
| | - Laura Fernández-Vañes
- Department of Otolaryngology, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (L.L.); (L.F.-V.); (J.L.L.)
| | - Virginia N. Cabal
- Department of Head and Neck Cancer, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (V.N.C.); (R.G.-M.); (L.S.-F.); (H.C.-M.); (S.L.L.-G.); (M.A.H.)
| | - Rocío García-Marín
- Department of Head and Neck Cancer, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (V.N.C.); (R.G.-M.); (L.S.-F.); (H.C.-M.); (S.L.L.-G.); (M.A.H.)
| | - Laura Suárez-Fernández
- Department of Head and Neck Cancer, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (V.N.C.); (R.G.-M.); (L.S.-F.); (H.C.-M.); (S.L.L.-G.); (M.A.H.)
| | - Helena Codina-Martínez
- Department of Head and Neck Cancer, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (V.N.C.); (R.G.-M.); (L.S.-F.); (H.C.-M.); (S.L.L.-G.); (M.A.H.)
| | - Sara L. Lorenzo-Guerra
- Department of Head and Neck Cancer, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (V.N.C.); (R.G.-M.); (L.S.-F.); (H.C.-M.); (S.L.L.-G.); (M.A.H.)
| | - Blanca Vivanco
- Department of Pathology, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (B.V.); (V.B.-L.)
| | - Verónica Blanco-Lorenzo
- Department of Pathology, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (B.V.); (V.B.-L.)
| | - José L. Llorente
- Department of Otolaryngology, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (L.L.); (L.F.-V.); (J.L.L.)
| | - Fernando López
- Department of Otolaryngology, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (L.L.); (L.F.-V.); (J.L.L.)
| | - Mario A. Hermsen
- Department of Head and Neck Cancer, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain; (V.N.C.); (R.G.-M.); (L.S.-F.); (H.C.-M.); (S.L.L.-G.); (M.A.H.)
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12
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Aanei CM, Devêvre E, Șerban A, Tavernier-Tardy E, Guyotat D, Campos Catafal L. High-Dimensional Mass Cytometry Analysis of Embryonic Antigens and Their Signaling Pathways in Myeloid Cells from Bone Marrow Aspirates in AML Patients at Diagnosis. Cancers (Basel) 2023; 15:4707. [PMID: 37835401 PMCID: PMC10571794 DOI: 10.3390/cancers15194707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Embryonic antigens (EA) regulate pluripotency, self-renewal, and differentiation in embryonic stem (ES) cells during their development. In adult somatic cells, EA expression is normally inhibited; however, EAs can be re-expressed by cancer cells and are involved in the deregulation of different signaling pathways (SPs). In the context of AML, data concerning the expression of EAs are scarce and contradictory. METHODS We used mass cytometry to explore the expression of EAs and three SPs in myeloid cells from AML patients and normal bone marrow (NBM). Imaging flow cytometry was used for morphological assessment of cells in association with their OCT3/4 expression status (positive vs. negative). RESULTS An overall reduction in or absence of EA expression was observed in immature myeloid cells from AML patients compared to their normal counterparts. Stage-specific embryonic antigen-3 (SSEA-3) was consistently expressed at low levels in immature myeloid cells, whereas SSEA-1 was overexpressed in hematopoietic stem cells (HSCs) and myeloblasts from AML with monocytic differentiation (AML M4/M5). Therefore, these markers are valuable for distinguishing between normal and abnormal myeloid cells. These preliminary results show that the exploration of myeloid cell intracellular SPs in the setting of AML is very informative. Deregulation of three important leukemogenic SPs was also observed in myeloid cells from AML. CONCLUSIONS Exploring EAs and SPs in myeloid cells from AML patients by mass cytometry may help identify characteristic phenotypes and facilitate AML follow-up.
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Affiliation(s)
- Carmen-Mariana Aanei
- Laboratory of Hematology, University Hospital of Saint-Etienne, 42055 Saint-Etienne, France; (A.Ș.); (L.C.C.)
- Santé Ingénierie Biologie Saint-Etienne, INSERM SainBiose U1059, 42270 Saint-Priest-en-Jarez, France
| | - Estelle Devêvre
- Plateau de Cytométrie AniRA, SFR BioSciences (UAR3444-US8), 69367 Lyon, France;
| | - Adrian Șerban
- Laboratory of Hematology, University Hospital of Saint-Etienne, 42055 Saint-Etienne, France; (A.Ș.); (L.C.C.)
| | - Emmanuelle Tavernier-Tardy
- Department of Clinical Hematology, University Hospital of Saint-Etienne, 42100 Saint-Etienne, France; (E.T.-T.); (D.G.)
| | - Denis Guyotat
- Department of Clinical Hematology, University Hospital of Saint-Etienne, 42100 Saint-Etienne, France; (E.T.-T.); (D.G.)
| | - Lydia Campos Catafal
- Laboratory of Hematology, University Hospital of Saint-Etienne, 42055 Saint-Etienne, France; (A.Ș.); (L.C.C.)
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13
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Hamilton DJ, Hein AE, Wuttke DS, Batey RT. The DNA binding high mobility group box protein family functionally binds RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1778. [PMID: 36646476 PMCID: PMC10349909 DOI: 10.1002/wrna.1778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023]
Abstract
Nucleic acid binding proteins regulate transcription, splicing, RNA stability, RNA localization, and translation, together tailoring gene expression in response to stimuli. Upon discovery, these proteins are typically classified as either DNA or RNA binding as defined by their in vivo functions; however, recent evidence suggests dual DNA and RNA binding by many of these proteins. High mobility group box (HMGB) proteins have a DNA binding HMGB domain, act as transcription factors and chromatin remodeling proteins, and are increasingly understood to interact with RNA as means to regulate gene expression. Herein, multiple layers of evidence that the HMGB family are dual DNA and RNA binding proteins is comprehensively reviewed. For example, HMGB proteins directly interact with RNA in vitro and in vivo, are localized to RNP granules involved in RNA processing, and their protein interactors are enriched in RNA binding proteins involved in RNA metabolism. Importantly, in cell-based systems, HMGB-RNA interactions facilitate protein-protein interactions, impact splicing outcomes, and modify HMGB protein genomic or cellular localization. Misregulation of these HMGB-RNA interactions are also likely involved in human disease. This review brings to light that as a family, HMGB proteins are likely to bind RNA which is essential to HMGB protein biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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14
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Hu X, Wu J, Feng Y, Ma H, Zhang E, Zhang C, Sun Q, Wang T, Ge Y, Zong D, Chen W, He X. METTL3-stabilized super enhancers-lncRNA SUCLG2-AS1 mediates the formation of a long-range chromatin loop between enhancers and promoters of SOX2 in metastasis and radiosensitivity of nasopharyngeal carcinoma. Clin Transl Med 2023; 13:e1361. [PMID: 37658588 PMCID: PMC10474317 DOI: 10.1002/ctm2.1361] [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: 01/04/2023] [Revised: 07/23/2023] [Accepted: 07/28/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND Super enhancers (SE) play pivotal roles in cell identity and diseases occur including tumorigenesis. The depletion of SE-associated lncRNA transcripts, also known as super-lncRNA, causes the activity of SE to be dysregulated. METHODS We screened and identified an elevated metastasis-associated SE-lncRNA SUCLG2-AS1 in nasopharyngeal carcinoma (NPC) using RNA-sequencing, real-time quantitative polymerase chain reaction (RT-qPCR) and bioinformatics. Western blotting, RT-qPCR, methylated RNA immunoprecipitation (MeRIP), RNA immunoprecipitation, chromatin immunoprecipitation, RNA pull-down and 3C (chromosome conformation capture assays) were used for mechanistic studies. RESULTS SUCLG2-AS1 was correlated with a poor prognosis. SUCLG2-AS1 promotes NPC cell invasion and metastasis while repressing apoptosis and radiosensitivity in vitro and in vivo. Mechanistically, high SUCLG2-AS1 expression occurred in an m6A-dependent manner. SUCLG2-AS1 was found to be located in the SE region of SOX2, and it regulated the expression of SOX2 via long-range chromatin loop formation, which via mediating CTCF (transcription factor) occupied the SE and promoter region of SOX2, thus regulating the metastasis and radiosensitivity of NPC. CONCLUSIONS Taken together, our data suggest that SUCLG2-AS1 may serve as a novel intervention target for the clinical treatment of NPC.
