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Saha D, Animireddy S, Lee J, Thommen A, Murvin MM, Lu Y, Calabrese JM, Bartholomew B. Enhancer switching in cell lineage priming is linked to eRNA, Brg1's AT-hook, and SWI/SNF recruitment. Mol Cell 2024; 84:1855-1869.e5. [PMID: 38593804 PMCID: PMC11104297 DOI: 10.1016/j.molcel.2024.03.013] [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: 05/08/2023] [Revised: 11/24/2023] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
RNA transcribed from enhancers, i.e., eRNA, has been suggested to directly activate transcription by recruiting transcription factors and co-activators. Although there have been specific examples of eRNA functioning in this way, it is not clear how general this may be. We find that the AT-hook of SWI/SNF preferentially binds RNA and, as part of the esBAF complex, associates with eRNA transcribed from intronic and intergenic regions. Our data suggest that SWI/SNF is globally recruited in cis by eRNA to cell-type-specific enhancers, representative of two distinct stages that mimic early mammalian development, and not at enhancers that are shared between the two stages. In this manner, SWI/SNF facilitates recruitment and/or activation of MLL3/4, p300/CBP, and Mediator to stage-specific enhancers and super-enhancers that regulate the transcription of metabolic and cell lineage priming-related genes. These findings highlight a connection between ATP-dependent chromatin remodeling and eRNA in cell identity and typical- and super-enhancer activation.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Srinivas Animireddy
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Junwoo Lee
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA
| | - Anna Thommen
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - McKenzie M Murvin
- Department of Pharmacology, RNA Discovery Center, Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA; Curriculum in Mechanistic, Interdisciplinary Studies in Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA
| | - J Mauro Calabrese
- Department of Pharmacology, RNA Discovery Center, Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA; Curriculum in Mechanistic, Interdisciplinary Studies in Biology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Center, Houston, TX 77054, USA; UT MD Anderson Cancer, Center for Cancer Epigenetics, Houston, TX 77054, USA.
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Mathies LD, Kim AC, Soukup EM, Thomas AE, Bettinger JC. PBRM-1/PBAF-regulated genes in a multipotent progenitor in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2024; 14:jkad297. [PMID: 38150396 PMCID: PMC10917506 DOI: 10.1093/g3journal/jkad297] [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: 10/15/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
The Caenorhabditis elegans somatic gonadal precursors (SGPs) are multipotent progenitors that generate all somatic cells of the adult reproductive system. The 2 SGPs originate in the mesodermal layer and are born through a division that produces one SGP and one head mesodermal cell (hmc). One hmc terminally differentiates, and the other dies by programmed cell death. The polybromo-associated BAF (PBAF) chromatin remodeling complex promotes the multipotent SGP fate. The complete loss of PBAF causes lethality, so we used a combination of Cre/lox recombination and GFP nanobody-directed protein degradation to eliminate PBRM-1, the signature subunit of the PBAF complex, from 83 mesodermal cells, including SGPs, body muscles, and the hmc. We used RNA sequencing to identify genes acting downstream of PBAF in these cells and identified 1,955 transcripts that were significantly differentially expressed between pbrm-1(-) and pbrm-1(+) in the mesoderm of L1 larvae. We found that genes involved in muscle cell function were overrepresented; most of these genes had lower expression in the absence of PBRM-1, suggesting that PBAF promotes muscle differentiation. Among the differentially expressed genes were 125 that are normally expressed at higher levels in SGP vs hmc and positively regulated by pbrm-1 and 53 that are normally expressed at higher levels in hmc vs SGP and are negatively regulated by pbrm-1; these are candidate regulators of the SGP/hmc fate decision. We validated one candidate gene using a fluorescent reporter; the hsp-12.3 reporter was derepressed in SGPs in pbrm-1 mutants, suggesting that hsp-12.3 expression is normally repressed by pbrm-1 in SGPs.
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Affiliation(s)
- Laura D Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Andrew C Kim
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Evan M Soukup
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Alan’da E Thomas
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jill C Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA 23298, USA
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3
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Liu H, Zhao Y, Zhao G, Deng Y, Chen YE, Zhang J. SWI/SNF Complex in Vascular Smooth Muscle Cells and Its Implications in Cardiovascular Pathologies. Cells 2024; 13:168. [PMID: 38247859 PMCID: PMC10814623 DOI: 10.3390/cells13020168] [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: 11/07/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Mature vascular smooth muscle cells (VSMC) exhibit a remarkable degree of plasticity, a characteristic that has intrigued cardiovascular researchers for decades. Recently, it has become increasingly evident that the chromatin remodeler SWItch/Sucrose Non-Fermentable (SWI/SNF) complex plays a pivotal role in orchestrating chromatin conformation, which is critical for gene regulation. In this review, we provide a summary of research related to the involvement of the SWI/SNF complexes in VSMC and cardiovascular diseases (CVD), integrating these discoveries into the current landscape of epigenetic and transcriptional regulation in VSMC. These novel discoveries shed light on our understanding of VSMC biology and pave the way for developing innovative therapeutic strategies in CVD treatment.
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Affiliation(s)
- Hongyu Liu
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
- Department of Molecular & Integrative Physiology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
- Department of Vascular Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yang Zhao
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
| | - Guizhen Zhao
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
| | - Yongjie Deng
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
| | - Y. Eugene Chen
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
- Department of Cardiac Surgery, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
| | - Jifeng Zhang
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, 2800 Plymouth Road, Ann Arbor, MI 48109, USA; (H.L.); (Y.Z.)
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Kretschmer M, Fischer V, Gapp K. When Dad's Stress Gets under Kid's Skin-Impacts of Stress on Germline Cargo and Embryonic Development. Biomolecules 2023; 13:1750. [PMID: 38136621 PMCID: PMC10742275 DOI: 10.3390/biom13121750] [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] [Received: 11/04/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
Multiple lines of evidence suggest that paternal psychological stress contributes to an increased prevalence of neuropsychiatric and metabolic diseases in the progeny. While altered paternal care certainly plays a role in such transmitted disease risk, molecular factors in the germline might additionally be at play in humans. This is supported by findings on changes to the molecular make up of germ cells and suggests an epigenetic component in transmission. Several rodent studies demonstrate the correlation between paternal stress induced changes in epigenetic modifications and offspring phenotypic alterations, yet some intriguing cases also start to show mechanistic links in between sperm and the early embryo. In this review, we summarise efforts to understand the mechanism of intergenerational transmission from sperm to the early embryo. In particular, we highlight how stress alters epigenetic modifications in sperm and discuss the potential for these modifications to propagate modified molecular trajectories in the early embryo to give rise to aberrant phenotypes in adult offspring.
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Affiliation(s)
- Miriam Kretschmer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Vincent Fischer
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
| | - Katharina Gapp
- Laboratory of Epigenetics and Neuroendocrinology, Department of Health Sciences and Technology, Institute for Neuroscience, ETH Zürich, 8057 Zürich, Switzerland; (M.K.); (V.F.)
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, 8057 Zürich, Switzerland
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5
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Ling X, Wei S, Ling D, Cao S, Chang R, Wang Q, Yuan Z. Irf7 regulates the expression of Srg3 and ferroptosis axis aggravated sepsis-induced acute lung injury. Cell Mol Biol Lett 2023; 28:91. [PMID: 37946128 PMCID: PMC10634032 DOI: 10.1186/s11658-023-00495-0] [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: 05/24/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
OBJECTIVE To investigate the mechanism of action of Srg3 in acute lung injury caused by sepsis. METHODS First, a sepsis-induced acute lung injury rat model was established using cecal ligation and puncture (CLP). RNA sequencing (RNA-seq) was used to screen for highly expressed genes in sepsis-induced acute lung injury (ALI), and the results showed that Srg3 was significantly upregulated. Then, SWI3-related gene 3 (Srg3) was knocked down using AAV9 vector in vivo, and changes in ALI symptoms in rats were analyzed. In vitro experiments were conducted by establishing a cell model using lipopolysaccharide (LPS)-induced BEAS-2B cells and coculturing them with phorbol 12-myristate 13-acetate (PMA)-treated THP-1 cells to analyze macrophage polarization. Next, downstream signaling pathways regulated by Srg3 and transcription factors involved in regulating Srg3 expression were analyzed using the KEGG database. Finally, gain-of-loss functional validation experiments were performed to analyze the role of downstream signaling pathways regulated by Srg3 and transcription factors involved in regulating Srg3 expression in sepsis-induced acute lung injury. RESULTS Srg3 was significantly upregulated in sepsis-induced acute lung injury, and knocking down Srg3 significantly improved the symptoms of ALI in rats. Furthermore, in vitro experiments showed that knocking down Srg3 significantly weakened the inhibitory effect of LPS on the viability of BEAS-2B cells and promoted alternative activation phenotype (M2) macrophage polarization. Subsequent experiments showed that Srg3 can regulate the activation of the NF-κB signaling pathway and promote ferroptosis. Specific activation of the NF-κB signaling pathway or ferroptosis significantly weakened the effect of Srg3 knockdown. It was then found that Srg3 can be transcriptionally activated by interferon regulatory factor 7 (Irf7), and specific inhibition of Irf7 significantly improved the symptoms of ALI. CONCLUSIONS Irf7 transcriptionally activates the expression of Srg3, which can promote ferroptosis and activate classical activation phenotype (M1) macrophage polarization by regulating the NF-κB signaling pathway, thereby exacerbating the symptoms of septic lung injury.
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Affiliation(s)
- Xinyu Ling
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China
| | - Shiyou Wei
- Department of Anesthesiology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China
| | - Dandan Ling
- Department of Anesthesiology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Siqi Cao
- School of Clinical Medicine, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Rui Chang
- Medical Department, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China
| | - Qiuyun Wang
- Department of Anesthesiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Zhize Yuan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, 200433, China.
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6
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Kufe D. Dependence on MUC1-C in Progression of Neuroendocrine Prostate Cancer. Int J Mol Sci 2023; 24:3719. [PMID: 36835130 PMCID: PMC9967814 DOI: 10.3390/ijms24043719] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/11/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
Castration resistant prostate cancer (CRPC) is responsive to androgen receptor (AR) axis targeted agents; however, patients invariably relapse with resistant disease that often progresses to neuroendocrine prostate cancer (NEPC). Treatment-related NEPC (t-NEPC) is highly aggressive with limited therapeutic options and poor survival outcomes. The molecular basis for NEPC progression remains incompletely understood. The MUC1 gene evolved in mammals to protect barrier tissues from loss of homeostasis. MUC1 encodes the transmembrane MUC1-C subunit, which is activated by inflammation and contributes to wound repair. However, chronic activation of MUC1-C contributes to lineage plasticity and carcinogenesis. Studies in human NEPC cell models have demonstrated that MUC1-C suppresses the AR axis and induces the Yamanaka OSKM pluripotency factors. MUC1-C interacts directly with MYC and activates the expression of the BRN2 neural transcription factor (TF) and other effectors, such as ASCL1, of the NE phenotype. MUC1-C also induces the NOTCH1 stemness TF in promoting the NEPC cancer stem cell (CSC) state. These MUC1-C-driven pathways are coupled with activation of the SWI/SNF embryonic stem BAF (esBAF) and polybromo-BAF (PBAF) chromatin remodeling complexes and global changes in chromatin architecture. The effects of MUC1-C on chromatin accessibility integrate the CSC state with the control of redox balance and induction of self-renewal capacity. Importantly, targeting MUC1-C inhibits NEPC self-renewal, tumorigenicity and therapeutic resistance. This dependence on MUC1-C extends to other NE carcinomas, such as SCLC and MCC, and identify MUC1-C as a target for the treatment of these aggressive malignancies with the anti-MUC1 agents now under clinical and preclinical development.
