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Aich M, Ansari AH, Ding L, Iesmantavicius V, Paul D, Choudhary C, Maiti S, Buchholz F, Chakraborty D. TOBF1 modulates mouse embryonic stem cell fate through regulating alternative splicing of pluripotency genes. Cell Rep 2023; 42:113177. [PMID: 37751355 DOI: 10.1016/j.celrep.2023.113177] [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: 02/08/2023] [Revised: 06/28/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Embryonic stem cells (ESCs) can undergo lineage-specific differentiation, giving rise to different cell types that constitute an organism. Although roles of transcription factors and chromatin modifiers in these cells have been described, how the alternative splicing (AS) machinery regulates their expression has not been sufficiently explored. Here, we show that the long non-coding RNA (lncRNA)-associated protein TOBF1 modulates the AS of transcripts necessary for maintaining stem cell identity in mouse ESCs. Among the genes affected is serine/arginine splicing factor 1 (SRSF1), whose AS leads to global changes in splicing and expression of a large number of downstream genes involved in the maintenance of ESC pluripotency. By overlaying information derived from TOBF1 chromatin occupancy, the distribution of its pluripotency-associated OCT-SOX binding motifs, and transcripts undergoing differential expression and AS upon its knockout, we describe local nuclear territories where these distinct events converge. Collectively, these contribute to the maintenance of mouse ESC identity.
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Affiliation(s)
- Meghali Aich
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Asgar Hussain Ansari
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Li Ding
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Vytautas Iesmantavicius
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Deepanjan Paul
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India
| | - Chunaram Choudhary
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Souvik Maiti
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Debojyoti Chakraborty
- CSIR- Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Guo Z, Zhu J, Qin G, Jia Y, Liu Z, Yang N, Guo R. Static Magnetic Fields Promote Generation of Muscle Lineage Cells from Pluripotent Stem Cells and Myoblasts. Stem Cell Rev Rep 2023; 19:1402-1414. [PMID: 37000377 DOI: 10.1007/s12015-023-10535-z] [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] [Accepted: 03/21/2023] [Indexed: 04/01/2023]
Abstract
Static magnetic fields (SMFs) exhibit numerous biological effects and regulate the proliferation and differentiation of several adult stem cells. However, the role of SMFs in the self-renewal maintenance and developmental potential of pluripotent embryonic stem cells (ESCs) remains largely uninvestigated. Here, we show that SMFs promote the expression of the core pluripotent markers Sox2 and SSEA-1. Furthermore, SMFs facilitate the differentiation of ESCs into cardiomyocytes and skeletal muscle cells. Consistently, transcriptome analysis reveals that muscle lineage differentiation and skeletal system specification of ESCs are remarkably strengthened by SMF stimuli. Additionally, when treated with SMFs, C2C12 myoblasts exhibit an increased proliferation rate, improved expression of skeletal muscle markers and elevated myogenic differentiation capacity compared with control cells. Together, our data show that SMFs effectively promote muscle cell generation from pluripotent stem cells and myoblasts. The noninvasive and convenient physical stimuli can be used to increase the production of muscle cells in regenerative medicine and the manufacture of cultured meat in cellular agriculture.
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Affiliation(s)
- Zhaoyuan Guo
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiahao Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guanyu Qin
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yumei Jia
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zheng Liu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Na Yang
- School of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
- INDUC Scientific Co., Ltd, No. 28-132 Jinshan North Photoelectric Science and Technology Park, Wuxi, 214000, China
| | - Renpeng Guo
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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Kwon YS, Park CB, Lee SM, Zee S, Kim GE, Kim YJ, Sim HJ, Kim JH, Seo JS. Proteomic analysis of zebrafish (Danio rerio) embryos exposed to benzyl benzoate. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:26375-26386. [PMID: 36367642 PMCID: PMC9995408 DOI: 10.1007/s11356-022-24081-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Benzyl benzoate (BB) is widely used in the food, cosmetics, agriculture, and pharmaceutical industries and is discharged into the aquatic environment via various water sources, including wastewater. Research on the bioaccumulation and possible toxicity of BB has been conducted, but the biochemical responses to BB toxicity are not fully understood, and the specific molecular pathways by which BB causes toxicity remain unknown. In this study, label-free quantitative proteomics based on mass spectrometry was applied to investigate protein profiles in zebrafish (Danio rerio) embryos exposed to BB (1 µg/mL) for 7 days. A total of 83 differentially expressed proteins (DEPs) were identified, including 49 up-regulated and 34 down-regulated proteins. The biological functions of proteins regulated by BB were grouped into functional categories and subcategories, including the biosynthesis of organonitrogen compound biosynthetic process, translation, amide biosynthetic process, lipid transport, stress response, and cytoskeletal activity. The results provide novel insight into the molecular basis of the ecotoxicity of BB in aquatic ecosystems.