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Affiliation(s)
- Xinyu Hu
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Jianfeng Wu
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Yong Feng
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Hongxia Ma
- Department of Epidemiology and BiostatisticsInternational Joint Research Center On Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical UniversityNanjingChina
| | - Erbao Zhang
- Department of Epidemiology and BiostatisticsInternational Joint Research Center On Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical UniversityNanjingChina
| | - Chang Zhang
- Department of Epidemiology and BiostatisticsInternational Joint Research Center On Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical UniversityNanjingChina
| | - Qi Sun
- Department of Epidemiology and BiostatisticsInternational Joint Research Center On Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical UniversityNanjingChina
| | - Tingting Wang
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Yizhi Ge
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Dan Zong
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Wei Chen
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
| | - Xia He
- Department of RadiotherapyThe Afliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer ResearchNanjingChina
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15
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Kleiner RE. Chemical Approaches To Investigate Post-transcriptional RNA Regulation. ACS Chem Biol 2023; 18:1684-1697. [PMID: 37540831 PMCID: PMC11031734 DOI: 10.1021/acschembio.3c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
RNA plays a central role in biological processes, and its activity is regulated by a host of diverse chemical and biochemical mechanisms including post-transcriptional modification and interactions with RNA-binding proteins. Here, we describe our efforts to illuminate RNA biology through the application of chemical tools, focusing on post-transcriptional regulatory mechanisms. We describe the development of an activity-based protein profiling approach for discovery and characterization of RNA-modifying enzymes. Next, we highlight novel approaches for RNA imaging based upon metabolic labeling with modified nucleosides and engineering of the nucleotide salvage pathway. Finally, we discuss profiling RNA-protein interactions using small molecule-dependent RNA editing and synthetic photo-cross-linkable oligonucleotide probes. Our work provides enabling technologies for deciphering the complexity of RNA and its diverse functions in biology.
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Affiliation(s)
- Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ, USA 08544
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16
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Camera F, Romero-Camarero I, Revell BH, Amaral FM, Sinclair OJ, Simeoni F, Wiseman DH, Stojic L, Somervaille TC. Differentiation block in acute myeloid leukemia regulated by intronic sequences of FTO. iScience 2023; 26:107319. [PMID: 37539037 PMCID: PMC10393733 DOI: 10.1016/j.isci.2023.107319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/23/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023] Open
Abstract
Iroquois transcription factor gene IRX3 is highly expressed in 20-30% of acute myeloid leukemia (AML) and contributes to the pathognomonic differentiation block. Intron 8 FTO sequences ∼220kB downstream of IRX3 exhibit histone acetylation, DNA methylation, and contacts with the IRX3 promoter, which correlate with IRX3 expression. Deletion of these intronic elements confirms a role in positively regulating IRX3. RNAseq revealed long non-coding (lnc) transcripts arising from this locus. FTO-lncAML knockdown (KD) induced differentiation of AML cells, loss of clonogenic activity, and reduced FTO intron 8:IRX3 promoter contacts. While both FTO-lncAML KD and IRX3 KD induced differentiation, FTO-lncAML but not IRX3 KD led to HOXA downregulation suggesting transcript activity in trans. FTO-lncAMLhigh AML samples expressed higher levels of HOXA and lower levels of differentiation genes. Thus, a regulatory module in FTO intron 8 consisting of clustered enhancer elements and a long non-coding RNA is active in human AML, impeding myeloid differentiation.
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Affiliation(s)
- Francesco Camera
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Isabel Romero-Camarero
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Bradley H. Revell
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Fabio M.R. Amaral
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Oliver J. Sinclair
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Fabrizio Simeoni
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
| | - Daniel H. Wiseman
- Epigenetics of Haematopoiesis Group, Oglesby Cancer Research Building, The University of Manchester, M20 4GJ Manchester, UK
| | - Lovorka Stojic
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, EC1M 6BQ London, UK
| | - Tim C.P. Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, The Oglesby Cancer Research Centre Building, 555 Wilmslow Road, M20 4GJ Manchester, UK
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17
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Oksuz O, Henninger JE, Warneford-Thomson R, Zheng MM, Erb H, Vancura A, Overholt KJ, Hawken SW, Banani SF, Lauman R, Reich LN, Robertson AL, Hannett NM, Lee TI, Zon LI, Bonasio R, Young RA. Transcription factors interact with RNA to regulate genes. Mol Cell 2023; 83:2449-2463.e13. [PMID: 37402367 PMCID: PMC10529847 DOI: 10.1016/j.molcel.2023.06.012] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/16/2023] [Accepted: 06/06/2023] [Indexed: 07/06/2023]
Abstract
Transcription factors (TFs) orchestrate the gene expression programs that define each cell's identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA binding contributes to TF function by promoting the dynamic association between DNA, RNA, and TF on chromatin. TF-RNA interactions are a conserved feature important for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA, and protein is a general property of many TFs and is fundamental to their gene regulatory function.
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Affiliation(s)
- Ozgur Oksuz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Robert Warneford-Thomson
- Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ming M Zheng
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hailey Erb
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Adrienne Vancura
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kalon J Overholt
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Susana Wilson Hawken
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Program of Computational & Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Salman F Banani
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Richard Lauman
- Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Lauren N Reich
- Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Anne L Robertson
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Nancy M Hannett
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Tong I Lee
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Leonard I Zon
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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18
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Tang X, Cao Y, Wu D, Sun L, Xu Y. Downregulated DUXAP8 lncRNA impedes trophoblast cell proliferation and migration by epigenetically upregulating TFPI2 expression. Reprod Biol Endocrinol 2023; 21:58. [PMID: 37349838 PMCID: PMC10286381 DOI: 10.1186/s12958-023-01108-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Preeclampsia (PE), a pregnancy complication characterized by new-onset hypertension and proteinuria during the second trimester, is the leading cause of neonatal and maternal morbidity and mortality. In the etiology of PE, failure of uterine spiral artery remodeling may be related to functioning abnormally of trophoblast cells, leading to the occurrence and progression of PE. Recently, long noncoding RNAs (lncRNAs) have been reported to play critical roles in PE nowadays. This study aimed to investigate the expression and functions of the TFPI2 pathway-related lncRNA DUXAP8. METHODS DUXAP8 expression in the placenta from pregnancies was examined using qPCR. Then, the in vitro functions of DUXAP8 were investigated through MTT, EdU, colony, transwell, and flow cytometry experiments. The downstream gene expression profiles were assessed using RNA transcriptome sequencing analysis and verified using qPCR and western blot. Furthermore, Immunoprecipitation (RIP), chromatin immunoprecipitation (CHIP) and fluorescence in situ hybridization (FISH) were used to detect the interaction between lncDUXAP8/EZH2/TFPI2. RESULTS The expression of lncRNA DUXAP8 in placenta of patients with eclampsia was significantly decreased. After knockout of DUXAP8, the proliferation and migration of trophoblasts were significantly decreased, and the percentage of apoptosis was increased. Flow cytometry showed that low expression of DUXAP8 increased the accumulation of cells in G2/M phase, while overexpression of DUXAP8 had the opposite effect. We also proved that DUXAP8 epigenetically inhibited TFPI2 expression by recruiting EZH2 and mediating H3K27me3 modification. CONCLUSION Together, these resulting data clarify that aberrant expression of DUXAP8 is involved in the potential PE development and progress. Unraveling the role of DUXAP8 will provide novel insights into the pathogenesis of PE.
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Affiliation(s)
- Xiaotong Tang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, P.R. China
| | - Yueying Cao
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, P.R. China
| | - Dan Wu
- Department of Obstetrics and Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, 123 Tianfeixiang, Mochou Road, Qinhuai District, Nanjing, 210004, P.R. China.
| | - Lizhou Sun
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, P.R. China.
| | - Yetao Xu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, Jiangsu Province, P.R. China.
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19
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Lammer NC, Ashraf HM, Ugay DA, Spencer SL, Allen MA, Batey RT, Wuttke DS. RNA binding by the glucocorticoid receptor attenuates dexamethasone-induced gene activation. Sci Rep 2023; 13:9385. [PMID: 37296231 PMCID: PMC10251336 DOI: 10.1038/s41598-023-35549-y] [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: 12/14/2022] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The glucocorticoid receptor (GR) is a ligand-activated transcription factor that regulates a suite of genes through direct binding of GR to specific DNA promoter elements. GR also interacts with RNA, but the function of this RNA-binding activity remains elusive. Current models speculate that RNA could repress the transcriptional activity of GR. To investigate the function of the GR-RNA interaction on GR's transcriptional activity, we generated cells that stably express a mutant of GR with reduced RNA binding affinity and treated the cells with the GR agonist dexamethasone. Changes in the dexamethasone-driven transcriptome were quantified using 4-thiouridine labeling of RNAs followed by high-throughput sequencing. We find that while many genes are unaffected, GR-RNA binding is repressive for specific subsets of genes in both dexamethasone-dependent and independent contexts. Genes that are dexamethasone-dependent are activated directly by chromatin-bound GR, suggesting a competition-based repression mechanism in which increasing local concentrations of RNA may compete with DNA for binding to GR at sites of transcription. Unexpectedly, genes that are dexamethasone-independent instead display a localization to specific chromosomal regions, which points to changes in chromatin accessibility or architecture. These results show that RNA binding plays a fundamental role in regulating GR function and highlights potential functions for transcription factor-RNA interactions.
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Affiliation(s)
- Nickolaus C Lammer
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Humza M Ashraf
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Daniella A Ugay
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
| | - Sabrina L Spencer
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Mary A Allen
- BioFrontiers Institute, University of Colorado, Boulder, CO, 80309, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA.
