1
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Favarolo MB, Revinski DR, Garavaglia MJ, López SL. Nodal and churchill1 position the expression of a notch ligand during Xenopus germ layer segregation. Life Sci Alliance 2022; 5:5/12/e202201693. [PMID: 36180230 PMCID: PMC9604498 DOI: 10.26508/lsa.202201693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/13/2022] [Accepted: 09/14/2022] [Indexed: 11/24/2022] Open
Abstract
Churchill and Nodal signaling, which participate in vertebrates’ germ layer induction, position a domain of Delta/Notch activity, which refines germ layer boundaries during frog gastrulation. In vertebrates, Nodal signaling plays a major role in endomesoderm induction, but germ layer delimitation is poorly understood. In avian embryos, the neural/mesoderm boundary is controlled by the transcription factor CHURCHILL1, presumably through the repressor ZEB2, but there is scarce knowledge about its role in other vertebrates. During amphibian gastrulation, Delta/Notch signaling refines germ layer boundaries in the marginal zone, but it is unknown the place this pathway occupies in the network comprising Churchill1 and Nodal. Here, we show that Xenopus churchill1 is expressed in the presumptive neuroectoderm at mid-blastula transition and during gastrulation, upregulates zeb2, prevents dll1 expression in the neuroectoderm, and favors neuroectoderm over endomesoderm development. Nodal signaling prevents dll1 expression in the endoderm but induces it in the presumptive mesoderm, from where it activates Notch1 and its target gene hes4 in the non-involuting marginal zone. We propose a model where Nodal and Churchill1 position Dll1/Notch1/Hes4 domains in the marginal zone, ensuring the delimitation between mesoderm and neuroectoderm.
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Affiliation(s)
- María Belén Favarolo
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Biología Celular e Histología/1° U.A. Departamento de Histología, Embriología, Biología Celular y Genética, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), Laboratorio de Embriología Molecular "Prof. Dr. Andrés E. Carrasco", Buenos Aires, Argentina
| | - Diego R Revinski
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Biología Celular e Histología/1° U.A. Departamento de Histología, Embriología, Biología Celular y Genética, Buenos Aires, Argentina.,CONICET-Universidad de Buenos Aires, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), Laboratorio de Embriología Molecular "Prof. Dr. Andrés E. Carrasco", Buenos Aires, Argentina
| | - Matías J Garavaglia
- Laboratorio de Bioinsumos, Instituto de Biotecnología, Universidad Nacional de Hurlingham, Buenos Aires, Argentina
| | - Silvia L López
- Universidad de Buenos Aires, Facultad de Medicina, Departamento de Biología Celular e Histología/1° U.A. Departamento de Histología, Embriología, Biología Celular y Genética, Buenos Aires, Argentina .,CONICET-Universidad de Buenos Aires, Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis" (IBCN), Laboratorio de Embriología Molecular "Prof. Dr. Andrés E. Carrasco", Buenos Aires, Argentina
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2
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Park S, Mossmann D, Chen Q, Wang X, Dazert E, Colombi M, Schmidt A, Ryback B, Ng CKY, Terracciano LM, Heim MH, Hall MN. Transcription factors TEAD2 and E2A globally repress acetyl-CoA synthesis to promote tumorigenesis. Mol Cell 2022; 82:4246-4261.e11. [PMID: 36400009 DOI: 10.1016/j.molcel.2022.10.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 08/22/2022] [Accepted: 10/24/2022] [Indexed: 11/18/2022]
Abstract
Acetyl-coenzyme A (acetyl-CoA) plays an important role in metabolism, gene expression, signaling, and other cellular processes via transfer of its acetyl group to proteins and metabolites. However, the synthesis and usage of acetyl-CoA in disease states such as cancer are poorly characterized. Here, we investigated global acetyl-CoA synthesis and protein acetylation in a mouse model and patient samples of hepatocellular carcinoma (HCC). Unexpectedly, we found that acetyl-CoA levels are decreased in HCC due to transcriptional downregulation of all six acetyl-CoA biosynthesis pathways. This led to hypo-acetylation specifically of non-histone proteins, including many enzymes in metabolic pathways. Importantly, repression of acetyl-CoA synthesis promoted oncogenic dedifferentiation and proliferation. Mechanistically, acetyl-CoA synthesis was repressed by the transcription factors TEAD2 and E2A, previously unknown to control acetyl-CoA synthesis. Knockdown of TEAD2 and E2A restored acetyl-CoA levels and inhibited tumor growth. Our findings causally link transcriptional reprogramming of acetyl-CoA metabolism, dedifferentiation, and cancer.
