1
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Kaplan HS, Logeman BL, Zhang K, Santiago C, Sohail N, Naumenko S, Ho Sui SJ, Ginty DD, Ren B, Dulac C. Sensory Input, Sex, and Function Shape Hypothalamic Cell Type Development. bioRxiv 2024:2024.01.23.576835. [PMID: 38328205 PMCID: PMC10849564 DOI: 10.1101/2024.01.23.576835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Mammalian behavior and physiology undergo dramatic changes in early life. Young animals rely on conspecifics to meet their homeostatic needs, until weaning and puberty initiate nutritional independence and sex-specific social interactions, respectively. How neuronal populations regulating homeostatic functions and social behaviors develop and mature during these transitions remains unclear. We used paired transcriptomic and chromatin accessibility profiling to examine the developmental trajectories of neuronal populations in the hypothalamic preoptic region, where cell types with key roles in physiological and behavioral control have been identified1-6. These data reveal a remarkable diversity of developmental trajectories shaped by the sex of the animal, and the location and behavioral or physiological function of the corresponding cell types. We identify key stages of preoptic development, including the perinatal emergence of sex differences, postnatal maturation and subsequent refinement of signaling networks, and nonlinear transcriptional changes accelerating at the time of weaning and puberty. We assessed preoptic development in various sensory mutants and find a major role for vomeronasal sensing in the timing of preoptic cell type maturation. These results provide novel insights into the development of neurons controlling homeostatic functions and social behaviors and lay ground for examining the dynamics of these functions in early life.
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Affiliation(s)
- Harris S. Kaplan
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Brandon L. Logeman
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Kai Zhang
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA 92093, USA
- Current address: Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, China
| | - Celine Santiago
- Department of Neurobiology, Harvard Medical School, Howard Hughes Medical Institute, 220 Longwood Ave, Boston, MA, 02115, USA
| | - Noor Sohail
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
| | - Serhiy Naumenko
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
- Newborn Screening Ontario, Ottawa, ON, Canada
| | - Shannan J. Ho Sui
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, USA
| | - David D. Ginty
- Department of Neurobiology, Harvard Medical School, Howard Hughes Medical Institute, 220 Longwood Ave, Boston, MA, 02115, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
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2
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Liu D, Rahman M, Johnson A, Tsutsui-Kimura I, Pena N, Talay M, Logeman BL, Finkbeiner S, Choi S, Capo-Battaglia A, Abdus-Saboor I, Ginty DD, Uchida N, Watabe-Uchida M, Dulac C. A Hypothalamic Circuit Underlying the Dynamic Control of Social Homeostasis. bioRxiv 2023:2023.05.19.540391. [PMID: 37293031 PMCID: PMC10245688 DOI: 10.1101/2023.05.19.540391] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Social grouping increases survival in many species, including humans1,2. By contrast, social isolation generates an aversive state (loneliness) that motivates social seeking and heightens social interaction upon reunion3-5. The observed rebound in social interaction triggered by isolation suggests a homeostatic process underlying the control of social drive, similar to that observed for physiological needs such as hunger, thirst or sleep3,6. In this study, we assessed social responses in multiple mouse strains and identified the FVB/NJ line as exquisitely sensitive to social isolation. Using FVB/NJ mice, we uncovered two previously uncharacterized neuronal populations in the hypothalamic preoptic nucleus that are activated during social isolation and social rebound and that orchestrate the behavior display of social need and social satiety, respectively. We identified direct connectivity between these two populations of opposite function and with brain areas associated with social behavior, emotional state, reward, and physiological needs, and showed that animals require touch to assess the presence of others and fulfill their social need, thus revealing a brain-wide neural system underlying social homeostasis. These findings offer mechanistic insight into the nature and function of circuits controlling instinctive social need and for the understanding of healthy and diseased brain states associated with social context.
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Affiliation(s)
- Ding Liu
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Mostafizur Rahman
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Autumn Johnson
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Iku Tsutsui-Kimura
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
- Present address: Division of Brain Sciences, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, Japan
| | - Nicolai Pena
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Mustafa Talay
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Brandon L. Logeman
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Samantha Finkbeiner
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Seungwon Choi
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Present address: Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Athena Capo-Battaglia
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Ishmail Abdus-Saboor
- Zuckerman Mind Brain Behavior Institute, Department of Biological Sciences, Columbia University, New York, NY, USA
| | - David D. Ginty
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Naoshige Uchida
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Mitsuko Watabe-Uchida
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
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3
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Allen WE, Blosser TR, Sullivan ZA, Dulac C, Zhuang X. Molecular and spatial signatures of mouse brain aging at single-cell resolution. Cell 2023; 186:194-208.e18. [PMID: 36580914 PMCID: PMC10024607 DOI: 10.1016/j.cell.2022.12.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/08/2022] [Accepted: 12/05/2022] [Indexed: 12/29/2022]
Abstract
The diversity and complex organization of cells in the brain have hindered systematic characterization of age-related changes in its cellular and molecular architecture, limiting our ability to understand the mechanisms underlying its functional decline during aging. Here, we generated a high-resolution cell atlas of brain aging within the frontal cortex and striatum using spatially resolved single-cell transcriptomics and quantified changes in gene expression and spatial organization of major cell types in these regions over the mouse lifespan. We observed substantially more pronounced changes in cell state, gene expression, and spatial organization of non-neuronal cells over neurons. Our data revealed molecular and spatial signatures of glial and immune cell activation during aging, particularly enriched in the subcortical white matter, and identified both similarities and notable differences in cell-activation patterns induced by aging and systemic inflammatory challenge. These results provide critical insights into age-related decline and inflammation in the brain.
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Affiliation(s)
- William E Allen
- Society of Fellows, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, and Department of Physics, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Timothy R Blosser
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Zuri A Sullivan
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Catherine Dulac
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, and Department of Physics, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
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4
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Osterhout JA, Kapoor V, Eichhorn SW, Vaughn E, Moore JD, Liu D, Lee D, DeNardo LA, Luo L, Zhuang X, Dulac C. A preoptic neuronal population controls fever and appetite during sickness. Nature 2022; 606:937-944. [PMID: 35676482 PMCID: PMC9327738 DOI: 10.1038/s41586-022-04793-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/21/2022] [Indexed: 01/07/2023]
Abstract
During infection, animals exhibit adaptive changes in physiology and behaviour aimed at increasing survival. Although many causes of infection exist, they trigger similar stereotyped symptoms such as fever, warmth-seeking, loss of appetite and fatigue1,2. Yet exactly how the nervous system alters body temperature and triggers sickness behaviours to coordinate responses to infection remains unknown. Here we identify a previously uncharacterized population of neurons in the ventral medial preoptic area (VMPO) of the hypothalamus that are activated after sickness induced by lipopolysaccharide (LPS) or polyinosinic:polycytidylic acid. These neurons are crucial for generating a fever response and other sickness symptoms such as warmth-seeking and loss of appetite. Single-nucleus RNA-sequencing and multiplexed error-robust fluorescence in situ hybridization uncovered the identity and distribution of LPS-activated VMPO (VMPOLPS) neurons and non-neuronal cells. Gene expression and electrophysiological measurements implicate a paracrine mechanism in which the release of immune signals by non-neuronal cells during infection activates nearby VMPOLPS neurons. Finally, we show that VMPOLPS neurons exert a broad influence on the activity of brain areas associated with behavioural and homeostatic functions and are synaptically and functionally connected to circuit nodes controlling body temperature and appetite. Together, these results uncover VMPOLPS neurons as a control hub that integrates immune signals to orchestrate multiple sickness symptoms in response to infection.
