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Kim N, Byun S, Um SJ. Additional Sex Combs-like Family Associated with Epigenetic Regulation. Int J Mol Sci 2024; 25:5119. [PMID: 38791157 PMCID: PMC11121404 DOI: 10.3390/ijms25105119] [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: 04/12/2024] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The additional sex combs-like (ASXL) family, a mammalian homolog of the additional sex combs (Asx) of Drosophila, has been implicated in transcriptional regulation via chromatin modifications. Abnormal expression of ASXL family genes leads to myelodysplastic syndromes and various types of leukemia. De novo mutation of these genes also causes developmental disorders. Genes in this family and their neighbor genes are evolutionary conserved in humans and mice. This review provides a comprehensive summary of epigenetic regulations associated with ASXL family genes. Their expression is commonly regulated by DNA methylation at CpG islands preceding transcription starting sites. Their proteins primarily engage in histone tail modifications through interactions with chromatin regulators (PRC2, TrxG, PR-DUB, SRC1, HP1α, and BET proteins) and with transcription factors, including nuclear hormone receptors (RAR, PPAR, ER, and LXR). Histone modifications associated with these factors include histone H3K9 acetylation and methylation, H3K4 methylation, H3K27 methylation, and H2AK119 deubiquitination. Recently, non-coding RNAs have been identified following mutations in the ASXL1 or ASXL3 gene, along with circular ASXLs and microRNAs that regulate ASXL1 expression. The diverse epigenetic regulations linked to ASXL family genes collectively contribute to tumor suppression and developmental processes. Our understanding of ASXL-regulated epigenetics may provide insights into the development of therapeutic epigenetic drugs.
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Affiliation(s)
| | | | - Soo-Jong Um
- Department of Integrative Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Gwangjin-Gu, Seoul 05006, Republic of Korea; (N.K.)
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2
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Brown AL, Meiborg AB, Franz-Wachtel M, Macek B, Gordon S, Rog O, Weadick CJ, Werner MS. Characterization of the Pristionchus pacificus "epigenetic toolkit" reveals the evolutionary loss of the histone methyltransferase complex PRC2. Genetics 2024; 227:iyae041. [PMID: 38513719 PMCID: PMC11075575 DOI: 10.1093/genetics/iyae041] [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: 12/04/2023] [Revised: 12/04/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Comparative approaches have revealed both divergent and convergent paths to achieving shared developmental outcomes. Thus, only through assembling multiple case studies can we understand biological principles. Yet, despite appreciating the conservation-or lack thereof-of developmental networks, the conservation of epigenetic mechanisms regulating these networks is poorly understood. The nematode Pristionchus pacificus has emerged as a model system of plasticity and epigenetic regulation as it exhibits a bacterivorous or omnivorous morph depending on its environment. Here, we determined the "epigenetic toolkit" available to P. pacificus as a resource for future functional work on plasticity, and as a comparison with Caenorhabditis elegans to investigate the conservation of epigenetic mechanisms. Broadly, we observed a similar cast of genes with putative epigenetic function between C. elegans and P. pacificus. However, we also found striking differences. Most notably, the histone methyltransferase complex PRC2 appears to be missing in P. pacificus. We described the deletion/pseudogenization of the PRC2 genes mes-2 and mes-6 and concluded that both were lost in the last common ancestor of P. pacificus and a related species P. arcanus. Interestingly, we observed the enzymatic product of PRC2 (H3K27me3) by mass spectrometry and immunofluorescence, suggesting that a currently unknown methyltransferase has been co-opted for heterochromatin silencing. Altogether, we have provided an inventory of epigenetic genes in P. pacificus to compare with C. elegans. This inventory will enable reverse-genetic experiments related to plasticity and has revealed the first loss of PRC2 in a multicellular organism.