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Affiliation(s)
- Donald Kufe
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
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7
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Roy A, Padhi SS, Khyriem I, Nikose S, Sankar S. H H, Bharathavikru RS. Resetting the epigenome: Methylation dynamics in cancer stem cells. Front Cell Dev Biol 2022; 10:909424. [PMID: 36225315 PMCID: PMC9549938 DOI: 10.3389/fcell.2022.909424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022] Open
Abstract
The molecular mechanisms that regulate stem cell pluripotency and differentiation has shown the crucial role that methylation plays in this process. DNA methylation has been shown to be important in the context of developmental pathways, and the role of histone methylation in establishment of the bivalent state of genes is equally important. Recent studies have shed light on the role of RNA methylation changes in stem cell biology. The dynamicity of these methylation changes not only regulates the effective maintenance of pluripotency or differentiation, but also provides an amenable platform for perturbation by cellular stress pathways that are inherent in immune responses such as inflammation or oncogenic programs involving cancer stem cells. We summarize the recent research on the role of methylation dynamics and how it is reset during differentiation and de-differentiation.
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Affiliation(s)
- Aiendrila Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, Transit campus (Govt. ITI Building), Berhampur, Odisha, India
- EMBL, Rome, Italy
| | - Swati Shree Padhi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, Transit campus (Govt. ITI Building), Berhampur, Odisha, India
| | - Ibakordor Khyriem
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, Transit campus (Govt. ITI Building), Berhampur, Odisha, India
| | - Saket Nikose
- Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra, India
| | - Harsha Sankar S. H
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, Transit campus (Govt. ITI Building), Berhampur, Odisha, India
| | - Ruthrotha Selvi Bharathavikru
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, Transit campus (Govt. ITI Building), Berhampur, Odisha, India
- *Correspondence: Ruthrotha Selvi Bharathavikru,
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8
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Weisberg E, Chowdhury B, Meng C, Case AE, Ni W, Garg S, Sattler M, Azab AK, Sun J, Muz B, Sanchez D, Toure A, Stone RM, Galinsky I, Winer E, Gleim S, Gkountela S, Kedves A, Harrington E, Abrams T, Zoller T, Vaupel A, Manley P, Faller M, Chung B, Chen X, Busenhart P, Stephan C, Calkins K, Bonenfant D, Thoma CR, Forrester W, Griffin JD. BRD9 degraders as chemosensitizers in acute leukemia and multiple myeloma. Blood Cancer J 2022; 12:110. [PMID: 35853853 PMCID: PMC9296512 DOI: 10.1038/s41408-022-00704-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/28/2022] [Indexed: 11/12/2022] Open
Abstract
Bromodomain-containing protein 9 (BRD9), an essential component of the SWI/SNF chromatin remodeling complex termed ncBAF, has been established as a therapeutic target in a subset of sarcomas and leukemias. Here, we used novel small molecule inhibitors and degraders along with RNA interference to assess the dependency on BRD9 in the context of diverse hematological malignancies, including acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), and multiple myeloma (MM) model systems. Following depletion of BRD9 protein, AML cells undergo terminal differentiation, whereas apoptosis was more prominent in ALL and MM. RNA-seq analysis of acute leukemia and MM cells revealed both unique and common signaling pathways affected by BRD9 degradation, with common pathways including those associated with regulation of inflammation, cell adhesion, DNA repair and cell cycle progression. Degradation of BRD9 potentiated the effects of several chemotherapeutic agents and targeted therapies against AML, ALL, and MM. Our findings support further development of therapeutic targeting of BRD9, alone or combined with other agents, as a novel strategy for acute leukemias and MM.
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Affiliation(s)
- Ellen Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Basudev Chowdhury
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Chengcheng Meng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Abigail E Case
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wei Ni
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Swati Garg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Martin Sattler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Abdel Kareem Azab
- Washington University in Saint Louis School of Medicine, St. Louis, MO, USA
| | - Jennifer Sun
- Washington University in Saint Louis School of Medicine, St. Louis, MO, USA
| | - Barbara Muz
- Washington University in Saint Louis School of Medicine, St. Louis, MO, USA
| | - Dana Sanchez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anthia Toure
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ilene Galinsky
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eric Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | | | - Alexia Kedves
- Novartis Pharma AG, Basel, Switzerland.,Alphina Therapeutics, Westport, CT, USA
| | | | | | | | | | | | | | | | - Xin Chen
- Novartis Pharma AG, Basel, Switzerland
| | | | | | | | | | | | | | - James D Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, USA.
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9
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Guo T, Han X, He J, Feng J, Jing J, Janečková E, Lei J, Ho TV, Xu J, Chai Y. KDM6B interacts with TFDP1 to activate P53 signalling in regulating mouse palatogenesis. eLife 2022; 11:74595. [PMID: 35212626 PMCID: PMC9007587 DOI: 10.7554/elife.74595] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenetic regulation plays extensive roles in diseases and development. Disruption of epigenetic regulation not only increases the risk of cancer, but can also cause various developmental defects. However, the question of how epigenetic changes lead to tissue-specific responses during neural crest fate determination and differentiation remains understudied. Using palatogenesis as a model, we reveal the functional significance of Kdm6b, an H3K27me3 demethylase, in regulating mouse embryonic development. Our study shows that Kdm6b plays an essential role in cranial neural crest development, and loss of Kdm6b disturbs P53 pathway-mediated activity, leading to complete cleft palate along with cell proliferation and differentiation defects in mice. Furthermore, activity of H3K27me3 on the promoter of Trp53 is antagonistically controlled by Kdm6b, and Ezh2 in cranial neural crest cells. More importantly, without Kdm6b, the transcription factor TFDP1, which normally binds to the promoter of Trp53, cannot activate Trp53 expression in palatal mesenchymal cells. Furthermore, the function of Kdm6b in activating Trp53 in these cells cannot be compensated for by the closely related histone demethylase Kdm6a. Collectively, our results highlight the important role of the epigenetic regulator KDM6B and how it specifically interacts with TFDP1 to achieve its functional specificity in regulating Trp53 expression, and further provide mechanistic insights into the epigenetic regulatory network during organogenesis.
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Affiliation(s)
- Tingwei Guo
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Xia Han
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jinzhi He
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jifan Feng
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Junjun Jing
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Eva Janečková
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jie Lei
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Jian Xu
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, United States
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10
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Park SY, Cho HS, Chung KH, Lee BN, Kim SH, Kim WJ, Jung JY. Inactivation of PI3K/Akt promotes the odontoblastic differentiation and suppresses the stemness with autophagic flux in dental pulp cells. J Dent Sci 2022; 17:145-154. [PMID: 35028032 PMCID: PMC8739242 DOI: 10.1016/j.jds.2021.05.013] [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: 03/30/2021] [Revised: 05/06/2021] [Indexed: 12/16/2022] Open
Abstract
Background/purpose Autophagy is involved in controlling differentiation of various cell types. The present study aimed to investigate the mechanism related to autophagy in regulating odontogenic differentiation of dental pulp cells. Materials and methods Human dental pulp cells (HDPCs) were cultured in differentiation inductive medium (DM) and odontoblastic differentiation and mineralization were evaluated by alkaline phosphatase (ALP) staining and Alizarin red S staining, respectively. Tooth cavity preparation was made on the mesial surface of lower first molars in rat. The expression of autophagy-related signal molecules was detected using Western blot analysis and Immunohistochemistry. Results HDPCs cultured in DM showed increased autophagic flux and declined phosphorylation of phosphoinositide 3-kinases (PI3K), protein kinase B (Akt), and mTOR. Dentin matrix protein-1 (DMP-1) and dentin sialoprotein (DSP), markers of odontoblastic differentiation, were upregulated and autophagic activation showing increased LC3-II and decreased p62 levels was observed during odontogenic differentiation of HDPCs. However, PI3K blocker 3-methyladenine (3MA), lentiviral shLC3 and Akt activator SC79 attenuated the expression of LC3II as well as DMP-1, ALP activity and mineralization enhanced in HDPCs under DM condition. In addition, 3MA, shLC3 and SC79 recovered the expression of pluripotency factor CD146, Oct4 and Nanog downregulated in DM condition. In rat tooth cavity preparation model, the expression of LC3B and DMP-1 was elevated near odontoblast-dentin layer during reparative dentin formation, whereas 3MA significantly reduced the expression of LC3B and DMP-1. Conclusion These findings indicated autophagy promotes the odontogenic differentiation of dental pulp cells modulating stemness via PI3K/Akt inactivation and the repair of pulp.
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Affiliation(s)
- Sam Young Park
- Department of Oral Physiology, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea
| | - Heui Seung Cho
- Department of Oral Physiology, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea
| | - Kyung Hwun Chung
- Dental Research Institute, School of Dentistry, Seoul National University, Seoul, Republic of Korea
| | - Bin Na Lee
- Department of Operative Dentistry, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea
| | - Sun Hun Kim
- Department of Oral Anatomy, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea
| | - Won Jae Kim
- Department of Oral Physiology, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea
| | - Ji Yeon Jung
- Department of Oral Physiology, Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea
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11
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Induced pluripotency in the context of stem cell expansion bioprocess development, optimization, and manufacturing: a roadmap to the clinic. NPJ Regen Med 2021; 6:72. [PMID: 34725374 PMCID: PMC8560749 DOI: 10.1038/s41536-021-00183-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/07/2021] [Indexed: 11/09/2022] Open
Abstract
The translation of laboratory-scale bioprocess protocols and technologies to industrial scales and the application of human induced pluripotent stem cell (hiPSC) derivatives in clinical trials globally presents optimism for the future of stem-cell products to impact healthcare. However, while many promising therapeutic approaches are being tested in pre-clinical studies, hiPSC-derived products currently account for a small fraction of active clinical trials. The complexity and volatility of hiPSCs present several bioprocessing challenges, where the goal is to generate a sufficiently large, high-quality, homogeneous population for downstream differentiation-the derivatives of which must retain functional efficacy and meet regulatory safety criteria in application. It is argued herein that one of the major challenges currently faced in improving the robustness of routine stem-cell biomanufacturing is in utilizing continuous, meaningful assessments of molecular and cellular characteristics from process to application. This includes integrating process data with biological characteristic and functional assessment data to model the interplay between variables in the search for global optimization strategies. Coupling complete datasets with relevant computational methods will contribute significantly to model development and automation in achieving process robustness. This overarching approach is thus crucially important in realizing the potential of hiPSC biomanufacturing for transformation of regenerative medicine and the healthcare industry.
