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Zhou H, Wu S, Liu L, Li R, Jin P, Li S. Drosophila Relish Activating lncRNA-CR33942 Transcription Facilitates Antimicrobial Peptide Expression in Imd Innate Immune Response. Front Immunol 2022; 13:905899. [PMID: 35720331 PMCID: PMC9201911 DOI: 10.3389/fimmu.2022.905899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 12/29/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are an emerging class of regulators that play crucial roles in regulating the strength and duration of innate immunity. However, little is known about the regulation of Drosophila innate immunity-related lncRNAs. In this study, we first revealed that overexpression of lncRNA-CR33942 could strengthen the expression of the Imd pathway antimicrobial peptide (AMP) genes Diptericin (Dpt) and Attacin-A (AttA) after infection, and vice versa. Secondly, RNA-seq analysis of lncRNA-CR33942-overexpressing flies post Gram-negative bacteria infection confirmed that lncRNA-CR33942 positively regulated the Drosophila immune deficiency (Imd) pathway. Mechanistically, we found that lncRNA-CR33942 interacts and enhances the binding of NF-κB transcription factor Relish to Dpt and AttA promoters, thereby facilitating Dpt and AttA expression. Relish could also directly promote lncRNA-CR33942 transcription by binding to its promoter. Finally, rescue experiments and dynamic expression profiling post-infection demonstrated the vital role of the Relish/lncRNA-CR33942/AMP regulatory axis in enhancing Imd pathway and maintaining immune homeostasis. Our study elucidates novel mechanistic insights into the role of lncRNA-CR33942 in activating Drosophila Imd pathway and the complex regulatory interaction during the innate immune response of animals.
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Affiliation(s)
- Hongjian Zhou
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Shanshan Wu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Li Liu
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China
| | - Ruimin Li
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, China,*Correspondence: Ping Jin, ; Shengjie Li,
| | - Shengjie Li
- Jiangsu Provincial Key Construction Laboratory of Special Biomass Byproduct Resource Utilization, School of Food Science, Nanjing Xiaozhuang University, Nanjing, China,*Correspondence: Ping Jin, ; Shengjie Li,
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Vallot C, Ouimette JF, Makhlouf M, Féraud O, Pontis J, Côme J, Martinat C, Bennaceur-Griscelli A, Lalande M, Rougeulle C. Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape. Cell Stem Cell 2015; 16:533-46. [PMID: 25921272 DOI: 10.1016/j.stem.2015.03.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 01/07/2015] [Accepted: 03/22/2015] [Indexed: 10/23/2022]
Abstract
Human pluripotent stem cells (hPSCs) display extensive epigenetic instability, particularly on the X chromosome. In this study, we show that, in hPSCs, the inactive X chromosome has a specific heterochromatin landscape that predisposes it to erosion of X chromosome inactivation (XCI), a process that occurs spontaneously in hPSCs. Heterochromatin remodeling and gene reactivation occur in a non-random fashion and are confined to specific H3K27me3-enriched domains, leaving H3K9me3-marked regions unaffected. Using single-cell monitoring of XCI erosion, we show that this instability only occurs in pluripotent cells. We also provide evidence that loss of XIST expression is not the primary cause of XCI instability and that gene reactivation from the inactive X (Xi) precedes loss of XIST coating. Notably, expression and coating by the long non-coding RNA XACT are early events in XCI erosion and, therefore, may play a role in mediating this process.
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Affiliation(s)
- Céline Vallot
- Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France; CNRS, UMR7216 Epigenetics and Cell Fate, 75013 Paris, France
| | - Jean-François Ouimette
- Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France; CNRS, UMR7216 Epigenetics and Cell Fate, 75013 Paris, France
| | - Mélanie Makhlouf
- Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France; CNRS, UMR7216 Epigenetics and Cell Fate, 75013 Paris, France
| | - Olivier Féraud
- ESTeam Paris Sud, INSERM U935, Université Paris Sud 11, AP-HP, Villejuif 94802, France
| | - Julien Pontis
- Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France; CNRS, UMR7216 Epigenetics and Cell Fate, 75013 Paris, France
| | - Julien Côme
- INSERM/UEVE UMR 861, ISTEM, AFM, 91030 Evry Cedex, France
| | | | | | - Marc Lalande
- Stem Cell and Systems Genomics Institutes, University of Connecticut, Farmington, CT 06030, USA
| | - Claire Rougeulle
- Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France; CNRS, UMR7216 Epigenetics and Cell Fate, 75013 Paris, France.
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XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells. Nat Genet 2013; 45:239-41. [PMID: 23334669 DOI: 10.1038/ng.2530] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 12/20/2012] [Indexed: 12/14/2022]
Abstract
X-chromosome inactivation (XCI) in mammals relies on XIST, a long noncoding transcript that coats and silences the X chromosome in cis. Here we report the discovery of a long noncoding RNA, XACT, that is expressed from and coats the active X chromosome specifically in human pluripotent cells. In the absence of XIST, XACT is expressed from both X chromosomes in humans but not in mice, suggesting a unique role for XACT in the control of human XCI initiation.
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Kobari L, Yates F, Oudrhiri N, Francina A, Kiger L, Mazurier C, Rouzbeh S, El-Nemer W, Hebert N, Giarratana MC, François S, Chapel A, Lapillonne H, Luton D, Bennaceur-Griscelli A, Douay L. Human induced pluripotent stem cells can reach complete terminal maturation: in vivo and in vitro evidence in the erythropoietic differentiation model. Haematologica 2012; 97:1795-803. [PMID: 22733021 DOI: 10.3324/haematol.2011.055566] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Human induced pluripotent stem cells offer perspectives for cell therapy and research models for diseases. We applied this approach to the normal and pathological erythroid differentiation model by establishing induced pluripotent stem cells from normal and homozygous sickle cell disease donors. DESIGN AND METHODS We addressed the question as to whether these cells can reach complete erythroid terminal maturation notably with a complete switch from fetal to adult hemoglobin. Sickle cell disease induced pluripotent stem cells were differentiated in vitro into red blood cells and characterized for their terminal maturation in terms of hemoglobin content, oxygen transport capacity, deformability, sickling and adherence. Nucleated erythroblast populations generated from normal and pathological induced pluripotent stem cells were then injected into non-obese diabetic severe combined immunodeficiency mice to follow the in vivo hemoglobin maturation. RESULTS We observed that in vitro erythroid differentiation results in predominance of fetal hemoglobin which rescues the functionality of red blood cells in the pathological model of sickle cell disease. We observed, in vivo, the switch from fetal to adult hemoglobin after infusion of nucleated erythroid precursors derived from either normal or pathological induced pluripotent stem cells into mice. CONCLUSIONS These results demonstrate that human induced pluripotent stem cells: i) can achieve complete terminal erythroid maturation, in vitro in terms of nucleus expulsion and in vivo in terms of hemoglobin maturation; and ii) open the way to generation of functionally corrected red blood cells from sickle cell disease induced pluripotent stem cells, without any genetic modification or drug treatment.
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Affiliation(s)
- Ladan Kobari
- UPMC Univ Paris 06, UMR_S938 CDR Saint-Antoine, Prolifération et Différentiation des Cellules Souches, Paris, France
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