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Affiliation(s)
- Audrey L Brown
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | - Adriaan B Meiborg
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Faculty of Biosciences, Collaboration for joint PhD degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, 72074 Tübingen, Germany
| | - Spencer Gordon
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | - Ofer Rog
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
| | | | - Michael S Werner
- School of Biological Sciences, The University of Utah, Salt Lake City, UT 84112, USA
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3
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Li Y, Mo Y, Chen C, He J, Guo Z. Research advances of polycomb group proteins in regulating mammalian development. Front Cell Dev Biol 2024; 12:1383200. [PMID: 38505258 PMCID: PMC10950033 DOI: 10.3389/fcell.2024.1383200] [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: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Polycomb group (PcG) proteins are a subset of epigenetic factors that are highly conserved throughout evolution. In mammals, PcG proteins can be classified into two muti-proteins complexes: Polycomb repressive complex 1 (PRC1) and PRC2. Increasing evidence has demonstrated that PcG complexes play critical roles in the regulation of gene expression, genomic imprinting, chromosome X-inactivation, and chromatin structure. Accordingly, the dysfunction of PcG proteins is tightly orchestrated with abnormal developmental processes. Here, we summarized and discussed the current knowledge of the biochemical and molecular functions of PcG complexes, especially the PRC1 and PRC2 in mammalian development including embryonic development and tissue development, which will shed further light on the deep understanding of the basic knowledge of PcGs and their functions for reproductive health and developmental disorders.
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Affiliation(s)
| | | | | | - Jin He
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhiheng Guo
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, Jilin, China
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4
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Bharti H, Han S, Chang HW, Reinberg D. Polycomb repressive complex 2 accessory factors: rheostats for cell fate decision? Curr Opin Genet Dev 2024; 84:102137. [PMID: 38091876 DOI: 10.1016/j.gde.2023.102137] [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: 10/04/2023] [Accepted: 11/15/2023] [Indexed: 02/12/2024]
Abstract
Epigenetic reprogramming during development is key to cell identity and the activities of the Polycomb repressive complexes are vital for this process. We focus on polycomb repressive complex 2 (PRC2), which catalyzes H3K27me1/2/3 and safeguards cellular integrity by ensuring proper gene repression. Notably, various accessory factors associate with PRC2, strongly influencing cell fate decisions, and their deregulation contributes to various illnesses. Yet, the exact role of these factors during development and carcinogenesis is not fully understood. Here, we present recent progress toward addressing these points and an analysis of the expression levels of PRC2 accessory factors in various tissues and developmental stages to highlight their abundance and roles. Last, we evaluate their contribution to cancer-specific phenotypes, providing insight into novel anticancer therapies.
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Affiliation(s)
- Hina Bharti
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Sungwook Han
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Han-Wen Chang
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Danny Reinberg
- Howard Hughes Medical Institute, University of Miami, Miller School of Medicine and Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA.
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5
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Yan X, Xia Y, Li B, Ye Z, Li L, Yuan T, Song B, Yu W, Rao T, Ning J, Lin F, Mei S, Mao Z, Zhou X, Li W, Cheng F. The SOX4/EZH2/SLC7A11 signaling axis mediates ferroptosis in calcium oxalate crystal deposition-induced kidney injury. J Transl Med 2024; 22:9. [PMID: 38169402 PMCID: PMC10763321 DOI: 10.1186/s12967-023-04793-1] [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: 07/14/2023] [Accepted: 12/09/2023] [Indexed: 01/05/2024] Open
Abstract
Epigenetic regulation is reported to play a significant role in the pathogenesis of various kidney diseases, including renal cell carcinoma, acute kidney injury, renal fibrosis, diabetic nephropathy, and lupus nephritis. However, the role of epigenetic regulation in calcium oxalate (CaOx) crystal deposition-induced kidney injury remains unclear. Our study demonstrated that the upregulation of enhancer of zeste homolog 2 (EZH2)-mediated ferroptosis facilitates CaOx-induced kidney injury. CaOx crystal deposition promoted ferroptosis in vivo and in vitro. Usage of liproxstatin-1 (Lip-1), a ferroptosis inhibitor, mitigated CaOx-induced kidney damage. Single-nucleus RNA-sequencing, RNA-sequencing, immunohistochemical and western blotting analyses revealed that EZH2 was upregulated in kidney stone patients, kidney stone mice, and oxalate-stimulated HK-2 cells. Experiments involving in vivo EZH2 knockout, in vitro EZH2 knockdown, and in vivo GSK-126 (an EZH2 inhibitor) treatment confirmed the protective effects of EZH2 inhibition on kidney injury and ferroptosis. Mechanistically, the results of RNA-sequencing and chromatin immunoprecipitation assays demonstrated that EZH2 regulates ferroptosis by suppressing solute carrier family 7, member 11 (SLC7A11) expression through trimethylation of histone H3 lysine 27 (H3K27me3) modification. Additionally, SOX4 regulated ferroptosis by directly modulating EZH2 expression. Thus, this study demonstrated that SOX4 facilitates ferroptosis in CaOx-induced kidney injury through EZH2/H3K27me3-mediated suppression of SLC7A11.