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12
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Building Pluripotency Identity in the Early Embryo and Derived Stem Cells. Cells 2021; 10:cells10082049. [PMID: 34440818 PMCID: PMC8391114 DOI: 10.3390/cells10082049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 07/27/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
The fusion of two highly differentiated cells, an oocyte with a spermatozoon, gives rise to the zygote, a single totipotent cell, which has the capability to develop into a complete, fully functional organism. Then, as development proceeds, a series of programmed cell divisions occur whereby the arising cells progressively acquire their own cellular and molecular identity, and totipotency narrows until when pluripotency is achieved. The path towards pluripotency involves transcriptome modulation, remodeling of the chromatin epigenetic landscape to which external modulators contribute. Both human and mouse embryos are a source of different types of pluripotent stem cells whose characteristics can be captured and maintained in vitro. The main aim of this review is to address the cellular properties and the molecular signature of the emerging cells during mouse and human early development, highlighting similarities and differences between the two species and between the embryos and their cognate stem cells.
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13
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Novo CL. A Tale of Two States: Pluripotency Regulation of Telomeres. Front Cell Dev Biol 2021; 9:703466. [PMID: 34307383 PMCID: PMC8300013 DOI: 10.3389/fcell.2021.703466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/08/2021] [Indexed: 01/01/2023] Open
Abstract
Inside the nucleus, chromatin is functionally organized and maintained as a complex three-dimensional network of structures with different accessibility such as compartments, lamina associated domains, and membraneless bodies. Chromatin is epigenetically and transcriptionally regulated by an intricate and dynamic interplay of molecular processes to ensure genome stability. Phase separation, a process that involves the spontaneous organization of a solution into separate phases, has been proposed as a mechanism for the timely coordination of several cellular processes, including replication, transcription and DNA repair. Telomeres, the repetitive structures at the end of chromosomes, are epigenetically maintained in a repressed heterochromatic state that prevents their recognition as double-strand breaks (DSB), avoiding DNA damage repair and ensuring cell proliferation. In pluripotent embryonic stem cells, telomeres adopt a non-canonical, relaxed epigenetic state, which is characterized by a low density of histone methylation and expression of telomere non-coding transcripts (TERRA). Intriguingly, this telomere non-canonical conformation is usually associated with chromosome instability and aneuploidy in somatic cells, raising the question of how genome stability is maintained in a pluripotent background. In this review, we will explore how emerging technological and conceptual developments in 3D genome architecture can provide novel mechanistic perspectives for the pluripotent epigenetic paradox at telomeres. In particular, as RNA drives the formation of LLPS, we will consider how pluripotency-associated high levels of TERRA could drive and coordinate phase separation of several nuclear processes to ensure genome stability. These conceptual advances will provide a better understanding of telomere regulation and genome stability within the highly dynamic pluripotent background.
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Affiliation(s)
- Clara Lopes Novo
- The Francis Crick Institute, London, United Kingdom
- Imperial College London, London, United Kingdom
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14
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Mendonca A, Sánchez OF, Xie J, Carneiro A, Lin L, Yuan C. Identifying distinct heterochromatin regions using combinatorial epigenetic probes in live cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194725. [PMID: 34174495 DOI: 10.1016/j.bbagrm.2021.194725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 10/21/2022]
Abstract
The 3D spatial organization of the genome controls gene expression and cell functionality. Heterochromatin (HC), which is the densely compacted and largely silenced part of the chromatin, is the driver for the formation and maintenance of nuclear organization in the mammalian nucleus. It is functionally divided into highly compact constitutive heterochromatin (cHC) and transcriptionally poised facultative heterochromatin (fHC). Long regarded as a static structure, the highly dynamic nature of the heterochromatin is being slowly understood and studied. These changes in HC occur on various temporal scales during the cell cycle and differentiation processes. Most methods that capture information about the heterochromatin are static techniques that cannot provide a readout of how the HC organization evolves with time. The delineation of specific areas such as fHC are also rendered difficult due to its diffusive nature and lack of specific features. Another degree of complexity in characterizing changes in heterochromatin occurs due to the heterogeneity in the HC organization of individual cells, necessitating single cell studies. Overall, there is a need for live cell compatible tools that can stably track the heterochromatin as it undergoes re-organization. In this work, we present an approach to track cHC and fHC based on the epigenetic hallmarks associated with them. Unlike conventional immunostaining approaches, we use small recombinant protein probes that allow us to dynamically monitor the HC by binding to modifications specific to the cHC and fHC, such as H3K9me3, DNA methylation and H3K27me3. We demonstrate the use of the probes to follow the changes in HC induced by drug perturbations at the single cell level. We also use the probe sets combinatorically to simultaneously track chromatin regions enriched in two selected epigenetic modifications using a FRET based approach that enabled us tracking distinctive chromatin features in situ.
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Affiliation(s)
- Agnes Mendonca
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Oscar F Sánchez
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Junkai Xie
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Ana Carneiro
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Li Lin
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA
| | - Chongli Yuan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, IN 47906, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47906, USA.
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15
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Bluemn T, Schmitz J, Chen Y, Zheng Y, Zhang Y, Zheng S, Burns R, DeJong J, Christiansen L, Izaguirre-Carbonell J, Wang D, Zhu N. Arid2 regulates hematopoietic stem cell differentiation in normal hematopoiesis. Exp Hematol 2021; 94:37-46. [PMID: 33346030 PMCID: PMC10041880 DOI: 10.1016/j.exphem.2020.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 01/25/2023]
Abstract
The switch/sugar nonfermenting (SWI/SNF) family of chromatin remodeling complexes have been implicated in normal hematopoiesis. The ARID2 protein is a component of the polybromo-associated BAF (PBAF), one of the two main SWI/SNF complexes. In the current study, we used a conditional Arid2 knockout mouse model to determine its role in normal hematopoiesis. We found that the loss of Arid2 has no discernable effects on steady-state hematopoiesis, with the exception of a modest effect on erythropoiesis. On bone marrow transplantation, however, the loss of Arid2 affects HSC differentiation in a cell-autonomous manner, resulting in significant decreases in the ability to reconstitute the lymphoid lineage. Gene expression analysis of Arid2 knockout cells revealed enrichment of myeloid-biased multipotent progenitor (MPP) cell signatures, while the lymphoid-biased MPPs are enriched in the wild type, consistent with the observed phenotype. Moreover, Arid2 knockout cells revealed enrichment of inflammatory pathways with upregulation of TLR receptors, as well as downstream signaling cascade genes. Furthermore, under lymphocyte-biased growth conditions in vitro, Arid2 null bone marrow cells have significantly impaired proliferation, which decreased further on lipopolysaccharide stimulation. Overall, these data suggest that the loss of Arid2 impairs HSC differentiation ability, and this effect may be mediated through upregulation of inflammatory pathways.
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Affiliation(s)
- Theresa Bluemn
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI
| | | | - Yuhong Chen
- Blood Research Institute, Versiti, Milwaukee, WI
| | | | | | - Shikan Zheng
- Blood Research Institute, Versiti, Milwaukee, WI
| | - Robert Burns
- Blood Research Institute, Versiti, Milwaukee, WI
| | | | - Luke Christiansen
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI
| | | | - Demin Wang
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI
| | - Nan Zhu
- Blood Research Institute, Versiti, Milwaukee, WI; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI.
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16
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Jiang TX, Ma S, Han X, Luo ZY, Zhu QQ, Chiba T, Xie W, Lin K, Qiu XB. Proteasome activator PA200 maintains stability of histone marks during transcription and aging. Am J Cancer Res 2021; 11:1458-1472. [PMID: 33391545 PMCID: PMC7738882 DOI: 10.7150/thno.48744] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/01/2020] [Indexed: 12/13/2022] Open
Abstract
The epigenetic inheritance relies on stability of histone marks, but various diseases, including aging-related disorders, are usually associated with alterations of histone marks. Whether and how the proteasome is responsible for maintaining the histone marks during transcription and aging remain unclear. The core histones can be degraded by the atypical proteasome, which contains the proteasome activator PA200, in an acetylation-dependent manner during somatic DNA damage response and spermiogenesis. Methods: By utilizing a substitute of methionine to label proteins metabolically, we analyzed histone degradation genome-wide by sequencing the DNA fragments following pulse-chase assays. The genome-wide RNA-sequencing analysis was performed to analyze transcription and chromatin-immunoprecipitation (ChIP)-sequencing was used for analyses of histone marks. The experimental models included gene-manipulated cells (including both mouse and yeast), mouse liver, and mice. Results: Degradation of H4 or the transcription-coupled histone variant H3.3 could be suppressed by deletion of PA200 or its yeast ortholog Blm10. The histone deacetylase inhibitor accelerated the degradation rates of H3, while the mutations of the putative acetyl-lysine-binding region of PA200 abolished histone degradation in the G1-arrested cells. Deletion of PA200 dramatically altered deposition of the active transcriptional hallmarks (H3K4me3 and H3K56ac) and transcription, especially during cellular aging. Furthermore, deletion of PA200 or Blm10 accelerated cellular aging. Notably, the PA200-deficient mice displayed a range of aging-related deteriorations, including immune malfunction, anxiety-like behavior and shorter lifespan. Conclusion: PA200 promotes the transcription-coupled degradation of the core histones, and plays an important role in maintaining the stability of histone marks during transcription and aging.
