1
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Patierno BM, Emerson MM. Enhanced Plasmid-Based Transcriptional Activation in Developing Mouse Photoreceptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597220. [PMID: 38895286 PMCID: PMC11185626 DOI: 10.1101/2024.06.06.597220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Rod photoreceptor formation in the postnatal mouse is a widely used model system for studying mammalian photoreceptor development. This experimental paradigm provides opportunities for both gain and loss-of-function studies which can be accomplished through in vivo plasmid delivery and electroporation. However, the cis-regulatory elements used to implement this approach have not been fully evaluated or optimized for the unique transcriptional environment of photoreceptors. Here we report that the use of a photoreceptor cis-regulatory element from the Crx gene in combination with broadly active promoter elements can increase the targeting of developing rod photoreceptors in the mouse. This can lead to greater reporter expression, as well as enhanced misexpression and loss-of-function phenotypes in these cells. This study also highlights the importance of identifying and testing relevant cis-regulatory elements when planning cell subtype specific experiments. The use of the specific hybrid elements in this study will provide a more efficacious gene delivery system to study mammalian photoreceptor formation.
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Affiliation(s)
- Brendon M. Patierno
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, 10031
| | - Mark M. Emerson
- Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, 10031
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031
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2
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Sun C, Ruzycki PA, Chen S. Rho enhancers play unexpectedly minor roles in Rhodopsin transcription and rod cell integrity. Sci Rep 2023; 13:12899. [PMID: 37558693 PMCID: PMC10412641 DOI: 10.1038/s41598-023-39979-6] [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: 12/06/2022] [Accepted: 08/02/2023] [Indexed: 08/11/2023] Open
Abstract
Enhancers function with a basal promoter to control the transcription of target genes. Enhancer regulatory activity is often studied using reporter-based transgene assays. However, unmatched results have been reported when selected enhancers are silenced in situ. In this study, using genomic deletion analysis in mice, we investigated the roles of two previously identified enhancers and the promoter of the Rho gene that codes for the visual pigment rhodopsin. The Rho gene is robustly expressed by rod photoreceptors of the retina, and essential for the subcellular structure and visual function of rod photoreceptors. Mutations in RHO cause severe vision loss in humans. We found that each Rho regulatory region can independently mediate local epigenomic changes, but only the promoter is absolutely required for establishing active Rho chromatin configuration and transcription and maintaining the cell integrity and function of rod photoreceptors. To our surprise, two Rho enhancers that enable strong promoter activation in reporter assays are largely dispensable for Rho expression in vivo. Only small and age-dependent impact is detectable when both enhancers are deleted. Our results demonstrate context-dependent roles of enhancers and highlight the importance of studying functions of cis-regulatory regions in the native genomic context.
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Affiliation(s)
- Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University, Saint Louis, MO, USA
| | - Philip A Ruzycki
- Department of Ophthalmology and Visual Sciences, Washington University, Saint Louis, MO, USA.
- Department of Genetics, Washington University, 660 South Euclid Avenue, MSC 8096-0006-11, Saint Louis, MO, 63110, USA.
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University, Saint Louis, MO, USA.
- Department of Developmental Biology, Washington University, 660 South Euclid Avenue, MSC 8096-0006-06, Saint Louis, MO, 63110, USA.
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3
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Li L, Sun Y, Davis AE, Shah SH, Hamed LK, Wu MR, Lin CH, Ding JB, Wang S. Mettl14-mediated m 6A modification ensures the cell-cycle progression of late-born retinal progenitor cells. Cell Rep 2023; 42:112596. [PMID: 37269288 PMCID: PMC10543643 DOI: 10.1016/j.celrep.2023.112596] [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: 10/24/2022] [Revised: 03/31/2023] [Accepted: 05/17/2023] [Indexed: 06/05/2023] Open
Abstract
Neural progenitor cells lengthen their cell cycle to prime themselves for differentiation as development proceeds. It is currently not clear how they counter this lengthening and avoid being halted in the cell cycle. We show that N6-methyladenosine (m6A) methylation of cell-cycle-related mRNAs ensures the proper cell-cycle progression of late-born retinal progenitor cells (RPCs), which are born toward the end of retinogenesis and have long cell-cycle length. Conditional deletion of Mettl14, which is required for depositing m6A, led to delayed cell-cycle exit of late-born RPCs but has no effect on retinal development prior to birth. m6A sequencing and single-cell transcriptomics revealed that mRNAs involved in elongating the cell cycle were highly enriched for m6A, which could target them for degradation and guarantee proper cell-cycle progression. In addition, we identified Zfp292 as a target of m6A and potent inhibitor of RPC cell-cycle progression.
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Affiliation(s)
- Liang Li
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Yue Sun
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA; Department of Neurosurgery, Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Alexander E Davis
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Sahil H Shah
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Lobna K Hamed
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Man-Ru Wu
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Cheng-Hui Lin
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Jun B Ding
- Department of Neurosurgery, Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Sui Wang
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA.
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4
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Ge Y, Chen X, Nan N, Bard J, Wu F, Yergeau D, Liu T, Wang J, Mu X. Key transcription factors influence the epigenetic landscape to regulate retinal cell differentiation. Nucleic Acids Res 2023; 51:2151-2176. [PMID: 36715342 PMCID: PMC10018358 DOI: 10.1093/nar/gkad026] [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: 04/29/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/31/2023] Open
Abstract
How the diverse neural cell types emerge from multipotent neural progenitor cells during central nervous system development remains poorly understood. Recent scRNA-seq studies have delineated the developmental trajectories of individual neural cell types in many neural systems including the neural retina. Further understanding of the formation of neural cell diversity requires knowledge about how the epigenetic landscape shifts along individual cell lineages and how key transcription factors regulate these changes. In this study, we dissect the changes in the epigenetic landscape during early retinal cell differentiation by scATAC-seq and identify globally the enhancers, enriched motifs, and potential interacting transcription factors underlying the cell state/type specific gene expression in individual lineages. Using CUT&Tag, we further identify the enhancers bound directly by four key transcription factors, Otx2, Atoh7, Pou4f2 and Isl1, including those dependent on Atoh7, and uncover the sequential and combinatorial interactions of these factors with the epigenetic landscape to control gene expression along individual retinal cell lineages such as retinal ganglion cells (RGCs). Our results reveal a general paradigm in which transcription factors collaborate and compete to regulate the emergence of distinct retinal cell types such as RGCs from multipotent retinal progenitor cells (RPCs).
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Affiliation(s)
- Yichen Ge
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Xushen Chen
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Nan Nan
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
- Department of Biostatistics, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Jonathan Bard
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Fuguo Wu
- Department of Ophthalmology/Ross Eye Institute, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Donald Yergeau
- New York State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY, USA
| | - Tao Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jie Wang
- Correspondence may also be addressed to Jie Wang.
| | - Xiuqian Mu
- To whom correspondence should be addressed. Tel: +1 716 881 7463; Fax: +1 716 887 2991;
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5
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Sun C, Chen S. Disease-causing mutations in genes encoding transcription factors critical for photoreceptor development. Front Mol Neurosci 2023; 16:1134839. [PMID: 37181651 PMCID: PMC10172487 DOI: 10.3389/fnmol.2023.1134839] [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: 12/30/2022] [Accepted: 04/04/2023] [Indexed: 05/16/2023] Open
Abstract
Photoreceptor development of the vertebrate visual system is controlled by a complex transcription regulatory network. OTX2 is expressed in the mitotic retinal progenitor cells (RPCs) and controls photoreceptor genesis. CRX that is activated by OTX2 is expressed in photoreceptor precursors after cell cycle exit. NEUROD1 is also present in photoreceptor precursors that are ready to specify into rod and cone photoreceptor subtypes. NRL is required for the rod fate and regulates downstream rod-specific genes including the orphan nuclear receptor NR2E3 which further activates rod-specific genes and simultaneously represses cone-specific genes. Cone subtype specification is also regulated by the interplay of several transcription factors such as THRB and RXRG. Mutations in these key transcription factors are responsible for ocular defects at birth such as microphthalmia and inherited photoreceptor diseases such as Leber congenital amaurosis (LCA), retinitis pigmentosa (RP) and allied dystrophies. In particular, many mutations are inherited in an autosomal dominant fashion, including the majority of missense mutations in CRX and NRL. In this review, we describe the spectrum of photoreceptor defects that are associated with mutations in the above-mentioned transcription factors, and summarize the current knowledge of molecular mechanisms underlying the pathogenic mutations. At last, we deliberate the outstanding gaps in our understanding of the genotype-phenotype correlations and outline avenues for future research of the treatment strategies.
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Affiliation(s)
- Chi Sun
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, United States
- *Correspondence: Chi Sun,
| | - Shiming Chen
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, United States
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6
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Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
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Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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7
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Bian F, Daghsni M, Lu F, Liu S, Gross JM, Aldiri I. Functional analysis of the Vsx2 super-enhancer uncovers distinct cis-regulatory circuits controlling Vsx2 expression during retinogenesis. Development 2022; 149:dev200642. [PMID: 35831950 PMCID: PMC9440754 DOI: 10.1242/dev.200642] [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: 02/14/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022]
Abstract
Vsx2 is a transcription factor essential for retinal proliferation and bipolar cell differentiation, but the molecular mechanisms underlying its developmental roles are unclear. Here, we have profiled VSX2 genomic occupancy during mouse retinogenesis, revealing extensive retinal genetic programs associated with VSX2 during development. VSX2 binds and transactivates its enhancer in association with the transcription factor PAX6. Mice harboring deletions in the Vsx2 regulatory landscape exhibit specific abnormalities in retinal proliferation and in bipolar cell differentiation. In one of those deletions, a complete loss of bipolar cells is associated with a bias towards photoreceptor production. VSX2 occupies cis-regulatory elements nearby genes associated with photoreceptor differentiation and homeostasis in the adult mouse and human retina, including a conserved region nearby Prdm1, a factor implicated in the specification of rod photoreceptors and suppression of bipolar cell fate. VSX2 interacts with the transcription factor OTX2 and can act to suppress OTX2-dependent enhancer transactivation of the Prdm1 enhancer. Taken together, our analyses indicate that Vsx2 expression can be temporally and spatially uncoupled at the enhancer level, and they illuminate important mechanistic insights into how VSX2 is engaged with gene regulatory networks that are essential for retinal proliferation and cell fate acquisition.