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Affiliation(s)
- Young Sang Kwon
- Environmental Safety Assessment Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Chang-Beom Park
- Environmental Exposure and Toxicology Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Seung-Min Lee
- Environmental Safety Assessment Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Seonggeun Zee
- Environmental Exposure and Toxicology Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Go-Eun Kim
- Environmental Exposure and Toxicology Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Yeong-Jin Kim
- Environmental Safety Assessment Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Hee-Jung Sim
- Environmental Safety Assessment Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Jong-Hwan Kim
- Environmental Safety Assessment Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea
| | - Jong-Su Seo
- Environmental Safety Assessment Center, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju, 52834, Republic of Korea.
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4
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Jia Y, Guo Z, Zhu J, Qin G, Sun W, Yin Y, Wang H, Guo R. Snap29 Is Dispensable for Self-Renewal Maintenance but Required for Proper Differentiation of Mouse Embryonic Stem Cells. Int J Mol Sci 2023; 24:ijms24010750. [PMID: 36614195 PMCID: PMC9821219 DOI: 10.3390/ijms24010750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Pluripotent embryonic stem cells (ESCs) can self-renew indefinitely and are able to differentiate into all three embryonic germ layers. Synaptosomal-associated protein 29 (Snap29) is implicated in numerous intracellular membrane trafficking pathways, including autophagy, which is involved in the maintenance of ESC pluripotency. However, the function of Snap29 in the self-renewal and differentiation of ESCs remains elusive. Here, we show that Snap29 depletion via CRISPR/Cas does not impair the self-renewal and expression of pluripotency-associated factors in mouse ESCs. However, Snap29 deficiency enhances the differentiation of ESCs into cardiomyocytes, as indicated by heart-like beating cells. Furthermore, transcriptome analysis reveals that Snap29 depletion significantly decreased the expression of numerous genes required for germ layer differentiation. Interestingly, Snap29 deficiency does not cause autophagy blockage in ESCs, which might be rescued by the SNAP family member Snap47. Our data show that Snap29 is dispensable for self-renewal maintenance, but required for the proper differentiation of mouse ESCs.
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Affiliation(s)
- Yumei Jia
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoyuan Guo
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiahao Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guanyu Qin
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenwen Sun
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Yin
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
| | - Haiying Wang
- State Key Laboratory of Medicinal Chemical Biology, Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Renpeng Guo
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Su G, Wang W, Zhao X, Chen J, Zheng J, Liu M, Bi J, Guo D, Chen B, Zhao Z, Shi J, Zhang L, Lu W. Enhancer architecture-dependent multilayered transcriptional regulation orchestrates RA signaling-induced early lineage differentiation of ESCs. Nucleic Acids Res 2021; 49:11575-11595. [PMID: 34723340 PMCID: PMC8599802 DOI: 10.1093/nar/gkab1001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
Signaling pathway-driven target gene transcription is critical for fate determination of embryonic stem cells (ESCs), but enhancer-dependent transcriptional regulation in these processes remains poorly understood. Here, we report enhancer architecture-dependent multilayered transcriptional regulation at the Halr1–Hoxa1 locus that orchestrates retinoic acid (RA) signaling-induced early lineage differentiation of ESCs. We show that both homeobox A1 (Hoxa1) and Hoxa adjacent long non-coding RNA 1 (Halr1) are identified as direct downstream targets of RA signaling and regulated by RARA/RXRA via RA response elements (RAREs). Chromosome conformation capture-based screens indicate that RA signaling promotes enhancer interactions essential for Hoxa1 and Halr1 expression and mesendoderm differentiation of ESCs. Furthermore, the results also show that HOXA1 promotes expression of Halr1 through binding to enhancer; conversely, loss of Halr1 enhances interaction between Hoxa1 chromatin and four distal enhancers but weakens interaction with chromatin inside the HoxA cluster, leading to RA signaling-induced Hoxa1 overactivation and enhanced endoderm differentiation. These findings reveal complex transcriptional regulation involving synergistic regulation by enhancers, transcription factors and lncRNA. This work provides new insight into intrinsic molecular mechanisms underlying ESC fate determination during RA signaling-induced early differentiation.