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado, Boulder, CO, 80309, USA.
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20
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 403] [Impact Index Per Article: 403.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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21
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Shabna A, Bindhya S, Sidhanth C, Garg M, Ganesan TS. Long non-coding RNAs: Fundamental regulators and emerging targets of cancer stem cells. Biochim Biophys Acta Rev Cancer 2023; 1878:188899. [PMID: 37105414 DOI: 10.1016/j.bbcan.2023.188899] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]
Abstract
Cancer is one of the leading causes of death worldwide, primarily due to the dearth of efficient therapies that result in long-lasting remission. This is especially true in cases of metastatic cancer where drug resistance causes the disease to recur after treatment. One of the factors contributing to drug resistance, metastasis, and aggressiveness of the cancer is cancer stem cells (CSCs) or tumor-initiating cells. As a result, CSCs have emerged as a potential target for drug development. In the present review, we have examined and highlighted the lncRNAs with their regulatory functions specific to CSCs. Moreover, we have discussed the difficulties and various methods involved in identifying lncRNAs that can play a particular role in regulating and maintaining CSCs. Interestingly, this review only focuses on those lncRNAs with strong functional evidence for CSC specificity and the mechanistic role that allows them to be CSC regulators and be the focus of CSC-specific drug development.
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Affiliation(s)
- Aboo Shabna
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India; Laboratory for Cancer Biology, Department of Medical Oncology, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai 610016, India; Department of Endocrinology, Indian Council of Medical Research - National Institute of Nutrtion, Tarnaka, Hyderabad 50007, India
| | - Sadanadhan Bindhya
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India
| | - Chirukandath Sidhanth
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Sector-125, Noida 201301, India
| | - Trivadi S Ganesan
- Laboratory for Cancer Biology, Departments of Medical Oncology and Clinical Research, Cancer Institute (WIA), Chennai 600020, India; Laboratory for Cancer Biology, Department of Medical Oncology, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai 610016, India.
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22
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Mikhaylina A, Svoeglazova A, Stolboushkina E, Tishchenko S, Kostareva O. The RNA-Binding and RNA-Melting Activities of the Multifunctional Protein Nucleobindin 1. Int J Mol Sci 2023; 24:ijms24076193. [PMID: 37047165 PMCID: PMC10093973 DOI: 10.3390/ijms24076193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Nucleobindin 1 (NUCB1) is a ubiquitous multidomain protein that belongs to the EF-hand Ca2+-binding superfamily. NUCB1 interacts with Galphai3 protein, cyclooxygenase, amyloid precursor protein, and lipids. It is involved in stress response and human diseases. In addition, this protein is a transcription factor that binds to the DNA E-box motif. Using surface plasmon resonance and molecular beacon approaches, we first showed the RNA binding and RNA melting activities of NUCB1. We suggest that NUCB1 could induce local changes in structured RNAs via binding to the GGAUAU loop sequence. Our results demonstrate the importance of the multidomain structure of NUCB1 for its RNA-chaperone activity in vitro.
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23
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Boumpas P, Merabet S, Carnesecchi J. Integrating transcription and splicing into cell fate: Transcription factors on the block. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1752. [PMID: 35899407 DOI: 10.1002/wrna.1752] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/22/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022]
Abstract
Transcription factors (TFs) are present in all life forms and conserved across great evolutionary distances in eukaryotes. From yeast to complex multicellular organisms, they are pivotal players of cell fate decision by orchestrating gene expression at diverse molecular layers. Notably, TFs fine-tune gene expression by coordinating RNA fate at both the expression and splicing levels. They regulate alternative splicing, an essential mechanism for cell plasticity, allowing the production of many mRNA and protein isoforms in precise cell and tissue contexts. Despite this apparent role in splicing, how TFs integrate transcription and splicing to ultimately orchestrate diverse cell functions and cell fate decisions remains puzzling. We depict substantial studies in various model organisms underlining the key role of TFs in alternative splicing for promoting tissue-specific functions and cell fate. Furthermore, we emphasize recent advances describing the molecular link between the transcriptional and splicing activities of TFs. As TFs can bind both DNA and/or RNA to regulate transcription and splicing, we further discuss their flexibility and compatibility for DNA and RNA substrates. Finally, we propose several models integrating transcription and splicing activities of TFs in the coordination and diversification of cell and tissue identities. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Mechanisms.
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Affiliation(s)
- Panagiotis Boumpas
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
| | - Samir Merabet
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
| | - Julie Carnesecchi
- Institut de Génomique Fonctionnelle de Lyon, UMR5242, Ecole Normale Supérieure de Lyon, Centre National de la Recherche Scientifique, Université Claude Bernard-Lyon 1, Lyon, France
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24
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Zhou H, Shi BJ. New roles of DNA-binding and forkhead-associated domains of Fkh1 and Fkh2 in cellular functions. Cell Biochem Funct 2022; 40:888-902. [PMID: 36121195 DOI: 10.1002/cbf.3750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 12/15/2022]
Abstract
Two yeast forkhead transcription factors Fkh1 and Fkh2 regulate the transcription of CLB2 cluster genes important for mitosis. Both proteins contain a DNA-binding domain (DBD) and a forkhead-associated domain (FHAD), which are essential for ternary complex formation with transcription factor Mcm1, the transcription of CLB2 cluster genes and the physical interaction with Ndd1 and Clb2. Fkh2 also contains an additional C' domain that contains six consensus Cdk phosphorylation sites, but the function of this domain is dispensable. Here, we found new roles of the DBD, the FHAD, and the C' domain of Fkh1 and Fkh2 in cellular functions. The Fkh2 DBD determines the genetic interaction with NDD1, while both the FHAD and DBD of Fkh1 or Fkh2 determine cell morphology and stability of their own transcripts. Both HFADs, but not DBDs, also mediate physical interaction between Fkh1 and Fkh2. DBD and HFAD of Fkh1 and DBD, but not HFAD, of Fkh2 are also fundamental for nuclear localization. However, the Fkh2-specific C' domain has no role in these aspects except in the stability of some fkh mutant transcripts, which is either increased or decreased in the presence of this domain. These findings reveal that Fkh1 and Fkh2 have multiple cellular functions and function mainly via their DBD and FHAD through a domain-controlled feedback regulation mechanism.
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Affiliation(s)
- Hui Zhou
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
| | - Bu-Jun Shi
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
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25
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Wang Y, Deng XW, Zhu D. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2290-2308. [PMID: 36453685 DOI: 10.1111/jipb.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.
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Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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26
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Song L, Li W, Chen X. Transcription factor is not just a transcription factor. TRENDS IN PLANT SCIENCE 2022; 27:1087-1089. [PMID: 35981952 DOI: 10.1016/j.tplants.2022.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Plant transcription factors (TFs) play important roles in diverse biological processes, including immunity. A recent study by Zhang et al. reported that the rice TF APIP5 regulates immunity through its roles on transcription and mRNA turnover, advancing our conceptual understanding that plant TF may not only function as a TF.
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Affiliation(s)
- Li Song
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China
| | - Weitao Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China; Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China.
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University at Wenjiang, Chengdu, Sichuan 611130, China.
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27
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Steiner H, Lammer NC, Batey RT, Wuttke DS. An Extended DNA Binding Domain of the Estrogen Receptor Alpha Directly Interacts with RNAs in Vitro. Biochemistry 2022; 61:2490-2494. [PMID: 36239332 PMCID: PMC9798703 DOI: 10.1021/acs.biochem.2c00536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Estrogen receptor alpha (ERα) is a ligand-responsive transcription factor critical for sex determination and development. Recent reports challenge the canonical view of ERα function by suggesting an activity beyond binding dsDNA at estrogen-responsive promotor elements: association with RNAs in vivo. Whether these interactions are direct or indirect remains unknown, which limits the ability to understand the extent, specificity, and biological role of ERα-RNA binding. Here we demonstrate that an extended DNA-binding domain of ERα directly binds a wide range of RNAs in vitro with structural specificity. ERα binds RNAs that adopt a range of hairpin-derived structures independent of sequence, while interacting poorly with single- and double-stranded RNA. RNA affinities are only 4-fold weaker than consensus dsDNA and significantly tighter than nonconsensus dsDNA sequences. Moreover, RNA binding is competitive with DNA binding. Together, these data show that ERα utilizes an extended DNA-binding domain to achieve a high-affinity/low-specificity mode for interacting with RNA.