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Affiliation(s)
- Fuyun Bian
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Marwa Daghsni
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Fangfang Lu
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jeffrey M Gross
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Issam Aldiri
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
- Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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8
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Zibetti C. Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives. Cells 2022; 11:cells11050806. [PMID: 35269428 PMCID: PMC8908986 DOI: 10.3390/cells11050806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 02/01/2023] Open
Abstract
Retinal neurogenesis is driven by concerted actions of transcription factors, some of which are expressed in a continuum and across several cell subtypes throughout development. While seemingly redundant, many factors diversify their regulatory outcome on gene expression, by coordinating variations in chromatin landscapes to drive divergent retinal specification programs. Recent studies have furthered the understanding of the epigenetic contribution to the progression of age-related macular degeneration, a leading cause of blindness in the elderly. The knowledge of the epigenomic mechanisms that control the acquisition and stabilization of retinal cell fates and are evoked upon damage, holds the potential for the treatment of retinal degeneration. Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming. A pipeline is then reviewed to functionally interrogate the epigenetic and transcriptional networks underlying cell fate specification, relying on a truly unbiased screening of open chromatin states. The related work proposes an inferential model to identify gene regulatory networks, features the first footprinting analysis and the first tentative, systematic query of candidate pioneer factors in the retina ever conducted in any model organism, leading to the identification of previously uncharacterized master regulators of retinal cell identity, such as the nuclear factor I, NFI. This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context. Finally, challenges and limitations intrinsic to the current next-generation sequencing techniques are discussed, as well as recent advances in super-resolution imaging, enabling spatio-temporal resolution of the genome.
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Affiliation(s)
- Cristina Zibetti
- Department of Ophthalmology, Institute of Clinical Medicine, University of Oslo, Kirkeveien 166, Building 36, 0455 Oslo, Norway
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9
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Honnell V, Norrie JL, Patel AG, Ramirez C, Zhang J, Lai YH, Wan S, Dyer MA. Identification of a modular super-enhancer in murine retinal development. Nat Commun 2022; 13:253. [PMID: 35017532 PMCID: PMC8752785 DOI: 10.1038/s41467-021-27924-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 12/20/2021] [Indexed: 11/23/2022] Open
Abstract
Super-enhancers are expansive regions of genomic DNA comprised of multiple putative enhancers that contribute to the dynamic gene expression patterns during development. This is particularly important in neurogenesis because many essential transcription factors have complex developmental stage- and cell-type specific expression patterns across the central nervous system. In the developing retina, Vsx2 is expressed in retinal progenitor cells and is maintained in differentiated bipolar neurons and Müller glia. A single super-enhancer controls this complex and dynamic pattern of expression. Here we show that deletion of one region disrupts retinal progenitor cell proliferation but does not affect cell fate specification. The deletion of another region has no effect on retinal progenitor cell proliferation but instead leads to a complete loss of bipolar neurons. This prototypical super-enhancer may serve as a model for dissecting the complex gene expression patterns for neurogenic transcription factors during development. Moreover, it provides a unique opportunity to alter expression of individual transcription factors in particular cell types at specific stages of development. This provides a deeper understanding of function that cannot be achieved with traditional knockout mouse approaches.
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Affiliation(s)
- Victoria Honnell
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jackie L Norrie
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Anand G Patel
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cody Ramirez
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jiakun Zhang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yu-Hsuan Lai
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shibiao Wan
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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10
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Daghsni M, Aldiri I. Building a Mammalian Retina: An Eye on Chromatin Structure. Front Genet 2021; 12:775205. [PMID: 34764989 PMCID: PMC8576187 DOI: 10.3389/fgene.2021.775205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
Regulation of gene expression by chromatin structure has been under intensive investigation, establishing nuclear organization and genome architecture as a potent and effective means of regulating developmental processes. The substantial growth in our knowledge of the molecular mechanisms underlying retinogenesis has been powered by several genome-wide based tools that mapped chromatin organization at multiple cellular and biochemical levels. Studies profiling the retinal epigenome and transcriptome have allowed the systematic annotation of putative cis-regulatory elements associated with transcriptional programs that drive retinal neural differentiation, laying the groundwork to understand spatiotemporal retinal gene regulation at a mechanistic level. In this review, we outline recent advances in our understanding of the chromatin architecture in the mammalian retina during development and disease. We focus on the emerging roles of non-coding regulatory elements in controlling retinal cell-type specific transcriptional programs, and discuss potential implications in untangling the etiology of eye-related disorders.
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Affiliation(s)
- Marwa Daghsni
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Issam Aldiri
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Louis J. Fox Center for Vision Restoration, University of Pittsburgh, Pittsburgh, PA, United States
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11
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Shiau F, Ruzycki PA, Clark BS. A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq. Dev Biol 2021; 478:41-58. [PMID: 34146533 PMCID: PMC8386138 DOI: 10.1016/j.ydbio.2021.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/20/2022]
Abstract
Recent advances in high throughput single-cell RNA sequencing (scRNA-seq) technology have enabled the simultaneous transcriptomic profiling of thousands of individual cells in a single experiment. To investigate the intrinsic process of retinal development, researchers have leveraged this technology to quantify gene expression in retinal cells across development, in multiple species, and from numerous important models of human disease. In this review, we summarize recent applications of scRNA-seq and discuss how these datasets have complemented and advanced our understanding of retinal progenitor cell competence, cell fate specification, and differentiation. Finally, we also highlight the outstanding questions in the field that advances in single-cell data generation and analysis will soon be able to answer.
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Affiliation(s)
- Fion Shiau
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Philip A Ruzycki
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Brian S Clark
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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12
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Chen X, Emerson MM. Notch signaling represses cone photoreceptor formation through the regulation of retinal progenitor cell states. Sci Rep 2021; 11:14525. [PMID: 34267251 PMCID: PMC8282820 DOI: 10.1038/s41598-021-93692-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/25/2021] [Indexed: 11/29/2022] Open
Abstract
Notch signaling is required to repress the formation of vertebrate cone photoreceptors and to maintain the proliferative potential of multipotent retinal progenitor cells. However, the mechanism by which Notch signaling controls these processes is unknown. Recently, restricted retinal progenitor cells with limited proliferation capacity and that preferentially generate cone photoreceptors have been identified. Thus, there are several potential steps during cone genesis that Notch signaling could act. Here we use cell type specific cis-regulatory elements to localize the primary role of Notch signaling in cone genesis to the formation of restricted retinal progenitor cells from multipotent retinal progenitor cells. Localized inhibition of Notch signaling in restricted progenitor cells does not alter the number of cones derived from these cells. Cell cycle promotion is not a primary effect of Notch signaling but an indirect effect on progenitor cell state transitions that leads to depletion of the multipotent progenitor cell population. Taken together, this suggests that the role of Notch signaling in cone photoreceptor formation and proliferation are both mediated by a localized function of Notch in multipotent retinal progenitor cells to repress the formation of restricted progenitor cells.
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Affiliation(s)
- Xueqing Chen
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Mark M Emerson
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA.
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA.
- Biochemistry PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA.
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13
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Kaufman ML, Goodson NB, Park KU, Schwanke M, Office E, Schneider SR, Abraham J, Hensley A, Jones KL, Brzezinski JA. Initiation of Otx2 expression in the developing mouse retina requires a unique enhancer and either Ascl1 or Neurog2 activity. Development 2021; 148:dev199399. [PMID: 34143204 PMCID: PMC8254865 DOI: 10.1242/dev.199399] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/10/2021] [Indexed: 11/20/2022]
Abstract
During retinal development, a large subset of progenitors upregulates the transcription factor Otx2, which is required for photoreceptor and bipolar cell formation. How these retinal progenitor cells initially activate Otx2 expression is unclear. To address this, we investigated the cis-regulatory network that controls Otx2 expression in mice. We identified a minimal enhancer element, DHS-4D, that drove expression in newly formed OTX2+ cells. CRISPR/Cas9-mediated deletion of DHS-4D reduced OTX2 expression, but this effect was diminished in postnatal development. Systematic mutagenesis of the enhancer revealed that three basic helix-loop-helix (bHLH) transcription factor-binding sites were required for its activity. Single cell RNA-sequencing of nascent Otx2+ cells identified the bHLH factors Ascl1 and Neurog2 as candidate regulators. CRISPR/Cas9 targeting of these factors showed that only the simultaneous loss of Ascl1 and Neurog2 prevented OTX2 expression. Our findings suggest that Ascl1 and Neurog2 act either redundantly or in a compensatory fashion to activate the DHS-4D enhancer and Otx2 expression. We observed redundancy or compensation at both the transcriptional and enhancer utilization levels, suggesting that the mechanisms governing Otx2 regulation in the retina are flexible and robust.