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Affiliation(s)
- Jessica A. Osterhout
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA,Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Vikrant Kapoor
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA,Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Stephen W. Eichhorn
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA,Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA,Department of Physics, Harvard University, Howard Hughes Medical Institute, Cambridge, MA 02138, USA
| | - Eric Vaughn
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA,Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Jeffrey D. Moore
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA,Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Ding Liu
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA,Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Dean Lee
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA,Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Laura A. DeNardo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA,Current address: Department of Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Xiaowei Zhuang
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA,Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA,Department of Physics, Harvard University, Howard Hughes Medical Institute, Cambridge, MA 02138, USA
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA,Center for Brain Science, Harvard University, Cambridge, MA 02138, USA,Corresponding author:
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5
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Lauer J, Zhou M, Ye S, Menegas W, Schneider S, Nath T, Rahman MM, Di Santo V, Soberanes D, Feng G, Murthy VN, Lauder G, Dulac C, Mathis MW, Mathis A. Multi-animal pose estimation, identification and tracking with DeepLabCut. Nat Methods 2022; 19:496-504. [PMID: 35414125 PMCID: PMC9007739 DOI: 10.1038/s41592-022-01443-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 03/04/2022] [Indexed: 11/23/2022]
Abstract
Estimating the pose of multiple animals is a challenging computer vision problem: frequent interactions cause occlusions and complicate the association of detected keypoints to the correct individuals, as well as having highly similar looking animals that interact more closely than in typical multi-human scenarios. To take up this challenge, we build on DeepLabCut, an open-source pose estimation toolbox, and provide high-performance animal assembly and tracking-features required for multi-animal scenarios. Furthermore, we integrate the ability to predict an animal's identity to assist tracking (in case of occlusions). We illustrate the power of this framework with four datasets varying in complexity, which we release to serve as a benchmark for future algorithm development.
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Affiliation(s)
- Jessy Lauer
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA
| | - Mu Zhou
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Shaokai Ye
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - William Menegas
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Steffen Schneider
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Tanmay Nath
- Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA
| | - Mohammed Mostafizur Rahman
- Department for Molecular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute (HHMI), Chevy Chase, MD, USA
| | - Valentina Di Santo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Daniel Soberanes
- Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA
| | - Guoping Feng
- Department of Brain and Cognitive Sciences and McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Venkatesh N Murthy
- Department for Molecular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - George Lauder
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Catherine Dulac
- Department for Molecular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute (HHMI), Chevy Chase, MD, USA
| | - Mackenzie Weygandt Mathis
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA.
| | - Alexander Mathis
- Brain Mind Institute, School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- Rowland Institute at Harvard, Harvard University, Cambridge, MA, USA.
- Department for Molecular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA.
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6
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Autry AE, Wu Z, Kapoor V, Kohl J, Bambah-Mukku D, Rubinstein ND, Marin-Rodriguez B, Carta I, Sedwick V, Tang M, Dulac C. Urocortin-3 neurons in the mouse perifornical area promote infant-directed neglect and aggression. eLife 2021; 10:e64680. [PMID: 34423776 PMCID: PMC8452308 DOI: 10.7554/elife.64680] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 08/19/2021] [Indexed: 12/18/2022] Open
Abstract
While recent studies have uncovered dedicated neural pathways mediating the positive control of parenting, the regulation of infant-directed aggression and how it relates to adult-adult aggression is poorly understood. Here we show that urocortin-3 (Ucn3)-expressing neurons in the hypothalamic perifornical area (PeFAUcn3) are activated during infant-directed attacks in males and females, but not other behaviors. Functional manipulations of PeFAUcn3 neurons demonstrate the role of this population in the negative control of parenting in both sexes. PeFAUcn3 neurons receive input from areas associated with vomeronasal sensing, stress, and parenting, and send projections to hypothalamic and limbic areas. Optogenetic activation of PeFAUcn3 axon terminals in these regions triggers various aspects of infant-directed agonistic responses, such as neglect, repulsion, and aggression. Thus, PeFAUcn3 neurons emerge as a dedicated circuit component controlling infant-directed neglect and aggression, providing a new framework to understand the positive and negative regulation of parenting in health and disease.
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Affiliation(s)
- Anita E Autry
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard UniversityCambridgeUnited States
- Dominick P. Purpura Department of Neuroscience, Department of Psychiatry and Behavioral Sciences, Albert Einstein College of MedicineBronxUnited States
| | - Zheng Wu
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard UniversityCambridgeUnited States
| | - Vikrant Kapoor
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard UniversityCambridgeUnited States
| | - Johannes Kohl
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard UniversityCambridgeUnited States
| | - Dhananjay Bambah-Mukku
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard UniversityCambridgeUnited States
| | - Nimrod D Rubinstein
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard UniversityCambridgeUnited States
| | - Brenda Marin-Rodriguez
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard UniversityCambridgeUnited States
| | - Ilaria Carta
- Dominick P. Purpura Department of Neuroscience, Department of Psychiatry and Behavioral Sciences, Albert Einstein College of MedicineBronxUnited States
| | - Victoria Sedwick
- Dominick P. Purpura Department of Neuroscience, Department of Psychiatry and Behavioral Sciences, Albert Einstein College of MedicineBronxUnited States
| | - Ming Tang
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard UniversityCambridgeUnited States
- FAS Informatics Group, Harvard UniversityCambridgeUnited States
| | - Catherine Dulac
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard UniversityCambridgeUnited States
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7
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Tang M, Kaymaz Y, Logeman BL, Eichhorn S, Liang ZS, Dulac C, Sackton TB. Evaluating single-cell cluster stability using the Jaccard similarity index. Bioinformatics 2021; 37:2212-2214. [PMID: 33165513 DOI: 10.1093/bioinformatics/btaa956] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/13/2020] [Accepted: 11/02/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION One major goal of single-cell RNA sequencing (scRNAseq) experiments is to identify novel cell types. With increasingly large scRNAseq datasets, unsupervised clustering methods can now produce detailed catalogues of transcriptionally distinct groups of cells in a sample. However, the interpretation of these clusters is challenging for both technical and biological reasons. Popular clustering algorithms are sensitive to parameter choices, and can produce different clustering solutions with even small changes in the number of principal components used, the k nearest neighbor and the resolution parameters, among others. RESULTS Here, we present a set of tools to evaluate cluster stability by subsampling, which can guide parameter choice and aid in biological interpretation. The R package scclusteval and the accompanying Snakemake workflow implement all steps of the pipeline: subsampling the cells, repeating the clustering with Seurat and estimation of cluster stability using the Jaccard similarity index and providing rich visualizations. AVAILABILITYAND IMPLEMENTATION R package scclusteval: https://github.com/crazyhottommy/scclusteval Snakemake workflow: https://github.com/crazyhottommy/pyflow_seuratv3_parameter Tutorial: https://crazyhottommy.github.io/EvaluateSingleCellClustering/.
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Affiliation(s)
- Ming Tang
- FAS Informatics Group, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Yasin Kaymaz
- FAS Informatics Group, Harvard University, Cambridge, MA, USA
| | - Brandon L Logeman
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA
| | | | - Zhengzheng S Liang
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA.,Howard Hughes Medical Institute, Cambridge, MA, USA
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8
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Miller BF, Bambah-Mukku D, Dulac C, Zhuang X, Fan J. Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities. Genome Res 2021; 31:1843-1855. [PMID: 34035045 DOI: 10.1101/gr.271288.120] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 05/13/2021] [Indexed: 11/24/2022]
Abstract
Recent technological advances have enabled spatially resolved measurements of expression profiles for hundreds to thousands of genes in fixed tissues at single-cell resolution. However, scalable computational analysis methods able to take into consideration the inherent 3D spatial organization of cell types and nonuniform cellular densities within tissues are still lacking. To address this, we developed MERINGUE, a computational framework based on spatial auto-correlation and cross-correlation analysis to identify genes with spatially heterogeneous expression patterns, infer putative cell-cell communication, and perform spatially informed cell clustering in 2D and 3D in a density-agnostic manner using spatially resolved transcriptomics data. We applied MERINGUE to a variety of spatially resolved transcriptomics datasets including multiplexed error-robust fluorescence in situ hybridization (MERFISH), spatial transcriptomics, Slide-Seq, and aligned in situ hybridization (ISH) data. We anticipate that such statistical analysis of spatially resolved transcriptomics data will facilitate our understanding of the interplay between cell state and spatial organization in tissue development and disease.
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9
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Abbott LF, Bock DD, Callaway EM, Denk W, Dulac C, Fairhall AL, Fiete I, Harris KM, Helmstaedter M, Jain V, Kasthuri N, LeCun Y, Lichtman JW, Littlewood PB, Luo L, Maunsell JHR, Reid RC, Rosen BR, Rubin GM, Sejnowski TJ, Seung HS, Svoboda K, Tank DW, Tsao D, Van Essen DC. The Mind of a Mouse. Cell 2021; 182:1372-1376. [PMID: 32946777 DOI: 10.1016/j.cell.2020.08.010] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Large scientific projects in genomics and astronomy are influential not because they answer any single question but because they enable investigation of continuously arising new questions from the same data-rich sources. Advances in automated mapping of the brain's synaptic connections (connectomics) suggest that the complicated circuits underlying brain function are ripe for analysis. We discuss benefits of mapping a mouse brain at the level of synapses.
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Affiliation(s)
- Larry F Abbott
- Zuckerman Mind, Brain and Behavior Institute, Department of Neuroscience, Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Davi D Bock
- Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | | | - Winfried Denk
- Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Catherine Dulac
- Howard Hughes Medical Institute and Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Adrienne L Fairhall
- Department of Physiology and Biophysics and Computational Neuroscience Center, University of Washington, Seattle, WA, USA
| | - Ila Fiete
- Department of Brain and Cognitive Sciences and McGovern Institute, MIT, Cambridge, MA, USA
| | - Kristen M Harris
- Center for Learning and Memory, Institute for Neuroscience, University of Texas - Austin, Austin, TX, USA
| | - Moritz Helmstaedter
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Viren Jain
- Google Research, Mountain View, CA, USA.
| | - Narayanan Kasthuri
- Argonne National Laboratory and Department of Neurobiology, University of Chicago, Chicago, IL, USA
| | - Yann LeCun
- Courant Institute, Center for Data Science and Center for Neural Science, New York University and Facebook AI Research, New York, NY, USA
| | - Jeff W Lichtman
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
| | - Peter B Littlewood
- Department of Physics and James Franck Institute, University of Chicago, Chicago, IL, USA
| | - Liqun Luo
- Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA, USA
| | - John H R Maunsell
- Department of Neurobiology and Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL, USA
| | - R Clay Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Bruce R Rosen
- Athinoula A. Martinos Center for Biomedical Imaging and Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Gerald M Rubin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Terrence J Sejnowski
- Salk Institute for Biological Studies, La Jolla, CA, USA; Division of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - H Sebastian Seung
- Department of Computer Science and Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - David W Tank
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
| | - Doris Tsao
- Division of Biology and Biological Engineering, Tianqiao and Chrissy Chen Institute for Neuroscience and Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
| | - David C Van Essen
- Neuroscience Department, Washington University School of Medicine, St. Louis, MO, USA
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10
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Isogai Y, Wu Z, Love MI, Ahn MHY, Bambah-Mukku D, Hua V, Farrell K, Dulac C. Multisensory Logic of Infant-Directed Aggression by Males. Cell 2019; 175:1827-1841.e17. [PMID: 30550786 DOI: 10.1016/j.cell.2018.11.032] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [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: 10/28/2017] [Revised: 10/11/2018] [Accepted: 11/20/2018] [Indexed: 12/24/2022]
Abstract
Newborn mice emit signals that promote parenting from mothers and fathers but trigger aggressive responses from virgin males. Although pup-directed attacks by males require vomeronasal function, the specific infant cues that elicit this behavior are unknown. We developed a behavioral paradigm based on reconstituted pup cues and showed that discrete infant morphological features combined with salivary chemosignals elicit robust male aggression. Seven vomeronasal receptors were identified based on infant-mediated activity, and the involvement of two receptors, Vmn2r65 and Vmn2r88, in infant-directed aggression was demonstrated by genetic deletion. Using the activation of these receptors as readouts for biochemical fractionation, we isolated two pheromonal compounds, the submandibular gland protein C and hemoglobins. Unexpectedly, none of the identified vomeronasal receptors and associated cues were specific to pups. Thus, infant-mediated aggression by virgin males relies on the recognition of pup's physical traits in addition to parental and infant chemical cues.
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Affiliation(s)
- Yoh Isogai
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK.
| | - Zheng Wu
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael I Love
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Michael Ho-Young Ahn
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Dhananjay Bambah-Mukku
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vivian Hua
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Karolina Farrell
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London W1T 4JG, UK
| | - Catherine Dulac
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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11
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12
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Moffitt JR, Bambah-Mukku D, Eichhorn SW, Vaughn E, Shekhar K, Perez JD, Rubinstein ND, Hao J, Regev A, Dulac C, Zhuang X. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science 2018; 362:eaau5324. [PMID: 30385464 PMCID: PMC6482113 DOI: 10.1126/science.aau5324] [Citation(s) in RCA: 585] [Impact Index Per Article: 97.5] [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: 06/20/2018] [Accepted: 09/21/2018] [Indexed: 12/23/2022]
Abstract
The hypothalamus controls essential social behaviors and homeostatic functions. However, the cellular architecture of hypothalamic nuclei-including the molecular identity, spatial organization, and function of distinct cell types-is poorly understood. Here, we developed an imaging-based in situ cell-type identification and mapping method and combined it with single-cell RNA-sequencing to create a molecularly annotated and spatially resolved cell atlas of the mouse hypothalamic preoptic region. We profiled ~1 million cells, identified ~70 neuronal populations characterized by distinct neuromodulatory signatures and spatial organizations, and defined specific neuronal populations activated during social behaviors in male and female mice, providing a high-resolution framework for mechanistic investigation of behavior circuits. The approach described opens a new avenue for the construction of cell atlases in diverse tissues and organisms.
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Affiliation(s)
- Jeffrey R Moffitt
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Dhananjay Bambah-Mukku
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Stephen W Eichhorn
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Eric Vaughn
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Karthik Shekhar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
| | - Julio D Perez
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nimrod D Rubinstein
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Junjie Hao
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Aviv Regev
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Koch Institute of Integrative Cancer Biology, Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Catherine Dulac
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
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13
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Abstract
Parenting is a multicomponent social behavior that is essential for the survival of offspring in many species. Despite extensive characterization of individual brain areas involved in parental care, we do not fully understand how discrete aspects of this behavior are orchestrated at the neural circuit level. Recent progress in identifying genetically specified neuronal populations critical for parenting, and the use of genetic and viral tools for circuit-cracking now allow us to deconstruct the underlying circuitry and, thus, to elucidate how different aspects of parental care are controlled. Here we review the latest advances, outline possible organizational principles of parental circuits and discuss future challenges.
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Affiliation(s)
- Johannes Kohl
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA.
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14
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Yao S, Bergan J, Lanjuin A, Dulac C. Oxytocin signaling in the medial amygdala is required for sex discrimination of social cues. eLife 2017; 6:31373. [PMID: 29231812 PMCID: PMC5768418 DOI: 10.7554/elife.31373] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 12/11/2017] [Indexed: 01/30/2023] Open
Abstract
The neural control of social behaviors in rodents requires the encoding of pheromonal cues by the vomeronasal system. Here we show that the typical preference of male mice for females is eliminated in mutants lacking oxytocin, a neuropeptide modulating social behaviors in many species. Ablation of the oxytocin receptor in aromatase-expressing neurons of the medial amygdala (MeA) fully recapitulates the elimination of female preference in males. Further, single-unit recording in the MeA uncovered significant changes in the sensory representation of conspecific cues in the absence of oxytocin signaling. Finally, acute manipulation of oxytocin signaling in adults is sufficient to alter social interaction preferences in males as well as responses of MeA neurons to chemosensory cues. These results uncover the critical role of oxytocin signaling in a molecularly defined neuronal population in order to modulate the behavioral and physiological responses of male mice to females on a moment-to-moment basis.
