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Leyva-Díaz E. CUT homeobox genes: transcriptional regulation of neuronal specification and beyond. Front Cell Neurosci 2023; 17:1233830. [PMID: 37744879 PMCID: PMC10515288 DOI: 10.3389/fncel.2023.1233830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
CUT homeobox genes represent a captivating gene class fulfilling critical functions in the development and maintenance of multiple cell types across a wide range of organisms. They belong to the larger group of homeobox genes, which encode transcription factors responsible for regulating gene expression patterns during development. CUT homeobox genes exhibit two distinct and conserved DNA binding domains, a homeodomain accompanied by one or more CUT domains. Numerous studies have shown the involvement of CUT homeobox genes in diverse developmental processes such as body axis formation, organogenesis, tissue patterning and neuronal specification. They govern these processes by exerting control over gene expression through their transcriptional regulatory activities, which they accomplish by a combination of classic and unconventional interactions with the DNA. Intriguingly, apart from their roles as transcriptional regulators, they also serve as accessory factors in DNA repair pathways through protein-protein interactions. They are highly conserved across species, highlighting their fundamental importance in developmental biology. Remarkably, evolutionary analysis has revealed that CUT homeobox genes have experienced an extraordinary degree of rearrangements and diversification compared to other classes of homeobox genes, including the emergence of a novel gene family in vertebrates. Investigating the functions and regulatory networks of CUT homeobox genes provides significant understanding into the molecular mechanisms underlying embryonic development and tissue homeostasis. Furthermore, aberrant expression or mutations in CUT homeobox genes have been associated with various human diseases, highlighting their relevance beyond developmental processes. This review will overview the well known roles of CUT homeobox genes in nervous system development, as well as their functions in other tissues across phylogeny.
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Wilkes MC, Chae HD, Scanlon V, Cepika AM, Wentworth EP, Saxena M, Eskin A, Chen Z, Glader B, Grazia Roncarolo M, Nelson SF, Sakamoto KM. SATB1 Chromatin Loops Regulate Megakaryocyte/Erythroid Progenitor Expansion by Facilitating HSP70 and GATA1 Induction. Stem Cells 2023; 41:560-569. [PMID: 36987811 PMCID: PMC10267687 DOI: 10.1093/stmcls/sxad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/21/2023] [Indexed: 03/30/2023]
Abstract
Diamond Blackfan anemia (DBA) is an inherited bone marrow failure syndrome associated with severe anemia, congenital malformations, and an increased risk of developing cancer. The chromatin-binding special AT-rich sequence-binding protein-1 (SATB1) is downregulated in megakaryocyte/erythroid progenitors (MEPs) in patients and cell models of DBA, leading to a reduction in MEP expansion. Here we demonstrate that SATB1 expression is required for the upregulation of the critical erythroid factors heat shock protein 70 (HSP70) and GATA1 which accompanies MEP differentiation. SATB1 binding to specific sites surrounding the HSP70 genes promotes chromatin loops that are required for the induction of HSP70, which, in turn, promotes GATA1 induction. This demonstrates that SATB1, although gradually downregulated during myelopoiesis, maintains a biological function in early myeloid progenitors.
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Affiliation(s)
- Mark C Wilkes
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Hee-Don Chae
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Vanessa Scanlon
- Department of Laboratory Medicine, Yale Stem Cell Center, Yale Cooperative Center of Excellence in Hematology, Yale School of Medicine, New Haven, CT, USA
| | - Alma-Martina Cepika
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ethan P Wentworth
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Mallika Saxena
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Ascia Eskin
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Zugen Chen
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Bert Glader
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Maria Grazia Roncarolo
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stanley F Nelson
- Department of Pathology and Laboratory Medicine¸ David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Kathleen M Sakamoto
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, USA
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Wang B, Ji L, Bian Q. SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites. Cell Rep 2023; 42:112323. [PMID: 37000624 DOI: 10.1016/j.celrep.2023.112323] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 01/20/2023] [Accepted: 03/16/2023] [Indexed: 04/01/2023] Open
Abstract
Special AT-rich sequence binding protein 1 (SATB1) has long been proposed to act as a global chromatin loop organizer in T cells. However, the exact functions of SATB1 in spatial genome organization remain elusive. Here we show that the depletion of SATB1 in human and murine T cells leads to transcriptional dysregulation for genes involved in T cell activation, as well as alterations of 3D genome architecture at multiple levels, including compartments, topologically associating domains, and loops. Importantly, SATB1 extensively colocalizes with CTCF throughout the genome. Depletion of SATB1 leads to increased chromatin contacts among and across the SATB1/CTCF co-occupied sites, thereby affecting the transcription of critical regulators of T cell activation. The loss of SATB1 does not affect CTCF occupancy but significantly reduces the retention of CTCF in the nuclear matrix. Collectively, our data show that SATB1 contributes to 3D genome organization by constraining chromatin topology surrounding CTCF-binding sites.
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Affiliation(s)
- Bao Wang
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Luzhang Ji
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China
| | - Qian Bian
- Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Shanghai Institute of Precision Medicine, Shanghai 200125, China; Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Antonio Urrutia G, Ramachandran H, Cauchy P, Boo K, Ramamoorthy S, Boller S, Dogan E, Clapes T, Trompouki E, Torres-Padilla ME, Palvimo JJ, Pichler A, Grosschedl R. ZFP451-mediated SUMOylation of SATB2 drives embryonic stem cell differentiation. Genes Dev 2021; 35:1142-1160. [PMID: 34244292 PMCID: PMC8336893 DOI: 10.1101/gad.345843.120] [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: 10/16/2020] [Accepted: 06/08/2021] [Indexed: 12/15/2022]
Abstract
Here, Urrutia et al. set out to study the mechanism that regulates the choice between pluripotency and differentiation in embryonic stem cells (ESCs). Using biochemical and genomic analyses, the authors identify SUMO2 modification of Satb2 by the E3 ligase Zfp451 as a driver of ESC differentiation. The establishment of cell fates involves alterations of transcription factor repertoires and repurposing of transcription factors by post-translational modifications. In embryonic stem cells (ESCs), the chromatin organizers SATB2 and SATB1 balance pluripotency and differentiation by activating and repressing pluripotency genes, respectively. Here, we show that conditional Satb2 gene inactivation weakens ESC pluripotency, and we identify SUMO2 modification of SATB2 by the E3 ligase ZFP451 as a potential driver of ESC differentiation. Mutations of two SUMO-acceptor lysines of Satb2 (Satb2K →R) or knockout of Zfp451 impair the ability of ESCs to silence pluripotency genes and activate differentiation-associated genes in response to retinoic acid (RA) treatment. Notably, the forced expression of a SUMO2-SATB2 fusion protein in either Satb2K →R or Zfp451−/− ESCs rescues, in part, their impaired differentiation potential and enhances the down-regulation of Nanog. The differentiation defect of Satb2K →R ESCs correlates with altered higher-order chromatin interactions relative to Satb2wt ESCs. Upon RA treatment of Satb2wt ESCs, SATB2 interacts with ZFP451 and the LSD1/CoREST complex and gains binding at differentiation genes, which is not observed in RA-treated Satb2K →R cells. Thus, SATB2 SUMOylation may contribute to the rewiring of transcriptional networks and the chromatin interactome of ESCs in the transition of pluripotency to differentiation.
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Affiliation(s)
- Gustavo Antonio Urrutia
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Haribaskar Ramachandran
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Pierre Cauchy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Kyungjin Boo
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Soeren Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Esen Dogan
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Clapes
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | | | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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Feng Y, Wang X, Wang Q. Expression of SATB1 and E-cad in tissues of patients with endometrial carcinoma and the relationship with clinicopathological features. Exp Ther Med 2018; 15:4339-4343. [PMID: 29725375 PMCID: PMC5920497 DOI: 10.3892/etm.2018.5954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/12/2017] [Indexed: 12/29/2022] Open
Abstract
The expression of special AT-rich sequence binding protein 1 (SATB1) and E-cadherin (E-cad) in tissues of patients with endometrial carcinoma and the relationships with clinicopathological features were investigated. One hundred and four cases of carcinoma tissues and 104 cases of para-carcinoma tissues of patients pathologically diagnosed as endometrial carcinoma in Affiliated Hospital of Jining Medical University (Jining, China) from August 2015 to August 2016 were selected. The expressions of SATB1 and E-cad in tissues was detected via streptavidin peroxidase biotin (SP) immunohistochemical method, and the relationship with clinicopathological features of patients was analyzed. SATB1 was positively expressed in 71 out of 104 cases of endometrial carcinoma tissues (the expression rate was 68.27%) and in 25 out of 104 cases of para-carcinoma tissues (the expression rate was 24.03%). The expression of SATB1 in endometrial carcinoma tissues was significantly higher than that in para-carcinoma tissues (P<0.05). E-cad was positively expressed in 60 out of 104 cases of carcinoma tissues (the expression rate was 57.6%) and 95 out of 104 cases of para-carcinoma tissues (the positive expression rate was 91.3%) (P<0.05). The expression of SATB1 and E-cad in endometrial carcinoma tissues was not associated with the menopausal status or age of patients (P>0.05), but correlated with the histological grade of endometrial carcinoma, depth of tumor invasion, lymph node metastasis and tumor lymph node metastasis (TNM) staging (P<0.05). In conclusion, SATB1 and E-cad play important roles in the occurrence and development of endometrial carcinoma, which are of great significance to the potential therapeutic target and prognosis estimation of endometrial carcinoma.
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Affiliation(s)
- Yanli Feng
- Department of Gynecology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
| | - Xin Wang
- Jining Hospital of Traditional Chinese Medicine, Jining, Shandong 272029, P.R. China
| | - Quanyi Wang
- Department of Pathology, Affiliated Hospital of Jining Medical University, Jining, Shandong 272029, P.R. China
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