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Affiliation(s)
- Michael L. Kaufman
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Noah B. Goodson
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ko Uoon Park
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael Schwanke
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emma Office
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sophia R. Schneider
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Joy Abraham
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Austin Hensley
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kenneth L. Jones
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Joseph A. Brzezinski
- Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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14
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Lonfat N, Wang S, Lee C, Garcia M, Choi J, Park PJ, Cepko C. Cis-regulatory dissection of cone development reveals a broad role for Otx2 and Oc transcription factors. Development 2021; 148:dev198549. [PMID: 33929509 PMCID: PMC8126413 DOI: 10.1242/dev.198549] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/31/2021] [Indexed: 11/20/2022]
Abstract
The vertebrate retina is generated by retinal progenitor cells (RPCs), which produce >100 cell types. Although some RPCs produce many cell types, other RPCs produce restricted types of daughter cells, such as a cone photoreceptor and a horizontal cell (HC). We used genome-wide assays of chromatin structure to compare the profiles of a restricted cone/HC RPC and those of other RPCs in chicks. These data nominated regions of regulatory activity, which were tested in tissue, leading to the identification of many cis-regulatory modules (CRMs) active in cone/HC RPCs and developing cones. Two transcription factors, Otx2 and Oc1, were found to bind to many of these CRMs, including those near genes important for cone development and function, and their binding sites were required for activity. We also found that Otx2 has a predicted autoregulatory CRM. These results suggest that Otx2, Oc1 and possibly other Onecut proteins have a broad role in coordinating cone development and function. The many newly discovered CRMs for cones are potentially useful reagents for gene therapy of cone diseases.
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Affiliation(s)
- Nicolas Lonfat
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
- Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Su Wang
- Department of Biomedical Informatics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - ChangHee Lee
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Mauricio Garcia
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
- Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Jiho Choi
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
- Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Peter J. Park
- Department of Biomedical Informatics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
| | - Connie Cepko
- Department of Genetics, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
- Department of Ophthalmology, Blavatnik Institute; Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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15
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Repeated mutation of a developmental enhancer contributed to human thermoregulatory evolution. Proc Natl Acad Sci U S A 2021; 118:2021722118. [PMID: 33850016 PMCID: PMC8072367 DOI: 10.1073/pnas.2021722118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Humans sweat to cool their bodies and have by far the highest eccrine sweat gland density among primates. Humans' high eccrine gland density has long been recognized as a hallmark human evolutionary adaptation, but its genetic basis has been unknown. In humans, expression of the Engrailed 1 (EN1) transcription factor correlates with the onset of eccrine gland formation. In mice, regulation of ectodermal En1 expression is a major determinant of natural variation in eccrine gland density between strains, and increased En1 expression promotes the specification of more eccrine glands. Here, we show that regulation of EN1 has evolved specifically on the human lineage to promote eccrine gland formation. Using comparative genomics and validation of ectodermal enhancer activity in mice, we identified a human EN1 skin enhancer, hECE18. We showed that multiple epistatically interacting derived substitutions in the human ECE18 enhancer increased its activity compared with nonhuman ape orthologs in cultured keratinocytes. Repression of hECE18 in human cultured keratinocytes specifically attenuated EN1 expression, indicating this element positively regulates EN1 in this context. In a humanized enhancer knock-in mouse, hECE18 increased developmental En1 expression in the skin to induce the formation of more eccrine glands. Our study uncovers a genetic basis contributing to the evolution of one of the most singular human adaptations and implicates multiple interacting mutations in a single enhancer as a mechanism for human evolutionary change.
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16
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Schick E, Gonzalez KC, Dutta P, Hossain K, Ghinia Tegla MG, Emerson MM. Early cis-regulatory events in the formation of retinal horizontal cells. Dev Biol 2021; 476:88-100. [PMID: 33774011 DOI: 10.1016/j.ydbio.2021.03.016] [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: 12/01/2020] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 11/25/2022]
Abstract
During retinal development, multipotent and restricted progenitor cells generate all of the neuronal cells of the retina. Among these are horizontal cells, which are interneurons that modulate the light-induced signal from photoreceptors. This study utilizes the identification of novel cis-regulatory elements as a method to examine the gene regulatory networks that direct the development of horizontal cells. Here we describe a screen for cis-regulatory elements, or enhancers, for the horizontal cell-associated genes PTF1A, ONECUT1 (OC1), TFAP2A (AP2A), and LHX1. The OC1ECR22 and Tfap2aACR5 elements were shown to be potential enhancers for OC1 and TFAP2A, respectively, and to be specifically active in developing horizontal cells. The OC1ECR22 element is activated by PTF1A and RBPJ, which translates to regulation of OC1 expression and suggests that PTF1A is a direct activator of OC1 expression in developing horizontal cells. The region within the Tfap2aACR5 element that is responsible for its activation was determined to be a 100 bp sequence named Motif 4. Both OC1ECR22 and Tfap2aACR5 are negatively regulated by the nuclear receptors THRB and RXRG, as is the expression of OC1 and AP2A, suggesting that nuclear receptors may have a role in the negative regulation of horizontal cell development.
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Affiliation(s)
- Estie Schick
- Biology PhD Program, Graduate Center, City University of New York, New York, NY, 10016, USA
| | - Kevin C Gonzalez
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Pooja Dutta
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Kazi Hossain
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Miruna G Ghinia Tegla
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Mark M Emerson
- Biology PhD Program, Graduate Center, City University of New York, New York, NY, 10016, USA; Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA; Biochemistry PhD Program, Graduate Center, City University of New York, New York, NY, 10016, USA.
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17
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Zhang Q, Li T, Zhang Y, Lin J, Chen X, Gui Y, Li Q. Comparative sequence analysis and functional validation identified a retina-specific enhancer around zic5 and zic2a. Gene Expr Patterns 2020; 39:119162. [PMID: 33359848 DOI: 10.1016/j.gep.2020.119162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 11/19/2022]
Abstract
The spatiotemporal development of vertebrate retina is regulated by a variety of genes. The zinc finger transcription factors zic5 and zic2a are located close to each other in the chromosome. They have similar expression patterns, and both play important roles in the development of the retina and nervous system. Here, we used ECR browser and gfp fluorescence report experiment to identify a 290bp enhancer sequence ECR3, which is located at 3 kb upstream of zic5 and 10 kb downstream of zic2a, and it can drive the specific expression of gfp in the retina. pT2KXIGQ-ECR3 was used to construct a transgenic zebrafish line Tg(ECR3-290: gfp) which first exhibits specific green fluorescence in the whole retina area at 24hpf. Then the expression region was gradually limited to ganglion cell layer (GCL) and lasted through adulthood. This expression pattern is highly consistent with the zic5 and zic2a at retina. These results indicate that the 290bp enhancer might be an important element to regulate the expression of zic5 and zic2a genes in ganglion cells, and this transgenic line is an important tool for studying the development of retina.
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Affiliation(s)
- Qi Zhang
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Tingting Li
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Yinglan Zhang
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Jia Lin
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Xudong Chen
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Yiting Gui
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China
| | - Qiang Li
- Translational Medical Center for Development and Disease, Institute of Pediatrics, Shanghai Key Laboratory of Birth Defect, Children's Hospital of Fudan University, Shanghai, China.
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18
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Chan CSY, Lonfat N, Zhao R, Davis AE, Li L, Wu MR, Lin CH, Ji Z, Cepko CL, Wang S. Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors and cis-regulatory modules in the retina. Development 2020; 147:dev187922. [PMID: 32631829 PMCID: PMC7406324 DOI: 10.1242/dev.187922] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
Abstract
Transcription factors (TFs) are often used repeatedly during development and homeostasis to control distinct processes in the same and/or different cellular contexts. Considering the limited number of TFs in the genome and the tremendous number of events that need to be regulated, re-use of TFs is necessary. We analyzed how the expression of the homeobox TF, orthodenticle homeobox 2 (Otx2), is regulated in a cell type- and stage-specific manner during development in the mouse retina. We identified seven Otx2 cis-regulatory modules (CRMs), among which the O5, O7 and O9 CRMs mark three distinct cellular contexts of Otx2 expression. We discovered that Otx2, Crx and Sox2, which are well-known TFs regulating retinal development, bind to and activate the O5, O7 or O9 CRMs, respectively. The chromatin status of these three CRMs was found to be distinct in vivo in different retinal cell types and at different stages. We conclude that retinal cells use a cohort of TFs with different expression patterns and multiple CRMs with different chromatin configurations to regulate the expression of Otx2 precisely.
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Affiliation(s)
- Candace S Y Chan
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Nicolas Lonfat
- Departments of Genetics and Ophthalmology, Blavatnik Institute, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Rong Zhao
- Departments of Genetics and Ophthalmology, Blavatnik Institute, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander E Davis
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Liang Li
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Man-Ru Wu
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Cheng-Hui Lin
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
| | - Zhe Ji
- Department of Bioengineering, Northwestern University, Evanston, IL 60208, USA
| | - Constance L Cepko
- Departments of Genetics and Ophthalmology, Blavatnik Institute, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sui Wang
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, CA 94304, USA
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19
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Ghinia Tegla MG, Buenaventura DF, Kim DY, Thakurdin C, Gonzalez KC, Emerson MM. OTX2 represses sister cell fate choices in the developing retina to promote photoreceptor specification. eLife 2020; 9:e54279. [PMID: 32347797 PMCID: PMC7237216 DOI: 10.7554/elife.54279] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
During vertebrate retinal development, subsets of progenitor cells generate progeny in a non-stochastic manner, suggesting that these decisions are tightly regulated. However, the gene-regulatory network components that are functionally important in these progenitor cells are largely unknown. Here we identify a functional role for the OTX2 transcription factor in this process. CRISPR/Cas9 gene editing was used to produce somatic mutations of OTX2 in the chick retina and identified similar phenotypes to those observed in human patients. Single cell RNA sequencing was used to determine the functional consequences OTX2 gene editing on the population of cells derived from OTX2-expressing retinal progenitor cells. This confirmed that OTX2 is required for the generation of photoreceptors, but also for repression of specific retinal fates and alternative gene regulatory networks. These include specific subtypes of retinal ganglion and horizontal cells, suggesting that in this context, OTX2 functions to repress sister cell fate choices.