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28
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29
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Bonczek O, Wang L, Gnanasundram SV, Chen S, Haronikova L, Zavadil-Kokas F, Vojtesek B. DNA and RNA Binding Proteins: From Motifs to Roles in Cancer. Int J Mol Sci 2022; 23:ijms23169329. [PMID: 36012592 PMCID: PMC9408909 DOI: 10.3390/ijms23169329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
DNA and RNA binding proteins (DRBPs) are a broad class of molecules that regulate numerous cellular processes across all living organisms, creating intricate dynamic multilevel networks to control nucleotide metabolism and gene expression. These interactions are highly regulated, and dysregulation contributes to the development of a variety of diseases, including cancer. An increasing number of proteins with DNA and/or RNA binding activities have been identified in recent years, and it is important to understand how their activities are related to the molecular mechanisms of cancer. In addition, many of these proteins have overlapping functions, and it is therefore essential to analyze not only the loss of function of individual factors, but also to group abnormalities into specific types of activities in regard to particular cancer types. In this review, we summarize the classes of DNA-binding, RNA-binding, and DRBPs, drawing particular attention to the similarities and differences between these protein classes. We also perform a cross-search analysis of relevant protein databases, together with our own pipeline, to identify DRBPs involved in cancer. We discuss the most common DRBPs and how they are related to specific cancers, reviewing their biochemical, molecular biological, and cellular properties to highlight their functions and potential as targets for treatment.
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Affiliation(s)
- Ondrej Bonczek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
- Correspondence: (O.B.); (B.V.)
| | - Lixiao Wang
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | | | - Sa Chen
- Department of Medical Biosciences, Umea University, 90187 Umea, Sweden
| | - Lucia Haronikova
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Filip Zavadil-Kokas
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
| | - Borivoj Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53 Brno, Czech Republic
- Correspondence: (O.B.); (B.V.)
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30
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Nguyen T, Li S, Chang JTH, Watters JW, Ng H, Osunsade A, David Y, Liu S. Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA. Nat Commun 2022; 13:3988. [PMID: 35810158 PMCID: PMC9271091 DOI: 10.1038/s41467-022-31738-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 06/29/2022] [Indexed: 11/08/2022] Open
Abstract
Biomolecular condensation constitutes an emerging mechanism for transcriptional regulation. Recent studies suggest that the co-condensation between transcription factors (TFs) and DNA can generate mechanical forces driving genome rearrangements. However, the reported forces generated by protein-DNA co-condensation are typically below one piconewton (pN), questioning its physiological significance. Moreover, the force-generating capacity of these condensates in the chromatin context remains unknown. Here, we show that Sox2, a nucleosome-binding pioneer TF, forms co-condensates with DNA and generates forces up to 7 pN, exerting considerable mechanical tension on DNA strands. We find that the disordered domains of Sox2 are required for maximum force generation but not for condensate formation. Furthermore, we show that nucleosomes dramatically attenuate the mechanical stress exerted by Sox2 by sequestering it from coalescing on bare DNA. Our findings reveal that TF-mediated DNA condensation can exert significant mechanical stress on the genome which can nonetheless be attenuated by the chromatin architecture.
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Affiliation(s)
- Tuan Nguyen
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Sai Li
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Jeremy T-H Chang
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - John W Watters
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Htet Ng
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Adewola Osunsade
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yael David
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA.
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31
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Zhang F, Fang H, Wang M, He F, Tao H, Wang R, Long J, Wang J, Wang GL, Ning Y. APIP5 functions as a transcription factor and an RNA-binding protein to modulate cell death and immunity in rice. Nucleic Acids Res 2022; 50:5064-5079. [PMID: 35524572 PMCID: PMC9122607 DOI: 10.1093/nar/gkac316] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/08/2022] [Accepted: 04/20/2022] [Indexed: 01/13/2023] Open
Abstract
Many transcription factors (TFs) in animals bind to both DNA and mRNA, regulating transcription and mRNA turnover. However, whether plant TFs function at both the transcriptional and post-transcriptional levels remains unknown. The rice (Oryza sativa) bZIP TF AVRPIZ-T-INTERACTING PROTEIN 5 (APIP5) negatively regulates programmed cell death and blast resistance and is targeted by the effector AvrPiz-t of the blast fungus Magnaporthe oryzae. We demonstrate that the nuclear localization signal of APIP5 is essential for APIP5-mediated suppression of cell death and blast resistance. APIP5 directly targets two genes that positively regulate blast resistance: the cell wall-associated kinase gene OsWAK5 and the cytochrome P450 gene CYP72A1. APIP5 inhibits OsWAK5 expression and thus limits lignin accumulation; moreover, APIP5 inhibits CYP72A1 expression and thus limits reactive oxygen species production and defense compounds accumulation. Remarkably, APIP5 acts as an RNA-binding protein to regulate mRNA turnover of the cell death- and defense-related genes OsLSD1 and OsRac1. Therefore, APIP5 plays dual roles, acting as TF to regulate gene expression in the nucleus and as an RNA-binding protein to regulate mRNA turnover in the cytoplasm, a previously unidentified regulatory mechanism of plant TFs at the transcriptional and post-transcriptional levels.
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Affiliation(s)
- Fan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hong Fang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Min Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Feng He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hui Tao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ruyi Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiawei Long
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiyang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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32
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Lenz J, Konecna P, Tichy F, Machacova D, Fiala L, Hurnik P, Kyllar M. Unique expression patterns of the embryonal stem cell marker SOX2 and hormone receptors suggest the existence of a subpopulation of epithelial stem/progenitor cells in porcine and bovine endometrium. Vet Med Sci 2022; 8:1489-1501. [PMID: 35561288 PMCID: PMC9297784 DOI: 10.1002/vms3.802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND There are currently insufficient data on the population of endometrial epithelial stem/progenitor cells in farm animals. OBJECTIVES With the aim of identifying a potential population of epithelial stem/progenitor cells in the porcine and bovine endometrium, this study immunohistochemically examined the expression patterns of the oestrogen and progesterone receptors, as well as that of the embryonal stem cell marker SOX2. METHODS A total of 24 endometrial tissue samples obtained from cycling pigs (n = 12) and cows (n = 12) were included in our study. Each endometrium was divided into basal, middle and luminal portions. The percentage of marker-positive cells and the intensity of the immunoreaction in each portion of the endometrium were determined. RESULTS Inverse expression patterns of SOX2 and progesterone receptors were found in both animal species throughout the oestrous cycle. Strong diffuse SOX2 expression was detected in the basal portions of the glands, while a significant decrease in positivity and a weak immunoreaction were found in the luminal two thirds of the glandular epithelium. Strong progesterone receptor expression was observed in at least 90% of glandular cells in the middle and luminal portions, whereas weak staining and significant decrease in positivity were detected in the basal portions of the glands. One oestrogen receptor expression pattern resembled that of progesterone receptors. CONCLUSION The inverse expression patterns of SOX2 and hormone (especially progesterone) receptors suggest that endometrial epithelial stem/progenitor cells represent a subset of cells that reside in the basal portions of the endometrial glands in both the bovine and porcine endometrium.
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Affiliation(s)
- Jiri Lenz
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic.,Department of Pathology, Znojmo Hospital, Znojmo, Czech Republic.,Cytohisto s.r.o., Břeclav, Czech Republic
| | - Petra Konecna
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Frantisek Tichy
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Dominika Machacova
- Department of Anatomy, Histology and Embryology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Brno, Czech Republic
| | - Ludek Fiala
- Cytohisto s.r.o., Břeclav, Czech Republic.,Department of Sexology, Psychiatric Clinic, Faculty of Medicine, Charles University Pilsen, Pilsen, Czech Republic.,Institute of Sexology, First Faculty of Medicine, Charles University Prague, Prague, Czech Republic
| | | | - Michal Kyllar
- Department of Pathobiology, Institute of Morphology, University of Veterinary Medicine Vienna, Vienna, Austria
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lncRNA LUCAT1/ELAVL1/LIN28B/SOX2 Positive Feedback Loop Promotes Cell Stemness in Triple-Negative Breast Cancer. Breast J 2022; 2022:7689718. [PMID: 35711895 PMCID: PMC9187271 DOI: 10.1155/2022/7689718] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/25/2022] [Accepted: 03/15/2022] [Indexed: 11/17/2022]
Abstract
Background. Triple-negative breast cancer (TNBC), as a subtype of breast cancer (BC), features an aggressive nature. Long noncoding RNAs (lncRNAs) are proved to get involved in the processes of cancers. lncRNA lung cancer associated transcript 1 (LUCAT1) has been reported in multiple cancers. The role of LUCAT1 in TNBC and its latent regulatory mechanism were investigated. Methods. RT-qPCR was performed to examine LUCAT1 expression. Functional experiments were implemented to disclose the role of LUCAT1 in TNBC. The underlying regulatory mechanism of LUCAT1 in TNBC was explored by chromatin immunoprecipitation (ChIP), RNA-binding protein immunoprecipitation (RIP), luciferase reporter, and RNA pull-down assays. Results. LUCAT1 is significantly overexpressed in TNBC cells. LUCAT1 interference impedes cell stemness in TNBC cells. SRY-box transcription factor 2 (SOX2) is an active transcription factor of LUCAT1. LUCAT1 recruits ELAV-like RNA binding protein 1 (ELAVL1) protein to stabilize lin-28 homolog B (LIN28B) mRNA, thereby further modulating SOX2 expression, which forms a positive feedback loop. Conclusion. The lncRNA LUCAT1/ELAVL1/LIN28B/SOX2 positive feedback loop promotes cell stemness in TNBC. The exploration of the mechanisms underlying TNBC stemness might be beneficial to TNBC treatment.