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Affiliation(s)
- Sujin Park
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Dirk Mossmann
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Qian Chen
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland; Division of Gastroenterology and Hepatology, Clarunis, University Center for Gastrointestinal and Liver Diseases, 4031 Basel, Switzerland
| | - Xueya Wang
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland; Division of Gastroenterology and Hepatology, Clarunis, University Center for Gastrointestinal and Liver Diseases, 4031 Basel, Switzerland
| | - Eva Dazert
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Marco Colombi
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Brendan Ryback
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Charlotte K Y Ng
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland; Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | | | - Markus H Heim
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland; Division of Gastroenterology and Hepatology, Clarunis, University Center for Gastrointestinal and Liver Diseases, 4031 Basel, Switzerland
| | - Michael N Hall
- Biozentrum, University of Basel, 4056 Basel, Switzerland.
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3
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Johnson K, Freedman S, Braun R, LaBonne C. Quantitative analysis of transcriptome dynamics provides novel insights into developmental state transitions. BMC Genomics 2022; 23:723. [PMID: 36273135 PMCID: PMC9588240 DOI: 10.1186/s12864-022-08953-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
Background During embryogenesis, the developmental potential of initially pluripotent cells becomes progressively restricted as they transit to lineage restricted states. The pluripotent cells of Xenopus blastula-stage embryos are an ideal system in which to study cell state transitions during developmental decision-making, as gene expression dynamics can be followed at high temporal resolution. Results Here we use transcriptomics to interrogate the process by which pluripotent cells transit to four different lineage-restricted states: neural progenitors, epidermis, endoderm and ventral mesoderm, providing quantitative insights into the dynamics of Waddington’s landscape. Our findings provide novel insights into why the neural progenitor state is the default lineage state for pluripotent cells and uncover novel components of lineage-specific gene regulation. These data reveal an unexpected overlap in the transcriptional responses to BMP4/7 and Activin signaling and provide mechanistic insight into how the timing of signaling inputs such as BMP are temporally controlled to ensure correct lineage decisions. Conclusions Together these analyses provide quantitative insights into the logic and dynamics of developmental decision making in early embryos. They also provide valuable lineage-specific time series data following the acquisition of specific lineage states during development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08953-3.
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Affiliation(s)
- Kristin Johnson
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Simon Freedman
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, 60208, USA.,Department of Engineering Sciences and Applied Math, Northwestern University, Evanston, IL, USA
| | - Rosemary Braun
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, 60208, USA.,Department of Engineering Sciences and Applied Math, Northwestern University, Evanston, IL, USA.,Northwestern Institute On Complex Systems, Northwestern University, Evanston, IL, USA
| | - Carole LaBonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA. .,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, 60208, USA.
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4
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Abstract
The EPH receptor tyrosine kinases and their signaling partners, the EPHRINS, comprise a large class of cell signaling molecules that plays diverse roles in development. As cell membrane-anchored signaling molecules, they regulate cellular organization by modulating the strength of cellular contacts, usually by impacting the actin cytoskeleton or cell adhesion programs. Through these cellular functions, EPH/EPHRIN signaling often regulates tissue shape. Indeed, recent evidence indicates that this signaling family is ancient and associated with the origin of multicellularity. Though extensively studied, our understanding of the signaling mechanisms employed by this large family of signaling proteins remains patchwork, and a truly "canonical" EPH/EPHRIN signal transduction pathway is not known and may not exist. Instead, several foundational evolutionarily conserved mechanisms are overlaid by a myriad of tissue -specific functions, though common themes emerge from these as well. Here, I review recent advances and the related contexts that have provided new understanding of the conserved and varied molecular and cellular mechanisms employed by EPH/EPHRIN signaling during development.
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Affiliation(s)
- Jeffrey O Bush
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, United States; Program in Craniofacial Biology, University of California San Francisco, San Francisco, CA, United States; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, United States; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, United States.