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Affiliation(s)
| | - Diego F Buenaventura
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
- PhD Program in Biology, The Graduate Center of the City University of New York (CUNY)New YorkUnited States
| | - Diana Y Kim
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
| | - Cassandra Thakurdin
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
| | - Kevin C Gonzalez
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York (CUNY)New YorkUnited States
- PhD Program in Biology, The Graduate Center of the City University of New York (CUNY)New YorkUnited States
- PhD Program in Biochemistry, The Graduate Center of the City University of New York (CUNY)New YorkUnited States
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20
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Perez-Cervantes C, Smith LA, Nadadur RD, Hughes AEO, Wang S, Corbo JC, Cepko C, Lonfat N, Moskowitz IP. Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types. Development 2020; 147:dev184432. [PMID: 31915147 PMCID: PMC7033740 DOI: 10.1242/dev.184432] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/13/2019] [Indexed: 12/30/2022]
Abstract
Identification of cell type-specific cis-regulatory elements (CREs) is crucial for understanding development and disease, although identification of functional regulatory elements remains challenging. We hypothesized that context-specific CREs could be identified by context-specific non-coding RNA (ncRNA) profiling, based on the observation that active CREs produce ncRNAs. We applied ncRNA profiling to identify rod and cone photoreceptor CREs from wild-type and mutant mouse retinas, defined by presence or absence, respectively, of the rod-specific transcription factor (TF) NrlNrl-dependent ncRNA expression strongly correlated with epigenetic profiles of rod and cone photoreceptors, identified thousands of candidate rod- and cone-specific CREs, and identified motifs for rod- and cone-specific TFs. Colocalization of NRL and the retinal TF CRX correlated with rod-specific ncRNA expression, whereas CRX alone favored cone-specific ncRNA expression, providing quantitative evidence that heterotypic TF interactions distinguish cell type-specific CRE activity. We validated the activity of novel Nrl-dependent ncRNA-defined CREs in developing cones. This work supports differential ncRNA profiling as a platform for the identification of cell type-specific CREs and the discovery of molecular mechanisms underlying TF-dependent CRE activity.
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Affiliation(s)
- Carlos Perez-Cervantes
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Linsin A Smith
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Rangarajan D Nadadur
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Andrew E O Hughes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sui Wang
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph C Corbo
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Constance Cepko
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nicolas Lonfat
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ivan P Moskowitz
- Departments of Pediatrics, Pathology, and Human Genetics, University of Chicago, Chicago, IL 60637, USA
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21
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Bhansali P, Cvekl A, Liu W. A distal enhancer that directs Otx2 expression in the retinal pigment epithelium and neuroretina. Dev Dyn 2020; 249:209-221. [PMID: 31658410 PMCID: PMC10518783 DOI: 10.1002/dvdy.127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/09/2019] [Accepted: 10/19/2019] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Homeodomain transcription factor Otx2 is essential for embryonic development of multiple head tissues, including retinal pigment epithelium (RPE) and neuroretina. Temporospatial regulation of Otx2 expression is critical for its functions. Molecular dissection of the cis-acting enhancers will help elucidate how Otx2 expression is regulated. RESULTS We comprehensively characterized distal enhancer hs1150 that was previously identified in a high throughput study. We established multiple transgenic mouse lines in which human hs1150, corresponding mouse hs1150, and two highly conserved sub-fragments in the mouse hs1150 were individually fused to a minimal hsp68 promoter to drive reporter expression. We found that hs1150 enhancer directed reporter expression in the RPE, neuroretina, and brain in a developmentally regulated manner. Human hs1150-directed reporter expression largely recapitulated Otx2 expression in the RPE, in the early neuroretina, and to a lesser degree in the early brain. Mouse hs1150, although shorter than human hs1150, exhibited similar enhancer activity, indicating functional conservation of hs1150 enhancer across species. Both of the highly conserved subfragments in mouse hs1150 enhancer directed reporter expression in the early neuroretina, indicating that the hs1150 enhancer has two functional components. CONCLUSIONS Our findings provide insight into the molecular mechanisms underlying the regulation of Otx2 retinal expression.
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Affiliation(s)
- Punita Bhansali
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Ales Cvekl
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Wei Liu
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
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22
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Buenaventura DF, Corseri A, Emerson MM. Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors. Invest Ophthalmol Vis Sci 2019; 60:2787-2799. [PMID: 31260032 PMCID: PMC6607928 DOI: 10.1167/iovs.19-26951] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Purpose The early transcriptional events that occur in newly generated cone photoreceptors are not well described. Knowledge of these events is critical to provide benchmarks for in vitro-derived cone photoreceptors and to understand the process of cone and rod photoreceptor diversification. We sought to identify genes with differential gene expression in embryonic mouse cone photoreceptors. Methods The specificity of expression of the LHX4 transcription factor in developing cone photoreceptors was examined using immunofluorescence visualization in both mouse and chicken retinas. A LHX4 transgenic reporter line with high specificity for developing mouse cone photoreceptors was identified and used to purify early-stage cone photoreceptors for profiling by single-cell RNA sequencing. Comparisons were made to previous datasets targeting photoreceptors. Results The LHX4 transcription factor and a transgenic reporter were determined to be highly specific to early developing cone photoreceptors in the mouse. Single-cell transcriptional profiling identified new genes with enriched expression in cone photoreceptors relative to concurrent cell populations. Comparison to previous profiling datasets allowed for further characterization of these genes across developmental time, species, photoreceptor type, and gene regulatory network. Conclusions The LHX4 gene is highly enriched in developing cone photoreceptors as are several new genes identified through transcriptional profiling, some of which are expressed in subclusters of cones. Many of these cone-enriched genes do not show obvious de-repression in profiling of retinas mutant for the rod-specific transcription factor NRL, highlighting differences between endogenous cones and those induced in NRL mutants.
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Affiliation(s)
- Diego F Buenaventura
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States.,Biology PhD Program, Graduate Center, City University of New York, New York, New York, United States
| | - Adrianne Corseri
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York, New York, New York, United States.,Biology PhD Program, Graduate Center, City University of New York, New York, New York, United States.,Biochemistry PhD Program, Graduate Center, City University of New York, New York, New York, United States
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23
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Lineage tracing analysis of cone photoreceptor associated cis-regulatory elements in the developing chicken retina. Sci Rep 2019; 9:9358. [PMID: 31249345 PMCID: PMC6597718 DOI: 10.1038/s41598-019-45750-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/14/2019] [Indexed: 02/02/2023] Open
Abstract
During vertebrate retinal development, transient populations of retinal progenitor cells with restricted cell fate choices are formed. One of these progenitor populations expresses the Thrb gene and can be identified by activity of the ThrbCRM1 cis-regulatory element. Short-term assays have concluded that these cells preferentially generate cone photoreceptors and horizontal cells, however developmental timing has precluded an extensive cell type characterization of their progeny. Here we describe the development and validation of a recombinase-based lineage tracing system for the chicken embryo to further characterize the lineage of these cells. The ThrbCRM1 element was found to preferentially form photoreceptors and horizontal cells, as well as a small number of retinal ganglion cells. The photoreceptor cell progeny are exclusively cone photoreceptors and not rod photoreceptors, confirming that ThrbCRM1 progenitor cells are restricted from the rod fate. In addition, specific subtypes of horizontal cells and retinal ganglion cells were overrepresented, suggesting that ThrbCRM1 progenitor cells are not only restricted for cell type, but for cell subtype as well.
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24
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Kishi JY, Lapan SW, Beliveau BJ, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P. SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. Nat Methods 2019; 16:533-544. [PMID: 31110282 PMCID: PMC6544483 DOI: 10.1038/s41592-019-0404-0] [Citation(s) in RCA: 236] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 04/03/2019] [Indexed: 12/24/2022]
Abstract
Fluorescence in situ hybridization (FISH) reveals the abundance and positioning of nucleic acid sequences in fixed samples. Despite recent advances in multiplexed amplification of FISH signals, it remains challenging to achieve high levels of simultaneous amplification and sequential detection with high sampling efficiency and simple workflows. Here we introduce signal amplification by exchange reaction (SABER), which endows oligonucleotide-based FISH probes with long, single-stranded DNA concatemers that aggregate a multitude of short complementary fluorescent imager strands. We show that SABER amplified RNA and DNA FISH signals (5- to 450-fold) in fixed cells and tissues. We also applied 17 orthogonal amplifiers against chromosomal targets simultaneously and detected mRNAs with high efficiency. We then used 10-plex SABER-FISH to identify in vivo introduced enhancers with cell-type-specific activity in the mouse retina. SABER represents a simple and versatile molecular toolkit for rapid and cost-effective multiplexed imaging of nucleic acid targets.
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Affiliation(s)
- Jocelyn Y Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sylvain W Lapan
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Brian J Beliveau
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Emma R West
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Allen Zhu
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Hiroshi M Sasaki
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Constance L Cepko
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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25
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Abstract
Enhancer activity is determined by both the activity and occupancy of transcription factors as well as the specific sequences they bind. Experimental investigation of this dynamic requires the ability to manipulate components of the system, ideally in as close to an in vivo context as possible. Here we use electroporation of plasmid reporters to define critical parameters of a specific cis-regulatory element, ThrbCRM1, during retinal development. ThrbCRM1 is associated with cone photoreceptor genesis and activated in a subset of developing retinal cells that co-express the Otx2 and Onecut1 (OC1) transcription factors. Variation of reporter plasmid concentration was used to generate dose response curves and revealed an effect of binding site availability on the number and strength of cells with reporter activity. Critical sequence elements of the ThrbCRM1 element were defined using both mutagenesis and misexpression of the Otx2 and OC1 transcription factors in the developing retina. Additionally, these experiments suggest that the ThrbCRM1 element is co-regulated by Otx2 and OC1 even under conditions of sub-optimal binding of OC1.