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Hamilton DJ, Hein AE, Holmes ZE, Wuttke DS, Batey RT. The DNA-Binding High-Mobility Group Box Domain of Sox Family Proteins Directly Interacts with RNA In Vitro. Biochemistry 2022; 61:10.1021/acs.biochem.2c00218. [PMID: 35511045 PMCID: PMC9636074 DOI: 10.1021/acs.biochem.2c00218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is a growing body of evidence that a substantial number of protein domains identified as DNA-binding also interact with RNA to regulate biological processes. Several recent studies have revealed that the Sox2 transcription factor binds RNA through its high-mobility group box (HMGB) domain in vitro and in vivo. A high degree of conservation of this domain among members of the Sox family of transcription factors suggests that RNA-binding activity may be a general feature of these proteins. To address this hypothesis, we examined a subset of HMGB domains from human Sox family of proteins for their ability to bind both DNA and RNA in vitro. We observed selective, high-affinity interactions between Sox family HMGB domains and various model RNA elements, including a four-way junction RNA, a hairpin RNA with an internal bulge, G-quadruplex RNA, and a fragment of long noncoding RNA ES2, which is known to directly interact with Sox2. Importantly, the HMGB domains bind these RNA ligands significantly tighter than nonconsensus dsDNA and in some cases with affinities rivaling those of their consensus dsDNA sequences. These data suggest that RNA binding is a conserved feature of the Sox family of transcription factors with the potential to modulate unappreciated biological functions.
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Affiliation(s)
- Desmond J Hamilton
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Abigail E Hein
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Zachariah E Holmes
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Robert T Batey
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
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Chen HH, Lu HY, Chang CH, Lin SH, Huang CW, Wei PH, Chen YW, Lin YR, Huang HS, Wang PY, Tsao YP, Chen SL. Breast carcinoma-amplified sequence 2 regulates adult neurogenesis via β-catenin. Stem Cell Res Ther 2022; 13:160. [PMID: 35410459 PMCID: PMC8996563 DOI: 10.1186/s13287-022-02837-9] [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: 09/23/2021] [Accepted: 03/31/2022] [Indexed: 11/10/2022] Open
Abstract
Background Breast carcinoma-amplified sequence 2 (BCAS2) regulates β-catenin gene splicing. The conditional knockout of BCAS2 expression in the forebrain (BCAS2 cKO) of mice confers impaired learning and memory along with decreased β-catenin expression. Because β-catenin reportedly regulates adult neurogenesis, we wondered whether BCAS2 could regulate adult neurogenesis via β-catenin. Methods BCAS2-regulating neurogenesis was investigated by characterizing BCAS2 cKO mice. Also, lentivirus-shBCAS2 was intracranially injected into the hippocampus of wild-type mice to knock down BCAS2 expression. We evaluated the rescue effects of BCAS2 cKO by intracranial injection of adeno-associated virus encoding BCAS2 (AAV-DJ8-BCAS2) and AAV-β-catenin gene therapy. Results To show that BCAS2-regulating adult neurogenesis via β-catenin, first, BCAS2 cKO mice showed low SRY-box 2-positive (Sox2+) neural stem cell proliferation and doublecortin-positive (DCX+) immature neurons. Second, stereotaxic intracranial injection of lentivirus-shBCAS2 knocked down BCAS2 in the hippocampus of wild-type mice, and we confirmed the BCAS2 regulation of adult neurogenesis via β-catenin. Third, AAV-DJ8-BCAS2 gene therapy in BCAS2 cKO mice reversed the low proliferation of Sox2+ neural stem cells and the decreased number of DCX+ immature neurons with increased β-catenin expression. Moreover, AAV-β-catenin gene therapy restored neuron stem cell proliferation and immature neuron differentiation, which further supports BCAS2-regulating adult neurogenesis via β-catenin. In addition, cells targeted by AAV-DJ8 injection into the hippocampus included Sox2 and DCX immature neurons, interneurons, and astrocytes. BCAS2 may regulate adult neurogenesis by targeting Sox2+ and DCX+ immature neurons for autocrine effects and interneurons or astrocytes for paracrine effects. Conclusions BCAS2 can regulate adult neurogenesis in mice via β-catenin. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02837-9.
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Affiliation(s)
- Hsin-Hsiung Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, 7F, No1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan
| | - Hao-Yu Lu
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, 7F, No1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan
| | - Chao-Hsin Chang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, 7F, No1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan
| | - Shih-Hao Lin
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, 7F, No1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan
| | - Chu-Wei Huang
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, 7F, No1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan
| | - Po-Han Wei
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, 7F, No1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan
| | - Yi-Wen Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, 7F, No1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan
| | - Yi-Rou Lin
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, 7F, No1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, No. 1, Section 1, Jen Ai Road, Taipei 100, Taiwan
| | - Pei-Yu Wang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, No. 1, Section 1, Jen Ai Road, Taipei 100, Taiwan
| | - Yeou-Ping Tsao
- Department of Ophthalmology, Mackay Memorial Hospital, No. 92, Sec. 2, Chung Shan North Road, Taipei 104, Taiwan
| | - Show-Li Chen
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, 7F, No1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan.
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NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation. Genes Dev 2022; 36:348-367. [PMID: 35241478 PMCID: PMC8973849 DOI: 10.1101/gad.347690.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/11/2022] [Indexed: 11/25/2022]
Abstract
Here, Huth et al. investigated the role of components of the nonsense-mediated mRNA decay (NMD) pathway in regulating embryonic stem cell (ESC) differentiation, and show that NMD controls expression levels of the translation initiation factor Eif4a2 and its premature termination codon-encoding isoform (Eif4a2PTC). Their findings expose an intricate link between mRNA homeostasis and mTORC1 activity that must be maintained for normal dynamics of cell state transitions. Cell fate transitions depend on balanced rewiring of transcription and translation programs to mediate ordered developmental progression. Components of the nonsense-mediated mRNA decay (NMD) pathway have been implicated in regulating embryonic stem cell (ESC) differentiation, but the exact mechanism is unclear. Here we show that NMD controls expression levels of the translation initiation factor Eif4a2 and its premature termination codon-encoding isoform (Eif4a2PTC). NMD deficiency leads to translation of the truncated eIF4A2PTC protein. eIF4A2PTC elicits increased mTORC1 activity and translation rates and causes differentiation delays. This establishes a previously unknown feedback loop between NMD and translation initiation. Furthermore, our results show a clear hierarchy in the severity of target deregulation and differentiation phenotypes between NMD effector KOs (Smg5 KO > Smg6 KO > Smg7 KO), which highlights heterodimer-independent functions for SMG5 and SMG7. Together, our findings expose an intricate link between mRNA homeostasis and mTORC1 activity that must be maintained for normal dynamics of cell state transitions.
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37
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Maldotti M, Lauria A, Anselmi F, Molineris I, Tamburrini A, Meng G, Polignano IL, Scrivano MG, Campestre F, Simon LM, Rapelli S, Morandi E, Incarnato D, Oliviero S. The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7. Nucleic Acids Res 2022; 50:2587-2602. [PMID: 35137201 PMCID: PMC8934626 DOI: 10.1093/nar/gkac083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/13/2022] Open
Abstract
The histone acetyltransferase p300 (also known as KAT3B) is a general transcriptional coactivator that introduces the H3K27ac mark on enhancers triggering their activation and gene transcription. Genome-wide screenings demonstrated that a large fraction of long non-coding RNAs (lncRNAs) plays a role in cellular processes and organ development although the underlying molecular mechanisms remain largely unclear (1,2). We found 122 lncRNAs that interacts directly with p300. In depth analysis of one of these, lncSmad7, is required to maintain ESC self-renewal and it interacts to the C-terminal domain of p300. lncSmad7 also contains predicted RNA-DNA Hoogsteen forming base pairing. Combined Chromatin Isolation by RNA precipitation followed by sequencing (ChIRP-seq) together with CRISPR/Cas9 mutagenesis of the target sites demonstrate that lncSmad7 binds and recruits p300 to enhancers in trans, to trigger enhancer acetylation and transcriptional activation of its target genes. Thus, these results unveil a new mechanism by which p300 is recruited to the genome.