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17
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Hagiwara M, Yasumizu Y, Yamashita N, Rajabi H, Fushimi A, Long MD, Li W, Bhattacharya A, Ahmad R, Oya M, Liu S, Kufe D. MUC1-C Activates the BAF (mSWI/SNF) Complex in Prostate Cancer Stem Cells. Cancer Res 2020; 81:1111-1122. [PMID: 33323379 DOI: 10.1158/0008-5472.can-20-2588] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/12/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022]
Abstract
The Brg/Brahma-associated factor (BAF, mSWI/SNF) chromatin remodeling complex is of importance in development and has been linked to prostate oncogenesis. The oncogenic MUC1-C protein promotes lineage plasticity in the progression of neuroendocrine prostate cancer (NEPC), however, there is no known association between MUC1-C and BAF. We report here that MUC1-C binds directly to the E2F1 transcription factor and that the MUC1-C→E2F1 pathway induces expression of embryonic stem cell-specific BAF (esBAF) components BRG1, ARID1A, BAF60a, BAF155, and BAF170 in castrate-resistant prostate cancer (CRPC) and NEPC cells. In concert with this previously unrecognized pathway, MUC1 was associated with increased expression of E2F1 and esBAF components in NEPC tumors as compared with CRPC, supporting involvement of MUC1-C in activating the E2F1→esBAF pathway with progression to NEPC. MUC1-C formed a nuclear complex with BAF and activated cancer stem cell (CSC) gene signatures and the core pluripotency factor gene network. The MUC1-C→E2F1→BAF pathway was necessary for induction of both the NOTCH1 effector of CSC function and the NANOG pluripotency factor, and collectively, this network drove CSC self-renewal. These findings indicate that MUC1-C promotes NEPC progression by integrating activation of E2F1 and esBAF with induction of NOTCH1, NANOG, and stemness. SIGNIFICANCE: These findings show that MUC1-C, which promotes prostate cancer progression, activates a novel pathway that drives the BAF remodeling complex, induces NOTCH1 and NANOG, and promotes self-renewal of prostate cancer stem cells.
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Affiliation(s)
- Masayuki Hagiwara
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Yota Yasumizu
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Nami Yamashita
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Hasan Rajabi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Atsushi Fushimi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Mark D Long
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Wei Li
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | - Rehan Ahmad
- King Khalid University Hospital College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Mototsugu Oya
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Donald Kufe
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
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18
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Innis SM, Cabot B. GBAF, a small BAF sub-complex with big implications: a systematic review. Epigenetics Chromatin 2020; 13:48. [PMID: 33143733 PMCID: PMC7607862 DOI: 10.1186/s13072-020-00370-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/23/2020] [Indexed: 12/01/2022] Open
Abstract
ATP-dependent chromatin remodeling by histone-modifying enzymes and chromatin remodeling complexes is crucial for maintaining chromatin organization and facilitating gene transcription. In the SWI/SNF family of ATP-dependent chromatin remodelers, distinct complexes such as BAF, PBAF, GBAF, esBAF and npBAF/nBAF are of particular interest regarding their implications in cellular differentiation and development, as well as in various diseases. The recently identified BAF subcomplex GBAF is no exception to this, and information is emerging linking this complex and its components to crucial events in mammalian development. Furthermore, given the essential nature of many of its subunits in maintaining effective chromatin remodeling function, it comes as no surprise that aberrant expression of GBAF complex components is associated with disease development, including neurodevelopmental disorders and numerous malignancies. It becomes clear that building upon our knowledge of GBAF and BAF complex function will be essential for advancements in both mammalian reproductive applications and the development of more effective therapeutic interventions and strategies. Here, we review the roles of the SWI/SNF chromatin remodeling subcomplex GBAF and its subunits in mammalian development and disease.
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Affiliation(s)
- Sarah M Innis
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Birgit Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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19
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Jing R, Guo X, Yang Y, Chen W, Kang J, Zhu S. Long noncoding RNA Q associates with Sox2 and is involved in the maintenance of pluripotency in mouse embryonic stem cells. Stem Cells 2020; 38:834-848. [PMID: 32277787 DOI: 10.1002/stem.3180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/11/2020] [Accepted: 03/17/2020] [Indexed: 11/11/2022]
Abstract
Large intergenic noncoding RNAs (lincRNAs) in ESCs may play an important role in the maintenance of pluripotency. The identification of stem cell-specific lincRNAs and their interacting partners will deepen our understanding of the maintenance of stem cell pluripotency. We identified a lincRNA, LincQ, which is specifically expressed in ESCs and is regulated by core pluripotent transcription factors. It was rapidly downregulated during the differentiation process. Knockdown of LincQ in ESCs led to differentiation, downregulation of pluripotency-related genes, and upregulation of differentiation-related genes. We found that exon 1 of LincQ can specifically bind to Sox2. The Soxp region in Sox2, rather than the high mobility group domain, is responsible for LincQ binding. Importantly, the interaction between LincQ and Sox2 is required for the maintenance of pluripotency in ESCs and the transcription of pluripotency genes. Esrrb and Tfcp2l1 are key downstream targets of LincQ and Sox2, since overexpression of Esrrb and Tfcp2l1 can restore the loss of ESC pluripotency that is induced by LincQ depletion. In summary, we found that LincQ specifically interacts with Sox2 and contributes to the maintenance of pluripotency, highlighting the critical role of lincRNA in the pluripotency regulatory network.
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Affiliation(s)
- Ruiqi Jing
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China.,Institute of Biophysics, Chinese Academy of Sciences, Beijing, People's Republic of China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China.,Institute for Advanced Study, Tongji University, Shanghai, People's Republic of China
| | - Yiwei Yang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Wen Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China.,Tsingtao Advanced Research Institute, Tongji University, Qingdao, People's Republic of China
| | - Songcheng Zhu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, School of Life Sciences and Technology, Tongji University, Shanghai, People's Republic of China
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20
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Han J, Kim I, Park JH, Yun JH, Joo K, Kim T, Park GY, Ryu KS, Ko YJ, Mizutani K, Park SY, Seong RH, Lee J, Suh JY, Lee W. A Coil-to-Helix Transition Serves as a Binding Motif for hSNF5 and BAF155 Interaction. Int J Mol Sci 2020; 21:E2452. [PMID: 32244797 PMCID: PMC7177284 DOI: 10.3390/ijms21072452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023] Open
Abstract
Human SNF5 and BAF155 constitute the core subunit of multi-protein SWI/SNF chromatin-remodeling complexes that are required for ATP-dependent nucleosome mobility and transcriptional control. Human SNF5 (hSNF5) utilizes its repeat 1 (RPT1) domain to associate with the SWIRM domain of BAF155. Here, we employed X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and various biophysical methods in order to investigate the detailed binding mechanism between hSNF5 and BAF155. Multi-angle light scattering data clearly indicate that hSNF5171-258 and BAF155SWIRM are both monomeric in solution and they form a heterodimer. NMR data and crystal structure of the hSNF5171-258/BAF155SWIRM complex further reveal a unique binding interface, which involves a coil-to-helix transition upon protein binding. The newly formed αN helix of hSNF5171-258 interacts with the β2-α1 loop of hSNF5 via hydrogen bonds and it also displays a hydrophobic interaction with BAF155SWIRM. Therefore, the N-terminal region of hSNF5171-258 plays an important role in tumorigenesis and our data will provide a structural clue for the pathogenesis of Rhabdoid tumors and malignant melanomas that originate from mutations in the N-terminal loop region of hSNF5.
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Affiliation(s)
- Jeongmin Han
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea; (J.H.); (J.-H.P.); (J.-H.Y.); (T.K.); (G.-Y.P.)
| | - Iktae Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea;
| | - Jae-Hyun Park
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea; (J.H.); (J.-H.P.); (J.-H.Y.); (T.K.); (G.-Y.P.)
| | - Ji-Hye Yun
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea; (J.H.); (J.-H.P.); (J.-H.Y.); (T.K.); (G.-Y.P.)
| | - Keehyoung Joo
- Center for In Silico Protein Science and Center for Advanced Computation, Korea Institute for Advanced Study, Seoul 130-722, Korea;
| | - Taehee Kim
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea; (J.H.); (J.-H.P.); (J.-H.Y.); (T.K.); (G.-Y.P.)
| | - Gye-Young Park
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea; (J.H.); (J.-H.P.); (J.-H.Y.); (T.K.); (G.-Y.P.)
| | - Kyoung-Seok Ryu
- Division of Magnetic Resonance Research, Korea Basic Science Institute, Yangcheong-Ri 804-1, Ochang-Eup, Cheongwon-Gun, Chungcheongbuk-Do 363-883, Korea;
| | - Yoon-Joo Ko
- National Center for Inter-University Research Facilities, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea;
| | - Kenji Mizutani
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan; (K.M.); (S.-Y.P.)
| | - Sam-Young Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan; (K.M.); (S.-Y.P.)
| | - Rho Hyun Seong
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Research Center for Functional Cellulomics, Seoul National University, Seoul 151-742, Korea;
| | - Jooyoung Lee
- Center for In Silico Protein Science and School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-722, Korea
| | - Jeong-Yong Suh
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea;
| | - Weontae Lee
- Structural Biochemistry & Molecular Biophysics Laboratory, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-740, Korea; (J.H.); (J.-H.P.); (J.-H.Y.); (T.K.); (G.-Y.P.)
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21
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Hasan N, Ahuja N. The Emerging Roles of ATP-Dependent Chromatin Remodeling Complexes in Pancreatic Cancer. Cancers (Basel) 2019; 11:E1859. [PMID: 31769422 PMCID: PMC6966483 DOI: 10.3390/cancers11121859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023] Open
Abstract
Pancreatic cancer is an aggressive cancer with low survival rates. Genetic and epigenetic dysregulation has been associated with the initiation and progression of pancreatic tumors. Multiple studies have pointed to the involvement of aberrant chromatin modifications in driving tumor behavior. ATP-dependent chromatin remodeling complexes regulate chromatin structure and have critical roles in stem cell maintenance, development, and cancer. Frequent mutations and chromosomal aberrations in the genes associated with subunits of the ATP-dependent chromatin remodeling complexes have been detected in different cancer types. In this review, we summarize the current literature on the genomic alterations and mechanistic studies of the ATP-dependent chromatin remodeling complexes in pancreatic cancer. Our review is focused on the four main subfamilies: SWItch/sucrose non-fermentable (SWI/SNF), imitation SWI (ISWI), chromodomain-helicase DNA-binding protein (CHD), and INOsitol-requiring mutant 80 (INO80). Finally, we discuss potential novel treatment options that use small molecules to target these complexes.
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Affiliation(s)
| | - Nita Ahuja
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520, USA;
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22
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Wang X. Stem cells in tissues, organoids, and cancers. Cell Mol Life Sci 2019; 76:4043-4070. [PMID: 31317205 PMCID: PMC6785598 DOI: 10.1007/s00018-019-03199-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/22/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022]
Abstract
Stem cells give rise to all cells and build the tissue structures in our body, and heterogeneity and plasticity are the hallmarks of stem cells. Epigenetic modification, which is associated with niche signals, determines stem cell differentiation and somatic cell reprogramming. Stem cells play a critical role in the development of tumors and are capable of generating 3D organoids. Understanding the properties of stem cells will improve our capacity to maintain tissue homeostasis. Dissecting epigenetic regulation could be helpful for achieving efficient cell reprograming and for developing new drugs for cancer treatment. Stem cell-derived organoids open up new avenues for modeling human diseases and for regenerative medicine. Nevertheless, in addition to the achievements in stem cell research, many challenges still need to be overcome for stem cells to have versatile application in clinics.