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Affiliation(s)
- Xinzhou Yan
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Yuqi Xia
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Bojun Li
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Zehua Ye
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Lei Li
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Tianhui Yuan
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Baofeng Song
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Weimin Yu
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Ting Rao
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Jinzhuo Ning
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Fangyou Lin
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China
| | - Shuqin Mei
- Department of Nephrology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, People's Republic of China
| | - Zhiguo Mao
- Department of Nephrology, Shanghai Changzheng Hospital, Naval Medical University, Shanghai, 200003, People's Republic of China
| | - Xiangjun Zhou
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China.
| | - Wei Li
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China.
| | - Fan Cheng
- Department of Urology, Renmin Hospital, Wuhan University, Wuhan, 430060, Hubei, People's Republic of China.
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6
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Josserand M, Rubanova N, Stefanutti M, Roumeliotis S, Espenel M, Marshall OJ, Servant N, Gervais L, Bardin AJ. Chromatin state transitions in the Drosophila intestinal lineage identify principles of cell-type specification. Dev Cell 2023; 58:3048-3063.e6. [PMID: 38056452 DOI: 10.1016/j.devcel.2023.11.005] [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: 02/06/2023] [Revised: 07/20/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023]
Abstract
Tissue homeostasis relies on rewiring of stem cell transcriptional programs into those of differentiated cells. Here, we investigate changes in chromatin occurring in a bipotent adult stem cells. Combining mapping of chromatin-associated factors with statistical modeling, we identify genome-wide transitions during differentiation in the adult Drosophila intestinal stem cell (ISC) lineage. Active, stem-cell-enriched genes transition to a repressive heterochromatin protein-1-enriched state more prominently in enteroendocrine cells (EEs) than in enterocytes (ECs), in which the histone H1-enriched Black state is preeminent. In contrast, terminal differentiation genes associated with metabolic functions follow a common path from a repressive, primed, histone H1-enriched Black state in ISCs to active chromatin states in EE and EC cells. Furthermore, we find that lineage priming has an important function in adult ISCs, and we identify histone H1 as a mediator of this process. These data define underlying principles of chromatin changes during adult multipotent stem cell differentiation.
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Affiliation(s)
- Manon Josserand
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France
| | - Natalia Rubanova
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France; Institut Curie Bioinformatics Core Facility, PSL Research University, INSERM U900, MINES ParisTech, Paris 75005, France
| | - Marine Stefanutti
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France
| | - Spyridon Roumeliotis
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France
| | - Marion Espenel
- Institut Curie, PSL University, ICGex Next-Generation Sequencing Platform, 75005 Paris, France
| | - Owen J Marshall
- Menzies Institute for Medical Research, University of Tasmania, Hobart 7000, Australia
| | - Nicolas Servant
- Institut Curie Bioinformatics Core Facility, PSL Research University, INSERM U900, MINES ParisTech, Paris 75005, France
| | - Louis Gervais
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France.
| | - Allison J Bardin
- Institut Curie, PSL Research University, Sorbonne University, CNRS UMR 3215, INSERM U934, Genetics and Developmental Biology Department, 75248 Paris, France.