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Affiliation(s)
- Benjamin Souferi
- Department of Biology, The City College of New York, City University of New York, New York, NY 10031, USA
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York, New York, NY 10031, USA .,Graduate Center, City University of New York, New York, NY 10031, USA
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26
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Jean-Charles N, Buenaventura DF, Emerson MM. Identification and characterization of early photoreceptor cis-regulatory elements and their relation to Onecut1. Neural Dev 2018; 13:26. [PMID: 30466480 PMCID: PMC6251108 DOI: 10.1186/s13064-018-0121-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/31/2018] [Indexed: 12/19/2022] Open
Abstract
Background Cone and rod photoreceptors are two of the primary cell types affected in human retinal disease. Potential strategies to combat these diseases are the use of gene therapy to rescue compromised photoreceptors or to generate new functional photoreceptors to replace those lost in the diseased retina. Cis-regulatory elements specific to cones, rods, or both types of photoreceptors are critical components of successful implementation of these two strategies. The purpose of this study was to identify and characterize the cell type specificity and activity of cis-regulatory elements active in developing photoreceptors. Methods Cis-regulatory elements were introduced into the developing chicken and mouse retina by electroporation. Characterization of reporter activity in relation with cell type markers was determined using confocal microscopy. In addition, two high-throughput flow cytometry assay were developed to assess whether these elements were downstream of Onecut1 in the photoreceptor specification network. Results The majority of cis-regulatory elements were active in both cone and rod photoreceptors and were largely uninfluenced by a Onecut1 dominant-negative construct. Elements associated with the Thrb, Nr2e3, and Rhodopsin genes showed highly enriched activity in cones or rods, and were affected by interference in Onecut1 signaling. Rhodopsin promoter activity was the most highly influenced by Onecut1 activity and its induction could be modulated by the Maf family transcription factor L-Maf. Nr2e3 elements were observed to have activity in cone photoreceptors and Nr2e3 protein was expressed in developing cone photoreceptors, suggesting a role for this predominant rod gene in cone photoreceptor development. Conclusions The analysis presented here provides an experimental framework to determine the specificity and strength of photoreceptor elements within specific genetic networks during development. The Onecut1 transcription factor is one such factor that influences the gene regulatory networks specific to cones and rods, but not those that are common to both. Electronic supplementary material The online version of this article (10.1186/s13064-018-0121-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nathalie Jean-Charles
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA.,Current Address: The Public Health Laboratory, NYC Department of Health and Mental Hygeine, New York, NY, 10016, USA
| | - Diego F Buenaventura
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA.,Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, 10031, USA
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA. .,Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY, 10031, USA.
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27
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Vancamp P, Bourgeois NMA, Houbrechts AM, Darras VM. Knockdown of the thyroid hormone transporter MCT8 in chicken retinal precursor cells hampers early retinal development and results in a shift towards more UV/blue cones at the expense of green/red cones. Exp Eye Res 2018; 178:135-147. [PMID: 30273578 DOI: 10.1016/j.exer.2018.09.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/21/2018] [Accepted: 09/27/2018] [Indexed: 12/19/2022]
Abstract
Thyroid hormones (THs) play a crucial role in coordinating brain development in vertebrates. They fine-tune processes like cell proliferation, migration, and differentiation mainly by regulating the transcriptional activity of many essential genes. Regulators of TH availability thereby define the cellular concentration of the bioactive 3,5,3'-triiodothyronine, which binds to nuclear TH receptors. One important regulator, the monocarboxylate transporter 8 (MCT8), facilitates cellular TH uptake and is known to be necessary for correct brain development, but data on its potential role during retinal development is lacking. The retinal cyto-architecture has been conserved throughout vertebrate evolution, and we used the chicken embryo to study the need for MCT8 during retinal development. Its external development allows easy manipulation, and MCT8 is abundantly expressed in the retina from early stages onwards. We induced MCT8 knockdown by electroporating a pRFP-MCT8-RNAi vector into the retinal precursor cells (RPCs) at embryonic day 4 (E4), and studied the consequences for early (E6) and late (E18) retinal development. The empty pRFP-RNAi vector was used as a control. RPC proliferation was reduced at E6. This resulted in cellular hypoplasia and a thinner retina at E18 where mainly photoreceptors and horizontal cells were lost, the two predominant cell types that are born around the stage of electroporation. At E6, differentiation into retinal ganglion cells and amacrine cells was delayed. However, since the proportion of a given cell type within the transfected cell population at E18 was similar in knockdown and controls, the partial loss of some cell types was most-likely due to reduced RPC proliferation and not impaired cell differentiation. Photoreceptors displayed delayed migration at first, but had successfully reached the outer nuclear layer at E18. However, they increasingly differentiated into short wavelength-sensitive cones at the expense of medium/long wavelength-sensitive cones, while the proportion of rods was unaltered. Improperly formed sublaminae in the inner plexiform layer additionally suggested defects in synaptogenesis. Altogether, our data echoes effects of hypothyroidism and the loss of some other regulators of TH availability in the developing zebrafish and rodent retina. Therefore, the expression of MCT8 in RPCs is crucial for adequate TH uptake during cell type-specific events in retinal development.
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Affiliation(s)
- Pieter Vancamp
- KU Leuven, Laboratory of Comparative Endocrinology, Department of Biology, B-3000, Leuven, Belgium
| | - Nele M A Bourgeois
- KU Leuven, Laboratory of Comparative Endocrinology, Department of Biology, B-3000, Leuven, Belgium
| | - Anne M Houbrechts
- KU Leuven, Laboratory of Comparative Endocrinology, Department of Biology, B-3000, Leuven, Belgium
| | - Veerle M Darras
- KU Leuven, Laboratory of Comparative Endocrinology, Department of Biology, B-3000, Leuven, Belgium.
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28
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Buenaventura DF, Ghinia-Tegla MG, Emerson MM. Fate-restricted retinal progenitor cells adopt a molecular profile and spatial position distinct from multipotent progenitor cells. Dev Biol 2018; 443:35-49. [PMID: 30145104 DOI: 10.1016/j.ydbio.2018.06.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/14/2018] [Accepted: 06/23/2018] [Indexed: 12/22/2022]
Abstract
During development, multipotent retinal progenitor cells generate a large number of unique cell types. Recent evidence suggests that there are fate-restricted progenitor cell states in addition to multipotent ones. Here we report a transcriptomic analysis of fate- restricted progenitor cells biased to produce cone photoreceptors and horizontal cells, marked by the THRB cis-regulatory element ThrbCRM1. Comparison to a control population enriched in multipotent progenitor cells identified several genes considered to be pan-progenitor, such as VSX2, LHX2, and PAX6, as downregulated in these fate- restricted retinal progenitor cells. This differential regulation occurs in chick and in a different restricted progenitor population in mouse suggesting that this is a conserved feature of progenitor dynamics during retinal development. S-phase labeling also revealed that nuclear positions of restricted progenitor populations occupy distinct spatial niches within the developing chick retina. Using a conserved regulatory element proximal to the VSX2 gene, a potential negative feedback mechanism from specific transcription factors enriched in cone/horizontal cell progenitor cells was identified. This study identifies conserved molecular and cellular changes that occur during the generation of fate restricted retinal progenitor cells from multipotent retinal progenitor cells.
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Affiliation(s)
- Diego F Buenaventura
- Department of Biology, The City College of New York, City University of New York, New York, NY 10031, United States; Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY 10031, United States
| | - Miruna G Ghinia-Tegla
- Department of Biology, The City College of New York, City University of New York, New York, NY 10031, United States
| | - Mark M Emerson
- Department of Biology, The City College of New York, City University of New York, New York, NY 10031, United States; Biology Ph.D. Program, Graduate Center, City University of New York, New York, NY 10031, United States.
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29
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Zhou J, Benito-Martin A, Mighty J, Chang L, Ghoroghi S, Wu H, Wong M, Guariglia S, Baranov P, Young M, Gharbaran R, Emerson M, Mark MT, Molina H, Canto-Soler MV, Selgas HP, Redenti S. Retinal progenitor cells release extracellular vesicles containing developmental transcription factors, microRNA and membrane proteins. Sci Rep 2018; 8:2823. [PMID: 29434302 PMCID: PMC5809580 DOI: 10.1038/s41598-018-20421-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 01/15/2018] [Indexed: 12/27/2022] Open
Abstract
A range of cell types, including embryonic stem cells, neurons and astrocytes have been shown to release extracellular vesicles (EVs) containing molecular cargo. Across cell types, EVs facilitate transfer of mRNA, microRNA and proteins between cells. Here we describe the release kinetics and content of EVs from mouse retinal progenitor cells (mRPCs). Interestingly, mRPC derived EVs contain mRNA, miRNA and proteins associated with multipotency and retinal development. Transcripts enclosed in mRPC EVs, include the transcription factors Pax6, Hes1, and Sox2, a mitotic chromosome stabilizer Ki67, and the neural intermediate filaments Nestin and GFAP. Proteomic analysis of EV content revealed retinogenic growth factors and morphogen proteins. mRPC EVs were shown to transfer GFP mRNA between cell populations. Finally, analysis of EV mediated functional cargo delivery, using the Cre-loxP recombination system, revealed transfer and uptake of Cre+ EVs, which were then internalized by target mRPCs activating responder loxP GFP expression. In summary, the data supports a paradigm of EV genetic material encapsulation and transfer within RPC populations. RPC EV transfer may influence recipient RPC transcriptional and post-transcriptional regulation, representing a novel mechanism of differentiation and fate determination during retinal development.