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Affiliation(s)
- Xusheng Wang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou, 510275, China.
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Chabanon RM, Morel D, Postel-Vinay S. Exploiting epigenetic vulnerabilities in solid tumors: Novel therapeutic opportunities in the treatment of SWI/SNF-defective cancers. Semin Cancer Biol 2019; 61:180-198. [PMID: 31568814 DOI: 10.1016/j.semcancer.2019.09.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/12/2022]
Abstract
Mammalian switch/sucrose non-fermentable (mSWI/SNF) family complexes are pivotal elements of the chromatin remodeling machinery, which contribute to the regulation of several major cellular functions. Large-scale exome-wide sequencing studies have identified mutations in genes encoding mSWI/SNF subunits in 20% of all human cancers, establishing mSWI/SNF deficiency as a recurrent oncogenic alteration. Accumulating evidence now supports that several mSWI/SNF defects represent targetable vulnerabilities in cancer; notably, recent research advances have unveiled unexpected synthetic lethal opportunities that foster the development of novel biomarker-driven and mechanism-based therapeutic approaches for the treatment of mSWI/SNF-deficient tumors. Here, we review the latest breakthroughs and discoveries that inform our understanding of the mSWI/SNF complexes biology in carcinogenesis, and discuss the most promising therapeutic strategies to target mSWI/SNF defects in human solid malignancies.
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Affiliation(s)
- Roman M Chabanon
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, France; ATIP-Avenir Group, Inserm Unit U981, Gustave Roussy, Villejuif, France; The Breast Cancer Now Toby Robins Breast Cancer Research Centre, France; CRUK Gene Function Laboratory, The Institute of Cancer Research, London, United Kingdom
| | - Daphné Morel
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, France; ATIP-Avenir Group, Inserm Unit U981, Gustave Roussy, Villejuif, France
| | - Sophie Postel-Vinay
- Université Paris Saclay, Université Paris-Sud, Faculté de médicine, Le Kremlin Bicêtre, France; ATIP-Avenir Group, Inserm Unit U981, Gustave Roussy, Villejuif, France; DITEP (Département d'Innovations Thérapeutiques et Essais Précoces), Gustave Roussy, Villejuif, France.
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Prozzillo Y, Delle Monache F, Ferreri D, Cuticone S, Dimitri P, Messina G. The True Story of Yeti, the "Abominable" Heterochromatic Gene of Drosophila melanogaster. Front Physiol 2019; 10:1093. [PMID: 31507454 PMCID: PMC6713933 DOI: 10.3389/fphys.2019.01093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/08/2019] [Indexed: 12/21/2022] Open
Abstract
The Drosophila Yeti gene (CG40218) was originally identified by recessive lethal mutation and subsequently mapped to the deep pericentromeric heterochromatin of chromosome 2. Functional studies have shown that Yeti encodes a 241 amino acid protein called YETI belonging to the evolutionarily conserved family of Bucentaur (BCNT) proteins and exhibiting a widespread distribution in animals and plants. Later studies have demonstrated that YETI protein: (i) is able to bind both subunits of the microtubule-based motor kinesin-I; (ii) is required for proper chromosome organization in both mitosis and meiosis divisions; and more recently (iii) is a new subunit of dTip60 chromatin remodeling complex. To date, other functions of YETI counterparts in chicken (CENtromere Protein 29, CENP-29), mouse (Cranio Protein 27, CP27), zebrafish and human (CranioFacial Development Protein 1, CFDP1) have been reported in literature, but the fully understanding of the multifaceted molecular function of this protein family remains still unclear. In this review we comprehensively highlight recent work and provide a more extensive hypothesis suggesting a broader range of YETI protein functions in different cellular processes.
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Affiliation(s)
- Yuri Prozzillo
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Francesca Delle Monache
- "Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Diego Ferreri
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Stefano Cuticone
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Patrizio Dimitri
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
| | - Giovanni Messina
- Pasteur Institute of Italy, Fondazione Cenci Bolognetti, Rome, Italy.,"Charles Darwin" Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy
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Strikoudis A, Lazaris C, Ntziachristos P, Tsirigos A, Aifantis I. Opposing functions of H2BK120 ubiquitylation and H3K79 methylation in the regulation of pluripotency by the Paf1 complex. Cell Cycle 2019; 16:2315-2322. [PMID: 28272987 DOI: 10.1080/15384101.2017.1295194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Maintenance of stem cell plasticity is determined by the ability to balance opposing forces that control gene expression. Regulation of transcriptional networks, signaling cues and chromatin-modifying mechanisms constitute crucial determinants of tissue equilibrium. Histone modifications can affect chromatin compaction, therefore co-transcriptional events that influence their deposition determine the propensities toward quiescence, self-renewal, or cell specification. The Paf1 complex (Paf1C) is a critical regulator of RNA PolII elongation that controls gene expression and deposition of histone modifications, however few studies have focused on its role affecting stem cell fate decisions. Here we delineate the functions of Paf1C in pluripotency and characterize its impact in deposition of H2B ubiquitylation (H2BK120-ub) and H3K79 methylation (H3K79me), 2 fundamental histone marks that shape transcriptional regulation. We identify that H2BK120-ub is increased in the absence of Paf1C on its embryonic stem cell targets, in sharp contrast to H3K79me, suggesting opposite functions in the maintenance of self-renewal. Furthermore, we found that core pluripotency genes are characterized by a dual gain of H2BK120-ub and loss of H3K79me on their gene bodies. Our findings elucidate molecular mechanisms of cellular adaptation and reveal novel functions of Paf1C in the regulation of the self-renewal network.
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Affiliation(s)
- Alexandros Strikoudis
- a Department of Pathology , NYU School of Medicine , New York , NY , USA.,b Laura & Isaac Perlmutter Cancer Center , NYU School of Medicine , New York , NY , USA.,c Helen L. & Martin S. Kimmel Center for Stem Cell Biology , NYU School of Medicine , New York , NY , USA
| | - Charalampos Lazaris
- a Department of Pathology , NYU School of Medicine , New York , NY , USA.,b Laura & Isaac Perlmutter Cancer Center , NYU School of Medicine , New York , NY , USA.,c Helen L. & Martin S. Kimmel Center for Stem Cell Biology , NYU School of Medicine , New York , NY , USA
| | - Panagiotis Ntziachristos
- d Department of Biochemistry and Molecular Genetics , Feinberg School of Medicine and Robert H. Lurie Comprehensive Cancer Center, Northwestern University , Chicago , IL , USA
| | - Aristotelis Tsirigos
- a Department of Pathology , NYU School of Medicine , New York , NY , USA.,b Laura & Isaac Perlmutter Cancer Center , NYU School of Medicine , New York , NY , USA.,e Applied Bioinformatics Laboratories, Office of Science & Research , NYU School of Medicine , NY , USA
| | - Iannis Aifantis
- a Department of Pathology , NYU School of Medicine , New York , NY , USA.,b Laura & Isaac Perlmutter Cancer Center , NYU School of Medicine , New York , NY , USA.,c Helen L. & Martin S. Kimmel Center for Stem Cell Biology , NYU School of Medicine , New York , NY , USA
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26
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Li W, Yang L, He Q, Hu C, Zhu L, Ma X, Ma X, Bao S, Li L, Chen Y, Deng X, Zhang X, Cen J, Zhang L, Wang Z, Xie WF, Li H, Li Y, Hui L. A Homeostatic Arid1a-Dependent Permissive Chromatin State Licenses Hepatocyte Responsiveness to Liver-Injury-Associated YAP Signaling. Cell Stem Cell 2019; 25:54-68.e5. [DOI: 10.1016/j.stem.2019.06.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/23/2019] [Accepted: 06/13/2019] [Indexed: 02/02/2023]
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Mathies LD, Ray S, Lopez-Alvillar K, Arbeitman MN, Davies AG, Bettinger JC. mRNA profiling reveals significant transcriptional differences between a multipotent progenitor and its differentiated sister. BMC Genomics 2019; 20:427. [PMID: 31138122 PMCID: PMC6540470 DOI: 10.1186/s12864-019-5821-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/21/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The two Caenorhabditis elegans somatic gonadal precursors (SGPs) are multipotent progenitors that generate all somatic tissues of the adult reproductive system. The sister cells of the SGPs are two head mesodermal cells (hmcs); one hmc dies by programmed cell death and the other terminally differentiates. Thus, a single cell division gives rise to one multipotent progenitor and one differentiated cell with identical lineage histories. We compared the transcriptomes of SGPs and hmcs in order to learn the determinants of multipotency and differentiation in this lineage. RESULTS We generated a strain that expressed fluorescent markers specifically in SGPs (ehn-3A::tdTomato) and hmcs (bgal-1::GFP). We dissociated cells from animals after the SGP/hmc cell division, but before the SGPs had further divided, and subjected the dissociated cells to fluorescence-activated cell sorting to collect isolated SGPs and hmcs. We analyzed the transcriptomes of these cells and found that 5912 transcripts were significantly differentially expressed, with at least two-fold change in expression, between the two cell types. The hmc-biased genes were enriched with those that are characteristic of neurons. The SGP-biased genes were enriched with those indicative of cell proliferation and development. We assessed the validity of our differentially expressed genes by examining existing reporters for five of the 10 genes with the most significantly biased expression in SGPs and found that two showed expression in SGPs. For one reporter that did not show expression in SGPs, we generated a GFP knock-in using CRISPR/Cas9. This reporter, in the native genomic context, was expressed in SGPs. CONCLUSIONS We found that the transcriptional profiles of SGPs and hmcs are strikingly different. The hmc-biased genes are enriched with those that encode synaptic transmission machinery, which strongly suggests that it has neuron-like signaling properties. In contrast, the SGP-biased genes are enriched with genes that encode factors involved in transcription and translation, as would be expected from a cell preparing to undergo proliferative divisions. Mediators of multipotency are likely to be among the genes differentially expressed in SGPs.