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7
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Heo G, Lee SH, Kim JD, Lee GH, Sim JM, Zhou D, Guo J, Cui XS. GRP78 acts as a cAMP/PKA signaling modulator through the MC4R pathway in porcine embryonic development. FASEB J 2023; 37:e23274. [PMID: 37917004 DOI: 10.1096/fj.202301356r] [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: 07/05/2023] [Revised: 09/23/2023] [Accepted: 10/08/2023] [Indexed: 11/03/2023]
Abstract
Glucose-regulated protein 78 (GRP78) binds to and stabilizes melanocortin 4 receptor (MC4R), which activates protein kinase A (PKA) by regulating G proteins. GRP78 is primarily used as a marker for endoplasmic reticulum stress; however, its other functions have not been well studied. Therefore, in this study, we aimed to investigate the function of GRP78 during porcine embryonic development. The developmental quality of porcine embryos, expression of cell cycle proteins, and function of mitochondria were evaluated by inhibiting the function of GRP78. Porcine oocytes were activated to undergo parthenogenesis, and blastocysts were obtained after 7 days of in vitro culture. GRP78 function was inhibited by adding 20 μM HA15 to the in vitro culture medium. The inhibition in GRP78 function led to a decrease in G proteins release, which subsequently downregulated the cyclic adenosine monophosphate (cAMP)/PKA pathway. Ultimately, inhibition of GRP78 function induced the inhibition of CDK1 and cyclin B expression and disruption of the cell cycle. In addition, inhibition of GRP78 function regulated DRP1 and SIRT1 expression, resulting in mitochondrial dysfunction. This study provides new insights into the role of GRP78 in porcine embryonic development, particularly its involvement in the regulation of the MC4R pathway and downstream cAMP/PKA signaling. The results suggest that the inhibition of GRP78 function in porcine embryos by HA15 treatment may have negative effects on embryo quality and development. This study also demonstrated that GRP78 plays a crucial role in the functioning of MC4R, which releases the G protein during porcine embryonic development.
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Affiliation(s)
- Geun Heo
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Song-Hee Lee
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Ji-Dam Kim
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Gyu-Hyun Lee
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jae-Min Sim
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Dongjie Zhou
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
| | - Jing Guo
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Xiang-Shun Cui
- Department of Animal Science, Chungbuk National University, Cheongju, Republic of Korea
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8
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Forston MD, Wei GZ, Chariker JH, Stephenson T, Andres K, Glover C, Rouchka EC, Whittemore SR, Hetman M. Enhanced oxidative phosphorylation, re-organized intracellular signaling, and epigenetic de-silencing as revealed by oligodendrocyte translatome analysis after contusive spinal cord injury. Sci Rep 2023; 13:21254. [PMID: 38040794 PMCID: PMC10692148 DOI: 10.1038/s41598-023-48425-6] [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: 07/12/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023] Open
Abstract
Reducing the loss of oligodendrocytes (OLs) is a major goal for neuroprotection after spinal cord injury (SCI). Therefore, the OL translatome was determined in Ribotag:Plp1-CreERT2 mice at 2, 10, and 42 days after moderate contusive T9 SCI. At 2 and 42 days, mitochondrial respiration- or actin cytoskeleton/cell junction/cell adhesion mRNAs were upregulated or downregulated, respectively. The latter effect suggests myelin sheath loss/morphological simplification which is consistent with downregulation of cholesterol biosynthesis transcripts on days 10 and 42. Various regulators of pro-survival-, cell death-, and/or oxidative stress response pathways showed peak expression acutely, on day 2. Many acutely upregulated OL genes are part of the repressive SUZ12/PRC2 operon suggesting that epigenetic de-silencing contributes to SCI effects on OL gene expression. Acute OL upregulation of the iron oxidoreductase Steap3 was confirmed at the protein level and replicated in cultured OLs treated with the mitochondrial uncoupler FCCP. Hence, STEAP3 upregulation may mark mitochondrial dysfunction. Taken together, in SCI-challenged OLs, acute and subchronic enhancement of mitochondrial respiration may be driven by axonal loss and subsequent myelin sheath degeneration. Acutely, the OL switch to oxidative phosphorylation may lead to oxidative stress that is further amplified by upregulation of such enzymes as STEAP3.