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Affiliation(s)
- Mara Maldotti
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Andrea Lauria
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Francesca Anselmi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Ivan Molineris
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Annalaura Tamburrini
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Guohua Meng
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Isabelle Laurence Polignano
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Mirko Giuseppe Scrivano
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Fabiola Campestre
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Lisa Marie Simon
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Stefania Rapelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Edoardo Morandi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
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Wang X, Nie P, Zhu D. LncRNA HOXA10-AS Activated by E2F1 Facilitates Proliferation and Migration of Nasopharyngeal Carcinoma Cells Through Sponging miR-582-3p to Upregulate RAB31. Am J Rhinol Allergy 2022; 36:348-359. [PMID: 35072529 DOI: 10.1177/19458924211064400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a kind of head and neck cancer with a characteristic regional distribution. Increasing evidence has illustrated that long noncoding RNAs (lncRNAs) exert the regulatory function in tumor development. Nevertheless, the specific functions of lncRNA HOXA10 antisense RNA (HOXA10-AS) in NPC remain to be clarified. In this research, quantitative reverse transcription polymerase chain reaction detected HOXA10-AS expression in NPC cells. Cell counting kit-8, colony formation, and transwell assays were utilized to measure the proliferation and migration of NPC cells. Moreover, mechanism assays detected the interaction of different genes. Briefly, HOXA10-AS was highly expressed in NPC cells. HOXA10-AS down-regulation restrained NPC cell proliferation and migration. Further, HOXA10-AS could bind to miR-582-3p by acting as a competing endogenous RNA. Besides, Ras-related protein Rab-31 (RAB31) was proven as the target gene of miR-582-3p. Additionally, E2F transcription factor 1 (E2F1) acted as a transcription factor to activate HOXA10-AS expression. In the final rescue assays, we observed that the effect of HOXA10-AS depletion on NPC cell growth could be fully reversed by RAB31 overexpression or miR-582-3p inhibition. In short, our research proved that HOXA10-AS activated by E2F1 facilitated proliferation and migration of NPC cells through sponging miR-582-3p to upregulate RAB31.
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Affiliation(s)
- Xinyan Wang
- Jinan Fourth People's Hospital, Jinan, China
| | - Peilan Nie
- Jinan Fourth People's Hospital, Jinan, China
| | - Dongmei Zhu
- Jinan Fourth People's Hospital, Jinan, China
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39
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Zhang YC, Zhou YF, Cheng Y, Huang JH, Lian JP, Yang L, He RR, Lei MQ, Liu YW, Yuan C, Zhao WL, Xiao S, Chen YQ. Genome-wide analysis and functional annotation of chromatin-enriched noncoding RNAs in rice during somatic cell regeneration. Genome Biol 2022; 23:28. [PMID: 35045887 PMCID: PMC8772118 DOI: 10.1186/s13059-022-02608-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 01/12/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Plants have the remarkable ability to generate callus, a pluripotent cell mass that acquires competence for subsequent tissue regeneration. Global chromatin remodeling is required for this cell fate transition, but how the process is regulated is not fully understood. Chromatin-enriched noncoding RNAs (cheRNAs) are thought to play important roles in maintaining chromatin state. However, whether cheRNAs participate in somatic cell regeneration in plants has not yet been clarified. RESULTS To uncover the characteristics and functions of cheRNAs during somatic cell reprogramming in plants, we systematically investigate cheRNAs during callus induction, proliferation and regeneration in rice. We identify 2284 cheRNAs, most of which are novel long non-coding RNAs or small nucleolar RNAs. These cheRNAs, which are highly conserved across plant species, shuttle between chromatin and the nucleoplasm during somatic cell regeneration. They positively regulate the expression of neighboring genes via specific RNA motifs, which may interact with DNA motifs around cheRNA loci. Large-scale mutant analysis shows that cheRNAs are associated with plant size and seed morphology. Further detailed functional investigation of two che-lncRNAs demonstrates that their loss of function impairs cell dedifferentiation and plant regeneration, highlighting the functions of cheRNAs in regulating the expression of neighboring genes via specific motifs. These findings support cis- regulatory roles of cheRNAs in influencing a variety of rice traits. CONCLUSIONS cheRNAs are a distinct subclass of regulatory non-coding RNAs that are required for somatic cell regeneration and regulate rice traits. Targeting cheRNAs has great potential for crop trait improvement and breeding in future.
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Affiliation(s)
- Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
| | - Yan-Fei Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu Cheng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jia-Hui Huang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Jian-Ping Lian
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Lu Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Rui-Rui He
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Meng-Qi Lei
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yu-Wei Liu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Chao Yuan
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Long Zhao
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shi Xiao
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
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Palacio M, Taatjes DJ. Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription. J Mol Biol 2022; 434:167216. [PMID: 34474085 PMCID: PMC8748285 DOI: 10.1016/j.jmb.2021.167216] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 01/17/2023]
Abstract
The regulation of RNA polymerase II (pol II) transcription requires a complex and context-specific array of proteins and protein complexes, as well as nucleic acids and metabolites. Every major physiological process requires coordinated transcription of specific sets of genes at the appropriate time, and a breakdown in this regulation is a hallmark of human disease. A proliferation of recent studies has revealed that many general transcription components, including sequence-specific, DNA-binding transcription factors, Mediator, and pol II itself, are capable of liquid-liquid phase separation, to form condensates that partition these factors away from the bulk aqueous phase. These findings hold great promise for next-level understanding of pol II transcription; however, many mechanistic aspects align with more conventional models, and whether phase separation per se regulates pol II activity in cells remains controversial. In this review, we describe the conventional and condensate-dependent models, and why their similarities and differences are important. We also compare and contrast these models in the context of genome organization and pol II transcription (initiation, elongation, and termination), and highlight the central role of RNA in these processes. Finally, we discuss mutations that disrupt normal partitioning of transcription factors, and how this may contribute to disease.
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Affiliation(s)
- Megan Palacio
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Dylan J. Taatjes
- Dept. of Biochemistry, University of Colorado, Boulder, CO, USA,corresponding author;
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Lachke SA. RNA-binding proteins and post-transcriptional regulation in lens biology and cataract: Mediating spatiotemporal expression of key factors that control the cell cycle, transcription, cytoskeleton and transparency. Exp Eye Res 2022; 214:108889. [PMID: 34906599 PMCID: PMC8792301 DOI: 10.1016/j.exer.2021.108889] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/29/2021] [Accepted: 12/05/2021] [Indexed: 01/03/2023]
Abstract
Development of the ocular lens - a transparent tissue capable of sustaining frequent shape changes for optimal focusing power - pushes the boundaries of what cells can achieve using the molecular toolkit encoded by their genomes. The mammalian lens contains broadly two types of cells, the anteriorly located monolayer of epithelial cells which, at the equatorial region of the lens, initiate differentiation into fiber cells that contribute to the bulk of the tissue. This differentiation program involves massive upregulation of select fiber cell-expressed RNAs and their subsequent translation into high amounts of proteins, such as crystallins. But intriguingly, fiber cells achieve this while also simultaneously undergoing significant morphological changes such as elongation - involving about 1000-fold length-wise increase - and migration, which requires modulation of cytoskeletal and cell adhesion factors. Adding further to the challenges, these molecular and cellular events have to be coordinated as fiber cells progress toward loss of their nuclei and organelles, which irreversibly compromises their potential for harnessing genetically hardwired information. A long-standing question is how processes downstream of signaling and transcription, which may also participate in feedback regulation, contribute toward orchestrating these cellular differentiation events in the lens. It is now becoming clear from findings over the past decade that post-transcriptional gene expression regulatory mechanisms are critical in controlling cellular proteomes and coordinating key processes in lens development and fiber cell differentiation. Indeed, RNA-binding proteins (RBPs) such as Caprin2, Celf1, Rbm24 and Tdrd7 have now been described in mediating post-transcriptional control over key factors (e.g. Actn2, Cdkn1a (p21Cip1), Cdkn1b (p27Kip1), various crystallins, Dnase2b, Hspb1, Pax6, Prox1, Sox2) that are variously involved in cell cycle, transcription, cytoskeleton maintenance and differentiation in the lens. Furthermore, deficiencies of these RBPs have been shown to result in various eye and lens defects and/or cataract. Because fiber cell differentiation in the lens occurs throughout life, the underlying regulatory mechanisms operational in development are expected to also be recruited for the maintenance of transparency in aged lenses. Indeed, in support of this, TDRD7 and CAPRIN2 loci have been linked to age-related cataract in humans. Here, I will review the role of key RBPs in the lens and their importance in understanding the pathology of lens defects. I will discuss advances in RBP-based gene expression control, in general, and the important challenges that need to be addressed in the lens to define the mechanisms that determine the epithelial and fiber cell proteome. Finally, I will also discuss in detail several key future directions including the application of bioinformatics approaches such as iSyTE to study RBP-based post-transcriptional gene expression control in the aging lens and in the context of age-related cataract.
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Affiliation(s)
- Salil A Lachke
- Department of Biological Sciences, University of Delaware, 105 The Green, Delaware Avenue, 236 Wolf Hall, Newark, DE, USA; Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA.