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Affiliation(s)
- Shenqin Yao
- Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Joseph Bergan
- Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Anne Lanjuin
- Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
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15
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Li Y, Mathis A, Grewe BF, Osterhout JA, Ahanonu B, Schnitzer MJ, Murthy VN, Dulac C. Neuronal Representation of Social Information in the Medial Amygdala of Awake Behaving Mice. Cell 2017; 171:1176-1190.e17. [PMID: 29107332 PMCID: PMC5731476 DOI: 10.1016/j.cell.2017.10.015] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/27/2017] [Accepted: 10/11/2017] [Indexed: 12/16/2022]
Abstract
The medial amygdala (MeA) plays a critical role in processing species- and sex-specific signals that trigger social and defensive behaviors. However, the principles by which this deep brain structure encodes social information is poorly understood. We used a miniature microscope to image the Ca2+ dynamics of large neural ensembles in awake behaving mice and tracked the responses of MeA neurons over several months. These recordings revealed spatially intermingled subsets of MeA neurons with distinct temporal dynamics. The encoding of social information in the MeA differed between males and females and relied on information from both individual cells and neuronal populations. By performing long-term Ca2+ imaging across different social contexts, we found that sexual experience triggers lasting and sex-specific changes in MeA activity, which, in males, involve signaling by oxytocin. These findings reveal basic principles underlying the brain's representation of social information and its modulation by intrinsic and extrinsic factors.
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Affiliation(s)
- Ying Li
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA; Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Alexander Mathis
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Benjamin F Grewe
- Howard Hughes Medical Institute, CNC Program, James H. Clark Center Biomedical Engineering & Sciences, Stanford University, Stanford, CA, USA
| | - Jessica A Osterhout
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA; Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Biafra Ahanonu
- Howard Hughes Medical Institute, CNC Program, James H. Clark Center Biomedical Engineering & Sciences, Stanford University, Stanford, CA, USA
| | - Mark J Schnitzer
- Howard Hughes Medical Institute, CNC Program, James H. Clark Center Biomedical Engineering & Sciences, Stanford University, Stanford, CA, USA
| | - Venkatesh N Murthy
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Catherine Dulac
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA; Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA.
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16
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Bendesky A, Kwon YM, Lassance JM, Lewarch CL, Yao S, Peterson BK, He MX, Dulac C, Hoekstra HE. The genetic basis of parental care evolution in monogamous mice. Nature 2017; 544:434-439. [PMID: 28424518 PMCID: PMC5600873 DOI: 10.1038/nature22074] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/16/2017] [Indexed: 12/15/2022]
Abstract
Parental care is essential for the survival of mammals, yet the mechanisms underlying its evolution remain largely unknown. Here we show that two sister species of mice, Peromyscus polionotus and P. maniculatus, have large and heritable differences in parental behaviour. Using quantitative genetics, we identify 12 genomic regions that affect parental care, eight of which have sex-specific effects, suggesting that parental care can evolve independently in males and females. Furthermore, some regions affect parental care broadly, whereas others affect specific behaviours, such as nest building. Of the genes linked to differences in nest-building behaviour, vasopressin is differentially expressed in the hypothalamus of the two species, with increased levels associated with less nest building. Using pharmacology in Peromyscus and chemogenetics in Mus, we show that vasopressin inhibits nest building but not other parental behaviours. Together, our results indicate that variation in an ancient neuropeptide contributes to interspecific differences in parental care.
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Affiliation(s)
- Andres Bendesky
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Young-Mi Kwon
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jean-Marc Lassance
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Caitlin L Lewarch
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Shenqin Yao
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Brant K Peterson
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Meng Xiao He
- Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Catherine Dulac
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Hopi E Hoekstra
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Graduate Program in Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA.,Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA
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17
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Abstract
Social interactions are essential for animals to reproduce, defend their territory, and raise their young. The conserved nature of social behaviors across animal species suggests that the neural pathways underlying the motivation for, and the execution of, specific social responses are also maintained. Modern tools of neuroscience have offered new opportunities for dissecting the molecular and neural mechanisms controlling specific social responses. We will review here recent insights into the neural circuits underlying a particularly fascinating and important form of social interaction, that of parental care. We will discuss how these findings open new avenues to deconstruct infant-directed behavioral control in males and females, and to help understand the neural basis of parenting in a variety of animal species, including humans. Please also see the video abstract here.
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Affiliation(s)
- Johannes Kohl
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, London, UK
| | - Anita E. Autry
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Center for Brain Science, Harvard University, Cambridge, MA, USA
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18
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19
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Renier N, Adams EL, Kirst C, Wu Z, Azevedo R, Kohl J, Autry AE, Kadiri L, Umadevi Venkataraju K, Zhou Y, Wang VX, Tang CY, Olsen O, Dulac C, Osten P, Tessier-Lavigne M. Mapping of Brain Activity by Automated Volume Analysis of Immediate Early Genes. Cell 2016; 165:1789-1802. [PMID: 27238021 DOI: 10.1016/j.cell.2016.05.007] [Citation(s) in RCA: 483] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/31/2016] [Accepted: 05/01/2016] [Indexed: 11/26/2022]
Abstract
Understanding how neural information is processed in physiological and pathological states would benefit from precise detection, localization, and quantification of the activity of all neurons across the entire brain, which has not, to date, been achieved in the mammalian brain. We introduce a pipeline for high-speed acquisition of brain activity at cellular resolution through profiling immediate early gene expression using immunostaining and light-sheet fluorescence imaging, followed by automated mapping and analysis of activity by an open-source software program we term ClearMap. We validate the pipeline first by analysis of brain regions activated in response to haloperidol. Next, we report new cortical regions downstream of whisker-evoked sensory processing during active exploration. Last, we combine activity mapping with axon tracing to uncover new brain regions differentially activated during parenting behavior. This pipeline is widely applicable to different experimental paradigms, including animal species for which transgenic activity reporters are not readily available.
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Affiliation(s)
- Nicolas Renier
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Eliza L Adams
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Christoph Kirst
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Zhuhao Wu
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Ricardo Azevedo
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Johannes Kohl
- Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Anita E Autry
- Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | | | - Kannan Umadevi Venkataraju
- Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA; Certerra, Cold Spring Harbor, NY 11724, USA
| | - Yu Zhou
- Department of Radiology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Victoria X Wang
- Department of Radiology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Cheuk Y Tang
- Department of Radiology, Mount Sinai School of Medicine, New York, NY 10029, USA
| | - Olav Olsen
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Center for Brain Science, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Pavel Osten
- Cold Spring Harbor Laboratories, Cold Spring Harbor, NY 11724, USA
| | - Marc Tessier-Lavigne
- Laboratory of Brain Development and Repair, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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20
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Perez JD, Rubinstein ND, Dulac C. New Perspectives on Genomic Imprinting, an Essential and Multifaceted Mode of Epigenetic Control in the Developing and Adult Brain. Annu Rev Neurosci 2016; 39:347-84. [PMID: 27145912 DOI: 10.1146/annurev-neuro-061010-113708] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mammalian evolution entailed multiple innovations in gene regulation, including the emergence of genomic imprinting, an epigenetic regulation leading to the preferential expression of a gene from its maternal or paternal allele. Genomic imprinting is highly prevalent in the brain, yet, until recently, its central roles in neural processes have not been fully appreciated. Here, we provide a comprehensive survey of adult and developmental brain functions influenced by imprinted genes, from neural development and wiring to synaptic function and plasticity, energy balance, social behaviors, emotions, and cognition. We further review the widespread identification of parental biases alongside monoallelic expression in brain tissues, discuss their potential roles in dosage regulation of key neural pathways, and suggest possible mechanisms underlying the dynamic regulation of imprinting in the brain. This review should help provide a better understanding of the significance of genomic imprinting in the normal and pathological brain of mammals including humans.
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Affiliation(s)
- Julio D Perez
- Department of Molecular and Cellular Biology, Harvard University, Howard Hughes Medical Institute, Cambridge, Massachusetts 02138;
| | - Nimrod D Rubinstein
- Department of Molecular and Cellular Biology, Harvard University, Howard Hughes Medical Institute, Cambridge, Massachusetts 02138;
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Harvard University, Howard Hughes Medical Institute, Cambridge, Massachusetts 02138;
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21
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Abstract
The broad diversity of cell types within vertebrates arises from a unique genetic blueprint by combining intrinsic cellular information with developmental and other extrinsic signals. Lying at the interface between cellular signals and the DNA is the chromatin, a dynamic nucleoprotein complex that helps to mediate gene regulation. The most basic subunit of chromatin, the nucleosome, consists of DNA wrapped around histones, a set of proteins that play crucial roles as scaffolding molecules and regulators of gene expression. Growing evidence indicates that canonical histones are commonly replaced by protein variants before and during cellular transitions. We highlight exciting new results suggesting that histone variants are essential players in the control of cellular plasticity during development and in the adult nervous system.
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Affiliation(s)
- Stephen W Santoro
- Neuroscience Program, Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA.
| | - Catherine Dulac
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
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22
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Perez JD, Rubinstein ND, Fernandez DE, Santoro SW, Needleman LA, Ho-Shing O, Choi JJ, Zirlinger M, Chen SK, Liu JS, Dulac C. Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain. eLife 2015; 4:e07860. [PMID: 26140685 PMCID: PMC4512258 DOI: 10.7554/elife.07860] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/02/2015] [Indexed: 12/14/2022] Open
Abstract
The maternal and paternal genomes play different roles in mammalian brains as a result of genomic imprinting, an epigenetic regulation leading to differential expression of the parental alleles of some genes. Here we investigate genomic imprinting in the cerebellum using a newly developed Bayesian statistical model that provides unprecedented transcript-level resolution. We uncover 160 imprinted transcripts, including 41 novel and independently validated imprinted genes. Strikingly, many genes exhibit parentally biased--rather than monoallelic--expression, with different magnitudes according to age, organ, and brain region. Developmental changes in parental bias and overall gene expression are strongly correlated, suggesting combined roles in regulating gene dosage. Finally, brain-specific deletion of the paternal, but not maternal, allele of the paternally-biased Bcl-x, (Bcl2l1) results in loss of specific neuron types, supporting the functional significance of parental biases. These findings reveal the remarkable complexity of genomic imprinting, with important implications for understanding the normal and diseased brain.
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Affiliation(s)
- Julio D Perez
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Nimrod D Rubinstein
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | | | - Stephen W Santoro
- Neuroscience Program, Department of Zoology and Physiology, University of Wyoming, Laramie, United States
| | - Leigh A Needleman
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Olivia Ho-Shing
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - John J Choi
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | | | | | - Jun S Liu
- Department of Statistics, Harvard University, Cambridge, United States
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
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23
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Abstract
Parental care, including feeding and protection of young, is essential for the survival as well as mental and physical well-being of the offspring. A large variety of parental behaviors has been described across species and sexes, raising fascinating questions about how animals identify the young and how brain circuits drive and modulate parental displays in males and females. Recent studies have begun to uncover a striking antagonistic interplay between brain systems underlying parental care and infant-directed aggression in both males and females, as well as a large range of intrinsic and environmentally driven neural modulation and plasticity. Improved understanding of the neural control of parental interactions in animals should provide novel insights into the complex issue of human parental care in both health and disease.
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Affiliation(s)
- Catherine Dulac
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
| | - Lauren A O'Connell
- FAS Center for System Biology, Harvard University, Cambridge, MA 02138, USA
| | - Zheng Wu
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
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24
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Chalfin L, Dayan M, Levy DR, Austad SN, Miller RA, Iraqi FA, Dulac C, Kimchi T. Mapping ecologically relevant social behaviours by gene knockout in wild mice. Nat Commun 2014; 5:4569. [DOI: 10.1038/ncomms5569] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 07/01/2014] [Indexed: 11/10/2022] Open
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25
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Abstract
Animal–animal recognition within, and across species, is essential for predator avoidance and social interactions. Despite its essential role in orchestrating responses to animal cues, basic principles of information processing by the vomeronasal system are still unknown. The medial amygdala (MeA) occupies a central position in the vomeronasal pathway, upstream of hypothalamic centers dedicated to defensive and social responses. We have characterized sensory responses in the mouse MeA and uncovered emergent properties that shed new light onto the transformation of vomeronasal information into sex- and species-specific responses. In particular, we show that the MeA displays a degree of stimulus selectivity and a striking sexually dimorphic sensory representation that are not observed in the upstream relay of the accessory olfactory bulb (AOB). Furthermore, our results demonstrate that the development of sexually dimorphic circuits in the MeA requires steroid signaling near the time of puberty to organize the functional representation of sensory stimuli. DOI:http://dx.doi.org/10.7554/eLife.02743.001 Many animals emit and detect chemicals known as pheromones to communicate with other members of their own species. Animals also rely on chemical signals from other species to warn them, for example, that a predator is nearby. Many of these chemical signals—which are present in sweat, tears, urine, and saliva—are detected by a structure called the vomeronasal organ, which is located at the base of the nasal cavity. When this organ detects a particular chemical signal, it broadcasts this information to a network of brain regions that generates an appropriate behavioral response. Two structures within this network, the accessory olfactory bulb and the medial amygdala, play an important role in modifying this signal before it reaches its final destination—a region of the brain called the hypothalamus. Activation of the hypothalamus by the signal triggers changes in the animal's behavior. Although the anatomical details of this pathway have been widely studied, it is not clear how information is actually transmitted along it. Now, Bergan et al. have provided insights into this process by recording signals in the brains of anesthetized mice exposed to specific stimuli. Whereas neurons in the accessory olfactory bulb responded similarly in male and female mice, those in the medial amygdala showed a preference for female urine in male mice, and a preference for male urine in the case of females. This is the first direct demonstration of differences in sensory processing in the brains of male and female mammals. These differences are thought to result from the actions of sex hormones, particularly estrogen, on brain circuits during development. Consistent with this, neurons in the medial amygdala of male mice with reduced levels of estrogen showed a reduced preference for female urine compared to control males. Similarly, female mice that had been previously exposed to high levels of estrogen as pups showed a reduced preference for male urine compared to controls. In addition to increasing understanding of how chemical signals—including pheromones—influence the responses of rodents to other animals, the work of Bergan et al. has provided clues to the neural mechanisms that underlie sex-specific differences in behaviors. DOI:http://dx.doi.org/10.7554/eLife.02743.002
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Affiliation(s)
- Joseph F Bergan
- Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Yoram Ben-Shaul
- School of Medicine, Department of Medical Neurobiology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Catherine Dulac
- Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
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Abstract
Animal-animal recognition within, and across species, is essential for predator avoidance and social interactions. Despite its essential role in orchestrating responses to animal cues, basic principles of information processing by the vomeronasal system are still unknown. The medial amygdala (MeA) occupies a central position in the vomeronasal pathway, upstream of hypothalamic centers dedicated to defensive and social responses. We have characterized sensory responses in the mouse MeA and uncovered emergent properties that shed new light onto the transformation of vomeronasal information into sex- and species-specific responses. In particular, we show that the MeA displays a degree of stimulus selectivity and a striking sexually dimorphic sensory representation that are not observed in the upstream relay of the accessory olfactory bulb (AOB). Furthermore, our results demonstrate that the development of sexually dimorphic circuits in the MeA requires steroid signaling near the time of puberty to organize the functional representation of sensory stimuli.DOI: http://dx.doi.org/10.7554/eLife.02743.001.