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Affiliation(s)
- Michael D Forston
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - George Z Wei
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Julia H Chariker
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
- Neuroscience Training, University Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Tyler Stephenson
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Kariena Andres
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Charles Glover
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Eric C Rouchka
- Kentucky IDeA Networks of Biomedical Research Excellence (KY INBRE) Bioinformatics Core, University of Louisville, Louisville, KY, 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Scott R Whittemore
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Michal Hetman
- Kentucky Spinal Cord Injury Research Center, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Neurological Surgery, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Anatomical Sciences & Neurobiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
- MD/PhD Program, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
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Ong ALC, Kokaji T, Kishi A, Takihara Y, Shinozuka T, Shimamoto R, Isotani A, Shirai M, Sasai N. Acquisition of neural fate by combination of BMP blockade and chromatin modification. iScience 2023; 26:107887. [PMID: 37771660 PMCID: PMC10522999 DOI: 10.1016/j.isci.2023.107887] [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: 05/29/2023] [Revised: 08/07/2023] [Accepted: 09/07/2023] [Indexed: 09/30/2023] Open
Abstract
Neural induction is a process where naive cells are converted into committed cells with neural characteristics, and it occurs at the earliest step during embryogenesis. Although the signaling molecules and chromatin remodeling for neural induction have been identified, the mutual relationships between these molecules are yet to be fully understood. By taking advantage of the neural differentiation system of mouse embryonic stem (ES) cells, we discovered that the BMP signal regulates the expression of several polycomb repressor complex (PRC) component genes. We particularly focused on Polyhomeotic Homolog 1 (Phc1) and established Phc1-knockout (Phc1-KO) ES cells. We found that Phc1-KO failed to acquire the neural fate, and the cells remained in pluripotent or primitive non-neural states. Chromatin accessibility analysis suggests that Phc1 is essential for chromatin packing. Aberrant upregulation of the BMP signal was confirmed in the Phc1 homozygotic mutant embryos. Taken together, Phc1 is required for neural differentiation through epigenetic modification.
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Affiliation(s)
- Agnes Lee Chen Ong
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Toshiya Kokaji
- Data-driven biology, NAIST Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Arisa Kishi
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Yoshihiro Takihara
- Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3, Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Takuma Shinozuka
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ren Shimamoto
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Ayako Isotani
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Manabu Shirai
- Omics Research Center (ORC), National Cerebral and Cardiovascular Center, 6-1 Kishibe Shinmachi, Suita, Osaka 564-8565, Japan
| | - Noriaki Sasai
- Division of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma 630-0192, Japan
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10
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Pang LY, DeLuca S, Zhu H, Urban JM, Spradling AC. Chromatin and gene expression changes during female Drosophila germline stem cell development illuminate the biology of highly potent stem cells. eLife 2023; 12:RP90509. [PMID: 37831064 PMCID: PMC10575629 DOI: 10.7554/elife.90509] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
Highly potent animal stem cells either self renew or launch complex differentiation programs, using mechanisms that are only partly understood. Drosophila female germline stem cells (GSCs) perpetuate without change over evolutionary time and generate cystoblast daughters that develop into nurse cells and oocytes. Cystoblasts initiate differentiation by generating a transient syncytial state, the germline cyst, and by increasing pericentromeric H3K9me3 modification, actions likely to suppress transposable element activity. Relatively open GSC chromatin is further restricted by Polycomb repression of testis or somatic cell-expressed genes briefly active in early female germ cells. Subsequently, Neijre/CBP and Myc help upregulate growth and reprogram GSC metabolism by altering mitochondrial transmembrane transport, gluconeogenesis, and other processes. In all these respects GSC differentiation resembles development of the totipotent zygote. We propose that the totipotent stem cell state was shaped by the need to resist transposon activity over evolutionary timescales.