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Affiliation(s)
- Guangsong Su
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Wenbin Wang
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Xueyuan Zhao
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Jun Chen
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Jian Zheng
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Man Liu
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Jinfang Bi
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Dianhao Guo
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Bohan Chen
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Zhongfang Zhao
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Jiandang Shi
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Lei Zhang
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
| | - Wange Lu
- College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin City, China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, 300071 Tianjin City, China
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6
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Shao JL, Li H, Zhang XR, Zhang X, Li ZZ, Jiao GL, Sun GD. Identification of Serum Exosomal MicroRNA Expression Profiling in Menopausal Females with Osteoporosis by High-throughput Sequencing. Curr Med Sci 2021; 40:1161-1169. [PMID: 33428145 DOI: 10.1007/s11596-020-2306-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/07/2020] [Indexed: 02/07/2023]
Abstract
Estrogen deficiency, which mainly occurs in postmenopausal women, is a primary reason for osteoporosis in clinical diagnosis. However, the molecular regulation of osteoporosis in menopausal females is still not adequately explained in the literature, with the diagnosis and treatment for osteoporosis being limited. Herein, exosomal microRNAs (miRNAs) were used to evaluate their diagnosis and prediction effects in menopausal females with osteoporosis. In this study, 6 menopausal females without osteoporosis and 12 menopausal females with osteoporosis were enrolled. The serum exosomes were isolated, and the miRNA expression was detected by miRNA high-throughput sequencing. Exosomal miRNA effects were analyzed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. The miRNA-targeted genes were evaluated by Targetscan 7.2 and the protein-protein interactions (PPI) by STRING. Hub genes were analyzed by the CytoHubba app of Cytoscape. The results showed that 191 aberrant miRNAs were found in the group of menopausal females with osteoporosis, including 72 upregulated miRNAs and 121 downregulated miRNAs. Aberrant miRNAs were involved in many signaling pathways, such as the Wnt, MAPK, and Hippo pathways. Based on PPI network analysis, FBXL3, FBXL13, COPS2, UBE2D3, DCUN1D1, DCUN1D4, CUL3, FBXO22, ASB6, and COMMD2 were the 10 most notable genes in the PPI network. In conclusion, aberrant serum exosomal miRNAs were associated with an altered risk of osteoporosis in menopausal females and may act as potential biomarkers for the prediction of risk of osteoporosis in menopausal females.
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Affiliation(s)
- Jian-Li Shao
- Department of Orthopedics and Traumatology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, China.
| | - Heng Li
- Department of Orthopedics, Central People's Hospital of Zhanjiang, Zhanjiang, 524045, China
| | - Xiao-Rong Zhang
- Department of Orthopedics and Traumatology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Xia Zhang
- Department of Ultrasound, Mental Hospital of Civil Affairs Bureau, Guangzhou, 510632, China.
| | - Zhi-Zhong Li
- Department of Orthopedics and Traumatology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Gen-Long Jiao
- Department of Orthopedics and Traumatology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Guo-Dong Sun
- Department of Orthopedics and Traumatology, First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
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Niu F, Kazimierska M, Nolte IM, Terpstra MM, de Jong D, Koerts J, van der Sluis T, Rutgers B, O’Connell RM, Kok K, van den Berg A, Dzikiewicz-Krawczyk A, Kluiver J. The miR-26b-5p/KPNA2 Axis Is an Important Regulator of Burkitt Lymphoma Cell Growth. Cancers (Basel) 2020; 12:E1464. [PMID: 32512858 PMCID: PMC7352454 DOI: 10.3390/cancers12061464] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/26/2022] Open
Abstract
The expression of several microRNAs (miRNAs) is known to be changed in Burkitt lymphoma (BL), compared to its normal counterparts. Although for some miRNAs, a role in BL was demonstrated, for most of them, their function is unclear. In this study, we aimed to identify miRNAs that control BL cell growth. Two BL cell lines were infected with lentiviral pools containing either 58 miRNA inhibitors or 44 miRNA overexpression constructs. Eighteen constructs showed significant changes in abundance over time, indicating that they affected BL growth. The screening results were validated by individual green fluorescent protein (GFP) growth competition assays for fifteen of the eighteen constructs. For functional follow-up studies, we focused on miR-26b-5p, whose overexpression inhibited BL cell growth. Argonaute 2 RNA immunoprecipitation (Ago2-IP) in two BL cell lines revealed 47 potential target genes of miR-26b-5p. Overlapping the list of putative targets with genes showing a growth repression phenotype in a genome-wide CRISPR/Cas9 knockout screen, revealed eight genes. The top-5 candidates included EZH2, COPS2, KPNA2, MRPL15, and NOL12. EZH2 is a known target of miR-26b-5p, with oncogenic properties in BL. The relevance of the latter four targets was confirmed using sgRNAs targeting these genes in individual GFP growth competition assays. Luciferase reporter assay confirmed binding of miR-26b-5p to the predicted target site for KPNA2, but not to the other genes. In summary, we identified 18 miRNAs that affected BL cell growth in a loss- or gain-of-function screening. A tumor suppressor role was confirmed for miR-26b-5p, and this effect could at least in part be attributed to KPNA2, a known regulator of OCT4, c-jun, and MYC.
