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Martersteck EM, Hirokawa KE, Evarts M, Bernard A, Duan X, Li Y, Ng L, Oh SW, Ouellette B, Royall JJ, Stoecklin M, Wang Q, Zeng H, Sanes JR, Harris JA. Diverse Central Projection Patterns of Retinal Ganglion Cells. Cell Rep 2017; 18:2058-2072. [PMID: 28228269 DOI: 10.1016/j.celrep.2017.01.075] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/09/2016] [Accepted: 01/27/2017] [Indexed: 11/27/2022] Open
Abstract
Understanding how >30 types of retinal ganglion cells (RGCs) in the mouse retina each contribute to visual processing in the brain will require more tools that label and manipulate specific RGCs. We screened and analyzed retinal expression of Cre recombinase using 88 transgenic driver lines. In many lines, Cre was expressed in multiple RGC types and retinal cell classes, but several exhibited more selective expression. We comprehensively mapped central projections from RGCs labeled in 26 Cre lines using viral tracers, high-throughput imaging, and a data processing pipeline. We identified over 50 retinorecipient regions and present a quantitative retina-to-brain connectivity map, enabling comparisons of target-specificity across lines. Projections to two major central targets were notably correlated: RGCs projecting to the outer shell or core regions of the lateral geniculate projected to superficial or deep layers within the superior colliculus, respectively. Retinal images and projection data are available online at http://connectivity.brain-map.org.
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Affiliation(s)
- Emily M Martersteck
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Mariah Evarts
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xin Duan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yang Li
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Seung W Oh
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Quanxin Wang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
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Peng YR, Tran NM, Krishnaswamy A, Kostadinov D, Martersteck EM, Sanes JR. Satb1 Regulates Contactin 5 to Pattern Dendrites of a Mammalian Retinal Ganglion Cell. Neuron 2017; 95:869-883.e6. [PMID: 28781169 DOI: 10.1016/j.neuron.2017.07.019] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 06/16/2017] [Accepted: 07/19/2017] [Indexed: 12/13/2022]
Abstract
The size and shape of dendritic arbors are prime determinants of neuronal connectivity and function. We asked how ON-OFF direction-selective ganglion cells (ooDSGCs) in mouse retina acquire their bistratified dendrites, in which responses to light onset and light offset are segregated to distinct strata. We found that the transcriptional regulator Satb1 is selectively expressed by ooDSGCs. In Satb1 mutant mice, ooDSGC dendrites lack ON arbors, and the cells selectively lose ON responses. Satb1 regulates expression of a homophilic adhesion molecule, Contactin 5 (Cntn5). Both Cntn5 and its co-receptor Caspr4 are expressed not only by ooDSGCs, but also by interneurons that form a scaffold on which ooDSGC ON dendrites fasciculate. Removing Cntn5 from either ooDSGCs or interneurons partially phenocopies Satb1 mutants, demonstrating that Satb1-dependent Cntn5 expression in ooDSGCs leads to branch-specific homophilic interactions with interneurons. Thus, Satb1 directs formation of a morphologically and functionally specialized compartment within a complex dendritic arbor.
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Affiliation(s)
- Yi-Rong Peng
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Nicholas M Tran
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Arjun Krishnaswamy
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Dimitar Kostadinov
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Emily M Martersteck
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, McCarroll SA. Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 2015; 161:1202-1214. [PMID: 26000488 PMCID: PMC4481139 DOI: 10.1016/j.cell.2015.05.002] [Citation(s) in RCA: 4294] [Impact Index Per Article: 477.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 03/04/2015] [Accepted: 04/30/2015] [Indexed: 02/06/2023]
Abstract
Cells, the basic units of biological structure and function, vary broadly in type and state. Single-cell genomics can characterize cell identity and function, but limitations of ease and scale have prevented its broad application. Here we describe Drop-seq, a strategy for quickly profiling thousands of individual cells by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together. Drop-seq analyzes mRNA transcripts from thousands of individual cells simultaneously while remembering transcripts' cell of origin. We analyzed transcriptomes from 44,808 mouse retinal cells and identified 39 transcriptionally distinct cell populations, creating a molecular atlas of gene expression for known retinal cell classes and novel candidate cell subtypes. Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution. VIDEO ABSTRACT.
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Affiliation(s)
- 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.
| | - Anindita Basu
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Rahul Satija
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, 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
| | - Karthik Shekhar
- Klarman Cell Observatory, 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
| | - Itay Tirosh
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Allison R Bialas
- The Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, MA 02115, USA
| | - Nolan Kamitaki
- 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
| | - Emily M Martersteck
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - John J Trombetta
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - David A Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Joshua R Sanes
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Alex K Shalek
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science and Department of Chemistry, MIT, Cambridge, MA 02139, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, 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.
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