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Affiliation(s)
- Liang-Yu Pang
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - Steven DeLuca
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - Haolong Zhu
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - John M Urban
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - Allan C Spradling
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
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11
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Forston MD, Wei G, Chariker JH, Stephenson T, Andres K, Glover C, Rouchka EC, Whittemore SR, Hetman M. Enhanced oxidative phosphorylation, re-organized intracellular signaling, and epigenetic de-silencing as revealed by oligodendrocyte translatome analysis after contusive spinal cord injury. RESEARCH SQUARE 2023:rs.3.rs-3164618. [PMID: 37546871 PMCID: PMC10402259 DOI: 10.21203/rs.3.rs-3164618/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Reducing the loss of oligodendrocytes (OLs) is a major goal for neuroprotection after spinal cord injury (SCI). Therefore, the OL translatome was determined in Ribotag:Plp1-CreERT2 mice at 2, 10, and 42 days after moderate contusive T9 SCI. At 2 and 42 days, mitochondrial respiration- or actin cytoskeleton/cell junction/cell adhesion mRNAs were upregulated or downregulated, respectively. The latter effect suggests myelin sheath loss/morphological simplification which is consistent with downregulation of cholesterol biosynthesis transcripts on days 10 and 42. Various regulators of pro-survival-, cell death-, and/or oxidative stress response pathways showed peak expression acutely, on day 2. Many acutely upregulated OL genes are part of the repressive SUZ12/PRC2 operon suggesting that epigenetic de-silencing contributes to SCI effects on OL gene expression. Acute OL upregulation of the iron oxidoreductase Steap3 was confirmed at the protein level and replicated in cultured OLs treated with the mitochondrial uncoupler FCCP. Hence, STEAP3 upregulation may mark mitochondrial dysfunction. Taken together, in SCI-challenged OLs, acute and subchronic enhancement of mitochondrial respiration may be driven by axonal loss and subsequent myelin sheath degeneration. Acutely, the OL switch to oxidative phosphorylation may lead to oxidative stress that is further amplified by upregulation of such enzymes as STEAP3.
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Affiliation(s)
| | - George Wei
- University of Louisville School of Medicine
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Naiyer S, Dwivedi L, Singh N, Phulera S, Mohan V, Kamran M. Role of Transcription Factor BEND3 and Its Potential Effect on Cancer Progression. Cancers (Basel) 2023; 15:3685. [PMID: 37509346 PMCID: PMC10377563 DOI: 10.3390/cancers15143685] [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: 05/29/2023] [Revised: 07/08/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
BEND3 is a transcription factor that plays a critical role in the regulation of gene expression in mammals. While there is limited research on the role of BEND3 as a tumor suppressor or an oncogene and its potential role in cancer therapy is still emerging, several studies suggest that it may be involved in both the processes. Its interaction and regulation with multiple other factors via p21 have already been reported to play a significant role in cancer development, which serves as an indication of its potential role in oncogenesis. Its interaction with chromatin modifiers such as NuRD and NoRC and its role in the recruitment of polycomb repressive complex 2 (PRC2) are some of the additional events indicative of its potential role in cancer development. Moreover, a few recent studies indicate BEND3 as a potential target for cancer therapy. Since the specific mechanisms by which BEND3 may contribute to cancer progression are not yet fully elucidated, in this review, we have discussed the possible pathways BEND3 may take to serve as an oncogenic driver or suppressor.
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Affiliation(s)
- Sarah Naiyer
- Department of Biomedical Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lalita Dwivedi
- Faculty of Science, Department of Biotechnology, Invertis University, Bareilly 243122, UP, India
| | - Nishant Singh
- Cell and Gene Therapy Division Absorption System, Exton, PA 19341, USA
| | - Swastik Phulera
- Initium Therapeutics, 22 Strathmore Rd., STE 453, Natick, MA 01760, USA
| | - Vijay Mohan
- Department of Biosciences, School of Basic and Applied Sciences, Galgotias University, Greater Noida 203201, UP, India
| | - Mohammad Kamran
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
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Parast SM, Yu D, Chen C, Dickinson AJ, Chang C, Wang H. Recognition of H2AK119ub plays an important role in RSF1-regulated early Xenopus development. Front Cell Dev Biol 2023; 11:1168643. [PMID: 37529237 PMCID: PMC10389277 DOI: 10.3389/fcell.2023.1168643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Abstract
Polycomb group (PcG) proteins are key regulators of gene expression and developmental programs via covalent modification of histones, but the factors that interpret histone modification marks to regulate embryogenesis are less studied. We previously identified Remodeling and Spacing Factor 1 (RSF1) as a reader of histone H2A lysine 119 ubiquitination (H2AK119ub), the histone mark deposited by Polycomb Repressive Complex 1 (PRC1). In the current study, we used Xenopus laevis as a model to investigate how RSF1 affects early embryonic development and whether recognition of H2AK119ub is important for the function of RSF1. We showed that knockdown of Xenopus RSF1, rsf1, not only induced gastrulation defects as reported previously, but specific targeted knockdown in prospective neural precursors induced neural and neural crest defects, with reductions of marker genes. In addition, similar to knockdown of PRC1 components in Xenopus, the anterior-posterior neural patterning was affected in rsf1 knockdown embryos. Binding of H2AK119ub appeared to be crucial for rsf1 function, as a construct with deletion of the UAB domain, which is required for RSF1 to recognize the H2AK119ub nucleosomes, failed to rescue rsf1 morphant embryos and was less effective in interfering with early Xenopus development when ectopically expressed. Furthermore, ectopic deposition of H2AK119ub on the Smad2 target gene gsc using a ring1a-smad2 fusion protein led to ectopic recruitment of RSF1. The fusion protein was inefficient in inducing mesodermal markers in the animal region or a secondary axis when expressed in the ventral tissues. Taken together, our results reveal that rsf1 modulates similar developmental processes in early Xenopus embryos as components of PRC1 do, and that RSF1 acts at least partially through binding to the H2AK119ub mark via the UAB domain during development.