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5
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Jansen C, Paraiso KD, Zhou JJ, Blitz IL, Fish MB, Charney RM, Cho JS, Yasuoka Y, Sudou N, Bright AR, Wlizla M, Veenstra GJC, Taira M, Zorn AM, Mortazavi A, Cho KWY. Uncovering the mesendoderm gene regulatory network through multi-omic data integration. Cell Rep 2022; 38:110364. [PMID: 35172134 PMCID: PMC8917868 DOI: 10.1016/j.celrep.2022.110364] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 10/30/2021] [Accepted: 01/19/2022] [Indexed: 01/01/2023] Open
Abstract
Mesendodermal specification is one of the earliest events in embryogenesis, where cells first acquire distinct identities. Cell differentiation is a highly regulated process that involves the function of numerous transcription factors (TFs) and signaling molecules, which can be described with gene regulatory networks (GRNs). Cell differentiation GRNs are difficult to build because existing mechanistic methods are low throughput, and high-throughput methods tend to be non-mechanistic. Additionally, integrating highly dimensional data composed of more than two data types is challenging. Here, we use linked self-organizing maps to combine chromatin immunoprecipitation sequencing (ChIP-seq)/ATAC-seq with temporal, spatial, and perturbation RNA sequencing (RNA-seq) data from Xenopus tropicalis mesendoderm development to build a high-resolution genome scale mechanistic GRN. We recover both known and previously unsuspected TF-DNA/TF-TF interactions validated through reporter assays. Our analysis provides insights into transcriptional regulation of early cell fate decisions and provides a general approach to building GRNs using highly dimensional multi-omic datasets.
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Affiliation(s)
- Camden Jansen
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Jeff J Zhou
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Margaret B Fish
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Rebekah M Charney
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jin Sun Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Norihiro Sudou
- Department of Anatomy, School of Medicine, Toho University, Tokyo, Japan
| | - Ann Rose Bright
- Department of Molecular Developmental Biology, Radboud University, Nijmegen, the Netherlands
| | - Marcin Wlizla
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Gert Jan C Veenstra
- Department of Molecular Developmental Biology, Radboud University, Nijmegen, the Netherlands
| | - Masanori Taira
- Department of Biological Sciences, Chuo University, Tokyo, Japan
| | - Aaron M Zorn
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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6
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Bou-Rouphael J, Durand BC. T-Cell Factors as Transcriptional Inhibitors: Activities and Regulations in Vertebrate Head Development. Front Cell Dev Biol 2021; 9:784998. [PMID: 34901027 PMCID: PMC8651982 DOI: 10.3389/fcell.2021.784998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
Since its first discovery in the late 90s, Wnt canonical signaling has been demonstrated to affect a large variety of neural developmental processes, including, but not limited to, embryonic axis formation, neural proliferation, fate determination, and maintenance of neural stem cells. For decades, studies have focused on the mechanisms controlling the activity of β-catenin, the sole mediator of Wnt transcriptional response. More recently, the spotlight of research is directed towards the last cascade component, the T-cell factor (TCF)/Lymphoid-Enhancer binding Factor (LEF), and more specifically, the TCF/LEF-mediated switch from transcriptional activation to repression, which in both embryonic blastomeres and mouse embryonic stem cells pushes the balance from pluri/multipotency towards differentiation. It has been long known that Groucho/Transducin-Like Enhancer of split (Gro/TLE) is the main co-repressor partner of TCF/LEF. More recently, other TCF/LEF-interacting partners have been identified, including the pro-neural BarH-Like 2 (BARHL2), which belongs to the evolutionary highly conserved family of homeodomain-containing transcription factors. This review describes the activities and regulatory modes of TCF/LEF as transcriptional repressors, with a specific focus on the functions of Barhl2 in vertebrate brain development. Specific attention is given to the transcriptional events leading to formation of the Organizer, as well as the roles and regulations of Wnt/β-catenin pathway in growth of the caudal forebrain. We present TCF/LEF activities in both embryonic and neural stem cells and discuss how alterations of this pathway could lead to tumors.
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Affiliation(s)
| | - Béatrice C. Durand
- Sorbonne Université, CNRS UMR7622, IBPS Developmental Biology Laboratory, Campus Pierre et Marie Curie, Paris, France
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7
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Cui N, Han Q, Cao Q, Wang K, Zhou X, Hou P, Liu C, Chen L, Xu L. Lefty A is involved in sunitinib resistance of renal cell carcinoma cells via regulation of IL-8. Biol Chem 2021; 402:1247-1256. [PMID: 34363384 DOI: 10.1515/hsz-2021-0280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 06/23/2021] [Indexed: 12/13/2022]
Abstract
Renal cell carcinoma (RCC) is the third most frequent malignancy within urological oncology. Sunitinib has been used as the standard of treatment for first-line RCC therapy. Understanding mechanisms of sunitinib resistance in RCC cell is important for clinical therapy and drug development. We established sunitinib resistant RCC cells by treating cells with increasing concentrations of sunitinib and named resistant cells as RCC/SR. Lefty A, an important embryonic morphogen, was increased in RCC/SR cells. Targeted inhibition of Lefty via its siRNAs restored the sensitivity of renal resistant cells to sunitinib treatment. It was due to that si-Lefty can decrease the expression of interleukin-8 (IL-8) in RCC/SR cells. Knockdown of IL-8 abolished Lefty-regulated sunitinib sensitivity of RCC cells. Mechanistically, Lefty can regulate IL-8 transcription via activation of p65, one major transcription factor of IL-8. Collectively, our present revealed that Lefty A can regulate sunitinib sensitivity of RCC cells of via NF-κB/IL-8 signals. It indicated that targeted inhibition of Lefty might be a potent approach to overcome sunitinib resistance of RCC.
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Affiliation(s)
- Ning Cui
- Medical Imaging Center, Taihe Hospital, No.32 Renmin South Road, Shiyan442000, Hubei Province, China
| | - Qiang Han
- Medical Imaging Center, Taihe Hospital, No.32 Renmin South Road, Shiyan442000, Hubei Province, China
| | - Qizhen Cao
- Medical Imaging Center, Taihe Hospital, No.32 Renmin South Road, Shiyan442000, Hubei Province, China
| | - Kejun Wang
- Medical Imaging Center, Taihe Hospital, No.32 Renmin South Road, Shiyan442000, Hubei Province, China
| | - Xujia Zhou
- Medical Imaging Center, Taihe Hospital, No.32 Renmin South Road, Shiyan442000, Hubei Province, China
| | - Pingzhi Hou
- Medical Imaging Center, Taihe Hospital, No.32 Renmin South Road, Shiyan442000, Hubei Province, China
| | - Chao Liu
- Medical Imaging Center, Taihe Hospital, No.32 Renmin South Road, Shiyan442000, Hubei Province, China
| | - Lungang Chen
- Medical Imaging Center, Taihe Hospital, No.32 Renmin South Road, Shiyan442000, Hubei Province, China
| | - Lin Xu
- Medical Imaging Center, Taihe Hospital, No.32 Renmin South Road, Shiyan442000, Hubei Province, China
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8
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Yi S, Huang X, Zhou S, Zhou Y, Anderson MK, Zúñiga-Pflücker JC, Luan Q, Li Y. E2A regulates neural ectoderm fate specification in human embryonic stem cells. Development 2020; 147:dev.190298. [PMID: 33144398 DOI: 10.1242/dev.190298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 10/27/2020] [Indexed: 11/20/2022]
Abstract
E protein transcription factors are crucial for many cell fate decisions. However, the roles of E proteins in the germ-layer specification of human embryonic stem cells (hESCs) are poorly understood. We disrupted the TCF3 gene locus to delete the E protein E2A in hESCs. E2A knockout (KO) hESCs retained key features of pluripotency, but displayed decreased neural ectoderm coupled with enhanced mesoendoderm outcomes. Genome-wide analyses showed that E2A directly regulates neural ectoderm and Nodal pathway genes. Accordingly, inhibition of Nodal or E2A overexpression partially rescued the neural ectoderm defect in E2A KO hESCs. Loss of E2A had little impact on the epigenetic landscape of hESCs, whereas E2A KO neural precursors displayed increased accessibility of the gene locus encoding the Nodal agonist CRIPTO. Double-deletion of both E2A and HEB (TCF12) resulted in a more severe neural ectoderm defect. Therefore, this study reveals critical context-dependent functions for E2A in human neural ectoderm fate specification.
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Affiliation(s)
- Siqi Yi
- Department of Periodontology, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China.,Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Xiaotian Huang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Shixin Zhou
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
| | - Yuan Zhou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Michele K Anderson
- Department of Immunology, University of Toronto, Sunnybrook Research Institute, Toronto, ON M4N 3M5, Canada
| | | | - Qingxian Luan
- Department of Periodontology, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - Yang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing 100191, China
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9
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Rao C, Malaguti M, Mason JO, Lowell S. The transcription factor E2A drives neural differentiation in pluripotent cells. Development 2020; 147:dev184093. [PMID: 32487737 PMCID: PMC7328008 DOI: 10.1242/dev.184093] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 05/26/2020] [Indexed: 12/21/2022]
Abstract
The intrinsic mechanisms that link extracellular signalling to the onset of neural differentiation are not well understood. In pluripotent mouse cells, BMP blocks entry into the neural lineage via transcriptional upregulation of inhibitor of differentiation (Id) factors. We have previously identified the major binding partner of Id proteins in pluripotent cells as the basic helix-loop-helix (bHLH) transcription factor (TF) E2A. Id1 can prevent E2A from forming heterodimers with bHLH TFs or from forming homodimers. Here, we show that overexpression of a forced E2A homodimer is sufficient to drive robust neural commitment in pluripotent cells, even under non-permissive conditions. Conversely, we find that E2A null cells display a defect in their neural differentiation capacity. E2A acts as an upstream activator of neural lineage genes, including Sox1 and Foxd4, and as a repressor of Nodal signalling. Our results suggest a crucial role for E2A in establishing neural lineage commitment in pluripotent cells.
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Affiliation(s)
- Chandrika Rao
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - Mattias Malaguti
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | - John O Mason
- Centre for Discovery Brain Sciences, University of Edinburgh, 15 George Square, Edinburgh EH8 9XD, UK
- Simons Initiative for the Developing Brain, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK
| | - Sally Lowell
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK
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10
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Paraiso KD, Blitz IL, Zhou JJ, Cho KWY. Morpholinos Do Not Elicit an Innate Immune Response during Early Xenopus Embryogenesis. Dev Cell 2020; 49:643-650.e3. [PMID: 31112700 DOI: 10.1016/j.devcel.2019.04.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/14/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023]
Abstract
It has recently been reported that a common side effect of translation-blocking morpholino antisense oligonucleotides is the induction of a set of innate immune response genes in Xenopus embryos and that splicing-blocking morpholinos lead to unexpected off-target mis-splicing events. Here, we present an analysis of all publicly available Xenopus RNA sequencing (RNA-seq) data in a reexamination of the effects of translation-blocking morpholinos on the innate immune response. Our analysis does not support the authors' general conclusion, which was based on a limited number of RNA-seq datasets. Moreover, the strong induction of an immune response appears to be specific to the tbxt/tbxt2 morpholinos. The more comprehensive study presented here indicates that using morpholinos for targeted gene knockdowns remains of considerable value for the rapid identification of gene function.
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Affiliation(s)
- Kitt D Paraiso
- Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ira L Blitz
- Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Jeff J Zhou
- Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Ken W Y Cho
- Developmental and Cell Biology, University of California, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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11
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Fiuza UM, Negishi T, Rouan A, Yasuo H, Lemaire P. A Nodal/Eph signalling relay drives the transition from apical constriction to apico-basal shortening in ascidian endoderm invagination. Development 2020; 147:dev.186965. [DOI: 10.1242/dev.186965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 07/02/2020] [Indexed: 01/13/2023]
Abstract
Gastrulation is the first major morphogenetic event during animal embryogenesis. Ascidian gastrulation starts with the invagination of 10 endodermal precursor cells between the 64- and late 112-cell stages. This process occurs in the absence of endodermal cell division and in two steps, driven by myosin-dependent contractions of the acto-myosin network. First, endoderm precursors constrict their apex. Second, they shorten apico-basally, while retaining small apical surfaces, thereby causing invagination. The mechanisms that prevent endoderm cell division, trigger the transition between step 1 and step 2, and drive apico-basal shortening have remained elusive. Here, we demonstrate a conserved role for Nodal and Eph signalling during invagination in two distantly related ascidian species, Phallusia mammillata and Ciona intestinalis. Specifically, we show that the transition to step 2 is triggered by Nodal relayed by Eph signalling. Additionally, our results indicate that Eph signalling lengthens the endodermal cell cycle, independently of Nodal. Finally, we find that both Nodal and Eph signals are dispensable for endoderm fate specification. These results illustrate commonalities as well as differences in the action of Nodal during ascidian and vertebrate gastrulation.
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Affiliation(s)
- Ulla-Maj Fiuza
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | - Takefumi Negishi
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, CNRS, Sorbonne Universités, 06230 Villefranche-sur-Mer, France
| | - Alice Rouan
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, CNRS, Sorbonne Universités, 06230 Villefranche-sur-Mer, France
| | - Hitoyoshi Yasuo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, CNRS, Sorbonne Universités, 06230 Villefranche-sur-Mer, France
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12
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Shoji M, Minato H, Ogaki S, Seki M, Suzuki Y, Kume S, Kuzuhara T. Different murine-derived feeder cells alter the definitive endoderm differentiation of human induced pluripotent stem cells. PLoS One 2018; 13:e0201239. [PMID: 30048506 PMCID: PMC6062072 DOI: 10.1371/journal.pone.0201239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/11/2018] [Indexed: 12/19/2022] Open
Abstract
The crosstalk between cells is important for differentiation of cells. Murine-derived feeder cells, SNL76/7 feeder cells (SNLs) or mouse primary embryonic fibroblast feeder cells (MEFs) are widely used for culturing undifferentiated human induced pluripotent stem cells (hiPSCs). It is still unclear whether different culture conditions affect the induction efficiency of definitive endoderm (DE) differentiation from hiPSCs. Here we show that the efficiency of DE differentiation from hiPSCs cultured on MEFs was higher than that of hiPSCs cultured on SNLs. The qPCR, immunofluorescent and flow cytometry analyses revealed that the expression levels of mRNA and/or proteins of the DE marker genes, SOX17, FOXA2 and CXCR4, in DE cells differentiated from hiPSCs cultured on MEFs were significantly higher than those cultured on SNLs. Comprehensive RNA sequencing and molecular network analyses showed the alteration of the gene expression and the signal transduction of hiPSCs cultured on SNLs and MEFs. Interestingly, the expression of non-coding hXIST exon 4 was up-regulated in hiPSCs cultured on MEFs, in comparison to that in hiPSCs cultured on SNLs. By qPCR analysis, the mRNA expression of undifferentiated stem cell markers KLF4, KLF5, OCT3/4, SOX2, NANOG, UTF1, and GRB7 were lower, while that of hXIST exon 4, LEFTY1, and LEFTY2 was higher in hiPSCs cultured on MEFs than in those cultured on SNLs. Taken together, our finding indicated that differences in murine-feeder cells used for maintenance of the undifferentiated state alter the expression of pluripotency-related genes in hiPSCs by the signaling pathways and affect DE differentiation from hiPSCs, suggesting that the feeder cells can potentiate hiPSCs for DE differentiation.
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Affiliation(s)
- Masaki Shoji
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Japan
- * E-mail: (MS); (TK)
| | - Hiroki Minato
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Japan
| | - Soichiro Ogaki
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Shoen Kume
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Takashi Kuzuhara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Tokushima, Japan
- * E-mail: (MS); (TK)
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13
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Abstract
TGF-β family ligands function in inducing and patterning many tissues of the early vertebrate embryonic body plan. Nodal signaling is essential for the specification of mesendodermal tissues and the concurrent cellular movements of gastrulation. Bone morphogenetic protein (BMP) signaling patterns tissues along the dorsal-ventral axis and simultaneously directs the cell movements of convergence and extension. After gastrulation, a second wave of Nodal signaling breaks the symmetry between the left and right sides of the embryo. During these processes, elaborate regulatory feedback between TGF-β ligands and their antagonists direct the proper specification and patterning of embryonic tissues. In this review, we summarize the current knowledge of the function and regulation of TGF-β family signaling in these processes. Although we cover principles that are involved in the development of all vertebrate embryos, we focus specifically on three popular model organisms: the mouse Mus musculus, the African clawed frog of the genus Xenopus, and the zebrafish Danio rerio, highlighting the similarities and differences between these species.
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Affiliation(s)
- Joseph Zinski
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
| | - Benjamin Tajer
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
| | - Mary C Mullins
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104-6058
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14
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Hill CS. Spatial and temporal control of NODAL signaling. Curr Opin Cell Biol 2018; 51:50-57. [PMID: 29153705 DOI: 10.1016/j.ceb.2017.10.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 12/21/2022]
Abstract
Embryonic development is orchestrated by the activity of signal transduction pathways, amongst which are those downstream of the transforming growth factor β (TGF-β) family. Here I focus on signalling by one of these ligands, NODAL, which is essential for early embryonic axis patterning. I review recent advances in our understanding of how NODAL signalling is transduced from the plasma membrane to the nucleus to regulate the transcription of target genes, and how domains of NODAL activity are established and refined during embryonic development. The duration of signalling is emerging as a key determinant of the specificity of downstream responses in terms of cell fate decisions and I will discuss what is currently known about the underlying mechanisms.
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Affiliation(s)
- Caroline S Hill
- Developmental Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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15
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Hepatocyte Nuclear Factor 4 Alpha Promotes Definitive Endoderm Differentiation from Human Induced Pluripotent Stem Cells. Stem Cell Rev Rep 2018; 13:542-551. [PMID: 28000155 DOI: 10.1007/s12015-016-9709-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hepatocyte nuclear factor 4 alpha (HNF4α) is a key transcription factor for liver development. Although HNF4α is necessary for hepatoblast differentiation, the function of HNF4α before the hepatoblast differentiation, such as in definitive endoderm differentiation, is not well known. In addition, it is known that there are nine HNF4α isoforms, but the expression and function of each HNF4α isoform during the definitive endoderm differentiation is also not clear. In this study, we examined the expression pattern of HNF4α and its functions in the definitive endoderm differentiation from human induced pluripotent stem (iPS) cells. We found that the HNF4α-1D isoform expression levels were significantly increased during the definitive endoderm differentiation, while the HNF4α-1A isoform expression levels did not change. Therefore, we further examined the function of the HNF4α-1D isoform in definitive endoderm differentiation. HNF4α-1D overexpression or knockdown was found to promote or prevent the definitive endoderm differentiation, respectively. Interestingly, Lefty1 was directly regulated by HNF4α-1D, and Lefty1 knockdown also prevented the definitive endoderm differentiation. These results suggest that HNF4α-1D promotes definitive endoderm differentiation through the regulation of Lefty1. To our knowledge, this is the first report to clarify the expression pattern and function of HNF4α during the definitive endoderm differentiation.
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16
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Cunningham TJ, Yu MS, McKeithan WL, Spiering S, Carrette F, Huang CT, Bushway PJ, Tierney M, Albini S, Giacca M, Mano M, Puri PL, Sacco A, Ruiz-Lozano P, Riou JF, Umbhauer M, Duester G, Mercola M, Colas AR. Id genes are essential for early heart formation. Genes Dev 2017; 31:1325-1338. [PMID: 28794185 PMCID: PMC5580654 DOI: 10.1101/gad.300400.117] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/17/2017] [Indexed: 01/08/2023]
Abstract
Deciphering the fundamental mechanisms controlling cardiac specification is critical for our understanding of how heart formation is initiated during embryonic development and for applying stem cell biology to regenerative medicine and disease modeling. Using systematic and unbiased functional screening approaches, we discovered that the Id family of helix-loop-helix proteins is both necessary and sufficient to direct cardiac mesoderm formation in frog embryos and human embryonic stem cells. Mechanistically, Id proteins specify cardiac cell fate by repressing two inhibitors of cardiogenic mesoderm formation-Tcf3 and Foxa2-and activating inducers Evx1, Grrp1, and Mesp1. Most importantly, CRISPR/Cas9-mediated ablation of the entire Id (Id1-4) family in mouse embryos leads to failure of anterior cardiac progenitor specification and the development of heartless embryos. Thus, Id proteins play a central and evolutionarily conserved role during heart formation and provide a novel means to efficiently produce cardiovascular progenitors for regenerative medicine and drug discovery applications.
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Affiliation(s)
- Thomas J Cunningham
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Michael S Yu
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Department of Bioengineering, University of California at San Diego, La Jolla, California 92037, USA
| | - Wesley L McKeithan
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA.,Department of Medicine and Cardiovascular Institute, Stanford University, Palo Alto, California 94305, USA
| | - Sean Spiering
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Florent Carrette
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Chun-Teng Huang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Paul J Bushway
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92037, USA
| | - Matthew Tierney
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Sonia Albini
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Mauro Giacca
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Miguel Mano
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal
| | - Pier Lorenzo Puri
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Istituti di Ricovero e Cura a Carattere Scientifico, Fondazione Santa Lucia, 00179 Rome, Italy
| | - Alessandra Sacco
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Pilar Ruiz-Lozano
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Regencor, Inc., Los Altos, California 94022, USA
| | - Jean-Francois Riou
- UMR 7622 Developmental Biology, Sorbonne Universités, University Pierre and Marie Curie, F- 75005 Paris, France
| | - Muriel Umbhauer
- UMR 7622 Developmental Biology, Sorbonne Universités, University Pierre and Marie Curie, F- 75005 Paris, France
| | - Gregg Duester
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
| | - Mark Mercola
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA.,Department of Medicine and Cardiovascular Institute, Stanford University, Palo Alto, California 94305, USA
| | - Alexandre R Colas
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA
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17
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Sampath K, Robertson EJ. Keeping a lid on nodal: transcriptional and translational repression of nodal signalling. Open Biol 2016; 6:150200. [PMID: 26791244 PMCID: PMC4736825 DOI: 10.1098/rsob.150200] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nodal is an evolutionarily conserved member of the transforming growth factor-β (TGF-β) superfamily of secreted signalling factors. Nodal factors are known to play key roles in embryonic development and asymmetry in a variety of organisms ranging from hydra and sea urchins to fish, mice and humans. In addition to embryonic patterning, Nodal signalling is required for maintenance of human embryonic stem cell pluripotency and mis-regulated Nodal signalling has been found associated with tumour metastases. Therefore, precise and timely regulation of this pathway is essential. Here, we discuss recent evidence from sea urchins, frogs, fish, mice and humans that show a role for transcriptional and translational repression of Nodal signalling during early development.