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Affiliation(s)
- Laura D. Mathies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA 23298 USA
| | - Surjyendu Ray
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306 USA
| | - Kayla Lopez-Alvillar
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA 23298 USA
| | - Michelle N. Arbeitman
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306 USA
| | - Andrew G. Davies
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA 23298 USA
| | - Jill C. Bettinger
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, PO Box 980613, Richmond, VA 23298 USA
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28
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An S, Park UH, Moon S, Kang M, Youn H, Hwang JT, Kim EJ, Um SJ. Asxl1 ablation in mouse embryonic stem cells impairs neural differentiation without affecting self-renewal. Biochem Biophys Res Commun 2018; 508:907-913. [PMID: 30545639 DOI: 10.1016/j.bbrc.2018.12.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 12/05/2018] [Indexed: 12/12/2022]
Abstract
Additional sex comb-like1 (Asxl1) is known as a chromatin modulator that plays dual functions in transcriptional regulation depending on the cell type. Recent studies using Asxl1 knockout mice revealed that Asxl1 is important for the proliferation and differentiation of hematopoietic progenitor cells, and the development of organs. Although we previously reported Asxl1 as a Sox2 target gene, its function in embryonic stem cells (ESCs) remains largely unknown. For this purpose, we isolated ESCs from the blastocyst inner cell mass of Asxl1-/- mice. Asxl1 deficiency in ESCs exhibited no effect on cell proliferation, expression of core pluripotent transcription factors, or alkaline phosphatase activity, suggesting dispensability of Asxl1 for self-renewal of ESCs. By contrast, the differentiation of Asxl1-/- ESCs was significantly affected as shown by size reductions of embryoid bodies accompanied with apoptosis, aberrant expression of differentiation genes, downregulation of bivalent neurogenesis genes, and abnormal axon formation in neurons. Overall, our findings indicated that Asxl1 played a critical role in regulating genes associated with neural differentiation without affecting self-renewal of mouse ESCs.
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Affiliation(s)
- SoJung An
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul 05006, South Korea
| | - Ui-Hyun Park
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul 05006, South Korea
| | - Seungtae Moon
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul 05006, South Korea
| | - Myengmo Kang
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul 05006, South Korea
| | - Hyesook Youn
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul 05006, South Korea
| | - Jin-Taek Hwang
- Korea Food Research Institute, 245 Nongsaengmyeong-ro, Jeonju, Jeonbuk 55365, South Korea
| | - Eun-Joo Kim
- Department of Molecular Biology, Dankook University, Chungnam 31116, South Korea
| | - Soo-Jong Um
- Department of Integrative Bioscience & Biotechnology, Sejong University, Seoul 05006, South Korea.
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29
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Characterizing the role of SWI/SNF-related chromatin remodeling complexes in planarian regeneration and stem cell function. Stem Cell Res 2018; 32:91-103. [DOI: 10.1016/j.scr.2018.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 08/18/2018] [Accepted: 09/06/2018] [Indexed: 11/21/2022] Open
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30
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Wang Q, Wang X, Lai D, Deng J, Hou Z, Liang H, Liu D. BIX-01294 promotes the differentiation of adipose mesenchymal stem cells into adipocytes and neural cells in Arbas Cashmere goats. Res Vet Sci 2018; 119:9-18. [PMID: 29783122 DOI: 10.1016/j.rvsc.2018.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/02/2018] [Accepted: 05/12/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Qing Wang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Xiao Wang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Defang Lai
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Jin Deng
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Zhuang Hou
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Hao Liang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Dongjun Liu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China.
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31
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Megaridis MR, Lu Y, Tevonian EN, Junger KM, Moy JM, Bohn-Wippert K, Dar RD. Fine-tuning of noise in gene expression with nucleosome remodeling. APL Bioeng 2018; 2:026106. [PMID: 31069303 PMCID: PMC6481717 DOI: 10.1063/1.5021183] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 03/16/2018] [Indexed: 01/08/2023] Open
Abstract
Engineering stochastic fluctuations of gene expression (or “noise”) is integral to precisely bias cellular-fate decisions and statistical phenotypes in both single-cell and multi-cellular systems. Epigenetic regulation has been shown to constitute a large source of noise, and thus, engineering stochasticity is deeply intertwined with epigenetics. Here, utilizing chromatin remodeling, we report that Caffeic acid phenethyl ester (CA) and Pyrimethamine (PYR), two inhibitors of BAF250a, a subunit of the Brahma-associated factor (BAF) nucleosome remodeling complex, enable differential and tunable control of noise in transcription and translation from the human immunodeficiency virus long terminal repeat promoter in a dose and time-dependent manner. CA conserves noise levels while increasing mean abundance, resulting in direct tuning of the transcriptional burst size, while PYR strictly increases transcriptional initiation frequency while conserving a constant transcriptional burst size. Time-dependent treatment with CA reveals non-continuous tuning with noise oscillating at a constant mean abundance at early time points and the burst size increasing for treatments after 5 h. Treatments combining CA and Protein Kinase C agonists result in an even larger increase of abundance while conserving noise levels with a highly non-linear increase in variance of up to 63× untreated controls. Finally, drug combinations provide non-antagonistic combinatorial tuning of gene expression noise and map a noise phase space for future applications with viral and synthetic gene vectors. Active remodeling of nucleosomes and BAF-mediated control of gene expression noise expand a toolbox for the future design and engineering of stochasticity in living systems.
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Affiliation(s)
- Melina R Megaridis
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yiyang Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Erin N Tevonian
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kendall M Junger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jennifer M Moy
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kathrin Bohn-Wippert
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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32
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Shanmugam MK, Arfuso F, Arumugam S, Chinnathambi A, Jinsong B, Warrier S, Wang LZ, Kumar AP, Ahn KS, Sethi G, Lakshmanan M. Role of novel histone modifications in cancer. Oncotarget 2018; 9:11414-11426. [PMID: 29541423 PMCID: PMC5834259 DOI: 10.18632/oncotarget.23356] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/01/2017] [Indexed: 01/02/2023] Open
Abstract
Oncogenesis is a multistep process mediated by a variety of factors including epigenetic modifications. Global epigenetic post-translational modifications have been detected in almost all cancers types. Epigenetic changes appear briefly and do not involve permanent changes to the primary DNA sequence. These epigenetic modifications occur in key oncogenes, tumor suppressor genes, and transcription factors, leading to cancer initiation and progression. The most commonly observed epigenetic changes include DNA methylation, histone lysine methylation and demethylation, histone lysine acetylation and deacetylation. However, there are several other novel post-translational modifications that have been observed in recent times such as neddylation, sumoylation, glycosylation, phosphorylation, poly-ADP ribosylation, ubiquitination as well as transcriptional regulation and these have been briefly discussed in this article. We have also highlighted the diverse epigenetic changes that occur during the process of tumorigenesis and described the role of histone modifications that can occur on tumor suppressor genes as well as oncogenes, which regulate tumorigenesis and can thus form the basis of novel strategies for cancer therapy.
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Affiliation(s)
- Muthu K. Shanmugam
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Frank Arfuso
- Stem Cell and Cancer Biology Laboratory, School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Surendar Arumugam
- Institute of Molecular and Cell Biology, A*STAR, Biopolis Drive, Proteos, Singapore, Singapore
| | - Arunachalam Chinnathambi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Kingdom of Saudi Arabia
| | - Bian Jinsong
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sudha Warrier
- Division of Cancer Stem Cells and Cardiovascular Regeneration, School of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore, India
| | - Ling Zhi Wang
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, WA, Australia
- National University Cancer Institute, National University Health System, Singapore, Singapore
- Department of Biological Sciences, University of North Texas, Denton, Texas, USA
| | - Kwang Seok Ahn
- College of Korean Medicine, Kyung Hee University, Dongdaemun-gu, Seoul, Korea
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Manikandan Lakshmanan
- Institute of Molecular and Cell Biology, A*STAR, Biopolis Drive, Proteos, Singapore, Singapore
- Department of Pathology, National University Hospital Singapore, Singapore, Singapore
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33
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Cabot B, Cabot RA. Chromatin remodeling in mammalian embryos. Reproduction 2018; 155:R147-R158. [PMID: 29339454 DOI: 10.1530/rep-17-0488] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/12/2018] [Indexed: 12/28/2022]
Abstract
The mammalian embryo undergoes a dramatic amount of epigenetic remodeling during the first week of development. In this review, we discuss several epigenetic changes that happen over the course of cleavage development, focusing on covalent marks (e.g., histone methylation and acetylation) and non-covalent remodeling (chromatin remodeling via remodeling complexes; e.g., SWI/SNF-mediated chromatin remodeling). Comparisons are also drawn between remodeling events that occur in embryos from a variety of mammalian species.
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Affiliation(s)
- Birgit Cabot
- Department of Animal SciencesPurdue University, West Lafayette, Indiana, USA
| | - Ryan A Cabot
- Department of Animal SciencesPurdue University, West Lafayette, Indiana, USA
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34
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Zhang Y, Cui P, Li Y, Feng G, Tong M, Guo L, Li T, Liu L, Li W, Zhou Q. Mitochondrially produced ATP affects stem cell pluripotency via Actl6a-mediated histone acetylation. FASEB J 2018; 32:1891-1902. [PMID: 29222327 DOI: 10.1096/fj.201700626rr] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
ATP is mainly generated by glycolysis in pluripotent stem cells (PSCs) and is consumed to maintain cell viability. Differences in mitochondrial activity among induced (i)PSCs with different degrees of pluripotency are poorly understood. In this study, by comparing gene expression and mitochondrial activity among iPSCs with different degrees of pluripotency, we found that mitochondrial complex I gene expression, complex I activity, and cellular ATP levels were much higher in fully pluripotent stem cell lines than in partially pluripotent stem cell lines. Actin-like protein 6a (Actl6a), a component of ATP-dependent chromatin remodeling and histone acetylation complexes, was more highly expressed in fully pluripotent stem cell lines. ATP promoted Actl6a expression and histone acetylation. Actl6a knockdown reduced the pluripotency of embryonic stem cells (ESCs), and this reduction could not be rescued by the addition of ATP. Furthermore, inhibiting ATP formation by treatment with rotenone reduced the pluripotency of ESCs. These data suggest that the abundance of mitochondrially produced ATP affects stem cell pluripotency via Actl6a-mediated histone acetylation.-Zhang, Y., Cui, P., Li, Y., Feng, G., Tong, M., Guo, L., Li, T., Liu, L., Li, W., Zhou, Q. Mitochondrially produced ATP affects stem cell pluripotency via Actl6a-mediated histone acetylation.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Peng Cui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yuhuan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Man Tong
- Key Laboratory of Genetic Network Biology, Collaborative Center for Genetics and Development, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lu Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tianda Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Lei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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35
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Ding D, Bergmaier P, Sachs P, Klangwart M, Rückert T, Bartels N, Demmers J, Dekker M, Poot RA, Mermoud JE. The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes. J Biol Chem 2017; 293:2711-2724. [PMID: 29284678 DOI: 10.1074/jbc.ra117.000959] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/13/2017] [Indexed: 12/13/2022] Open
Abstract
Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs. We found that this interaction occurs on chromatin and that SMARCAD1 binds to different classes of KAP1 target genes, including zinc finger protein (ZFP) and imprinted genes. We also found that the RING B-box coiled-coil (RBCC) domain in KAP1 and the proximal coupling of ubiquitin conjugation to ER degradation (CUE) domain in SMARCAD1 mediate their direct interaction. Of note, retention of SMARCAD1 in the nucleus depended on KAP1 in both mouse ESCs and human somatic cells. Mutations in the CUE1 domain of SMARCAD1 perturbed the binding to KAP1 in vitro and in vivo Accordingly, an intact CUE1 domain was required for tethering this remodeler to the nucleus. Moreover, mutation of the CUE1 domain compromised SMARCAD1 binding to KAP1 target genes. Taken together, our results reveal a mechanism that localizes SMARCAD1 to genomic sites through the interaction of SMARCAD1's CUE1 motif with KAP1.