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Affiliation(s)
- Jing Zhou
- Department of Biological Sciences, Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA.,Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Alberto Benito-Martin
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Jason Mighty
- Department of Biological Sciences, Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA.,Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Lynne Chang
- Nikon Instruments Inc, 1300 Walt Whitman Road, Melville, NY, 11747, USA
| | - Shima Ghoroghi
- Department of Biological Sciences, Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | - Hao Wu
- Department of Biological Sciences, Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA.,Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA
| | - Madeline Wong
- Department of Biological Sciences, Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | - Sara Guariglia
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, 722 West 168th St, New York, NY, 10032, USA
| | - Petr Baranov
- The Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, 20 Staniford Street, Boston, MA, 02114, USA
| | - Michael Young
- The Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, 20 Staniford Street, Boston, MA, 02114, USA
| | - Rajendra Gharbaran
- Department of Biological Sciences, Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA
| | - Mark Emerson
- Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA.,Department of Biology, The City College of New York, City University of New York, New York, NY, 10031, USA
| | - Milica Tesic Mark
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - M Valeria Canto-Soler
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Hector Peinado Selgas
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics, and Cell and Developmental Biology, Drukier Institute for Children's Health, Meyer Cancer Center, Weill Cornell Medical College, New York, New York, 10021, USA.,Microenvironment and Metastasis Laboratory, Department of Molecular Oncology, Spanish National Cancer Research Centre (CNIO), Melchor Fernández Almagro, 3, Madrid, E28029, Spain
| | - Stephen Redenti
- Department of Biological Sciences, Lehman College, City University of New York, 250 Bedford Park Boulevard West, Bronx, NY, 10468, USA. .,Biology Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA. .,Biochemistry Doctoral Program, The Graduate School and University Center, City University of New York, 365 5th Avenue, New York, NY, 10016, USA.
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30
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Mechanisms of Photoreceptor Patterning in Vertebrates and Invertebrates. Trends Genet 2017; 32:638-659. [PMID: 27615122 DOI: 10.1016/j.tig.2016.07.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/25/2016] [Accepted: 07/28/2016] [Indexed: 11/22/2022]
Abstract
Across the animal kingdom, visual systems have evolved to be uniquely suited to the environments and behavioral patterns of different species. Visual acuity and color perception depend on the distribution of photoreceptor (PR) subtypes within the retina. Retinal mosaics can be organized into three broad categories: stochastic/regionalized, regionalized, and ordered. We describe here the retinal mosaics of flies, zebrafish, chickens, mice, and humans, and the gene regulatory networks controlling proper PR specification in each. By drawing parallels in eye development between these divergent species, we identify a set of conserved organizing principles and transcriptional networks that govern PR subtype differentiation.
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31
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Abstract
Photoreceptors are highly specialized primary sensory neurons that sense light and initiate vision. This critical role is well demonstrated by the fact that visual impairment accompanies photoreceptor loss or dysfunction in many human diseases. With the remarkable advances in stem cell research, one therapeutic approach is to use stem cells to generate photoreceptors and then engraft them into diseased eyes. Knowledge of the molecular mechanisms that control photoreceptor genesis during normal development can greatly aid in the production of photoreceptor cells for this approach. This article will discuss advances in our understanding of the molecular mechanisms that regulate photoreceptor fate determination during development. Recent lineage studies have shown that there are distinct retinal progenitor cells (RPCs) that produce specific combinations of daughter cell types, including photoreceptors and other types of retinal cells. Gene regulatory networks, in which transcription factors interact via cis-regulatory DNA elements, have been discovered that operate within distinct RPCs, and/or newly postmitotic cells, to direct the choice of photoreceptor fate.
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Affiliation(s)
- Sui Wang
- Department of Genetics and Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States 2Howard Hughes Medical Institute, Boston, Massachusetts, United States
| | - Constance L Cepko
- Department of Genetics and Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States 2Howard Hughes Medical Institute, Boston, Massachusetts, United States
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32
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Woodworth MB, Girskis KM, Walsh CA. Building a lineage from single cells: genetic techniques for cell lineage tracking. Nat Rev Genet 2017; 18:230-244. [PMID: 28111472 PMCID: PMC5459401 DOI: 10.1038/nrg.2016.159] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Resolving lineage relationships between cells in an organism is a fundamental interest of developmental biology. Furthermore, investigating lineage can drive understanding of pathological states, including cancer, as well as understanding of developmental pathways that are amenable to manipulation by directed differentiation. Although lineage tracking through the injection of retroviral libraries has long been the state of the art, a recent explosion of methodological advances in exogenous labelling and single-cell sequencing have enabled lineage tracking at larger scales, in more detail, and in a wider range of species than was previously considered possible. In this Review, we discuss these techniques for cell lineage tracking, with attention both to those that trace lineage forwards from experimental labelling, and those that trace backwards across the life history of an organism.
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Affiliation(s)
- Mollie B Woodworth
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Kelly M Girskis
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, USA
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33
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Shekhar K, Lapan SW, Whitney IE, Tran NM, Macosko EZ, Kowalczyk M, Adiconis X, Levin JZ, Nemesh J, Goldman M, McCarroll SA, Cepko CL, Regev A, Sanes JR. Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics. Cell 2016; 166:1308-1323.e30. [PMID: 27565351 DOI: 10.1016/j.cell.2016.07.054] [Citation(s) in RCA: 710] [Impact Index Per Article: 88.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/10/2016] [Accepted: 07/28/2016] [Indexed: 12/15/2022]
Abstract
Patterns of gene expression can be used to characterize and classify neuronal types. It is challenging, however, to generate taxonomies that fulfill the essential criteria of being comprehensive, harmonizing with conventional classification schemes, and lacking superfluous subdivisions of genuine types. To address these challenges, we used massively parallel single-cell RNA profiling and optimized computational methods on a heterogeneous class of neurons, mouse retinal bipolar cells (BCs). From a population of ∼25,000 BCs, we derived a molecular classification that identified 15 types, including all types observed previously and two novel types, one of which has a non-canonical morphology and position. We validated the classification scheme and identified dozens of novel markers using methods that match molecular expression to cell morphology. This work provides a systematic methodology for achieving comprehensive molecular classification of neurons, identifies novel neuronal types, and uncovers transcriptional differences that distinguish types within a class.
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Affiliation(s)
- Karthik Shekhar
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sylvain W Lapan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Irene E Whitney
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA
| | - Nicholas M Tran
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA
| | - Evan Z Macosko
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | | | - Xian Adiconis
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Joshua Z Levin
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - James Nemesh
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Melissa Goldman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Constance L Cepko
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Aviv Regev
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology and Koch Institute, MIT, Cambridge, MA 02139, USA.
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA.
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34
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Liu H, Aramaki M, Fu Y, Forrest D. Retinoid-Related Orphan Receptor β and Transcriptional Control of Neuronal Differentiation. Curr Top Dev Biol 2016; 125:227-255. [PMID: 28527573 DOI: 10.1016/bs.ctdb.2016.11.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ability to generate neuronal diversity is central to the function of the nervous system. Here we discuss the key neurodevelopmental roles of retinoid-related orphan receptor β (RORβ) encoded by the Rorb (Nr1f2) gene. Recent studies have reported loss of function of the human RORB gene in cases of familial epilepsy and intellectual disability. Principal sites of expression of the Rorb gene in model species include sensory organs, the spinal cord, and brain regions that process sensory and circadian information. Genetic analyses in mice have indicated functions in circadian behavior, vision, and, at the cellular level, the differentiation of specific neuronal cell types. Studies in the retina and sensory areas of the cerebral cortex suggest that this orphan nuclear receptor acts at decisive steps in transcriptional hierarchies that determine neuronal diversity.
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Affiliation(s)
- Hong Liu
- Laboratory of Endocrinology and Receptor Biology, NIDDK, National Institutes of Health, Bethesda, MD, United States
| | - Michihiko Aramaki
- Laboratory of Endocrinology and Receptor Biology, NIDDK, National Institutes of Health, Bethesda, MD, United States
| | - Yulong Fu
- Laboratory of Endocrinology and Receptor Biology, NIDDK, National Institutes of Health, Bethesda, MD, United States
| | - Douglas Forrest
- Laboratory of Endocrinology and Receptor Biology, NIDDK, National Institutes of Health, Bethesda, MD, United States.
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35
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Blixt MKE, Hallböök F. A regulatory sequence from the retinoid X receptor γ gene directs expression to horizontal cells and photoreceptors in the embryonic chicken retina. Mol Vis 2016; 22:1405-1420. [PMID: 28003731 PMCID: PMC5166796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 12/12/2016] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Combining techniques of episomal vector gene-specific Cre expression and genomic integration using the piggyBac transposon system enables studies of gene expression-specific cell lineage tracing in the chicken retina. In this work, we aimed to target the retinal horizontal cell progenitors. METHODS A 208 bp gene regulatory sequence from the chicken retinoid X receptor γgene (RXRγ208) was used to drive Cre expression. RXRγ is expressed in progenitors and photoreceptors during development. The vector was combined with a piggyBac "donor" vector containing a floxed STOP sequence followed by enhanced green fluorescent protein (EGFP), as well as a piggyBac helper vector for efficient integration into the host cell genome. The vectors were introduced into the embryonic chicken retina with in ovo electroporation. Tissue electroporation targets specific developmental time points and in specific structures. RESULTS Cells that drove Cre expression from the regulatory RXRγ208 sequence excised the floxed STOP-sequence and expressed GFP. The approach generated a stable lineage with robust expression of GFP in retinal cells that have activated transcription from the RXRγ208 sequence. Furthermore, GFP was expressed in cells that express horizontal or photoreceptor markers when electroporation was performed between developmental stages 22 and 28. Electroporation of a stage 12 optic cup gave multiple cell types in accordance with RXRγ gene expression in the early retina. CONCLUSIONS In this study, we describe an easy, cost-effective, and time-efficient method for testing regulatory sequences in general. More specifically, our results open up the possibility for further studies of the RXRγ-gene regulatory network governing the formation of photoreceptor and horizontal cells. In addition, the method presents approaches to target the expression of effector genes, such as regulators of cell fate or cell cycle progression, to these cells and their progenitor.