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Carnesecchi J, Boumpas P, van Nierop Y Sanchez P, Domsch K, Pinto HD, Borges Pinto P, Lohmann I. The Hox transcription factor Ultrabithorax binds RNA and regulates co-transcriptional splicing through an interplay with RNA polymerase II. Nucleic Acids Res 2021; 50:763-783. [PMID: 34931250 PMCID: PMC8789087 DOI: 10.1093/nar/gkab1250] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription factors (TFs) play a pivotal role in cell fate decision by coordinating gene expression programs. Although most TFs act at the DNA layer, few TFs bind RNA and modulate splicing. Yet, the mechanistic cues underlying TFs activity in splicing remain elusive. Focusing on the Drosophila Hox TF Ultrabithorax (Ubx), our work shed light on a novel layer of Ubx function at the RNA level. Transcriptome and genome-wide binding profiles in embryonic mesoderm and Drosophila cells indicate that Ubx regulates mRNA expression and splicing to promote distinct outcomes in defined cellular contexts. Our results demonstrate a new RNA-binding ability of Ubx. We find that the N51 amino acid of the DNA-binding Homeodomain is non-essential for RNA interaction in vitro, but is required for RNA interaction in vivo and Ubx splicing activity. Moreover, mutation of the N51 amino acid weakens the interaction between Ubx and active RNA Polymerase II (Pol II). Our results reveal that Ubx regulates elongation-coupled splicing, which could be coordinated by a dynamic interplay with active Pol II on chromatin. Overall, our work uncovered a novel role of the Hox TFs at the mRNA regulatory layer. This could be an essential function for other classes of TFs to control cell diversity.
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Affiliation(s)
- Julie Carnesecchi
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany.,Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Panagiotis Boumpas
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany
| | - Patrick van Nierop Y Sanchez
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany
| | - Katrin Domsch
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany.,Friedrich-Alexander-University Erlangen-Nürnberg, Department Biology, Division of Developmental Biology, Erlangen, Germany
| | - Hugo Daniel Pinto
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Pedro Borges Pinto
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany.,Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR5242, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Ingrid Lohmann
- Heidelberg University, Centre for Organismal Studies (COS) Heidelberg, Department of Developmental Biology, Heidelberg, Germany
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Feng Z, Ye Z, Xie J, Chen W, Li W, Xing C. Study on the mechanism of LOXL1-AS1/miR-3614-5p/YY1 signal axis in the malignant phenotype regulation of hepatocellular carcinoma. Biol Direct 2021; 16:24. [PMID: 34863279 PMCID: PMC8645132 DOI: 10.1186/s13062-021-00312-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 11/16/2021] [Indexed: 01/29/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with high mortality worldwide. Accumulating researches have indicated that long non‑coding RNAs (lncRNAs) are involved in varies human cancers, including HCC. Nevertheless, the specific molecular mechanism of lncRNA lysyl oxidase like 1 antisense RNA 1 (LOXL1-AS1) in HCC is still unclear. Methods LOXL1-AS1 expression was tested via qRT-PCR in HCC cells. Functional and mechanism assays were respectively done to evaluate the biological functions of HCC cells and the potential interaction of LOXL1-AS1 and other factors. Results We discovered that LOXL1-AS1 was high expressed in HCC cells. Inhibition of LOXL1-AS1 repressed cell proliferation, migration and invasion, but enhanced cell apoptosis in HCC. Further, miR-3614-5p was proven to be sponged by LOXL1-AS1. Additionally, Yin Yang 1 (YY1) was proven as the target gene of miR-3614-5p, and YY1 depletion could repress HCC cell malignant behaviors. YY1 could also transcriptionally activate LOXL1-AS1 expression. In rescue assays, we confirmed that overexpression of YY1 or miR-3614-5p inhibition could reverse the suppressive effects of LOXL1-AS1 silence on the malignant behaviors of HCC cells. Conclusion In short, LOXL1-AS1/miR-3614-5p/YY1 forms a positive loop in modulating HCC cell malignant behaviors. Supplementary Information The online version contains supplementary material available at 10.1186/s13062-021-00312-8.
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Affiliation(s)
- ZhenYu Feng
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - ZhenYu Ye
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - JiaMing Xie
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Wei Chen
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - Wei Li
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, Jiangsu, China
| | - ChunGen Xing
- Department of General Surgery, The Second Affiliated Hospital of Soochow University, No. 1055 Sanxiang Road, Gusu District, Suzhou, 215004, Jiangsu, China.
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E2F1-Induced lncRNA BAIAP2-AS1 Overexpression Contributes to the Malignant Progression of Hepatocellular Carcinoma via miR-361-3p/SOX4 Axis. DISEASE MARKERS 2021; 2021:6256369. [PMID: 34616498 PMCID: PMC8487846 DOI: 10.1155/2021/6256369] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 01/10/2023]
Abstract
Currently, plenty of researches have revealed that long noncoding RNAs (lncRNAs) can act as crucial roles during the progression of various tumors, including hepatocellular carcinoma (HCC). Here, we measured the expression of lncRNA BAIAP2 antisense RNA 1(BAIAP2-AS1) as well as its contribution to the developments of HCC. In this study, the expressions of BAIAP2-AS1 and SOX4 were distinctly upregulated in HCC cells and tissues, and high BAIAP2-AS1 may be a novel biomarker for HCC. E2F1 activated BAIAP2-AS1 expression. The silence of BAIAP2-AS1 inhibited the proliferation and metastasis of HepG2 and PLC5 cells. Assays for relationship verification showed that BAIAP2-AS1 regulated the expression of SOX4 and miR-361-3p. Rescue experiments further confirmed the positive interaction between miR-361-3p and BAIAP2-AS1 as well as between miR-361-3p and SOX4. Overall, BAIAP2-AS1 modulated the miR-361-3p/SOX4 axis to promote the development of HCC. Thus, our study offers a potential therapeutic target for treating HCC.
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Ren H, Wei ZC, Sun YX, Qiu CY, Zhang WJ, Zhang W, Liu T, Che X. ATF2-Induced Overexpression of lncRNA LINC00882, as a Novel Therapeutic Target, Accelerates Hepatocellular Carcinoma Progression via Sponging miR-214-3p to Upregulate CENPM. Front Oncol 2021; 11:714264. [PMID: 34513693 PMCID: PMC8429907 DOI: 10.3389/fonc.2021.714264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/09/2021] [Indexed: 01/05/2023] Open
Abstract
Background Long intergenic non-protein coding RNA 882 (LINC00882) are abnormally expressed in several tumors. Our research aimed to uncover the functions and the potential mechanisms of LINC00882 in hepatocellular carcinoma (HCC) progression. Methods RT-qPCR was applied to identify LINC00882 and miR-214-3p levels in HCC specimens and cells. Luciferase reporter was applied for the exploration of whether activating transcription factor 2 (ATF2) could bind to the promoter region of LINC00882. Cell proliferation, invasion, and migration were evaluated. In vivo tumor xenograft models were constructed to assess tumorigenicity. RT-PCR, Western blot and Luciferase reporter assays were conducted to examine the regulatory relationships among LINC00882, miR-214-3p and ATF2. Results LINC00882 was markedly upregulated in HCC cells and clinical specimens. Additionally, ATF2 could bind directly to the LINC00882 promoter region and activate its transcription. Loss-of-function studies further demonstrated that LINC00882 knockdown inhibited proliferation, invasion, and migration of HCC cells. Mechanistically, LINC00882 adsorbed miR-214-3p, thus promoting the expressions of CENPM. Rescue assays demonstrated that functions of LINC00882 deficiency in HCC cells were reversed through suppressing miR-214-3p. Conclusion Our group identified a novel regulatory axis of ATF2/LINC00882/miR-214-3p/CENPM, which may provide potential therapeutic targets for HCC.
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Affiliation(s)
- Hua Ren
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Zhi-Cheng Wei
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Yan-Xia Sun
- Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chun-Yan Qiu
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Wen-Jue Zhang
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Wei Zhang
- Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tao Liu
- Department of Oncology Rehabilitation, Shenzhen Luohu People's Hospital, Shenzhen, China
| | - Xu Che
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China.,Department of Pancreatic and Gastric Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Du Z, Wen X, Wang Y, Jia L, Zhang S, Liu Y, Zhou L, Li H, Yang W, Wang C, Chen J, Hao Y, Salgado Figueroa D, Chen H, Li D, Chen N, Celik I, Zhu Y, Yan Z, Fu C, Liu S, Jiao B, Wang Z, Zhang H, Gülsoy G, Luo J, Qin B, Gao S, Kapranov P, Esteban MA, Zhang S, Li W, Ay F, Chen R, Hoffman AR, Cui J, Hu JF. Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network. Genome Biol 2021; 22:233. [PMID: 34412677 PMCID: PMC8375132 DOI: 10.1186/s13059-021-02444-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/29/2021] [Indexed: 02/04/2023] Open
Abstract
Background A specific 3-dimensional intrachromosomal architecture of core stem cell factor genes is required to reprogram a somatic cell into pluripotency. As little is known about the epigenetic readers that orchestrate this architectural remodeling, we used a novel chromatin RNA in situ reverse transcription sequencing (CRIST-seq) approach to profile long noncoding RNAs (lncRNAs) in the Oct4 promoter. Results We identify Platr10 as an Oct4 - Sox2 binding lncRNA that is activated in somatic cell reprogramming. Platr10 is essential for the maintenance of pluripotency, and lack of this lncRNA causes stem cells to exit from pluripotency. In fibroblasts, ectopically expressed Platr10 functions in trans to activate core stem cell factor genes and enhance pluripotent reprogramming. Using RNA reverse transcription-associated trap sequencing (RAT-seq), we show that Platr10 interacts with multiple pluripotency-associated genes, including Oct4, Sox2, Klf4, and c-Myc, which have been extensively used to reprogram somatic cells. Mechanistically, we demonstrate that Platr10 helps orchestrate intrachromosomal promoter-enhancer looping and recruits TET1, the enzyme that actively induces DNA demethylation for the initiation of pluripotency. We further show that Platr10 contains an Oct4 binding element that interacts with the Oct4 promoter and a TET1-binding element that recruits TET1. Mutation of either of these two elements abolishes Platr10 activity. Conclusion These data suggest that Platr10 functions as a novel chromatin RNA molecule to control pluripotency in trans by modulating chromatin architecture and regulating DNA methylation in the core stem cell factor network. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02444-6.