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Affiliation(s)
- Saeid Mohammad Parast
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Deli Yu
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Chunxu Chen
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Biomedical Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Amanda J. Dickinson
- Department of Biology, College of Humanities and Sciences, Virginia Commonwealth University, Richmond, VA, United States
| | - Chenbei Chang
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Hengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
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14
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Feng X, Wang AH, Juan AH, Ko KD, Jiang K, Riparini G, Ciuffoli V, Kaba A, Lopez C, Naz F, Jarnik M, Aliberti E, Hu S, Segalés J, Khateb M, Acevedo-Luna N, Randazzo D, Cheung TH, Muñoz-Cánoves P, Dell'Orso S, Sartorelli V. Polycomb Ezh1 maintains murine muscle stem cell quiescence through non-canonical regulation of Notch signaling. Dev Cell 2023; 58:1052-1070.e10. [PMID: 37105173 PMCID: PMC10330238 DOI: 10.1016/j.devcel.2023.04.005] [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: 12/16/2022] [Revised: 03/08/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023]
Abstract
Organismal homeostasis and regeneration are predicated on committed stem cells that can reside for long periods in a mitotically dormant but reversible cell-cycle arrest state defined as quiescence. Premature escape from quiescence is detrimental, as it results in stem cell depletion, with consequent defective tissue homeostasis and regeneration. Here, we report that Polycomb Ezh1 confers quiescence to murine muscle stem cells (MuSCs) through a non-canonical function. In the absence of Ezh1, MuSCs spontaneously exit quiescence. Following repeated injuries, the MuSC pool is progressively depleted, resulting in failure to sustain proper muscle regeneration. Rather than regulating repressive histone H3K27 methylation, Ezh1 maintains gene expression of the Notch signaling pathway in MuSCs. Selective genetic reconstitution of the Notch signaling corrects stem cell number and re-establishes quiescence of Ezh1-/- MuSCs.
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Affiliation(s)
- Xuesong Feng
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - A Hongjun Wang
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Aster H Juan
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Kyung Dae Ko
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Kan Jiang
- Biodata Mining & Discovery Section, NIAMS, NIH, Bethesda, MD, USA
| | - Giulia Riparini
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Veronica Ciuffoli
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Aissah Kaba
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Christopher Lopez
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Faiza Naz
- Genomic Technology Section, NIAMS, NIH, Bethesda, MD, USA
| | - Michal Jarnik
- Cell Biology and Neurobiology Branch, NICHD, NIH, Bethesda, MD, USA
| | - Elizabeth Aliberti
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Shenyuan Hu
- Division of Life Sciences, State Key Laboratory of Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Jessica Segalés
- Department of Medicine and Life Sciences (MELIS), Pompeu Fabra University (UPF), Barcelona, Spain
| | - Mamduh Khateb
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | - Natalia Acevedo-Luna
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA
| | | | - Tom H Cheung
- Division of Life Sciences, State Key Laboratory of Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Pura Muñoz-Cánoves
- Department of Medicine and Life Sciences (MELIS), Pompeu Fabra University (UPF), Barcelona, Spain; Altos Labs Inc, San Diego, CA, USA
| | | | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells & Gene Regulation, NIAMS, NIH, Bethesda, MD, USA.
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