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Affiliation(s)
- Maria K E Blixt
- Department of Neuroscience, Faculty of Medicine, Uppsala University, Uppsala, Sweden
| | - Finn Hallböök
- Department of Neuroscience, Faculty of Medicine, Uppsala University, Uppsala, Sweden
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36
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Tang JC, Drokhlyansky E, Etemad B, Rudolph S, Guo B, Wang S, Ellis EG, Li JZ, Cepko CL. Detection and manipulation of live antigen-expressing cells using conditionally stable nanobodies. eLife 2016; 5. [PMID: 27205882 PMCID: PMC4922844 DOI: 10.7554/elife.15312] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/19/2016] [Indexed: 12/18/2022] Open
Abstract
The ability to detect and/or manipulate specific cell populations based upon the presence of intracellular protein epitopes would enable many types of studies and applications. Protein binders such as nanobodies (Nbs) can target untagged proteins (antigens) in the intracellular environment. However, genetically expressed protein binders are stable regardless of antigen expression, complicating their use for applications that require cell-specificity. Here, we created a conditional system in which the stability of an Nb depends upon an antigen of interest. We identified Nb framework mutations that can be used to rapidly create destabilized Nbs. Fusion of destabilized Nbs to various proteins enabled applications in living cells, such as optogenetic control of neural activity in specific cell types in the mouse brain, and detection of HIV-infected human cells by flow cytometry. These approaches are generalizable to other protein binders, and enable the rapid generation of single-polypeptide sensors and effectors active in cells expressing specific intracellular epitopes. DOI:http://dx.doi.org/10.7554/eLife.15312.001 Biologists often wish to study the role of a particular cell type within an organism, but such studies are often not possible due to the lack of reagents that allow one to gain control of the cell type of interest. One method that can be used to detect and manipulate the cells that express specific proteins uses molecules called antibodies. An antibody can strongly bind to a specific part of a protein, and a diversity of antibodies that bind to different proteins can be isolated by animal immunization, or by using molecular or cell-based methods. Antibodies from camelid species (which include camels and llamas) are increasingly being used to detect and manipulate proteins in living cells. The variable region of these antibodies – also known as the nanobody – recognises the proteins that the antibody binds to, and often just this fragment of the antibody is used in protein detection experiments. However, nanobodies are stable even in cells that do not contain their target proteins, which makes it difficult to use nanobodies to study just a specific cell type within an organism. Tang, Drokhlyansky et al. have now developed a way of engineering the sequence of a nanobody so that it is broken down in living cells unless it is bound to its protein target inside the cell. Any protein that is tethered to the engineered nanobody is also broken down. For example, some tethered proteins with useful biological activities are fluorescent proteins and enzymes that can modify DNA. When one of these engineered nanobodies binds to a protein target of interest, the activity of the nanobody-tethered protein can be turned on in just those cells that produce the targeted protein. Thus, this strategy of engineering allows “conditionally stable” tools to be generated. A core set of sequence alterations can be used to modify different nanobodies that target different proteins. Tang, Drokhlyansky et al. have demonstrated the uses of several of the resulting conditionally stable nanobodies. In one application, the nanobodies were used to target specific cell types in the mouse brain in a way that allowed the activity of these cells to be controlled by light. Another application of the technique enables live human cells that have been infected with HIV to be detected and isolated. The conditionally stable nanobody tools can be used to detect and manipulate cells that express any protein for which a camelid antibody exists. Tang, Drokhlyansky et al. therefore hope that biologists who work in a wide range of fields will find the tools useful for studying many different types of organisms and biological processes. DOI:http://dx.doi.org/10.7554/eLife.15312.002
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Affiliation(s)
- Jonathan Cy Tang
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Eugene Drokhlyansky
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Behzad Etemad
- Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Stephanie Rudolph
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Binggege Guo
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Sui Wang
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Emily G Ellis
- Department of Neurobiology, Harvard Medical School, Boston, United States
| | - Jonathan Z Li
- Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Constance L Cepko
- Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
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Abstract
Photoreceptors have been the most intensively studied retinal cell type. Early lineage studies showed that photoreceptors are produced by retinal progenitor cells (RPCs) that produce only photoreceptor cells and by RPCs that produce both photoreceptor cells and other retinal cell types. More recent lineage studies have shown that there are intrinsic, molecular differences among these RPCs and that these molecular differences operate in gene regulatory networks (GRNs) that lead to the choice of the rod versus the cone fate. In addition, there are GRNs that lead to the choice of a photoreceptor fate and that of another retinal cell type. An example of such a GRN is one that drives the binary fate choice between a rod photoreceptor and bipolar cell. This GRN has many elements, including both feedforward and feedback regulatory loops, highlighting the complexity of such networks. This and other examples of retinal cell fate determination are reviewed here, focusing on the events that direct the choice of rod and cone photoreceptor fate.
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Affiliation(s)
- Constance L Cepko
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115;
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38
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Tang JCY, Rudolph S, Dhande OS, Abraira VE, Choi S, Lapan SW, Drew IR, Drokhlyansky E, Huberman AD, Regehr WG, Cepko CL. Cell type-specific manipulation with GFP-dependent Cre recombinase. Nat Neurosci 2015; 18:1334-41. [PMID: 26258682 PMCID: PMC4839275 DOI: 10.1038/nn.4081] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 07/02/2015] [Indexed: 12/12/2022]
Abstract
There are many transgenic GFP reporter lines that allow visualization of specific populations of cells. Using such lines for functional studies requires a method that transforms GFP into a molecule that enables genetic manipulation. Here we report the creation of a method that exploits GFP for gene manipulation, Cre Recombinase Dependent on GFP (CRE-DOG), a split component system that uses GFP and its derivatives to directly induce Cre/loxP recombination. Using plasmid electroporation and AAV viral vectors, we delivered CRE-DOG to multiple GFP mouse lines, leading to effective recombination selectively in GFP-labeled cells. Further, CRE-DOG enabled optogenetic control of these neurons. Beyond providing a new set of tools for manipulation of gene expression selectively in GFP+ cells, we demonstrate that GFP can be used to reconstitute the activity of a protein not known to have a modular structure, suggesting that this strategy might be applicable to a wide range of proteins.
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Affiliation(s)
- Jonathan C Y Tang
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Stephanie Rudolph
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Onkar S Dhande
- Department of Neurosciences, University of California, San Diego, California, USA.,Neurobiology Section in the Division of Biological Sciences, University of California, San Diego, California, USA.,Department of Ophthalmology, University of California, San Diego, California, USA
| | - Victoria E Abraira
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Seungwon Choi
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sylvain W Lapan
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Iain R Drew
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eugene Drokhlyansky
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew D Huberman
- Department of Neurosciences, University of California, San Diego, California, USA.,Neurobiology Section in the Division of Biological Sciences, University of California, San Diego, California, USA.,Department of Ophthalmology, University of California, San Diego, California, USA
| | - Wade G Regehr
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Constance L Cepko
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.,Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
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Wilken MS, Brzezinski JA, La Torre A, Siebenthall K, Thurman R, Sabo P, Sandstrom RS, Vierstra J, Canfield TK, Hansen RS, Bender MA, Stamatoyannopoulos J, Reh TA. DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements. Epigenetics Chromatin 2015; 8:8. [PMID: 25972927 PMCID: PMC4429822 DOI: 10.1186/1756-8935-8-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 01/27/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The brain, spinal cord, and neural retina comprise the central nervous system (CNS) of vertebrates. Understanding the regulatory mechanisms that underlie the enormous cell-type diversity of the CNS is a significant challenge. Whole-genome mapping of DNase I-hypersensitive sites (DHSs) has been used to identify cis-regulatory elements in many tissues. We have applied this approach to the mouse CNS, including developing and mature neural retina, whole brain, and two well-characterized brain regions, the cerebellum and the cerebral cortex. RESULTS For the various regions and developmental stages of the CNS that we analyzed, there were approximately the same number of DHSs; however, there were many DHSs unique to each CNS region and developmental stage. Many of the DHSs are likely to mark enhancers that are specific to the specific CNS region and developmental stage. We validated the DNase I mapping approach for identification of CNS enhancers using the existing VISTA Browser database and with in vivo and in vitro electroporation of the retina. Analysis of transcription factor consensus sites within the DHSs shows distinct region-specific profiles of transcriptional regulators particular to each region. Clustering developmentally dynamic DHSs in the retina revealed enrichment of developmental stage-specific transcriptional regulators. Additionally, we found reporter gene activity in the retina driven from several previously uncharacterized regulatory elements surrounding the neurodevelopmental gene Otx2. Identification of DHSs shared between mouse and human showed region-specific differences in the evolution of cis-regulatory elements. CONCLUSIONS Overall, our results demonstrate the potential of genome-wide DNase I mapping to cis-regulatory questions regarding the regional diversity within the CNS. These data represent an extensive catalogue of potential cis-regulatory elements within the CNS that display region and temporal specificity, as well as a set of DHSs common to CNS tissues. Further examination of evolutionary conservation of DHSs between CNS regions and different species may reveal important cis-regulatory elements in the evolution of the mammalian CNS.