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Affiliation(s)
- Dong Ding
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Philipp Bergmaier
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Parysatis Sachs
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Marius Klangwart
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Tamina Rückert
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Nora Bartels
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Jeroen Demmers
- Center for Proteomics, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Mike Dekker
- Department of Cell Biology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Raymond A Poot
- Department of Cell Biology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Jacqueline E Mermoud
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany.
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Wang L, Koutelou E, Hirsch C, McCarthy R, Schibler A, Lin K, Lu Y, Jeter C, Shen J, Barton MC, Dent SYR. GCN5 Regulates FGF Signaling and Activates Selective MYC Target Genes during Early Embryoid Body Differentiation. Stem Cell Reports 2017; 10:287-299. [PMID: 29249668 PMCID: PMC5768892 DOI: 10.1016/j.stemcr.2017.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/14/2017] [Accepted: 11/14/2017] [Indexed: 12/12/2022] Open
Abstract
Precise control of gene expression during development is orchestrated by transcription factors and co-regulators including chromatin modifiers. How particular chromatin-modifying enzymes affect specific developmental processes is not well defined. Here, we report that GCN5, a histone acetyltransferase essential for embryonic development, is required for proper expression of multiple genes encoding components of the fibroblast growth factor (FGF) signaling pathway in early embryoid bodies (EBs). Gcn5-/- EBs display deficient activation of ERK and p38, mislocalization of cytoskeletal components, and compromised capacity to differentiate toward mesodermal lineage. Genomic analyses identified seven genes as putative direct targets of GCN5 during early differentiation, four of which are cMYC targets. These findings established a link between GCN5 and the FGF signaling pathway and highlighted specific GCN5-MYC partnerships in gene regulation during early differentiation.
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Affiliation(s)
- Li Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Epigenetics and Molecular Carcinogenesis, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Calley Hirsch
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Ryan McCarthy
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Andria Schibler
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Genes and Development, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Collene Jeter
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Epigenetics and Molecular Carcinogenesis, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Program in Genes and Development, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Program in Epigenetics and Molecular Carcinogenesis, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Program in Genes and Development, The Graduate School of Biomedical Sciences (GSBS) of the University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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Rhee C, Kim J, Tucker HO. Transcriptional Regulation of the First Cell Fate Decision. JOURNAL OF DEVELOPMENTAL BIOLOGY & REGENERATIVE MEDICINE 2017; 1:102. [PMID: 29658952 PMCID: PMC5897107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding how the first cell fate decision has chosen is a fascinating biological question that was received consider attention over the last decade. Numerous transcription factors are required, and many have been shown to have essential roles in this process. Here we reexamine the function that transcription factors play primarily in the mouse-the model system most thoroughly examined in this process. We address how the first embryonic lineage is established and maintained, with a particular emphasis on subsequent trophectoderm development and the role of the recently established Arid3a transcription factor in this process. In addition, we review relevant aspects of embryonic stem cell reprogramming into trophoblast stem cells -the equivalent of the epiblast (inner cell mass) and the establishment of induced trophoblast stem cells-the in vitro equivalent of the trophectoderm.
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Affiliation(s)
- Catherine Rhee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge MA 02138, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Haley O. Tucker
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
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Zhu B, Ueda A, Song X, Horike SI, Yokota T, Akagi T. Baf53a is involved in survival of mouse ES cells, which can be compensated by Baf53b. Sci Rep 2017; 7:14059. [PMID: 29070872 PMCID: PMC5656580 DOI: 10.1038/s41598-017-14362-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 10/10/2017] [Indexed: 12/19/2022] Open
Abstract
The human Baf (Brg1/Brm associated factor) complex, also known as the mammalian SWI/SNF chromatin-remodeling complex, is involved in a variety of cellular processes. The pluripotency and self-renewal abilities are major characteristics of embryonic stem (ES) cells and are regulated by the ES cell-specific BAF (esBAF) complex. Baf53a is one of the subunits of the esBAF complex. Here, we found that Baf53a was expressed in undifferentiated ES cells and that it interacted with Oct3/4. Analyses of tetracycline-inducible Baf53a conditional knockout ES cells revealed that the undifferentiated markers, including Nanog and Oct3/4, were expressed in Baf53a-deficient ES cells; however, growth of the cells was repressed, and expression of p53, p21, and cleaved Caspase 3 was increased. Cell death of Baf53a-deficient ES cells was rescued by overexpression of Baf53a, but not by the Baf53a M3 mutant (E388A/R389A/R390A). Interestingly, Baf53b, a homologue of Baf53a, rescued cell death of Baf53a-deficient ES cells. Baf53a-deficient ES cells overexpressing exogenous Baf53a or Baf53b remained in the undifferentiated state, proliferated, and repressed expression of p21. In summary, our findings suggest that Baf53a is involved in the survival of ES cells by regulating p53 and Caspase3, and that Baf53b is able to compensate for this functional aspect of Baf53a.
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Affiliation(s)
- Bo Zhu
- Department of Stem Cell Biology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University., 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Atsushi Ueda
- Department of Stem Cell Biology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University., 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Xiaohong Song
- Department of Stem Cell Biology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University., 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Shin-Ichi Horike
- Advanced Science Research Center, Kanazawa University. 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan
| | - Takashi Yokota
- Department of Stem Cell Biology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University., 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan.
| | - Tadayuki Akagi
- Department of Stem Cell Biology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University., 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640, Japan.
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39
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Abulaiti X, Zhang H, Wang A, Li N, Li Y, Wang C, Du X, Li L. Phosphorylation of Threonine 343 Is Crucial for OCT4 Interaction with SOX2 in the Maintenance of Mouse Embryonic Stem Cell Pluripotency. Stem Cell Reports 2017; 9:1630-1641. [PMID: 28988986 PMCID: PMC5829306 DOI: 10.1016/j.stemcr.2017.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/31/2017] [Accepted: 09/01/2017] [Indexed: 12/22/2022] Open
Abstract
OCT4 is required to maintain the pluripotency of embryonic stem cells (ESCs); yet, overdose-expression of OCT4 induces ESC differentiation toward primitive endoderm. The molecular mechanism underlying this differentiation switch is not fully understood. Here, we found that substitution of threonine343 by alanine (T343A), but not aspartic acid (T343D), caused a significant loss of OCT4-phosphorylation signal in ESCs. Loss of such OCT4-phosphorylation compromises its interaction with SOX2 but promotes interaction with SOX17. We therefore propose that threonine343-based OCT4-phosphorylation is crucial for the maintenance of ESC pluripotency. This OCT4-phosphorylation-based mechanism may provide insight into the regulation of lineage specification during early embryonic development. Phosphorylation of threonine343 mediates global OCT4-phosphorylation (phos-OCT4T343) Phos-OCT4T343 is crucial for OCT4 to protect embryonic stem cell pluripotency Phos-OCT4T343 binds to SOX2 but non-phos-OCT4T343 binds to SOX17 in cell fate decision Phos-OCT4T343 may regulate lineage commitment in early embryonic development
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Affiliation(s)
- Xianmixinuer Abulaiti
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Han Zhang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Aifang Wang
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Li
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chenchen Wang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xiaojuan Du
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lingsong Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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40
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Alternative SET/TAFI Promoters Regulate Embryonic Stem Cell Differentiation. Stem Cell Reports 2017; 9:1291-1303. [PMID: 28966118 PMCID: PMC5639460 DOI: 10.1016/j.stemcr.2017.08.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/27/2017] [Accepted: 08/28/2017] [Indexed: 01/21/2023] Open
Abstract
Embryonic stem cells (ESCs) are regulated by pluripotency-related transcription factors in concert with chromatin regulators. To identify additional stem cell regulators, we screened a library of endogenously labeled fluorescent fusion proteins in mouse ESCs for fluorescence loss during differentiation. We identified SET, which displayed a rapid isoform shift during early differentiation from the predominant isoform in ESCs, SETα, to the primary isoform in differentiated cells, SETβ, through alternative promoters. SETα is selectively bound and regulated by pluripotency factors. SET depletion causes proliferation slowdown and perturbed neuronal differentiation in vitro and developmental arrest in vivo, and photobleaching methods demonstrate SET's role in maintaining a dynamic chromatin state in ESCs. This work identifies an important regulator of pluripotency and early differentiation, which is controlled by alternative promoter usage. We identify SETα to be rapidly downregulated during ESC differentiation SETα is regulated by pluripotency factors and replaced by SETβ during differentiation SETα/SETβ switch is crucial for ESC differentiation SETα regulates chromatin plasticity in ESCs
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Abstract
Skeletal muscle regeneration is an efficient stem cell-based repair system that ensures healthy musculature. For this repair system to function continuously throughout life, muscle stem cells must contribute to the process of myofiber repair as well as repopulation of the stem cell niche. The decision made by the muscle stem cells to commit to the muscle repair or to remain a stem cell depends upon patterns of gene expression, a process regulated at the epigenetic level. Indeed, it is well accepted that dynamic changes in epigenetic landscapes to control DNA accessibility and expression is a critical component during myogenesis for the effective repair of damaged muscle. Changes in the epigenetic landscape are governed by various posttranslational histone tail modifications, nucleosome repositioning, and DNA methylation events which collectively allow the control of changes in transcription networks during transitions of satellite cells from a dormant quiescent state toward terminal differentiation. This chapter focuses upon the specific epigenetic changes that occur during muscle stem cell-mediated regeneration to ensure myofiber repair and continuity of the stem cell compartment. Furthermore, we explore open questions in the field that are expected to be important areas of exploration as we move toward a more thorough understanding of the epigenetic mechanism regulating muscle regeneration.
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Affiliation(s)
- Daniel C L Robinson
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada; University of Ottawa, Ottawa, ON, Canada
| | - Francis J Dilworth
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada; University of Ottawa, Ottawa, ON, Canada.
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LaMere SA, Thompson RC, Meng X, Komori HK, Mark A, Salomon DR. H3K27 Methylation Dynamics during CD4 T Cell Activation: Regulation of JAK/STAT and IL12RB2 Expression by JMJD3. THE JOURNAL OF IMMUNOLOGY 2017; 199:3158-3175. [PMID: 28947543 DOI: 10.4049/jimmunol.1700475] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022]
Abstract
The changes to the epigenetic landscape in response to Ag during CD4 T cell activation have not been well characterized. Although CD4 T cell subsets have been mapped globally for numerous epigenetic marks, little has been done to study their dynamics early after activation. We have studied changes to promoter H3K27me3 during activation of human naive and memory CD4 T cells. Our results show that these changes occur relatively early (1 d) after activation of naive and memory cells and that demethylation is the predominant change to H3K27me3 at this time point, reinforcing high expression of target genes. Additionally, inhibition of the H3K27 demethylase JMJD3 in naive CD4 T cells demonstrates how critically important molecules required for T cell differentiation, such as JAK2 and IL12RB2, are regulated by H3K27me3. Our results show that H3K27me3 is a dynamic and important epigenetic modification during CD4 T cell activation and that JMJD3-driven H3K27 demethylation is critical for CD4 T cell function.
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Affiliation(s)
- Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Ryan C Thompson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Xiangzhi Meng
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Adam Mark
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
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JMJD1C Ensures Mouse Embryonic Stem Cell Self-Renewal and Somatic Cell Reprogramming through Controlling MicroRNA Expression. Stem Cell Reports 2017; 9:927-942. [PMID: 28826851 PMCID: PMC5599225 DOI: 10.1016/j.stemcr.2017.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 07/14/2017] [Accepted: 07/17/2017] [Indexed: 12/17/2022] Open
Abstract
The roles of histone demethylases (HDMs) for the establishment and maintenance of pluripotency are incompletely characterized. Here, we show that JmjC-domain-containing protein 1c (JMJD1C), an H3K9 demethylase, is required for mouse embryonic stem cell (ESC) self-renewal. Depletion of Jmjd1c leads to the activation of ERK/MAPK signaling and epithelial-to-mesenchymal transition (EMT) to induce differentiation of ESCs. Inhibition of ERK/MAPK signaling rescues the differentiation phenotype caused by Jmjd1c depletion. Mechanistically, JMJD1C, with the help of pluripotency factor KLF4, maintains ESC identity at least in part by regulating the expression of the miR-200 family and miR-290/295 cluster to suppress the ERK/MAPK signaling and EMT. Additionally, we uncover that JMJD1C ensures efficient generation and maintenance of induced pluripotent stem cells, at least partially through controlling the expression of microRNAs. Collectively, we propose an integrated model of epigenetic and transcriptional control mediated by the H3K9 demethylase for ESC self-renewal and somatic cell reprogramming. JMJD1C is required for the maintenance of ESC identity Depletion of Jmjd1c leads to the activation of ERK/MAPK signaling and EMT JMJD1C interplays with KLF4 to activate the expression of miR-200 family JMJD1C ensures efficient induction of pluripotency partially via miR-200 family
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Clapier CR, Iwasa J, Cairns BR, Peterson CL. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat Rev Mol Cell Biol 2017; 18:407-422. [PMID: 28512350 DOI: 10.1038/nrm.2017.26] [Citation(s) in RCA: 703] [Impact Index Per Article: 100.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells utilize diverse ATP-dependent nucleosome-remodelling complexes to carry out histone sliding, ejection or the incorporation of histone variants, suggesting that different mechanisms of action are used by the various chromatin-remodelling complex subfamilies. However, all chromatin-remodelling complex subfamilies contain an ATPase-translocase 'motor' that translocates DNA from a common location within the nucleosome. In this Review, we discuss (and illustrate with animations) an alternative, unifying mechanism of chromatin remodelling, which is based on the regulation of DNA translocation. We propose the 'hourglass' model of remodeller function, in which each remodeller subfamily utilizes diverse specialized proteins and protein domains to assist in nucleosome targeting or to differentially detect nucleosome epitopes. These modules converge to regulate a common DNA translocation mechanism, to inform the conserved ATPase 'motor' on whether and how to apply DNA translocation, which together achieve the various outcomes of chromatin remodelling: nucleosome assembly, chromatin access and nucleosome editing.
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Affiliation(s)
- Cedric R Clapier
- Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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45
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Brg1 chromatin remodeling ATPase balances germ layer patterning by amplifying the transcriptional burst at midblastula transition. PLoS Genet 2017; 13:e1006757. [PMID: 28498870 PMCID: PMC5428918 DOI: 10.1371/journal.pgen.1006757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 04/11/2017] [Indexed: 12/21/2022] Open
Abstract
Zygotic gene expression programs control cell differentiation in vertebrate development. In Xenopus, these programs are initiated by local induction of regulatory genes through maternal signaling activities in the wake of zygotic genome activation (ZGA) at the midblastula transition (MBT). These programs lay down the vertebrate body plan through gastrulation and neurulation, and are accompanied by massive changes in chromatin structure, which increasingly constrain cellular plasticity. Here we report on developmental functions for Brahma related gene 1 (Brg1), a key component of embyronic SWI/SNF chromatin remodeling complexes. Carefully controlled, global Brg1 protein depletion in X. tropicalis and X. laevis causes embryonic lethality or developmental arrest from gastrulation on. Transcriptome analysis at late blastula, before development becomes arrested, indicates predominantly a role for Brg1 in transcriptional activation of a limited set of genes involved in pattern specification processes and nervous system development. Mosaic analysis by targeted microinjection defines Brg1 as an essential amplifier of gene expression in dorsal (BCNE/Nieuwkoop Center) and ventral (BMP/Vent) signaling centers. Moreover, Brg1 is required and sufficient for initiating axial patterning in cooperation with maternal Wnt signaling. In search for a common denominator of Brg1 impact on development, we have quantitatively filtered global mRNA fluctuations at MBT. The results indicate that Brg1 is predominantly required for genes with the highest burst of transcriptional activity. Since this group contains many key developmental regulators, we propose Brg1 to be responsible for raising their expression above threshold levels in preparation for embryonic patterning. Brahma-related-gene-1 (Brg1) is a catalytic subunit of mammalian SWI/SNF chromatin remodeling complexes. Loss of maternal Brg1 protein arrests development in mice at the 2-cell stage, while null homozygotes die at the blastocyst stage. These early requirements have precluded any analysis of Brg1’s embryonic functions. Here we present data from X. laevis and X. tropicalis, which for the first time describe a role for Brg1 during germ layer patterning and axis formation. Brg1-depleted embryos fail to develop past gastrulation. Genome-wide transcriptome analysis at late blastula stage, before the developmental arrest, shows that Brg1 is required predominantly for transcriptional activation of a limited set of genes involved in pattern specification processes and nervous system development shortly after midblastula transition. Mosaic analysis by targeted microinjection defines Brg1 as an essential amplifier of gene expression in dorsal (BCNE and Nieuwkoop center) and ventral (BMP/Vent) signaling centers, being required and sufficient to initiate axial patterning by cooperating with canonical Wnt signaling. Since Brg1-dependent genes share a high burst of transcriptional activation before gastrulation, we propose a systemic role for Brg1 as transcriptional amplifier, which balances the embryonic patterning process.
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Structural Insights into BAF47 and BAF155 Complex Formation. J Mol Biol 2017; 429:1650-1660. [PMID: 28438634 DOI: 10.1016/j.jmb.2017.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/16/2017] [Accepted: 04/18/2017] [Indexed: 12/13/2022]
Abstract
Mammalian BAF complexes are a subfamily of SWI/SNF ATP-dependent chromatin remodelers that dynamically modulate chromatin structure to regulate fundamental cellular processes including gene transcription, cell cycle control, and DNA damage response. So far, many distinct BAF complexes have been identified with polymorphic assemblies of up to 15 subunits from 29 genes. The evolutionarily conserved BRG1/BRM, BAF47, and BAF155/BAF170 form a stable complex that carries out essential chromatin remodeling activity and therefore have been regarded as the core components of BAF complex. Here, we first confirmed that SWIRM domain of BAF155 is responsible for its interaction with BAF47 and then narrowed down the SWIRM-binding region in BAF47 to the Repeat 1 (RPT1) domain. We further presented the high-resolution crystal structure of SWIRM/RPT1 complex. Extensive mutagenesis experiments together with isothermal titration calorimetry and NMR titrations were performed to corroborate the interactions observed in crystal structure. Overall, we demonstrated that BAF155 SWIRM is a modular domain involved in BAF47 interaction, which is functionally distinct from other characterized SWIRM domains that possess DNA binding activity.
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47
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The BAF45a/PHF10 subunit of SWI/SNF-like chromatin remodeling complexes is essential for hematopoietic stem cell maintenance. Exp Hematol 2017; 48:58-71.e15. [DOI: 10.1016/j.exphem.2016.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/12/2016] [Accepted: 11/25/2016] [Indexed: 11/22/2022]
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48
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PHB Associates with the HIRA Complex to Control an Epigenetic-Metabolic Circuit in Human ESCs. Cell Stem Cell 2017; 20:274-289.e7. [DOI: 10.1016/j.stem.2016.11.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 08/30/2016] [Accepted: 10/28/2016] [Indexed: 02/07/2023]
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49
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Toto PC, Puri PL, Albini S. SWI/SNF-directed stem cell lineage specification: dynamic composition regulates specific stages of skeletal myogenesis. Cell Mol Life Sci 2016; 73:3887-96. [PMID: 27207468 PMCID: PMC5158306 DOI: 10.1007/s00018-016-2273-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/06/2016] [Accepted: 05/10/2016] [Indexed: 11/25/2022]
Abstract
SWI/SNF chromatin-remodeling complexes are key regulators of the epigenetic modifications that determine whether stem cells maintain pluripotency or commit toward specific lineages through development and during postnatal life. Dynamic combinatorial assembly of multiple variants of SWI/SNF subunits is emerging as the major determinant of the functional versatility of SWI/SNF. Here, we summarize the current knowledge on the structural and functional properties of the alternative SWI/SNF complexes that direct stem cell fate toward skeletal muscle lineage and control distinct stages of skeletal myogenesis. In particular, we will refer to recent evidence pointing to the essential role of two SWI/SNF components not expressed in embryonic stem cells-the catalytic subunit BRM and the structural component BAF60C-whose induction in muscle progenitors coincides with the expansion of their transcriptional repertoire.
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Affiliation(s)
- Paula Coutinho Toto
- Sanford Burnham Prebys Medical Discovery Institute, 10905 Road to the Cure, San Diego, CA, 92121, USA
| | - Pier Lorenzo Puri
- Sanford Burnham Prebys Medical Discovery Institute, 10905 Road to the Cure, San Diego, CA, 92121, USA.
- IRCCS Fondazione Santa Lucia, Via del Fosso di Fiorano, 64, 00143, Rome, Italy.
| | - Sonia Albini
- Sanford Burnham Prebys Medical Discovery Institute, 10905 Road to the Cure, San Diego, CA, 92121, USA.
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50
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Structural Insights into the Association of Hif1 with Histones H2A-H2B Dimer and H3-H4 Tetramer. Structure 2016; 24:1810-1820. [DOI: 10.1016/j.str.2016.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 08/01/2016] [Accepted: 08/01/2016] [Indexed: 11/22/2022]
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