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Affiliation(s)
- Fubiao Niu
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | - Marta Kazimierska
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland;
| | - Ilja M. Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands;
| | - Miente Martijn Terpstra
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (M.M.T.); (K.K.)
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | - Jasper Koerts
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | - Tineke van der Sluis
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | - Bea Rutgers
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | - Ryan M. O’Connell
- Division of Microbiology and Immunology, Huntsman Cancer Institute, Department of Pathology at the University of Utah, Salt Lake City, UT 84112, USA.;
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (M.M.T.); (K.K.)
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
| | | | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands; (F.N.); (D.d.J.); (J.K.); (T.v.d.S.); (B.R.); (A.v.d.B.)
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8
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Cops5 safeguards genomic stability of embryonic stem cells through regulating cellular metabolism and DNA repair. Proc Natl Acad Sci U S A 2020; 117:2519-2525. [PMID: 31964807 DOI: 10.1073/pnas.1915079117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The highly conserved COP9 signalosome (CSN), composed of 8 subunits (Cops1 to Cops8), has been implicated in pluripotency maintenance of human embryonic stem cells (ESCs). Yet, the mechanism for the CSN to regulate pluripotency remains elusive. We previously showed that Cops2, independent of the CSN, is essential for the pluripotency maintenance of mouse ESCs. In this study, we set out to investigate how Cops5 and Cops8 regulate ESC differentiation and tried to establish Cops5 and Cops8 knockout (KO) ESC lines by CRISPR/Cas9. To our surprise, no Cops5 KO ESC clones were identified out of 127 clones, while three Cops8 KO ESC lines were established out of 70 clones. We then constructed an inducible Cops5 KO ESC line. Cops5 KO leads to decreased expression of the pluripotency marker Nanog, proliferation defect, G2/M cell-cycle arrest, and apoptosis of ESCs. Further analysis revealed dual roles of Cops5 in maintaining genomic stability of ESCs. On one hand, Cops5 suppresses the autophagic degradation of Mtch2 to direct cellular metabolism toward glycolysis and minimize reactive oxygen species (ROS) production, thereby reducing endogenous DNA damage. On the other hand, Cops5 is required for high DNA damage repair (DDR) activities in ESCs. Without Cops5, elevated ROS and reduced DDR activities lead to DNA damage accumulation in ESCs. Subsequently, p53 is activated to trigger G2/M arrest and apoptosis. Altogether, our studies reveal an essential role of Cops5 in maintaining genome integrity and self-renewal of ESCs by regulating cellular metabolism and DDR pathways.
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9
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Su G, Guo D, Chen J, Liu M, Zheng J, Wang W, Zhao X, Yin Q, Zhang L, Zhao Z, Shi J, Lu W. A distal enhancer maintaining Hoxa1 expression orchestrates retinoic acid-induced early ESCs differentiation. Nucleic Acids Res 2020; 47:6737-6752. [PMID: 31147716 PMCID: PMC6649716 DOI: 10.1093/nar/gkz482] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 11/17/2022] Open
Abstract
Retinoic acid (RA) induces rapid differentiation of embryonic stem cells (ESCs), partly by activating expression of the transcription factor Hoxa1, which regulates downstream target genes that promote ESCs differentiation. However, mechanisms of RA-induced Hoxa1 expression and ESCs early differentiation remain largely unknown. Here, we identify a distal enhancer interacting with the Hoxa1 locus through a long-range chromatin loop. Enhancer deletion significantly inhibited expression of RA-induced Hoxa1 and endoderm master control genes such as Gata4 and Gata6. Transcriptome analysis revealed that RA-induced early ESCs differentiation was blocked in Hoxa1 enhancer knockout cells, suggesting a requirement for the enhancer. Restoration of Hoxa1 expression partly rescued expression levels of ∼40% of genes whose expression changed following enhancer deletion, and ∼18% of promoters of those rescued genes were directly bound by Hoxa1. Our data show that a distal enhancer maintains Hoxa1 expression through long-range chromatin loop and that Hoxa1 directly regulates downstream target genes expression and then orchestrates RA-induced early differentiation of ESCs. This discovery reveals mechanisms of a novel enhancer regulating RA-induced Hoxa genes expression and early ESCs differentiation.
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Affiliation(s)
- Guangsong Su
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Dianhao Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Jun Chen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Man Liu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Jian Zheng
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Wenbin Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Xueyuan Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Qingqing Yin
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Lei Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Zhongfang Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Jiandang Shi
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, 300071 Tianjin, China
| | - Wange Lu
- Department of Stem Cell Biology and Regenerative Medicine, Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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