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Affiliation(s)
- Matthew S Wilken
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Box 357420, Seattle, WA 98195 USA ; Molecular and Cellular Biology Program, University of Washington, MCB Program Office, T-466 Health Sciences Building, Box 357275, Seattle, WA 98195 USA
| | - Joseph A Brzezinski
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Box 357420, Seattle, WA 98195 USA ; Department of Ophthalmology, University of Colorado School of Medicine, 1675 Aurora Court, Aurora, CO 80045 USA
| | - Anna La Torre
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Box 357420, Seattle, WA 98195 USA
| | - Kyle Siebenthall
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Robert Thurman
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Peter Sabo
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Richard S Sandstrom
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Theresa K Canfield
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - R Scott Hansen
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Michael A Bender
- Department of Pediatrics, University of Washington, 1959 NE Pacific St, Health Sciences Building, Seattle, WA Box 356320, 98195 USA ; Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109 USA
| | - John Stamatoyannopoulos
- Department of Genome Sciences, University of Washington, Foege Building S-250, 3720 15th Ave NE, Box 355065, Seattle, WA 98195 USA
| | - Thomas A Reh
- Department of Biological Structure, University of Washington, 1959 NE Pacific Street, Box 357420, Seattle, WA 98195 USA
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40
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Abstract
Retinoblastoma is a rare childhood cancer of the developing retina. Most retinoblastomas initiate with biallelic inactivation of the RB1 gene through diverse mechanisms including point mutations, nucleotide insertions, deletions, loss of heterozygosity and promoter hypermethylation. Recently, a novel mechanism of retinoblastoma initiation was proposed. Gallie and colleagues discovered that a small proportion of retinoblastomas lack RB1 mutations and had MYCN amplification [1]. In this study, we identifed recurrent chromosomal, regional and focal genomic lesions in 94 primary retinoblastomas with their matched normal DNA using SNP 6.0 chips. We also analyzed the RB1 gene mutations and compared the mechanism of RB1 inactivation to the recurrent copy number variations in the retinoblastoma genome. In addition to the previously described focal amplification of MYCN and deletions in RB1 and BCOR, we also identifed recurrent focal amplification of OTX2, a transcription factor required for retinal photoreceptor development. We identifed 10 retinoblastomas in our cohort that lacked RB1 point mutations or indels. We performed whole genome sequencing on those 10 tumors and their corresponding germline DNA. In one of the tumors, the RB1 gene was unaltered, the MYCN gene was amplified and RB1 protein was expressed in the nuclei of the tumor cells. In addition, several tumors had complex patterns of structural variations and we identified 3 tumors with chromothripsis at the RB1 locus. This is the first report of chromothripsis as a mechanism for RB1 gene inactivation in cancer.
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41
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Wortham M, Guo C, Zhang M, Song L, Lee BK, Iyer VR, Furey TS, Crawford GE, Yan H, He Y. Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma. PLoS One 2014; 9:e107156. [PMID: 25198066 PMCID: PMC4157845 DOI: 10.1371/journal.pone.0107156] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 08/06/2014] [Indexed: 12/01/2022] Open
Abstract
Despite an emerging understanding of the genetic alterations giving rise to various tumors, the mechanisms whereby most oncogenes are overexpressed remain unclear. Here we have utilized an integrated approach of genomewide regulatory element mapping via DNase-seq followed by conventional reporter assays and transcription factor binding site discovery to characterize the transcriptional regulation of the medulloblastoma oncogene Orthodenticle Homeobox 2 (OTX2). Through these studies we have revealed that OTX2 is differentially regulated in medulloblastoma at the level of chromatin accessibility, which is in part mediated by DNA methylation. In cell lines exhibiting chromatin accessibility of OTX2 regulatory regions, we found that autoregulation maintains OTX2 expression. Comparison of medulloblastoma regulatory elements with those of the developing brain reveals that these tumors engage a developmental regulatory program to drive OTX2 transcription. Finally, we have identified a transcriptional regulatory element mediating retinoid-induced OTX2 repression in these tumors. This work characterizes for the first time the mechanisms of OTX2 overexpression in medulloblastoma. Furthermore, this study establishes proof of principle for applying ENCODE datasets towards the characterization of upstream trans-acting factors mediating expression of individual genes.
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Affiliation(s)
- Matthew Wortham
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Changcun Guo
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Monica Zhang
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Lingyun Song
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Bum-Kyu Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Vishwanath R. Iyer
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America
| | - Terrence S. Furey
- Department of Genetics, Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Gregory E. Crawford
- Duke Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Hai Yan
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (YH); (HY)
| | - Yiping He
- Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail: (YH); (HY)
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42
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A gene regulatory network controls the binary fate decision of rod and bipolar cells in the vertebrate retina. Dev Cell 2014; 30:513-27. [PMID: 25155555 PMCID: PMC4304698 DOI: 10.1016/j.devcel.2014.07.018] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/16/2014] [Accepted: 07/21/2014] [Indexed: 12/12/2022]
Abstract
Gene regulatory networks (GRNs) regulate critical events during development. In complex tissues, such as the mammalian central nervous system (CNS), networks likely provide the complex regulatory interactions needed to direct the specification of the many CNS cell types. Here, we dissect a GRN that regulates a binary fate decision between two siblings in the murine retina, the rod photoreceptor and bipolar interneuron. The GRN centers on Blimp1, one of the transcription factors (TFs) that regulates the rod versus bipolar cell fate decision. We identified a cis-regulatory module (CRM), B108, that mimics Blimp1 expression. Deletion of genomic B108 by CRISPR/Cas9 in vivo using electroporation abolished the function of Blimp1. Otx2 and RORβ were found to regulate Blimp1 expression via B108, and Blimp1 and Otx2 were shown to form a negative feedback loop that regulates the level of Otx2, which regulates the production of the correct ratio of rods and bipolar cells.
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43
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Tang JCY, Szikra T, Kozorovitskiy Y, Teixiera M, Sabatini BL, Roska B, Cepko CL. A nanobody-based system using fluorescent proteins as scaffolds for cell-specific gene manipulation. Cell 2013; 154:928-39. [PMID: 23953120 PMCID: PMC4096992 DOI: 10.1016/j.cell.2013.07.021] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 05/31/2013] [Accepted: 07/15/2013] [Indexed: 01/22/2023]
Abstract
Fluorescent proteins are commonly used to label cells across organisms, but the unmodified forms cannot control biological activities. Using GFP-binding proteins derived from Camelid antibodies, we co-opted GFP as a scaffold for inducing formation of biologically active complexes, developing a library of hybrid transcription factors that control gene expression only in the presence of GFP or its derivatives. The modular design allows for variation in key properties such as DNA specificity, transcriptional potency, and drug dependency. Production of GFP controlled cell-specific gene expression and facilitated functional perturbations in the mouse retina and brain. Further, retrofitting existing transgenic GFP mouse and zebrafish lines for GFP-dependent transcription enabled applications such as optogenetic probing of neural circuits. This work establishes GFP as a multifunctional scaffold and opens the door to selective manipulation of diverse GFP-labeled cells across transgenic lines. This approach may also be extended to exploit other intracellular products as cell-specific scaffolds in multicellular organisms.
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Affiliation(s)
- Jonathan C Y Tang
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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44
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Emerson MM, Surzenko N, Goetz JJ, Trimarchi J, Cepko CL. Otx2 and Onecut1 promote the fates of cone photoreceptors and horizontal cells and repress rod photoreceptors. Dev Cell 2013; 26:59-72. [PMID: 23867227 DOI: 10.1016/j.devcel.2013.06.005] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 04/22/2013] [Accepted: 06/06/2013] [Indexed: 10/26/2022]
Abstract
Cone photoreceptors carry out phototransduction in daylight conditions and provide the critical first step in color vision. Despite their importance, little is known about the developmental mechanisms involved in their generation, particularly how they are determined relative to rod photoreceptors, the cells that initiate vision in dim light. Here, we report the identification of a cis-regulatory module (CRM) for the thyroid hormone receptor beta (Thrb) gene, an early cone marker. We found that ThrbCRM1 is active in progenitor cells biased to the production of cones and an interneuronal cell type, the horizontal cell (HC). Molecular analysis of ThrbCRM1 revealed that it is combinatorially regulated by the Otx2 and Onecut1 transcription factors. Onecut1 is sufficient to induce cells with the earliest markers of cones and HCs. Conversely, interference with Onecut1 transcriptional activity leads to precocious rod development, suggesting that Onecut1 is critically important in defining cone versus rod fates.
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Affiliation(s)
- Mark M Emerson
- Departments of Genetics and Ophthalmology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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45
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Islam MM, Li Y, Luo H, Xiang M, Cai L. Meis1 regulates Foxn4 expression during retinal progenitor cell differentiation. Biol Open 2013; 2:1125-36. [PMID: 24244849 PMCID: PMC3828759 DOI: 10.1242/bio.20132279] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 08/12/2013] [Indexed: 12/20/2022] Open
Abstract
The transcription factor forkhead box N4 (Foxn4) is a key regulator in a variety of biological processes during development. In particular, Foxn4 plays an essential role in the genesis of horizontal and amacrine neurons from neural progenitors in the vertebrate retina. Although the functions of Foxn4 have been well established, the transcriptional regulation of Foxn4 expression during progenitor cell differentiation remains unclear. Here, we report that an evolutionarily conserved 129 bp noncoding DNA fragment (Foxn4CR4.2 or CR4.2), located ∼26 kb upstream of Foxn4 transcription start site, functions as a cis-element for Foxn4 regulation. CR4.2 directs gene expression in Foxn4-positive cells, primarily in progenitors, differentiating horizontal and amacrine cells. We further determined that the gene regulatory activity of CR4.2 is modulated by Meis1 binding motif, which is bound and activated by Meis1 transcription factor. Deletion of the Meis1 binding motif or knockdown of Meis1 expression abolishes the gene regulatory activity of CR4.2. In addition, knockdown of Meis1 expression diminishes the endogenous Foxn4 expression and affects cell lineage development. Together, we demonstrate that CR4.2 and its interacting Meis1 transcription factor play important roles in regulating Foxn4 expression during early retinogenesis. These findings provide new insights into molecular mechanisms that govern gene regulation in retinal progenitors and specific cell lineage development.
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Affiliation(s)
- Mohammed M Islam
- Department of Biomedical Engineering, Rutgers University , 599 Taylor Road, Piscataway, NJ 08854 , USA ; Present address: Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
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46
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Beby F, Lamonerie T. The homeobox gene Otx2 in development and disease. Exp Eye Res 2013; 111:9-16. [DOI: 10.1016/j.exer.2013.03.007] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/07/2013] [Accepted: 03/11/2013] [Indexed: 01/04/2023]
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