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Kiefer L, Gaudin S, Rajkumar SM, Servito GIF, Langen J, Mui MH, Nawsheen S, Canzio D. Tuning cohesin trajectories enables differential readout of the Pcdhα cluster across neurons. Science 2024; 385:eadm9802. [PMID: 39052779 DOI: 10.1126/science.adm9802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/16/2024] [Indexed: 07/27/2024]
Abstract
Expression of Protocadherin (Pcdh) genes is critical to the generation of neuron identity and wiring of the nervous system. Pcdhα genes are arranged in clusters and exhibit a range of expression profiles, from stochastic to deterministic. Because Pcdhα promoters have high sequence identity and share distal enhancers, how distinct neurons choose which gene to express remains unclear. We show that the interplay between multiple enhancers, epigenetics, and genome folding orchestrates differential readouts of the locus across neurons. The probability of Pcdhα promoter choice depends on enhancer/promoter encounters catalyzed by cohesin, whose extrusion trajectories determine the likelihood that an individual promoter can "escape" heterochromatin-mediated silencing. We propose that tunable locus-specific regulatory elements and cell type-specific cohesin activity underlie the generation of cellular diversity by Pcdh genes.
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Affiliation(s)
- Lea Kiefer
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Simon Gaudin
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biology, Ecole Normale Supérieure de Lyon, 69432 Lyon, France
| | - Sandy M Rajkumar
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gabrielle Isabelle F Servito
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jennifer Langen
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael H Mui
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shayra Nawsheen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniele Canzio
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub Investigator, San Francisco, San Francisco, CA 94158, USA
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2
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Mian Y, Wang L, Keikhosravi A, Guo K, Misteli T, Arda HE, Finn EH. Cell type- and transcription-independent spatial proximity between enhancers and promoters. Mol Biol Cell 2024; 35:ar96. [PMID: 38717453 PMCID: PMC11244156 DOI: 10.1091/mbc.e24-02-0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024] Open
Abstract
Cell type-specific enhancers are critically important for lineage specification. The mechanisms that determine cell-type specificity of enhancer activity, however, are not fully understood. Most current models for how enhancers function invoke physical proximity between enhancer elements and their target genes. Here, we use an imaging-based approach to examine the spatial relationship of cell type-specific enhancers and their target genes with single-cell resolution. Using high-throughput microscopy, we measure the spatial distance from target promoters to their cell type-specific active and inactive enhancers in individual pancreatic cells derived from distinct lineages. We find increased proximity of all promoter-enhancer pairs relative to non-enhancer pairs separated by similar genomic distances. Strikingly, spatial proximity between enhancers and target genes was unrelated to tissue-specific enhancer activity. Furthermore, promoter-enhancer proximity did not correlate with the expression status of target genes. Our results suggest that promoter-enhancer pairs exist in a distinctive chromatin environment but that genome folding is not a universal driver of cell-type specificity in enhancer function.
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Affiliation(s)
- Yasmine Mian
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Li Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Adib Keikhosravi
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Konnie Guo
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - H Efsun Arda
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elizabeth H Finn
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104
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3
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van Velthoven CTJ, Gao Y, Kunst M, Lee C, McMillen D, Chakka AB, Casper T, Clark M, Chakrabarty R, Daniel S, Dolbeare T, Ferrer R, Gloe J, Goldy J, Guzman J, Halterman C, Ho W, Huang M, James K, Nguy B, Pham T, Ronellenfitch K, Thomas ED, Torkelson A, Pagan CM, Kruse L, Dee N, Ng L, Waters J, Smith KA, Tasic B, Yao Z, Zeng H. The transcriptomic and spatial organization of telencephalic GABAergic neuronal types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.18.599583. [PMID: 38948843 PMCID: PMC11212977 DOI: 10.1101/2024.06.18.599583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The telencephalon of the mammalian brain comprises multiple regions and circuit pathways that play adaptive and integrative roles in a variety of brain functions. There is a wide array of GABAergic neurons in the telencephalon; they play a multitude of circuit functions, and dysfunction of these neurons has been implicated in diverse brain disorders. In this study, we conducted a systematic and in-depth analysis of the transcriptomic and spatial organization of GABAergic neuronal types in all regions of the mouse telencephalon and their developmental origins. This was accomplished by utilizing 611,423 single-cell transcriptomes from the comprehensive and high-resolution transcriptomic and spatial cell type atlas for the adult whole mouse brain we have generated, supplemented with an additional single-cell RNA-sequencing dataset containing 99,438 high-quality single-cell transcriptomes collected from the pre- and postnatal developing mouse brain. We present a hierarchically organized adult telencephalic GABAergic neuronal cell type taxonomy of 7 classes, 52 subclasses, 284 supertypes, and 1,051 clusters, as well as a corresponding developmental taxonomy of 450 clusters across different ages. Detailed charting efforts reveal extraordinary complexity where relationships among cell types reflect both spatial locations and developmental origins. Transcriptomically and developmentally related cell types can often be found in distant and diverse brain regions indicating that long-distance migration and dispersion is a common characteristic of nearly all classes of telencephalic GABAergic neurons. Additionally, we find various spatial dimensions of both discrete and continuous variations among related cell types that are correlated with gene expression gradients. Lastly, we find that cortical, striatal and some pallidal GABAergic neurons undergo extensive postnatal diversification, whereas septal and most pallidal GABAergic neuronal types emerge simultaneously during the embryonic stage with limited postnatal diversification. Overall, the telencephalic GABAergic cell type taxonomy can serve as a foundational reference for molecular, structural and functional studies of cell types and circuits by the entire community.
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Affiliation(s)
| | - Yuan Gao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Scott Daniel
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Windy Ho
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Mike Huang
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Beagan Nguy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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4
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Fan C, Xing X, Murphy SJH, Poursine-Laurent J, Schmidt H, Parikh BA, Yoon J, Choudhary MNK, Saligrama N, Piersma SJ, Yokoyama WM, Wang T. Cis-regulatory evolution of the recently expanded Ly49 gene family. Nat Commun 2024; 15:4839. [PMID: 38844462 PMCID: PMC11156856 DOI: 10.1038/s41467-024-48990-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Comparative genomics has revealed the rapid expansion of multiple gene families involved in immunity. Members within each gene family often evolved distinct roles in immunity. However, less is known about the evolution of their epigenome and cis-regulation. Here we systematically profile the epigenome of the recently expanded murine Ly49 gene family that mainly encode either inhibitory or activating surface receptors on natural killer cells. We identify a set of cis-regulatory elements (CREs) for activating Ly49 genes. In addition, we show that in mice, inhibitory and activating Ly49 genes are regulated by two separate sets of proximal CREs, likely resulting from lineage-specific losses of CRE activity. Furthermore, we find that some Ly49 genes are cross-regulated by the CREs of other Ly49 genes, suggesting that the Ly49 family has begun to evolve a concerted cis-regulatory mechanism. Collectively, we demonstrate the different modes of cis-regulatory evolution for a rapidly expanding gene family.
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Affiliation(s)
- Changxu Fan
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Samuel J H Murphy
- Department of Neurology, Washington University School of Medicine, St. Louis, 63110, USA
- Medical Scientist Training Program, Washington University School of Medicine, St. Louis, 63110, USA
| | - Jennifer Poursine-Laurent
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA
| | - Heather Schmidt
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Bijal A Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Jeesang Yoon
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA
| | - Mayank N K Choudhary
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA
| | - Naresha Saligrama
- Department of Neurology, Washington University School of Medicine, St. Louis, 63110, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, 63110, USA
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, 63110, USA
- Center for Brain Immunology and Glia (BIG), Washington University School of Medicine, St. Louis, 63110, USA
| | - Sytse J Piersma
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, 63110, USA.
| | - Wayne M Yokoyama
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, 63110, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, 63110, USA.
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, 63110, USA.
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, 63110, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, 63110, USA.
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5
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Rufenacht KE, Asson AJ, Hossain K, Santoro SW. The influence of olfactory experience on the birthrates of olfactory sensory neurons with specific odorant receptor identities. Genesis 2024; 62:e23611. [PMID: 38888221 PMCID: PMC11189617 DOI: 10.1002/dvg.23611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/20/2024]
Abstract
Olfactory sensory neurons (OSNs) are one of a few neuron types that are generated continuously throughout life in mammals. The persistence of olfactory sensory neurogenesis beyond early development has long been thought to function simply to replace neurons that are lost or damaged through exposure to environmental insults. The possibility that olfactory sensory neurogenesis may also serve an adaptive function has received relatively little consideration, largely due to the assumption that the generation of new OSNs is stochastic with respect to OSN subtype, as defined by the single odorant receptor gene that each neural precursor stochastically chooses for expression out of hundreds of possibilities. Accordingly, the relative birthrates of different OSN subtypes are predicted to be constant and impervious to olfactory experience. This assumption has been called into question, however, by evidence that the birthrates of specific OSN subtypes can be selectively altered by manipulating olfactory experience through olfactory deprivation, enrichment, and conditioning paradigms. Moreover, studies of recovery of the OSN population following injury provide further evidence that olfactory sensory neurogenesis may not be strictly stochastic with respect to subtype. Here we review this evidence and consider mechanistic and functional implications of the prospect that specific olfactory experiences can regulate olfactory sensory neurogenesis rates in a subtype-selective manner.
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Affiliation(s)
- Karlin E Rufenacht
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Alexa J Asson
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kawsar Hossain
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Stephen W Santoro
- Department of Pediatrics, Section of Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado, USA
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6
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Wu H, Zhang J, Jian F, Chen JP, Zheng Y, Tan L, Sunney Xie X. Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice. Nat Methods 2024; 21:974-982. [PMID: 38622459 PMCID: PMC11166570 DOI: 10.1038/s41592-024-02239-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 03/07/2024] [Indexed: 04/17/2024]
Abstract
The simultaneous measurement of three-dimensional (3D) genome structure and gene expression of individual cells is critical for understanding a genome's structure-function relationship, yet this is challenging for existing methods. Here we present 'Linking mRNA to Chromatin Architecture (LiMCA)', which jointly profiles the 3D genome and transcriptome with exceptional sensitivity and from low-input materials. Combining LiMCA and our high-resolution scATAC-seq assay, METATAC, we successfully characterized chromatin accessibility, as well as paired 3D genome structures and gene expression information, of individual developing olfactory sensory neurons. We expanded the repertoire of known olfactory receptor (OR) enhancers and discovered unexpected rules of their dynamics: OR genes and their enhancers are most accessible during early differentiation. Furthermore, we revealed the dynamic spatial relationship between ORs and enhancers behind stepwise OR expression. These findings offer valuable insights into how 3D connectivity of ORs and enhancers dynamically orchestrate the 'one neuron-one receptor' selection process.
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Affiliation(s)
- Honggui Wu
- Biomedical Pioneering Innovation Center (BIOPIC), and School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
| | - Jiankun Zhang
- Biomedical Pioneering Innovation Center (BIOPIC), and School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
| | - Fanchong Jian
- Biomedical Pioneering Innovation Center (BIOPIC), and School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jinxin Phaedo Chen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Yinghui Zheng
- Biomedical Pioneering Innovation Center (BIOPIC), and School of Life Sciences, Peking University, Beijing, China
| | - Longzhi Tan
- Department of Neurobiology, Stanford University, Stanford, CA, USA.
| | - X Sunney Xie
- Biomedical Pioneering Innovation Center (BIOPIC), and School of Life Sciences, Peking University, Beijing, China.
- Changping Laboratory, Beijing, China.
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7
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Kanata E, Duffié R, Schulz EG. Establishment and maintenance of random monoallelic expression. Development 2024; 151:dev201741. [PMID: 38813842 PMCID: PMC11166465 DOI: 10.1242/dev.201741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
This Review elucidates the regulatory principles of random monoallelic expression by focusing on two well-studied examples: the X-chromosome inactivation regulator Xist and the olfactory receptor gene family. Although the choice of a single X chromosome or olfactory receptor occurs in different developmental contexts, common gene regulatory principles guide monoallelic expression in both systems. In both cases, an event breaks the symmetry between genetically and epigenetically identical copies of the gene, leading to the expression of one single random allele, stabilized through negative feedback control. Although many regulatory steps that govern the establishment and maintenance of monoallelic expression have been identified, key pieces of the puzzle are still missing. We provide an overview of the current knowledge and models for the monoallelic expression of Xist and olfactory receptors. We discuss their similarities and differences, and highlight open questions and approaches that could guide the study of other monoallelically expressed genes.
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Affiliation(s)
- Eleni Kanata
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Rachel Duffié
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Edda G. Schulz
- Systems Epigenetics, Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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8
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Tomikawa J. Potential roles of inter-chromosomal interactions in cell fate determination. Front Cell Dev Biol 2024; 12:1397807. [PMID: 38774644 PMCID: PMC11106443 DOI: 10.3389/fcell.2024.1397807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/23/2024] [Indexed: 05/24/2024] Open
Abstract
Mammalian genomic DNA is packed in a small nucleus, and its folding and organization in the nucleus are critical for gene regulation and cell fate determination. In interphase, chromosomes are compartmentalized into certain nuclear spaces and territories that are considered incompatible with each other. The regulation of gene expression is influenced by the epigenetic characteristics of topologically associated domains and A/B compartments within chromosomes (intrachromosomal). Previously, interactions among chromosomes detected via chromosome conformation capture-based methods were considered noise or artificial errors. However, recent studies based on newly developed ligation-independent methods have shown that inter-chromosomal interactions play important roles in gene regulation. This review summarizes the recent understanding of spatial genomic organization in mammalian interphase nuclei and discusses the potential mechanisms that determine cell identity. In addition, this review highlights the potential role of inter-chromosomal interactions in early mouse development.
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Affiliation(s)
- Junko Tomikawa
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
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9
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Ordway AJ, Helt RN, Johnston RJ. Transcriptional priming and chromatin regulation during stochastic cell fate specification. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230046. [PMID: 38432315 PMCID: PMC10909510 DOI: 10.1098/rstb.2023.0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/19/2024] [Indexed: 03/05/2024] Open
Abstract
Stochastic cell fate specification, in which a cell chooses between two or more fates with a set probability, diversifies cell subtypes in development. Although this is a vital process across species, a common mechanism for these cell fate decisions remains elusive. This review examines two well-characterized stochastic cell fate decisions to identify commonalities between their developmental programmes. In the fly eye, two subtypes of R7 photoreceptors are specified by the stochastic ON/OFF expression of a transcription factor, spineless. In the mouse olfactory system, olfactory sensory neurons (OSNs) randomly select to express one copy of an olfactory receptor (OR) gene out of a pool of 2800 alleles. Despite the differences in these sensory systems, both stochastic fate choices rely on the dynamic interplay between transcriptional priming, chromatin regulation and terminal gene expression. The coupling of transcription and chromatin modifications primes gene loci in undifferentiated neurons, enabling later expression during terminal differentiation. Here, we compare these mechanisms, examine broader implications for gene regulation during development and posit key challenges moving forward. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Alison J. Ordway
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Rina N. Helt
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Robert J. Johnston
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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10
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Yusuf N, Monahan K. Epigenetic programming of stochastic olfactory receptor choice. Genesis 2024; 62:e23593. [PMID: 38562011 PMCID: PMC11003729 DOI: 10.1002/dvg.23593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/01/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
The mammalian sense of smell relies upon a vast array of receptor proteins to detect odorant compounds present in the environment. The proper deployment of these receptor proteins in olfactory sensory neurons is orchestrated by a suite of epigenetic processes that remodel the olfactory genes in differentiating neuronal progenitors. The goal of this review is to elucidate the central role of gene regulatory processes acting in neuronal progenitors of olfactory sensory neurons that lead to a singular expression of an odorant receptor in mature olfactory sensory neurons. We begin by describing the principal features of odorant receptor gene expression in mature olfactory sensory neurons. Next, we delineate our current understanding of how these features emerge from multiple gene regulatory mechanisms acting in neuronal progenitors. Finally, we close by discussing the key gaps in our understanding of how these regulatory mechanisms work and how they interact with each other over the course of differentiation.
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Affiliation(s)
- Nusrath Yusuf
- Division of Life Sciences-Molecular Biology and Biochemistry Department, Rutgers University-New Brunswick, New Brunswick, New Jersey, USA
| | - Kevin Monahan
- Division of Life Sciences-Molecular Biology and Biochemistry Department, Rutgers University-New Brunswick, New Brunswick, New Jersey, USA
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11
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Hirota J. Molecular mechanisms of differentiation and class choice of olfactory sensory neurons. Genesis 2024; 62:e23587. [PMID: 38454646 DOI: 10.1002/dvg.23587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/10/2024] [Accepted: 01/29/2024] [Indexed: 03/09/2024]
Abstract
The sense of smell is intricately linked to essential animal behaviors necessary for individual survival and species preservation. During vertebrate evolution, odorant receptors (ORs), responsible for detecting odor molecules, have evolved to adapt to changing environments, transitioning from aquatic to terrestrial habitats and accommodating increasing complex chemical environments. These evolutionary pressures have given rise to the largest gene family in vertebrate genomes. Vertebrate ORs are phylogenetically divided into two major classes; class I and class II. Class I OR genes, initially identified in fish and frog, have persisted across vertebrate species. On the other hand, class II OR genes are unique to terrestrial animals, accounting for ~90% of mammalian OR genes. In mice, each olfactory sensory neuron (OSN) expresses a single functional allele of a single OR gene from either the class I or class II OR repertoire. This one neuron-one receptor rule is established through two sequential steps: specification of OR class and subsequent exclusive OR expression from the corresponding OR class. Consequently, OSNs acquire diverse neuronal identities during the process of OSN differentiation, enabling animals to detect a wide array of odor molecules. This review provides an overview of the OSN differentiation process through which OSN diversity is achieved, primarily using the mouse as a model animal.
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Affiliation(s)
- Junji Hirota
- Department of Life Science and Technology, Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Center for Integrative Biosciences, Tokyo Institute of Technology, Yokohama, Japan
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12
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Ishii C, Nakano H, Higashiseto R, Ooki Y, Umemura M, Takahashi S, Takahashi Y. Nescient helix-loop-helix 1 (Nhlh1) is a novel activating transcription factor 5 (ATF5) target gene in olfactory and vomeronasal sensory neurons in mice. Cell Tissue Res 2024; 396:85-94. [PMID: 38388750 DOI: 10.1007/s00441-024-03871-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Activating transcription factor 5 (ATF5) is a transcription factor that belongs to the cAMP-response element-binding protein/ATF family and is essential for the differentiation and survival of sensory neurons in mouse olfactory organs. However, transcriptional target genes for ATF5 have yet to be identified. In the present study, chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-qPCR) experiments were performed to verify ATF5 target genes in the main olfactory epithelium and vomeronasal organ in the postnatal pups. ChIP-qPCR was conducted using hemagglutinin (HA)-tagged ATF5 knock-in olfactory organs. The results obtained demonstrated that ATF5-HA fusion proteins bound to the CCAAT/enhancer-binding protein-ATF response element (CARE) site in the enhancer region of nescient helix-loop-helix 1 (Nhlh1), a transcription factor expressed in differentiating olfactory and vomeronasal sensory neurons. Nhlh1 mRNA expression was downregulated in ATF5-deficient (ATF5-/-) olfactory organs. The LIM/homeobox protein transcription factor Lhx2 co-localized with ATF5 in the nuclei of olfactory and vomeronasal sensory neurons and bound to the homeodomain site proximal to the CARE site in the Nhlh1 gene. The CARE region of the Nhlh1 gene was enriched by the active enhancer marker, acetyl-histone H3 (Lys27). The present study identified Nhlh1 as a novel target gene for ATF5 in murine olfactory organs. ATF5 may upregulate Nhlh1 expression in concert with Lhx2, thereby promoting the differentiation of olfactory and vomeronasal sensory neurons.
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Affiliation(s)
- Chiharu Ishii
- Laboratory of Environmental Molecular Physiology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1, Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Haruo Nakano
- Laboratory of Environmental Molecular Physiology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1, Horinouchi, Hachioji, Tokyo 192-0392, Japan.
| | - Riko Higashiseto
- Laboratory of Environmental Molecular Physiology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1, Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yusaku Ooki
- Laboratory of Environmental Molecular Physiology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1, Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Mariko Umemura
- Laboratory of Environmental Molecular Physiology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1, Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Shigeru Takahashi
- Laboratory of Environmental Molecular Physiology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1, Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Yuji Takahashi
- Laboratory of Environmental Molecular Physiology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1, Horinouchi, Hachioji, Tokyo 192-0392, Japan
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13
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Destain H, Prahlad M, Kratsios P. Maintenance of neuronal identity in C. elegans and beyond: Lessons from transcription and chromatin factors. Semin Cell Dev Biol 2024; 154:35-47. [PMID: 37438210 PMCID: PMC10592372 DOI: 10.1016/j.semcdb.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/14/2023]
Abstract
Neurons are remarkably long-lived, non-dividing cells that must maintain their functional features (e.g., electrical properties, chemical signaling) for extended periods of time - decades in humans. How neurons accomplish this incredible feat is poorly understood. Here, we review recent advances, primarily in the nematode C. elegans, that have enhanced our understanding of the molecular mechanisms that enable post-mitotic neurons to maintain their functionality across different life stages. We begin with "terminal selectors" - transcription factors necessary for the establishment and maintenance of neuronal identity. We highlight new findings on five terminal selectors (CHE-1 [Glass], UNC-3 [Collier/Ebf1-4], LIN-39 [Scr/Dfd/Hox4-5], UNC-86 [Acj6/Brn3a-c], AST-1 [Etv1/ER81]) from different transcription factor families (ZNF, COE, HOX, POU, ETS). We compare the functions of these factors in specific neuron types of C. elegans with the actions of their orthologs in other invertebrate (D. melanogaster) and vertebrate (M. musculus) systems, highlighting remarkable functional conservation. Finally, we reflect on recent findings implicating chromatin-modifying proteins, such as histone methyltransferases and Polycomb proteins, in the control of neuronal terminal identity. Altogether, these new studies on transcription factors and chromatin modifiers not only shed light on the fundamental problem of neuronal identity maintenance, but also outline mechanistic principles of gene regulation that may operate in other long-lived, post-mitotic cell types.
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Affiliation(s)
- Honorine Destain
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Manasa Prahlad
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA; Committee on Development, Regeneration and Stem Cell Biology, University of Chicago, Chicago, IL, USA; Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA; University of Chicago Neuroscience Institute, Chicago, IL, USA.
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14
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Kim S, Morgunova E, Naqvi S, Goovaerts S, Bader M, Koska M, Popov A, Luong C, Pogson A, Swigut T, Claes P, Taipale J, Wysocka J. DNA-guided transcription factor cooperativity shapes face and limb mesenchyme. Cell 2024; 187:692-711.e26. [PMID: 38262408 PMCID: PMC10872279 DOI: 10.1016/j.cell.2023.12.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/23/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024]
Abstract
Transcription factors (TFs) can define distinct cellular identities despite nearly identical DNA-binding specificities. One mechanism for achieving regulatory specificity is DNA-guided TF cooperativity. Although in vitro studies suggest that it may be common, examples of such cooperativity remain scarce in cellular contexts. Here, we demonstrate how "Coordinator," a long DNA motif composed of common motifs bound by many basic helix-loop-helix (bHLH) and homeodomain (HD) TFs, uniquely defines the regulatory regions of embryonic face and limb mesenchyme. Coordinator guides cooperative and selective binding between the bHLH family mesenchymal regulator TWIST1 and a collective of HD factors associated with regional identities in the face and limb. TWIST1 is required for HD binding and open chromatin at Coordinator sites, whereas HD factors stabilize TWIST1 occupancy at Coordinator and titrate it away from HD-independent sites. This cooperativity results in the shared regulation of genes involved in cell-type and positional identities and ultimately shapes facial morphology and evolution.
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Affiliation(s)
- Seungsoo Kim
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Ekaterina Morgunova
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Seppe Goovaerts
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mervenaz Koska
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Christy Luong
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Angela Pogson
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Peter Claes
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium; Department of Human Genetics, KU Leuven, Leuven, Belgium; Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | - Jussi Taipale
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, Sweden; Department of Biochemistry, University of Cambridge, Cambridge, UK; Applied Tumor Genomics Program, University of Helsinki, Helsinki, Finland
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
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15
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Pourmorady AD, Bashkirova EV, Chiariello AM, Belagzhal H, Kodra A, Duffié R, Kahiapo J, Monahan K, Pulupa J, Schieren I, Osterhoudt A, Dekker J, Nicodemi M, Lomvardas S. RNA-mediated symmetry breaking enables singular olfactory receptor choice. Nature 2024; 625:181-188. [PMID: 38123679 PMCID: PMC10765522 DOI: 10.1038/s41586-023-06845-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/07/2023] [Indexed: 12/23/2023]
Abstract
Olfactory receptor (OR) choice provides an extreme example of allelic competition for transcriptional dominance, where every olfactory neuron stably transcribes one of approximately 2,000 or more OR alleles1,2. OR gene choice is mediated by a multichromosomal enhancer hub that activates transcription at a single OR3,4, followed by OR-translation-dependent feedback that stabilizes this choice5,6. Here, using single-cell genomics, we show formation of many competing hubs with variable enhancer composition, only one of which retains euchromatic features and transcriptional competence. Furthermore, we provide evidence that OR transcription recruits enhancers and reinforces enhancer hub activity locally, whereas OR RNA inhibits transcription of competing ORs over distance, promoting transition to transcriptional singularity. Whereas OR transcription is sufficient to break the symmetry between equipotent enhancer hubs, OR translation stabilizes transcription at the prevailing hub, indicating that there may be sequential non-coding and coding mechanisms that are implemented by OR alleles for transcriptional prevalence. We propose that coding OR mRNAs possess non-coding functions that influence nuclear architecture, enhance their own transcription and inhibit transcription from their competitors, with generalizable implications for probabilistic cell fate decisions.
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Affiliation(s)
- Ariel D Pourmorady
- Vagelos College of Physicians and Surgeons, Columbia University New York, New York, NY, USA
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Elizaveta V Bashkirova
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Andrea M Chiariello
- Department of Physics 'Ettore Pancini', University of Naples, and INFN, Napoli, Italy
| | - Houda Belagzhal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Albana Kodra
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, New York, NY, USA
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Rachel Duffié
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Jerome Kahiapo
- Department of Molecular Biology & Biochemistry, Rutgers School of Arts and Sciences, Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Kevin Monahan
- Department of Molecular Biology & Biochemistry, Rutgers School of Arts and Sciences, Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Joan Pulupa
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Ira Schieren
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
| | - Alexa Osterhoudt
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Job Dekker
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Mario Nicodemi
- Department of Physics 'Ettore Pancini', University of Naples, and INFN, Napoli, Italy
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, Brain, and Behavior Institute, Columbia University New York, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, New York, NY, USA.
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16
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Bashkirova EV, Klimpert N, Monahan K, Campbell CE, Osinski J, Tan L, Schieren I, Pourmorady A, Stecky B, Barnea G, Xie XS, Abdus-Saboor I, Shykind BM, Marlin BJ, Gronostajski RM, Fleischmann A, Lomvardas S. Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice. eLife 2023; 12:RP87445. [PMID: 38108811 PMCID: PMC10727497 DOI: 10.7554/elife.87445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023] Open
Abstract
Olfactory receptor (OR) choice represents an example of genetically hardwired stochasticity, where every olfactory neuron expresses one out of ~2000 OR alleles in the mouse genome in a probabilistic, yet stereotypic fashion. Here, we propose that topographic restrictions in OR expression are established in neuronal progenitors by two opposing forces: polygenic transcription and genomic silencing, both of which are influenced by dorsoventral gradients of transcription factors NFIA, B, and X. Polygenic transcription of OR genes may define spatially constrained OR repertoires, among which one OR allele is selected for singular expression later in development. Heterochromatin assembly and genomic compartmentalization of OR alleles also vary across the axes of the olfactory epithelium and may preferentially eliminate ectopically expressed ORs with more dorsal expression destinations from this 'privileged' repertoire. Our experiments identify early transcription as a potential 'epigenetic' contributor to future developmental patterning and reveal how two spatially responsive probabilistic processes may act in concert to establish deterministic, precise, and reproducible territories of stochastic gene expression.
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Affiliation(s)
- Elizaveta V Bashkirova
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Nell Klimpert
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Kevin Monahan
- Department of Biochemistry and Molecular Biology, Rutgers UniversityNewarkUnited States
| | - Christine E Campbell
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Jason Osinski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Longzhi Tan
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Ira Schieren
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Ariel Pourmorady
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Beka Stecky
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Gilad Barnea
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Xiaoliang Sunney Xie
- Beijing Innovation Center for Genomics, Peking UniversityBeijingChina
- Biomedical Pioneering Innovation Center, Peking UniversityBeijingChina
| | - Ishmail Abdus-Saboor
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Benjamin M Shykind
- Prevail Therapeutics- a wholly-owned subsidiary of Eli Lilly and CompanyNew YorkUnited States
| | - Bianca J Marlin
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
| | - Richard M Gronostajski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life SciencesBuffaloUnited States
| | - Alexander Fleischmann
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Stavros Lomvardas
- Zuckerman Mind, Brain, and Behavior Institute, Columbia UniversityNew YorkUnited States
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia UniversityNew YorkUnited States
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17
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Hristov BH, Noble WS, Bertero A. Systematic identification of inter-chromosomal interaction networks supports the existence of RNA factories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558852. [PMID: 37790381 PMCID: PMC10542540 DOI: 10.1101/2023.09.21.558852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Most studies of genome organization have focused on intra-chromosomal (cis) contacts because they harbor key features such as DNA loops and topologically associating domains. Inter-chromosomal (trans) contacts have received much less attention, and tools for interrogating potential biologically relevant trans structures are lacking. Here, we develop a computational framework to identify sets of loci that jointly interact in trans from Hi-C data. This method, trans-C, initiates probabilistic random walks with restarts from a set of seed loci to traverse an input Hi-C contact network, thereby identifying sets of trans-contacting loci. We validate trans-C in three increasingly complex models of established trans contacts: the Plasmodium falciparum var genes, the mouse olfactory receptor "Greek islands", and the human RBM20 cardiac splicing factory. We then apply trans-C to systematically test the hypothesis that genes co-regulated by the same trans-acting element (i.e., a transcription or splicing factor) co-localize in three dimensions to form "RNA factories" that maximize the efficiency and accuracy of RNA biogenesis. We find that many loci with multiple binding sites of the same transcription factor interact with one another in trans, especially those bound by transcription factors with intrinsically disordered domains. Similarly, clustered binding of a subset of RNA binding proteins correlates with trans interaction of the encoding loci. These findings support the existence of trans interacting chromatin domains (TIDs) driven by RNA biogenesis. Trans-C provides an efficient computational framework for studying these and other types of trans interactions, empowering studies of a poorly understood aspect of genome architecture.
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Affiliation(s)
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
| | - Alessandro Bertero
- Molecular Biotechnology Center “Guido Tarone”, Dept. of Molecular Biotechnology and Health Sciences, University of Turin, Torino, Italy
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18
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Bashkirova EV, Klimpert N, Monahan K, Campbell CE, Osinski JM, Tan L, Schieren I, Pourmorady A, Stecky B, Barnea G, Xie XS, Abdus-Saboor I, Shykind B, Jones-Marlin B, Gronostajski RM, Fleischmann A, Lomvardas S. Opposing, spatially-determined epigenetic forces impose restrictions on stochastic olfactory receptor choice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.15.532726. [PMID: 36993168 PMCID: PMC10055043 DOI: 10.1101/2023.03.15.532726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Olfactory receptor (OR) choice represents an example of genetically hardwired stochasticity, where every olfactory neuron expresses one out of ~2000 OR alleles in a probabilistic, yet stereotypic fashion. Here, we propose that topographic restrictions in OR expression are established in neuronal progenitors by two opposing forces: polygenic transcription and genomic silencing, both of which are influenced by dorsoventral gradients of transcription factors NFIA, B, and X. Polygenic transcription of OR genes may define spatially constrained OR repertoires, among which one OR allele is selected for singular expression later in development. Heterochromatin assembly and genomic compartmentalization of OR alleles also vary across the axes of the olfactory epithelium and may preferentially eliminate ectopically expressed ORs with more dorsal expression destinations from this "privileged" repertoire. Our experiments identify early transcription as a potential "epigenetic" contributor to future developmental patterning and reveal how two spatially responsive probabilistic processes may act in concert to establish deterministic, precise, and reproducible territories of stochastic gene expression.
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Affiliation(s)
- Elizaveta V Bashkirova
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Nell Klimpert
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Kevin Monahan
- Department of Biochemistry and Molecular Biology, Rutgers University, NJ, USA
| | - Christine E Campbell
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
| | - Jason M Osinski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
| | - Longzhi Tan
- Department of Bioengineering, Stanford University, CA, USA
| | - Ira Schieren
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Ariel Pourmorady
- Integrated Program in Cellular, Molecular and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Beka Stecky
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Gilad Barnea
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - X Sunnie Xie
- Beijing Innovation Center for Genomics, Peking University, Beijing, China
- Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Ishmail Abdus-Saboor
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Benjamin Shykind
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Bianca Jones-Marlin
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
| | - Richard M Gronostajski
- Department of Biochemistry, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
- Genetics, Genomics, and Bioinformatics Graduate Program, University at Buffalo and New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, NY, USA
| | - Alexander Fleischmann
- Department of Neuroscience, Division of Biology and Medicine and Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA
| | - Stavros Lomvardas
- Zuckerman Mind, Brain, and Behavior Institute, Columbia University, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, Columbia University, New York, NY, 10032, USA
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19
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Brovkina MV, Chapman MA, Holding ML, Clowney EJ. Emergence and influence of sequence bias in evolutionarily malleable, mammalian tandem arrays. BMC Biol 2023; 21:179. [PMID: 37612705 PMCID: PMC10463633 DOI: 10.1186/s12915-023-01673-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/01/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND The radiation of mammals at the extinction of the dinosaurs produced a plethora of new forms-as diverse as bats, dolphins, and elephants-in only 10-20 million years. Behind the scenes, adaptation to new niches is accompanied by extensive innovation in large families of genes that allow animals to contact the environment, including chemosensors, xenobiotic enzymes, and immune and barrier proteins. Genes in these "outward-looking" families are allelically diverse among humans and exhibit tissue-specific and sometimes stochastic expression. RESULTS Here, we show that these tandem arrays of outward-looking genes occupy AT-biased isochores and comprise the "tissue-specific" gene class that lack CpG islands in their promoters. Models of mammalian genome evolution have not incorporated the sharply different functions and transcriptional patterns of genes in AT- versus GC-biased regions. To examine the relationship between gene family expansion, sequence content, and allelic diversity, we use population genetic data and comparative analysis. First, we find that AT bias can emerge during evolutionary expansion of gene families in cis. Second, human genes in AT-biased isochores or with GC-poor promoters experience relatively low rates of de novo point mutation today but are enriched for non-synonymous variants. Finally, we find that isochores containing gene clusters exhibit low rates of recombination. CONCLUSIONS Our analyses suggest that tolerance of non-synonymous variation and low recombination are two forces that have produced the depletion of GC bases in outward-facing gene arrays. In turn, high AT content exerts a profound effect on their chromatin organization and transcriptional regulation.
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Affiliation(s)
- Margarita V Brovkina
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Margaret A Chapman
- Neurosciences Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - E Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA.
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20
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Senapati S, Irshad IU, Sharma AK, Kumar H. Fundamental insights into the correlation between chromosome configuration and transcription. Phys Biol 2023; 20:051002. [PMID: 37467757 DOI: 10.1088/1478-3975/ace8e5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Eukaryotic chromosomes exhibit a hierarchical organization that spans a spectrum of length scales, ranging from sub-regions known as loops, which typically comprise hundreds of base pairs, to much larger chromosome territories that can encompass a few mega base pairs. Chromosome conformation capture experiments that involve high-throughput sequencing methods combined with microscopy techniques have enabled a new understanding of inter- and intra-chromosomal interactions with unprecedented details. This information also provides mechanistic insights on the relationship between genome architecture and gene expression. In this article, we review the recent findings on three-dimensional interactions among chromosomes at the compartment, topologically associating domain, and loop levels and the impact of these interactions on the transcription process. We also discuss current understanding of various biophysical processes involved in multi-layer structural organization of chromosomes. Then, we discuss the relationships between gene expression and genome structure from perturbative genome-wide association studies. Furthermore, for a better understanding of how chromosome architecture and function are linked, we emphasize the role of epigenetic modifications in the regulation of gene expression. Such an understanding of the relationship between genome architecture and gene expression can provide a new perspective on the range of potential future discoveries and therapeutic research.
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Affiliation(s)
- Swayamshree Senapati
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
| | - Inayat Ullah Irshad
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
| | - Ajeet K Sharma
- Department of Physics, Indian Institute of Technology, Jammu, Jammu 181221, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Jammu, Jammu 181221, India
| | - Hemant Kumar
- School of Basic Sciences, Indian Institute of Technology, Bhubaneswar, Argul, Odisha 752050, India
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21
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Zhao Z, Parra OP, Musella F, Scrutton-Alvarado N, Fujita SI, Alber F, Yang Y, Yamada T. Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549737. [PMID: 37503219 PMCID: PMC10370079 DOI: 10.1101/2023.07.19.549737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Dynamic regulation of gene expression plays a key role in establishing the diverse neuronal cell types in the brain. Recent findings in genome biology suggest that three-dimensional (3D) genome organization has important, but mechanistically poorly understood functions in gene transcription. Beyond local genomic interactions between promoters and enhancers, we find that cerebellar granule neurons undergoing differentiation in vivo exhibit striking increases in long-distance genomic interactions between transcriptionally active genomic loci, which are separated by tens of megabases within a chromosome or located on different chromosomes. Among these interactions, we identify a nuclear subcompartment enriched for near-megabase long enhancers and their associated neuronal long genes encoding synaptic or signaling proteins. Neuronal long genes are differentially recruited to this enhancer-dense subcompartment to help shape the transcriptional identities of granule neuron subtypes in the cerebellum. SPRITE analyses of higher-order genomic interactions, together with IGM-based 3D genome modeling and imaging approaches, reveal that the enhancer-dense subcompartment forms prominent nuclear structures, which we term mega-enhancer bodies. These novel nuclear bodies reside in the nuclear periphery, away from other transcriptionally active structures, including nuclear speckles located in the nuclear interior. Together, our findings define additional layers of higher-order 3D genome organization closely linked to neuronal maturation and identity in the brain.
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22
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Chandra A, Yoon S, Michieletto MF, Goldman N, Ferrari EK, Abedi M, Johnson I, Fasolino M, Pham K, Joannas L, Kee BL, Henao-Mejia J, Vahedi G. Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation. Immunity 2023; 56:1451-1467.e12. [PMID: 37263273 PMCID: PMC10979463 DOI: 10.1016/j.immuni.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 06/03/2023]
Abstract
Multi-enhancer hubs are spatial clusters of enhancers present across numerous developmental programs. Here, we studied the functional relevance of these three-dimensional structures in T cell biology. Mathematical modeling identified a highly connected multi-enhancer hub at the Ets1 locus, comprising a noncoding regulatory element that was a hotspot for sequence variation associated with allergic disease in humans. Deletion of this regulatory element in mice revealed that the multi-enhancer connectivity was dispensable for T cell development but required for CD4+ T helper 1 (Th1) differentiation. These mice were protected from Th1-mediated colitis but exhibited overt allergic responses. Mechanistically, the multi-enhancer hub controlled the dosage of Ets1 that was required for CTCF recruitment and assembly of Th1-specific genome topology. Our findings establish a paradigm wherein multi-enhancer hubs control cellular competence to respond to an inductive cue through quantitative control of gene dosage and provide insight into how sequence variation within noncoding elements at the Ets1 locus predisposes individuals to allergic responses.
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Affiliation(s)
- Aditi Chandra
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sora Yoon
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michaël F Michieletto
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Naomi Goldman
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Emily K Ferrari
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maryam Abedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Isabelle Johnson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria Fasolino
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenneth Pham
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leonel Joannas
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Barbara L Kee
- Department of Pathology, Committees on Cancer Biology and Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Jorge Henao-Mejia
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Golnaz Vahedi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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23
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Kahiapo JK, Monahan K. Chromatin Immunoprecipitation from Formaldehyde Cross-Linked Olfactory Sensory Neurons. Methods Mol Biol 2023; 2710:71-82. [PMID: 37688725 DOI: 10.1007/978-1-0716-3425-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2023]
Abstract
Chromatin immunoprecipitation (ChIP) allows a researcher to determine the genomic occupancy of nuclear proteins, providing insight into the roles of transcription factors, chromatin modifiers, histone modifications, and other factors bound to DNA. Protein-DNA interactions are first fixed in vivo by chemical cross-linking, and then a target protein is captured together with any associated DNA by an antibody mediated pull-down. The co-immunoprecipitated DNA can then be assayed by quantitative PCR or deep sequencing. Here, we demonstrate this technique using murine olfactory sensory neurons (OSNs) purified using fluorescence-activated cell sorting (FACS) and antibodies for the ubiquitous chromatin protein CTCF.
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Affiliation(s)
- Jerome K Kahiapo
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Kevin Monahan
- Department of Molecular Biology and Biochemistry, Nelson Biological Laboratories, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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24
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Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
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Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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25
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Nair SJ, Suter T, Wang S, Yang L, Yang F, Rosenfeld MG. Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures. Trends Genet 2022; 38:1019-1047. [PMID: 35811173 PMCID: PMC9474616 DOI: 10.1016/j.tig.2022.05.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/05/2022] [Accepted: 05/31/2022] [Indexed: 02/08/2023]
Abstract
Gene regulation by transcriptional enhancers is the dominant mechanism driving cell type- and signal-specific transcriptional diversity in metazoans. However, over four decades since the original discovery, how enhancers operate in the nuclear space remains largely enigmatic. Recent multidisciplinary efforts combining real-time imaging, genome sequencing, and biophysical strategies provide insightful but conflicting models of enhancer-mediated gene control. Here, we review the discovery and progress in enhancer biology, emphasizing the recent findings that acutely activated enhancers assemble regulatory machinery as mesoscale architectural structures with distinct physical properties. These findings help formulate novel models that explain several mysterious features of the assembly of transcriptional enhancers and the mechanisms of spatial control of gene expression.
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Affiliation(s)
- Sreejith J Nair
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.
| | - Tom Suter
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Susan Wang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Cellular and Molecular Medicine Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lu Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Feng Yang
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Michael G Rosenfeld
- Howard Hughes Medical Institute, Department and School of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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26
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Hussainy M, Korsching SI, Tresch A. Pseudotime analysis reveals novel regulatory factors for multigenic onset and monogenic transition of odorant receptor expression. Sci Rep 2022; 12:16183. [PMID: 36171231 PMCID: PMC9519747 DOI: 10.1038/s41598-022-20106-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 09/08/2022] [Indexed: 12/02/2022] Open
Abstract
During their maturation from horizontal basal stem cells, olfactory sensory neurons (OSNs) are known to select exactly one out of hundreds of olfactory receptors (ORs) and express it on their surface, a process called monogenic selection. Monogenic expression is preceded by a multigenic phase during which several OR genes are expressed in a single OSN. Here, we perform pseudotime analysis of a single cell RNA-Seq dataset of murine olfactory epithelium to precisely align the multigenic and monogenic expression phases with the cell types occurring during OSN differentiation. In combination with motif analysis of OR gene cluster-associated enhancer regions, we identify known and novel transcription (co-)factors (Ebf1, Lhx2, Ldb1, Fos and Ssbp2) and chromatin remodelers (Kdm1a, Eed and Zmynd8) associated with OR expression. The inferred temporal order of their activity suggests novel mechanisms contributing to multigenic OR expression and monogenic selection.
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Affiliation(s)
- Mohammad Hussainy
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany.,Institute of Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Sigrun I Korsching
- Institute of Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Achim Tresch
- Institute of Medical Statistics and Computational Biology, Faculty of Medicine, University of Cologne, Cologne, Germany. .,Cologne Excellence Cluster On Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany. .,Center for Data and Simulation Science, University of Cologne, Cologne, Germany.
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27
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Lin JM, Mitchell TA, Rothstein M, Pehl A, Taroc EZM, Katreddi RR, Parra KE, Zuloaga DG, Simoes-Costa M, Forni PE. Sociosexual behavior requires both activating and repressive roles of Tfap2e/AP-2ε in vomeronasal sensory neurons. eLife 2022; 11:e77259. [PMID: 36111787 PMCID: PMC9525060 DOI: 10.7554/elife.77259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Neuronal identity dictates the position in an epithelium, and the ability to detect, process, and transmit specific signals to specified targets. Transcription factors (TFs) determine cellular identity via direct modulation of genetic transcription and recruiting chromatin modifiers. However, our understanding of the mechanisms that define neuronal identity and their magnitude remain a critical barrier to elucidate the etiology of congenital and neurodegenerative disorders. The rodent vomeronasal organ provides a unique system to examine in detail the molecular mechanisms underlying the differentiation and maturation of chemosensory neurons. Here, we demonstrated that the identity of postmitotic/maturing vomeronasal sensory neurons (VSNs), and vomeronasal-dependent behaviors can be reprogrammed through the rescue of Tfap2e/AP-2ε expression in the Tfap2eNull mice, and partially reprogrammed by inducing ectopic Tfap2e expression in mature apical VSNs. We suggest that the TF Tfap2e can reprogram VSNs bypassing cellular plasticity restrictions, and that it directly controls the expression of batteries of vomeronasal genes.
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Affiliation(s)
- Jennifer M Lin
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Tyler A Mitchell
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Megan Rothstein
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Alison Pehl
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Ed Zandro M Taroc
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Raghu R Katreddi
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
| | - Katherine E Parra
- Department of Psychology, University at Albany, State University of New YorkAlbanyUnited States
| | - Damian G Zuloaga
- Department of Psychology, University at Albany, State University of New YorkAlbanyUnited States
| | - Marcos Simoes-Costa
- Department of Molecular Biology and Genetics, Cornell UniversityIthacaUnited States
| | - Paolo Emanuele Forni
- Department of Biological Sciences, University at Albany, State University of New YorkAlbanyUnited States
- The RNA Institute, University at AlbanyAlbanyUnited States
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28
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Wang IH, Murray E, Andrews G, Jiang HC, Park SJ, Donnard E, Durán-Laforet V, Bear DM, Faust TE, Garber M, Baer CE, Schafer DP, Weng Z, Chen F, Macosko EZ, Greer PL. Spatial transcriptomic reconstruction of the mouse olfactory glomerular map suggests principles of odor processing. Nat Neurosci 2022; 25:484-492. [PMID: 35314823 PMCID: PMC9281876 DOI: 10.1038/s41593-022-01030-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 02/07/2022] [Indexed: 12/14/2022]
Abstract
The olfactory system's ability to detect and discriminate between the vast array of chemicals present in the environment is critical for an animal's survival. In mammals, the first step of this odor processing is executed by olfactory sensory neurons, which project their axons to a stereotyped location in the olfactory bulb (OB) to form glomeruli. The stereotyped positioning of glomeruli in the OB suggests an importance for this organization in odor perception. However, because the location of only a limited subset of glomeruli has been determined, it has been challenging to determine the relationship between glomerular location and odor discrimination. Using a combination of single-cell RNA sequencing, spatial transcriptomics and machine learning, we have generated a map of most glomerular positions in the mouse OB. These observations significantly extend earlier studies and suggest an overall organizational principle in the OB that may be used by the brain to assist in odor decoding.
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Affiliation(s)
- I-Hao Wang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Evan Murray
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Greg Andrews
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Hao-Ching Jiang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sung Jin Park
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Elisa Donnard
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Violeta Durán-Laforet
- Department of Neurobiology and Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Daniel M Bear
- Department of Psychology, Stanford University, Palo Alto, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Palo Alto, CA, USA
| | - Travis E Faust
- Department of Neurobiology and Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Manuel Garber
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christina E Baer
- Sanderson Center for Optical Imaging and Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dorothy P Schafer
- Department of Neurobiology and Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Fei Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Evan Z Macosko
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Paul L Greer
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
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29
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Ruiz Tejada Segura ML, Abou Moussa E, Garabello E, Nakahara TS, Makhlouf M, Mathew LS, Wang L, Valle F, Huang SSY, Mainland JD, Caselle M, Osella M, Lorenz S, Reisert J, Logan DW, Malnic B, Scialdone A, Saraiva LR. A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell. Cell Rep 2022; 38:110547. [PMID: 35320714 PMCID: PMC8995392 DOI: 10.1016/j.celrep.2022.110547] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/26/2022] [Accepted: 03/01/2022] [Indexed: 12/26/2022] Open
Abstract
The sense of smell helps us navigate the environment, but its molecular architecture and underlying logic remain understudied. The spatial location of odorant receptor genes (Olfrs) in the nose is thought to be independent of the structural diversity of the odorants they detect. Using spatial transcriptomics, we create a genome-wide 3D atlas of the mouse olfactory mucosa (OM). Topographic maps of genes differentially expressed in space reveal that both Olfrs and non-Olfrs are distributed in a continuous and overlapping fashion over at least five broad zones in the OM. The spatial locations of Olfrs correlate with the mucus solubility of the odorants they recognize, providing direct evidence for the chromatographic theory of olfaction. This resource resolves the molecular architecture of the mouse OM and will inform future studies on mechanisms underlying Olfr gene choice, axonal pathfinding, patterning of the nervous system, and basic logic for the peripheral representation of smell.
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Affiliation(s)
- Mayra L Ruiz Tejada Segura
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | | | - Elisa Garabello
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany; Physics Department, University of Turin and INFN, Via P. Giuria 1, 10125 Turin, Italy; Department of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Thiago S Nakahara
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | | | | | - Li Wang
- Sidra Medicine, P.O. Box 26999, Doha, Qatar
| | - Filippo Valle
- Physics Department, University of Turin and INFN, Via P. Giuria 1, 10125 Turin, Italy
| | | | - Joel D Mainland
- Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA 19104, USA; Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michele Caselle
- Physics Department, University of Turin and INFN, Via P. Giuria 1, 10125 Turin, Italy
| | - Matteo Osella
- Physics Department, University of Turin and INFN, Via P. Giuria 1, 10125 Turin, Italy
| | - Stephan Lorenz
- Sidra Medicine, P.O. Box 26999, Doha, Qatar; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Johannes Reisert
- Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA 19104, USA
| | - Darren W Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Bettina Malnic
- Department of Biochemistry, University of São Paulo, São Paulo, Brazil
| | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Feodor-Lynen-Strasse 21, 81377 München, Germany; Institute of Functional Epigenetics, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
| | - Luis R Saraiva
- Sidra Medicine, P.O. Box 26999, Doha, Qatar; Monell Chemical Senses Center, 3500 Market Street, Philadelphia, PA 19104, USA; College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar.
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30
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Zazhytska M, Kodra A, Hoagland DA, Frere J, Fullard JF, Shayya H, McArthur NG, Moeller R, Uhl S, Omer AD, Gottesman ME, Firestein S, Gong Q, Canoll PD, Goldman JE, Roussos P, tenOever BR, Jonathan B Overdevest, Lomvardas S. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia. Cell 2022; 185:1052-1064.e12. [PMID: 35180380 PMCID: PMC8808699 DOI: 10.1016/j.cell.2022.01.024] [Citation(s) in RCA: 146] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/06/2021] [Accepted: 01/26/2022] [Indexed: 12/22/2022]
Abstract
SARS-CoV-2 infects less than 1% of cells in the human body, yet it can cause severe damage in a variety of organs. Thus, deciphering the non-cell-autonomous effects of SARS-CoV-2 infection is imperative for understanding the cellular and molecular disruption it elicits. Neurological and cognitive defects are among the least understood symptoms of COVID-19 patients, with olfactory dysfunction being their most common sensory deficit. Here, we show that both in humans and hamsters, SARS-CoV-2 infection causes widespread downregulation of olfactory receptors (ORs) and of their signaling components. This non-cell-autonomous effect is preceded by a dramatic reorganization of the neuronal nuclear architecture, which results in dissipation of genomic compartments harboring OR genes. Our data provide a potential mechanism by which SARS-CoV-2 infection alters the cellular morphology and the transcriptome of cells it cannot infect, offering insight to its systemic effects in olfaction and beyond.
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Affiliation(s)
- Marianna Zazhytska
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Albana Kodra
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Genetics and Development, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Justin Frere
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Hani Shayya
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Genetics and Development, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Natalie G McArthur
- Department of Biological Sciences, Columbia University New York, NY 10027, USA
| | - