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Tran M, Askary A, Elowitz MB. Lineage motifs as developmental modules for control of cell type proportions. Dev Cell 2024; 59:812-826.e3. [PMID: 38359830 DOI: 10.1016/j.devcel.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/10/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024]
Abstract
In multicellular organisms, cell types must be produced and maintained in appropriate proportions. One way this is achieved is through committed progenitor cells or extrinsic interactions that produce specific patterns of descendant cell types on lineage trees. However, cell fate commitment is probabilistic in most contexts, making it difficult to infer these dynamics and understand how they establish overall cell type proportions. Here, we introduce Lineage Motif Analysis (LMA), a method that recursively identifies statistically overrepresented patterns of cell fates on lineage trees as potential signatures of committed progenitor states or extrinsic interactions. Applying LMA to published datasets reveals spatial and temporal organization of cell fate commitment in zebrafish and rat retina and early mouse embryonic development. Comparative analysis of vertebrate species suggests that lineage motifs facilitate adaptive evolutionary variation of retinal cell type proportions. LMA thus provides insight into complex developmental processes by decomposing them into simpler underlying modules.
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Affiliation(s)
- Martin Tran
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Amjad Askary
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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2
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Goh W, Sudholz H, Foroutan M, Scheer S, Pfefferle A, Delconte RB, Meng X, Shen Z, Hennessey R, Kong IY, Schuster IS, Andoniou CE, Davis MJ, Hediyeh-Zadeh S, Souza-Fonseca-Guimaraes F, Parish IA, Beavis P, Thiele D, Chopin M, Degli-Esposti MA, Cursons J, Kallies A, Rautela J, Nutt SL, Huntington ND. IKAROS and AIOLOS directly regulate AP-1 transcriptional complexes and are essential for NK cell development. Nat Immunol 2024; 25:240-255. [PMID: 38182668 DOI: 10.1038/s41590-023-01718-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/22/2023] [Indexed: 01/07/2024]
Abstract
Ikaros transcription factors are essential for adaptive lymphocyte function, yet their role in innate lymphopoiesis is unknown. Using conditional genetic inactivation, we show that Ikzf1/Ikaros is essential for normal natural killer (NK) cell lymphopoiesis and IKZF1 directly represses Cish, a negative regulator of interleukin-15 receptor resulting in impaired interleukin-15 receptor signaling. Both Bcl2l11 and BIM levels, and intrinsic apoptosis were increased in Ikzf1-null NK cells, which in part accounts for NK lymphopenia as both were restored to normal levels when Ikzf1 and Bcl2l11 were co-deleted. Ikzf1-null NK cells presented extensive transcriptional alterations with reduced AP-1 transcriptional complex expression and increased expression of Ikzf2/Helios and Ikzf3/Aiolos. IKZF1 and IKZF3 directly bound AP-1 family members and deletion of both Ikzf1 and Ikzf3 in NK cells resulted in further reductions in Jun/Fos expression and complete loss of peripheral NK cells. Collectively, we show that Ikaros family members are important regulators of apoptosis, cytokine responsiveness and AP-1 transcriptional activity.
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Affiliation(s)
- Wilford Goh
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Harrison Sudholz
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Momeneh Foroutan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Sebastian Scheer
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Aline Pfefferle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Rebecca B Delconte
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiangpeng Meng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Zihan Shen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Robert Hennessey
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Isabella Y Kong
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Iona S Schuster
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Christopher E Andoniou
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
- The South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Soroor Hediyeh-Zadeh
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paul Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Thiele
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Michael Chopin
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Mariapia A Degli-Esposti
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Centre for Experimental Immunology, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Joe Cursons
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Axel Kallies
- Department of Microbiology & Immunology, Faculty of Medicine, Dentistry and Health Sciences & Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jai Rautela
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research. Department of Medical Biology, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nicholas D Huntington
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia.
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Zhang X, Leavey P, Appel H, Makrides N, Blackshaw S. Molecular mechanisms controlling vertebrate retinal patterning, neurogenesis, and cell fate specification. Trends Genet 2023; 39:736-757. [PMID: 37423870 PMCID: PMC10529299 DOI: 10.1016/j.tig.2023.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023]
Abstract
This review covers recent advances in understanding the molecular mechanisms controlling neurogenesis and specification of the developing retina, with a focus on insights obtained from comparative single cell multiomic analysis. We discuss recent advances in understanding the mechanisms by which extrinsic factors trigger transcriptional changes that spatially pattern the optic cup (OC) and control the initiation and progression of retinal neurogenesis. We also discuss progress in unraveling the core evolutionarily conserved gene regulatory networks (GRNs) that specify early- and late-state retinal progenitor cells (RPCs) and neurogenic progenitors and that control the final steps in determining cell identity. Finally, we discuss findings that provide insight into regulation of species-specific aspects of retinal patterning and neurogenesis, including consideration of key outstanding questions in the field.
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Affiliation(s)
- Xin Zhang
- Department of Ophthalmology, Columbia University School of Medicine, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University School of Medicine, New York, NY, USA.
| | - Patrick Leavey
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Haley Appel
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neoklis Makrides
- Department of Ophthalmology, Columbia University School of Medicine, New York, NY, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Psychiatry and Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Liang J, Fang D, Yao F, Chen L, Zou Z, Tang X, Feng L, Zhuang Y, Xie T, Wei P, Li P, Zheng H, Zhang S. Analysis of shared ceRNA networks and related-hub genes in rats with primary and secondary photoreceptor degeneration. Front Neurosci 2023; 17:1259622. [PMID: 37811327 PMCID: PMC10552924 DOI: 10.3389/fnins.2023.1259622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Photoreceptor degenerative diseases are characterized by the progressive death of photoreceptor cells, resulting in irreversible visual impairment. However, the role of competing endogenous RNA (ceRNA) in photoreceptor degeneration is unclear. We aimed to explore the shared ceRNA regulation network and potential molecular mechanisms between primary and secondary photoreceptor degenerations. Methods We established animal models for both types of photoreceptor degenerations and conducted retina RNA sequencing to identify shared differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs). Using ceRNA regulatory principles, we constructed a shared ceRNA network and performed function enrichment and protein-protein interaction (PPI) analyses to identify hub genes and key pathways. Immune cell infiltration and drug-gene interaction analyses were conducted, and hub gene expression was validated by quantitative real-time polymerase chain reaction (qRT-PCR). Results We identified 37 shared differentially expressed lncRNAs, 34 miRNAs, and 247 mRNAs and constructed a ceRNA network consisting of 3 lncRNAs, 5 miRNAs, and 109 mRNAs. Furthermore, we examined 109 common differentially expressed genes (DEGs) through functional annotation, PPI analysis, and regulatory network analysis. We discovered that these diseases shared the complement and coagulation cascades pathway. Eight hub genes were identified and enriched in the immune system process. Immune infiltration analysis revealed increased T cells and decreased B cells in both photoreceptor degenerations. The expression of hub genes was closely associated with the quantities of immune cell types. Additionally, we identified 7 immune therapeutical drugs that target the hub genes. Discussion Our findings provide new insights and directions for understanding the common mechanisms underlying the development of photoreceptor degeneration. The hub genes and related ceRNA networks we identified may offer new perspectives for elucidating the mechanisms and hold promise for the development of innovative treatment strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Shaochong Zhang
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen, Guangdong, China
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Bosze B, Suarez-Navarro J, Cajias I, Brzezinski IV JA, Brown NL. Notch pathway mutants do not equivalently perturb mouse embryonic retinal development. PLoS Genet 2023; 19:e1010928. [PMID: 37751417 PMCID: PMC10522021 DOI: 10.1371/journal.pgen.1010928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/16/2023] [Indexed: 09/28/2023] Open
Abstract
In the vertebrate eye, Notch ligands, receptors, and ternary complex components determine the destiny of retinal progenitor cells in part by regulating Hes effector gene activity. There are multiple paralogues for nearly every node in this pathway, which results in numerous instances of redundancy and compensation during development. To dissect such complexity at the earliest stages of eye development, we used seven germline or conditional mutant mice and two spatiotemporally distinct Cre drivers. We perturbed the Notch ternary complex and multiple Hes genes to understand if Notch regulates optic stalk/nerve head development; and to test intracellular pathway components for their Notch-dependent versus -independent roles during retinal ganglion cell and cone photoreceptor competence and fate acquisition. We confirmed that disrupting Notch signaling universally blocks progenitor cell growth, but delineated specific pathway components that can act independently, such as sustained Hes1 expression in the optic stalk/nerve head. In retinal progenitor cells, we found that among the genes tested, they do not uniformly suppress retinal ganglion cell or cone differentiation; which is not due differences in developmental timing. We discovered that shifts in the earliest cell fates correlate with expression changes for the early photoreceptor factor Otx2, but not with Atoh7, a factor required for retinal ganglion cell formation. During photoreceptor genesis we also better defined multiple and simultaneous activities for Rbpj and Hes1 and identify redundant activities that occur downstream of Notch. Given its unique roles at the retina-optic stalk boundary and cone photoreceptor genesis, our data suggest Hes1 as a hub where Notch-dependent and -independent inputs converge.
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Affiliation(s)
- Bernadett Bosze
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Julissa Suarez-Navarro
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Illiana Cajias
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
| | - Joseph A. Brzezinski IV
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Nadean L. Brown
- Department of Cell Biology & Human Anatomy, University of California, Davis, California, United States of America
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Affar M, Bottardi S, Quansah N, Lemarié M, Ramón AC, Affar EB, Milot E. IKAROS: from chromatin organization to transcriptional elongation control. Cell Death Differ 2023:10.1038/s41418-023-01212-2. [PMID: 37620540 DOI: 10.1038/s41418-023-01212-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/26/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
IKAROS is a master regulator of cell fate determination in lymphoid and other hematopoietic cells. This transcription factor orchestrates the association of epigenetic regulators with chromatin, ensuring the expression pattern of target genes in a developmental and lineage-specific manner. Disruption of IKAROS function has been associated with the development of acute lymphocytic leukemia, lymphoma, chronic myeloid leukemia and immune disorders. Paradoxically, while IKAROS has been shown to be a tumor suppressor, it has also been identified as a key therapeutic target in the treatment of various forms of hematological malignancies, including multiple myeloma. Indeed, targeted proteolysis of IKAROS is associated with decreased proliferation and increased death of malignant cells. Although the molecular mechanisms have not been elucidated, the expression levels of IKAROS are variable during hematopoiesis and could therefore be a key determinant in explaining how its absence can have seemingly opposite effects. Mechanistically, IKAROS collaborates with a variety of proteins and complexes controlling chromatin organization at gene regulatory regions, including the Nucleosome Remodeling and Deacetylase complex, and may facilitate transcriptional repression or activation of specific genes. Several transcriptional regulatory functions of IKAROS have been proposed. An emerging mechanism of action involves the ability of IKAROS to promote gene repression or activation through its interaction with the RNA polymerase II machinery, which influences pausing and productive transcription at specific genes. This control appears to be influenced by IKAROS expression levels and isoform production. In here, we summarize the current state of knowledge about the biological roles and mechanisms by which IKAROS regulates gene expression. We highlight the dynamic regulation of this factor by post-translational modifications. Finally, potential avenues to explain how IKAROS destruction may be favorable in the treatment of certain hematological malignancies are also explored.
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Affiliation(s)
- Malik Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Stefania Bottardi
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Norreen Quansah
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Maud Lemarié
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - Ailyn C Ramón
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada
| | - El Bachir Affar
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
| | - Eric Milot
- Faculty of Medicine, University of Montreal, Montréal, QC, Canada.
- Maisonneuve-Rosemont Hospital Research Center, CIUSSS de l'Est-de-l'Île de Montréal, 5415 boulevard de l'Assomption, Montréal, QC, H1T 2M4, Canada.
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Zhang J, Roberts JM, Chang F, Schwakopf J, Vetter ML. Jarid2 promotes temporal progression of retinal progenitors via repression of Foxp1. Cell Rep 2023; 42:112237. [PMID: 36924502 PMCID: PMC10210259 DOI: 10.1016/j.celrep.2023.112237] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 01/14/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
Transitions in competence underlie the ability of CNS progenitors to generate a diversity of neurons and glia. Retinal progenitor cells in mouse generate early-born cell types embryonically and late-born cell types largely postnatally. We find that the transition from early to late progenitor competence is regulated by Jarid2. Loss of Jarid2 results in extended production of early cell types and extended expression of early progenitor genes. Jarid2 can regulate histone modifications, and we find reduction of repressive mark H3K27me3 on a subset of early progenitor genes with loss of Jarid2, most notably Foxp1. We show that Foxp1 regulates the competence to generate early-born retinal cell types, promotes early and represses late progenitor gene expression, and is required for extending early retinal cell production after loss of Jarid2. We conclude that Jarid2 facilitates progression of retinal progenitor temporal identity by repressing Foxp1, which is a primary regulator of early temporal patterning.
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Affiliation(s)
- Jianmin Zhang
- Department of Neurobiology, University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, UT 84112, USA
| | - Jacqueline M Roberts
- Department of Neurobiology, University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, UT 84112, USA
| | - Fei Chang
- Department of Neurobiology, University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, UT 84112, USA; Interdepartmental Program in Neuroscience, University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, UT 84112, USA
| | - Joon Schwakopf
- Department of Neurobiology, University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, UT 84112, USA
| | - Monica L Vetter
- Department of Neurobiology, University of Utah Spencer Fox Eccles School of Medicine, Salt Lake City, UT 84112, USA.
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