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Affiliation(s)
- Joseph F Bergan
- Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Yoram Ben-Shaul
- School of Medicine, Department of Medical Neurobiology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Catherine Dulac
- Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
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Abstract
We have identified a replication-independent histone variant, Hist2h2be (referred to herein as H2be), which is expressed exclusively by olfactory chemosensory neurons. Levels of H2BE are heterogeneous among olfactory neurons, but stereotyped according to the identity of the co-expressed olfactory receptor (OR). Gain- and loss-of-function experiments demonstrate that changes in H2be expression affect olfactory function and OR representation in the adult olfactory epithelium. We show that H2BE expression is reduced by sensory activity and that it promotes neuronal cell death, such that inactive olfactory neurons display higher levels of the variant and shorter life spans. Post-translational modifications (PTMs) of H2BE differ from those of the canonical H2B, consistent with a role for H2BE in altering transcription. We propose a physiological function for H2be in modulating olfactory neuron population dynamics to adapt the OR repertoire to the environment. DOI:http://dx.doi.org/10.7554/eLife.00070.001 A hallmark of the nervous systems of all mammals is their capacity to undergo changes in function that are shaped by experience. This phenomenon underlies the ability of our brains to develop properly and to learn, and also enables various sensory systems—including the visual, auditory and olfactory systems—to perform optimally in diverse environments. In most mammals, a high-functioning olfactory system is essential for carrying out tasks that are crucial for survival, such as finding food, avoiding predators and mating. In general, sensory systems have to decipher only a limited collection of stimuli, but the olfactory system must be able to process information from thousands of distinct odors that are found in a given environment and which may vary dramatically from one environment to the next. Each odor-sensing neuron in the nose of a mammal contains just one kind of odorant receptor protein, although mammalian genomes typically encode 1000 or so different kinds of receptor proteins. This suggests that it might be possible to ‘tune’ the olfactory system to a particular environment by changing the relative numbers of the different types of neurons. Indeed, it is known that the relative abundance of each type of odor-sensing neuron changes with age and experience, and that these changes might be caused by variations in the lifespans of the neurons. Although our understanding of how these experience-dependent changes are orchestrated at the molecular level is far from complete, it is clear that adjustments in the levels of specific gene products is necessary. But how do experiences alter the levels of gene products to give rise to lasting changes in the brain? One hypothesis is that changes to a structure called chromatin are key to this process: chromatin is an assembly of DNA molecules, which are quite long, and organizing proteins, mostly proteins known as histones, that together form a compact structure that can fit inside the nucleus of a cell. Santoro and Dulac have now discovered a previously uncharacterized protein called H2BE that is found only in the odor-sensing neurons of mice. H2BE is a variant of a protein called H2B, which is a well-known histone. They found that in odor-sensing neurons, H2BE replaces H2B to an extent that depends on the amount of activity experienced by the neuron: H2BE is nearly undetectable in highly active neurons, but almost completely replaces H2B in neurons that are inactive. Moreover, genetic manipulation showed that the deletion of H2BE significantly extended the lifespan of neurons, whereas elevated levels of H2BE shortened their lifespan. These findings reveal an extraordinary process that involves inactive odor-sensing neurons being depleted relative to active ones over time. How does H2BE, which differs from H2B by just five amino acids, cause such dramatic changes in neuronal composition? One hint comes from evidence that these amino acids disrupt interactions between chromatin and ‘effector’ proteins, which modulate gene activity. Consistent with this, Santoro and Dulac have found that the replacement of H2B by H2BE strongly alters gene activity, although the precise mechanism by which these alterations regulate neuronal lifespans remains to be determined. Understanding this process in detail, and exploring if similar phenomena are involved in experience-dependent changes elsewhere in the nervous system, are fascinating areas of future research. DOI:http://dx.doi.org/10.7554/eLife.00070.002
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Affiliation(s)
- Stephen W Santoro
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology , Harvard University , Cambridge , United States
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29
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Abstract
The vomeronasal organ (VNO) has a key role in mediating the social and defensive responses of many terrestrial vertebrates to species- and sex-specific chemosignals. More than 250 putative pheromone receptors have been identified in the mouse VNO, but the nature of the signals detected by individual VNO receptors has not yet been elucidated. To gain insight into the molecular logic of VNO detection leading to mating, aggression or defensive responses, we sought to uncover the response profiles of individual vomeronasal receptors to a wide range of animal cues. Here we describe the repertoire of behaviourally and physiologically relevant stimuli detected by a large number of individual vomeronasal receptors in mice, and define a global map of vomeronasal signal detection. We demonstrate that the two classes (V1R and V2R) of vomeronasal receptors use fundamentally different strategies to encode chemosensory information, and that distinct receptor subfamilies have evolved towards the specific recognition of certain animal groups or chemical structures. The association of large subsets of vomeronasal receptors with cognate, ethologically and physiologically relevant stimuli establishes the molecular foundation of vomeronasal information coding, and opens new avenues for further investigating the neural mechanisms underlying behaviour specificity.
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Affiliation(s)
- Yoh Isogai
- Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA
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30
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Abstract
Determination of the molecular architecture of synapses requires nanoscopic image resolution and specific molecular recognition, a task that has so far defied many conventional imaging approaches. Here, we present a superresolution fluorescence imaging method to visualize the molecular architecture of synapses in the brain. Using multicolor, three-dimensional stochastic optical reconstruction microscopy, the distributions of synaptic proteins can be measured with nanometer precision. Furthermore, the wide-field, volumetric imaging method enables high-throughput, quantitative analysis of a large number of synapses from different brain regions. To demonstrate the capabilities of this approach, we have determined the organization of ten protein components of the presynaptic active zone and the postsynaptic density. Variations in synapse morphology, neurotransmitter receptor composition, and receptor distribution were observed both among synapses and across different brain regions. Combination with optogenetics further allowed molecular events associated with synaptic plasticity to be resolved at the single-synapse level.
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Affiliation(s)
- Adish Dani
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Bo Huang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
- Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138
| | - Joseph Bergan
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Catherine Dulac
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Correspondence: ,
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
- Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138
- Correspondence: ,
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Rawson NE, Lischka FW, Yee KK, Peters AZ, Tucker ES, Meechan DW, Zirlinger M, Maynard TM, Burd GB, Dulac C, Pevny L, LaMantia AS. Specific mesenchymal/epithelial induction of olfactory receptor, vomeronasal, and gonadotropin-releasing hormone (GnRH) neurons. Dev Dyn 2010; 239:1723-38. [PMID: 20503368 DOI: 10.1002/dvdy.22315] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We asked whether specific mesenchymal/epithelial (M/E) induction generates olfactory receptor neurons (ORNs), vomeronasal neurons (VRNs), and gonadotropin-releasing hormone (GnRH) neurons, the major neuron classes associated with the olfactory epithelium (OE). To assess specificity of M/E-mediated neurogenesis, we compared the influence of frontonasal mesenchyme on frontonasal epithelium, which becomes the OE, with that of the forelimb bud. Despite differences in position, morphogenetic and cytogenic capacity, both mesenchymal tissues support neurogenesis, expression of several signaling molecules and neurogenic transcription factors in the frontonasal epithelium. Only frontonasal mesenchyme, however, supports OE-specific patterning and activity of a subset of signals and factors associated with OE differentiation. Moreover, only appropriate pairing of frontonasal epithelial and mesenchymal partners yields ORNs, VRNs, and GnRH neurons. Accordingly, the position and molecular identity of specialized frontonasal epithelia and mesenchyme early in gestation and subsequent inductive interactions specify the genesis and differentiation of peripheral chemosensory and neuroendocrine neurons.
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Affiliation(s)
- N E Rawson
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, USA
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32
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Abstract
Genomic imprinting results in preferential gene expression from paternally versus maternally inherited chromosomes. We used a genome-wide approach to uncover sex-specific parent-of-origin allelic effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex. Moreover, analysis of the cortex and hypothalamus identified 347 autosomal genes with sex-specific imprinting features. In the hypothalamus, sex-specific imprinted genes were mostly found in females, which suggests parental influence over the hypothalamic function of daughters. We show that interleukin-18, a gene linked to diseases with sex-specific prevalence, is subject to complex, regional, and sex-specific parental effects in the brain. Parent-of-origin effects thus provide new avenues for investigation of sexual dimorphism in brain function and disease.
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Affiliation(s)
- Christopher Gregg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jiangwen Zhang
- FAS Research Computing, Harvard University, Cambridge, MA 02138, USA
| | - James E. Butler
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Catherine Dulac
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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33
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Abstract
The characteristics of epigenetic control, including the potential for long-lasting, stable effects on gene expression that outlive an initial transient signal, could be of singular importance for post-mitotic neurons, which are subject to changes with short- to long-lasting influence on their activity and connectivity. Persistent changes in chromatin structure are thought to contribute to mechanisms of epigenetic inheritance. Recent advances in chromatin biology offer new avenues to investigate regulatory mechanisms underlying long-lasting changes in neurons, with direct implications for the study of brain function, behaviour and diseases.
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Affiliation(s)
- Catherine Dulac
- Howard Hughes Medical Institute, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA.
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Gregg C, Zhang J, Weissbourd B, Luo S, Schroth GP, Haig D, Dulac C. High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science 2010; 329:643-8. [PMID: 20616232 PMCID: PMC3005244 DOI: 10.1126/science.1190830] [Citation(s) in RCA: 448] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Genomic imprinting results in preferential expression of the paternal or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain. This approach uncovered parent-of-origin allelic effects of more than 1300 loci. We identified parental bias in the expression of individual genes and of specific transcript isoforms, with differences between brain regions. Many imprinted genes are expressed in neural systems associated with feeding and motivated behaviors, and parental biases preferentially target genetic pathways governing metabolism and cell adhesion. We observed a preferential maternal contribution to gene expression in the developing brain and a major paternal contribution in the adult brain. Thus, parental expression bias emerges as a major mode of epigenetic regulation in the brain.
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Affiliation(s)
- Christopher Gregg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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35
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Tucker ES, Lehtinen MK, Maynard T, Zirlinger M, Dulac C, Rawson N, Pevny L, Lamantia AS. Proliferative and transcriptional identity of distinct classes of neural precursors in the mammalian olfactory epithelium. Development 2010; 137:2471-81. [PMID: 20573694 DOI: 10.1242/dev.049718] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Neural precursors in the developing olfactory epithelium (OE) give rise to three major neuronal classes - olfactory receptor (ORNs), vomeronasal (VRNs) and gonadotropin releasing hormone (GnRH) neurons. Nevertheless, the molecular and proliferative identities of these precursors are largely unknown. We characterized two precursor classes in the olfactory epithelium (OE) shortly after it becomes a distinct tissue at midgestation in the mouse: slowly dividing self-renewing precursors that express Meis1/2 at high levels, and rapidly dividing neurogenic precursors that express high levels of Sox2 and Ascl1. Precursors expressing high levels of Meis genes primarily reside in the lateral OE, whereas precursors expressing high levels of Sox2 and Ascl1 primarily reside in the medial OE. Fgf8 maintains these expression signatures and proliferative identities. Using electroporation in the wild-type embryonic OE in vitro as well as Fgf8, Sox2 and Ascl1 mutant mice in vivo, we found that Sox2 dose and Meis1 - independent of Pbx co-factors - regulate Ascl1 expression and the transition from lateral to medial precursor state. Thus, we have identified proliferative characteristics and a dose-dependent transcriptional network that define distinct OE precursors: medial precursors that are most probably transit amplifying neurogenic progenitors for ORNs, VRNs and GnRH neurons, and lateral precursors that include multi-potent self-renewing OE neural stem cells.
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Affiliation(s)
- Eric S Tucker
- Department of Cell and Molecular Physiology, University of North Carolina at Chapel Hill, NC 27599, USA
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36
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Dulac C, Rizzolatti G. Neurobiology of behavior. Curr Opin Neurobiol 2009; 19:634-6. [PMID: 19896830 DOI: 10.1016/j.conb.2009.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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37
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Choi PS, Zakhary L, Choi WY, Caron S, Alvarez-Saavedra E, Miska EA, McManus M, Harfe B, Giraldez AJ, Horvitz HR, Schier AF, Dulac C. Members of the miRNA-200 family regulate olfactory neurogenesis. Neuron 2008; 57:41-55. [PMID: 18184563 PMCID: PMC2204047 DOI: 10.1016/j.neuron.2007.11.018] [Citation(s) in RCA: 203] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 09/10/2007] [Accepted: 11/14/2007] [Indexed: 12/27/2022]
Abstract
MicroRNAs (miRNAs) are highly expressed in vertebrate neural tissues, but the contribution of specific miRNAs to the development and function of different neuronal populations is still largely unknown. We report that miRNAs are required for terminal differentiation of olfactory precursors in both mouse and zebrafish but are dispensable for proper function of mature olfactory neurons. The repertoire of miRNAs expressed in olfactory tissues contains over 100 distinct miRNAs. A subset, including the miR-200 family, shows high olfactory enrichment and expression patterns consistent with a role during olfactory neurogenesis. Loss of function of the miR-200 family phenocopies the terminal differentiation defect observed in absence of all miRNA activity in olfactory progenitors. Our data support the notion that vertebrate tissue differentiation is controlled by conserved subsets of organ-specific miRNAs in both mouse and zebrafish and provide insights into control mechanisms underlying olfactory differentiation in vertebrates.
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Affiliation(s)
- Philip S Choi
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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38
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Kimchi T, Xu J, Dulac C. A functional circuit underlying male sexual behaviour in the female mouse brain. Nature 2007; 448:1009-14. [PMID: 17676034 DOI: 10.1038/nature06089] [Citation(s) in RCA: 293] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Accepted: 07/17/2007] [Indexed: 11/09/2022]
Abstract
In mice, pheromone detection is mediated by the vomeronasal organ and the main olfactory epithelium. Male mice that are deficient for Trpc2, an ion channel specifically expressed in VNO neurons and essential for VNO sensory transduction, are impaired in sex discrimination and male-male aggression. We report here that Trpc2-/- female mice show a reduction in female-specific behaviour, including maternal aggression and lactating behaviour. Strikingly, mutant females display unique characteristics of male sexual and courtship behaviours such as mounting, pelvic thrust, solicitation, anogenital olfactory investigation, and emission of complex ultrasonic vocalizations towards male and female conspecific mice. The same behavioural phenotype is observed after VNO surgical removal in adult animals, and is not accompanied by disruption of the oestrous cycle and sex hormone levels. These findings suggest that VNO-mediated pheromone inputs act in wild-type females to repress male behaviour and activate female behaviours. Moreover, they imply that functional neuronal circuits underlying male-specific behaviours exist in the normal female mouse brain.
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Affiliation(s)
- Tali Kimchi
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138, USA
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39
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Abstract
Molecular approaches and genetic manipulations have provided novel insights into the processing of pheromone-mediated information by the olfactory and vomeronasal systems of mammals. We will review and discuss the specific contribution of each of the two chemosensory systems that ensure specific behavioral responses to conspecific animals.
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Affiliation(s)
- C Dulac
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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40
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Affiliation(s)
- Catherine Dulac
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA.
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41
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Yamagata M, Weiner JA, Dulac C, Roth KA, Sanes JR. Labeled lines in the retinotectal system: markers for retinorecipient sublaminae and the retinal ganglion cell subsets that innervate them. Mol Cell Neurosci 2006; 33:296-310. [PMID: 16978878 DOI: 10.1016/j.mcn.2006.08.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2006] [Revised: 07/31/2006] [Accepted: 08/01/2006] [Indexed: 11/27/2022] Open
Abstract
Axons of retinal ganglion cells (RGCs) carry visual information to the brain. In most vertebrates, the major synaptic target of RGCs is the optic tectum. In the chick, RGC axons form synapses in just 4 of 16 histologically recognizable laminae (the retinorecipient laminae [RRLs]), and arbors of individual RGCs are confined to a single RRL. To analyze the development and function of these parallel pathways, markers are required that selectively label them. Here, we have identified molecular markers for individual RRLs and for RGCs that project to them. Some of the markers may mediate or modulate signaling through the separate pathways: neuropeptides (substance P, neuromedin B, somatostatin-I and -II) and their receptors (substance P receptor), neurotransmitter synthetic enzymes (choline acetyltransferase) and the corresponding receptors (acetylcholine receptor beta2) and calcium-binding proteins (parvalbumin and calbindin). Other markers are adhesive proteins that could mediate selective connectivity of RGC subsets within specific RRLs (cadherin-7, cadherin-11, reelin and neuropilin-1). We further show that RGC subsets whose axons project to specific RRLs are heterogeneous with respect to the retinal sublaminae within which their dendrites arborize. Our results define laminar-specified circuits from retina to brain and support a model in which RGCs transmit information from multiple sources to single central laminae, where it can be integrated.
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Affiliation(s)
- Masahito Yamagata
- Department of Anatomy and Neurobiology, Washington University Medical School, St. Louis, MO 63110, USA
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42
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Abstract
Natural scents are mixtures of tens to hundreds of individual chemical compounds. While previous studies have investigated how the olfactory bulb responds to simple odorants, how the nose and the brain respond to and interpret complex mixtures is less clear. In a paper in this issue of Neuron, Lin et al. combined gas chromatography and intrinsic signal imaging to examine the responses of individual olfactory bulb glomeruli in the mouse to natural odors and their component parts.
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Affiliation(s)
- Catherine Dulac
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Wagner S, Gresser AL, Torello AT, Dulac C. A multireceptor genetic approach uncovers an ordered integration of VNO sensory inputs in the accessory olfactory bulb. Neuron 2006; 50:697-709. [PMID: 16731509 DOI: 10.1016/j.neuron.2006.04.033] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [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: 02/24/2006] [Revised: 04/17/2006] [Accepted: 04/26/2006] [Indexed: 11/29/2022]
Abstract
Pheromone detection by the vomeronasal organ (VNO) is thought to rely on activation of specific receptors from the V1R and V2R gene families, but the central representation of pheromone receptor activation remains poorly understood. We generated transgenic mouse lines in which projections from multiple populations of VNO neurons, each expressing a distinct V1R, are differentially labeled with fluorescent proteins. This approach revealed that inputs from neurons expressing closely related V1Rs intermingle within shared, spatially conserved domains of the accessory olfactory bulb (AOB). Mitral cell-glomerular connectivity was examined by injecting intracellular dyes into AOB mitral cells and monitoring dendritic contacts with genetically labeled glomeruli. We show that individual mitral cells extend dendrites to glomeruli associated with different, but likely closely related, V1Rs. This organization differs from the labeled line of OR signaling in the main olfactory system and suggests that integration of information may already occur at the level of the AOB.
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Affiliation(s)
- Shlomo Wagner
- Department of Neurobiology, Hebrew University, Jerusalem 91904, Israel.
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Abstract
Major histocompatibility complex (MHC) molecules have been implicated in a number of non-immune roles in the central nervous system, particularly in synaptic development and plasticity. The discovery of M10 (50% sequence identity to classical MHC molecules) proteins expressed in the vomeronasal organ adds to the list of non-traditional roles of MHC homologs. M10 molecules associate with the V2R class of vomeronasal receptors, a family of G-protein coupled receptors thought to function as pheromone receptors. Recent studies showing that classical MHC-binding peptides activate V2R-expressing neurons offer tempting clues that M10s might participate directly in the recognition of pheromone ligands, but M10 proteins do not bind to these peptides with significant affinity. Instead of presenting MHC-binding peptides, M10s might function as molecular chaperones to V2R receptors or more generally as modulators of neuronal function, as demonstrated elsewhere in the brain for classical MHC molecules.
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Affiliation(s)
- Rich Olson
- Division of Biology, Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA
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45
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Yoon H, Enquist LW, Dulac C. Olfactory inputs to hypothalamic neurons controlling reproduction and fertility. Cell 2006; 123:669-82. [PMID: 16290037 DOI: 10.1016/j.cell.2005.08.039] [Citation(s) in RCA: 345] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Revised: 07/29/2005] [Accepted: 08/26/2005] [Indexed: 11/19/2022]
Abstract
In order to gain insight into sensory processing modulating reproductive behavioral and endocrine changes, we have aimed at identifying afferent pathways to neurons synthesizing luteinizing hormone-releasing hormone (LHRH, also known as gonadotropin-releasing hormone [GnRH]), a key neurohormone of reproduction. Injection of conditional pseudorabies virus into the brain of an LHRH::CRE mouse line led to the identification of neuronal networks connected to LHRH neurons. Remarkably, and in contrast to established notions on the nature of LHRH neuronal inputs, our data identify major olfactory projection pathways originating from a discrete population of olfactory sensory neurons but fail to document any synaptic connectivity with the vomeronasal system. Accordingly, chemosensory modulation of LHRH neuronal activity and mating behavior are dramatically impaired in absence of olfactory function, while they appear unaffected in mouse mutants lacking vomeronasal signaling. Further visualization of afferents to LHRH neurons across the brain offers a unique opportunity to uncover complex polysynaptic circuits modulating reproduction and fertility.
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Affiliation(s)
- Hayan Yoon
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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47
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Abstract
Pheromones have evolved as a discrete class of secreted chemicals that signal the sex and social status of an individual and that promote coordinated motor programs and endocrine changes essential for breeding and aggression. The highly reproducible and species-specific character of the response to pheromones offers a unique experimental system to elucidate the coding of sexual and social information within the brain, and to provide new insights into the molecular and cellular basis of information processing leading to specific behaviours.
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Affiliation(s)
- Catherine Dulac
- Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
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48
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Abstract
Drosophila male courtship offers a unique experimental system to uncover the molecular and neural basis of genetically preprogrammed behavior. In this issue of Cell, Demir and Dickson (2005) and Stockinger et al. (2005) demonstrate that this behavior relies on a single splicing of the fruitless transcript, and on a specific olfactory-based neuronal circuit.
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Affiliation(s)
- Catherine Dulac
- Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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49
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Olson R, Huey-Tubman KE, Dulac C, Bjorkman PJ. Structure of a pheromone receptor-associated MHC molecule with an open and empty groove. PLoS Biol 2005; 3:e257. [PMID: 16089503 PMCID: PMC1174912 DOI: 10.1371/journal.pbio.0030257] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2005] [Accepted: 05/18/2005] [Indexed: 11/24/2022] Open
Abstract
Neurons in the murine vomeronasal organ (VNO) express a family of class Ib major histocompatibility complex (MHC) proteins (M10s) that interact with the V2R class of VNO receptors. This interaction may play a direct role in the detection of pheromonal cues that initiate reproductive and territorial behaviors. The crystal structure of M10.5, an M10 family member, is similar to that of classical MHC molecules. However, the M10.5 counterpart of the MHC peptide-binding groove is open and unoccupied, revealing the first structure of an empty class I MHC molecule. Similar to empty MHC molecules, but unlike peptide-filled MHC proteins and non-peptide–binding MHC homologs, M10.5 is thermally unstable, suggesting that its groove is normally occupied. However, M10.5 does not bind endogenous peptides when expressed in mammalian cells or when offered a mixture of class I–binding peptides. The F pocket side of the M10.5 groove is open, suggesting that ligands larger than 8–10-mer class I–binding peptides could fit by extending out of the groove. Moreover, variable residues point up from the groove helices, rather than toward the groove as in classical MHC structures. These data suggest that M10s are unlikely to provide specific recognition of class I MHC–binding peptides, but are consistent with binding to other ligands, including proteins such as the V2Rs. MHC-like protein M10.5 is expressed in the vomeronasal organ. The structure does not bind endogenous class I-binding peptides, but is thought to interact with a larger V2R pheromone receptor.
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Affiliation(s)
- Rich Olson
- 1 Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Kathryn E Huey-Tubman
- 1 Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- 2 Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, United States of America
| | - Catherine Dulac
- 3 Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, United States of America
| | - Pamela J Bjorkman
- 1 Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- 2 Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California, United States of America
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50
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Cloutier JF, Sahay A, Chang EC, Tessier-Lavigne M, Dulac C, Kolodkin AL, Ginty DD. Differential requirements for semaphorin 3F and Slit-1 in axonal targeting, fasciculation, and segregation of olfactory sensory neuron projections. J Neurosci 2005; 24:9087-96. [PMID: 15483127 PMCID: PMC6730055 DOI: 10.1523/jneurosci.2786-04.2004] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The formation of precise stereotypic connections in sensory systems is critical for defining accurate internal representations of the external world; however, the molecular mechanisms underlying the formation of sensory maps are poorly understood. Here, we examine the roles of two structurally unrelated repulsive guidance cues, semaphorin 3F (Sema3F) and Slit-1, in olfactory sensory axon fasciculation, targeting, and segregation. Using sema3F-/- mice, we show that Sema3F is critical for vomeronasal sensory neuron axonal fasciculation and for segregation of these sensory afferents from the main olfactory system; however, Sema3F plays only a minor role in targeting of apical vomeronasal neuron axons to the anterior accessory olfactory bulb (AOB). In addition, we show that Sema3F is required for lamina-specific targeting of olfactory sensory axons within the main olfactory system. In contrast to Sema3F, Slit-1 is dispensable for fasciculation of basal vomeronasal neuron axons but is critical for targeting these axons to the posterior AOB. These results reveal discrete and complementary roles for secreted semaphorins and slits in axonal targeting, fasciculation, and segregation of olfactory sensory neuron projections.
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Affiliation(s)
- Jean-François Cloutier
- Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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