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Affiliation(s)
- Zhonghua Du
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China
| | - Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Yudi Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Hui Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China
| | - Wang Yang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China
| | - Jingcheng Chen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China
| | - Yajing Hao
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | | | - Huiling Chen
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA.,Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Dan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China
| | - Naifei Chen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China
| | - Ilkay Celik
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Yanbo Zhu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China
| | - Zi Yan
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Changhao Fu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Shanshan Liu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Benzheng Jiao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Zhuo Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA
| | - Hui Zhang
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, People's Republic of China
| | | | - Jianjun Luo
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Baoming Qin
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, People's Republic of China
| | - Sujun Gao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China
| | - Philipp Kapranov
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, Xiamen, 361021, People's Republic of China
| | - Miguel A Esteban
- Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong, 510530, People's Republic of China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, California, 92037, USA
| | - Runsheng Chen
- CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA.
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China.
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin, 130061, People's Republic of China. .,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA, 94304, USA.
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Bjarnason S, Ruidiaz SF, McIvor J, Mercadante D, Heidarsson PO. Protein intrinsic disorder on a dynamic nucleosomal landscape. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:295-354. [PMID: 34656332 DOI: 10.1016/bs.pmbts.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The complex nucleoprotein landscape of the eukaryotic cell nucleus is rich in dynamic proteins that lack a stable three-dimensional structure. Many of these intrinsically disordered proteins operate directly on the first fundamental level of genome compaction: the nucleosome. Here we give an overview of how disordered interactions with and within nucleosomes shape the dynamics, architecture, and epigenetic regulation of the genetic material, controlling cellular transcription patterns. We highlight experimental and computational challenges in the study of protein disorder and illustrate how integrative approaches are increasingly unveiling the fine details of nuclear interaction networks. We finally dissect sequence properties encoded in disordered regions and assess common features of disordered nucleosome-binding proteins. As drivers of many critical biological processes, disordered proteins are integral to a comprehensive molecular view of the dynamic nuclear milieu.
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Affiliation(s)
- Sveinn Bjarnason
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Sarah F Ruidiaz
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland
| | - Jordan McIvor
- School of Chemical Science, University of Auckland, Auckland, New Zealand
| | - Davide Mercadante
- School of Chemical Science, University of Auckland, Auckland, New Zealand.
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Reykjavík, Iceland.
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Cerebral Organoids Derived from a Parkinson's Patient Exhibit Unique Pathogenesis from Chikungunya Virus Infection When Compared to a Non-Parkinson's Patient. Pathogens 2021; 10:pathogens10070913. [PMID: 34358063 PMCID: PMC8308834 DOI: 10.3390/pathogens10070913] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/05/2021] [Accepted: 07/15/2021] [Indexed: 12/25/2022] Open
Abstract
(1) Background: Arboviruses of medical and veterinary significance have been identified on all seven continents, with every human and animal population at risk for exposure. Like arboviruses, chronic neurodegenerative diseases, like Alzheimer’s and Parkinson’s disease, are found wherever there are humans. Significant differences in baseline gene and protein expression have been determined between human-induced pluripotent stem cell lines derived from non-Parkinson’s disease individuals and from individuals with Parkinson’s disease. It was hypothesized that these inherent differences could impact cerebral organoid responses to viral infection. (2) Methods: In this study, cerebral organoids from a non-Parkinson’s and Parkinson’s patient were infected with Chikungunya virus and observed for two weeks. (3) Results: Parkinson’s organoids lost mass and exhibited a differential antiviral response different from non-Parkinson’s organoids. Neurotransmission data from both infected non-Parkinson’s and Parkinson’s organoids had dysregulation of IL-1, IL-10, and IL-6. These cytokines are associated with mood and could be contributing to persistent depression seen in patients following CHIKV infection. Both organoid types had increased expression of CXCL10, which is linked to demyelination. (4) Conclusions: The differential antiviral response of Parkinson’s organoids compared with non-Parkinson’s organoids highlights the need for more research in neurotropic infections in a neurologically compromised host.
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Liu XX, Bao QX, Li YM, Zhang YH. The promotion of cervical cancer progression by signal transducer and activator of transcription 1-induced up-regulation of lncRNA MEOX2-AS1 as a competing endogenous RNA through miR-143-3p/VDAC1 pathway. Bioengineered 2021; 12:3322-3335. [PMID: 34224325 PMCID: PMC8806930 DOI: 10.1080/21655979.2021.1947174] [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: 11/01/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are the new regulators and biomarkers for various tumors. However, in cervical cancer (CC), the potential roles of lncRNAs are not well characterized. This research aimed at exploring the roles of MEOX2 antisense RNA 1(MEOX2-AS1) in CC progression and the underlying mechanisms. The examination of MEOX2-AS1 levels in CC specimens and cell lines was conducted by RT-PCR. Loss-of-function experiments were performed for the assays of proliferation, migration, and invasion of CC cells after various treatments. Animal experiments were applied for the determination of the effects of MEOX2-AS1 in vivo. Bioinformatics analysis, together with dual-luciferase reporter assays, was applied to demonstrate the possible relationships among MEOX2-AS1, miR-143-3p and VDAC1. In the paper, we reported that MEOX2-AS1 levels were distinctly upregulated in CC cells and tissues, and higher MEOX2-AS1 expressions indicated a poor clinical outcome. Besides, STAT1 could activate transcriptions of MEOX2-AS1 by binding directly to its promoter region. The silence of MEOX2-AS1 suppressed the metastatic and proliferative ability of CC cells, as revealed by functional assays. Mechanistically, MEOX2-AS1 sponged miR-143-3p to regulate VDAC1 expressions. Furthermore, miR-143-3p inhibitor reversed the anti-proliferation and anti-metastasis effect of MEOX2-AS1 knockdown. Overall, the data indicated that the MEOX2-AS1/miR-143-3p/VDAC1 pathway participated in CC progression, making it a novel therapeutic target for CC cures.
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Affiliation(s)
- Xiao-Xing Liu
- Department of Obstetrics and Gynecology, Dongying People's Hospital, Dongying, Shandong, P.R. China
| | - Qi-Xiu Bao
- Department of Public Health, Dongying People's Hospital, Dongying, Shandong, P.R. China
| | - Yan-Mei Li
- Department of Obstetrics and Gynecology, Dongying People's Hospital, Dongying, Shandong, P.R. China
| | - Yan-Hua Zhang
- Department of Obstetrics and Gynecology, Dongying People's Hospital, Dongying, Shandong, P.R. China
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PBRM1 Cooperates with YTHDF2 to Control HIF-1α Protein Translation. Cells 2021; 10:cells10061425. [PMID: 34200988 PMCID: PMC8228889 DOI: 10.3390/cells10061425] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/27/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
PBRM1, a component of the chromatin remodeller SWI/SNF, is often deleted or mutated in human cancers, most prominently in renal cancers. Core components of the SWI/SNF complex have been shown to be important for the cellular response to hypoxia. Here, we investigated how PBRM1 controls HIF-1α activity. We found that PBRM1 is required for HIF-1α transcriptional activity and protein levels. Mechanistically, PBRM1 is important for HIF-1α mRNA translation, as absence of PBRM1 results in reduced actively translating HIF-1α mRNA. Interestingly, we found that PBRM1, but not BRG1, interacts with the m6A reader protein YTHDF2. HIF-1α mRNA is m6A-modified, bound by PBRM1 and YTHDF2. PBRM1 is necessary for YTHDF2 binding to HIF-1α mRNA and reduction of YTHDF2 results in reduced HIF-1α protein expression in cells. Our results identify a SWI/SNF-independent function for PBRM1, interacting with HIF-1α mRNA and the epitranscriptome machinery. Furthermore, our results suggest that the epitranscriptome-associated proteins play a role in the control of hypoxia signalling pathways.
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