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Affiliation(s)
- Karuna Sampath
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AJ, UK
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18
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Blitz IL, Paraiso KD, Patrushev I, Chiu WTY, Cho KWY, Gilchrist MJ. A catalog of Xenopus tropicalis transcription factors and their regional expression in the early gastrula stage embryo. Dev Biol 2016; 426:409-417. [PMID: 27475627 PMCID: PMC5596316 DOI: 10.1016/j.ydbio.2016.07.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/01/2016] [Accepted: 07/01/2016] [Indexed: 12/30/2022]
Abstract
Gene regulatory networks (GRNs) involve highly combinatorial interactions between transcription factors and short sequence motifs in cis-regulatory modules of target genes to control cellular phenotypes. The GRNs specifying most cell types are largely unknown and are the subject of wide interest. A catalog of transcription factors is a valuable tool toward obtaining a deeper understanding of the role of these critical effectors in any biological setting. Here we present a comprehensive catalog of the transcription factors for the diploid frog Xenopus tropicalis. We identify 1235 genes encoding DNA-binding transcription factors, comparable to the numbers found in typical mammalian species. In detail, the repertoire of X. tropicalis transcription factor genes is nearly identical to human and mouse, with the exception of zinc finger family members, and a small number of species/lineage-specific gene duplications and losses relative to the mammalian repertoires. We applied this resource to the identification of transcription factors differentially expressed in the early gastrula stage embryo. We find transcription factor enrichment in Spemann's organizer, the ventral mesoderm, ectoderm and endoderm, and report 218 TFs that show regionalized expression patterns at this stage. Many of these have not been previously reported as expressed in the early embryo, suggesting thus far unappreciated roles for many transcription factors in the GRNs regulating early development. We expect our transcription factor catalog will facilitate myriad studies using Xenopus as a model system to understand basic biology and human disease.
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Affiliation(s)
- Ira L Blitz
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States.
| | - Kitt D Paraiso
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States
| | - Ilya Patrushev
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK
| | - William T Y Chiu
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States
| | - Ken W Y Cho
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, United States.
| | - Michael J Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway Mill Hill, London NW7 1AA, UK.
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19
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Reid CD, Karra K, Chang J, Piskol R, Li Q, Li JB, Cherry JM, Baker JC. XenMine: A genomic interaction tool for the Xenopus community. Dev Biol 2016; 426:155-164. [PMID: 27157655 DOI: 10.1016/j.ydbio.2016.02.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 02/06/2016] [Accepted: 02/26/2016] [Indexed: 11/17/2022]
Abstract
The Xenopus community has embraced recent advances in sequencing technology, resulting in the accumulation of numerous RNA-Seq and ChIP-Seq datasets. However, easily accessing and comparing datasets generated by multiple laboratories is challenging. Thus, we have created a central space to view, search and analyze data, providing essential information on gene expression changes and regulatory elements present in the genome. XenMine (www.xenmine.org) is a user-friendly website containing published genomic datasets from both Xenopus tropicalis and Xenopus laevis. We have established an analysis pipeline where all published datasets are uniformly processed with the latest genome releases. Information from these datasets can be extracted and compared using an array of pre-built or custom templates. With these search tools, users can easily extract sequences for all putative regulatory domains surrounding a gene of interest, identify the expression values of a gene of interest over developmental time, and analyze lists of genes for gene ontology terms and publications. Additionally, XenMine hosts an in-house genome browser that allows users to visualize all available ChIP-Seq data, extract specifically marked sequences, and aid in identifying important regulatory elements within the genome. Altogether, XenMine is an excellent tool for visualizing, accessing and querying analyzed datasets rapidly and efficiently.
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Affiliation(s)
- Christine D Reid
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Jessica Chang
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Robert Piskol
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Qin Li
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University, Stanford CA 94305, USA
| | - Julie C Baker
- Department of Genetics, Stanford University, Stanford CA 94305, USA.
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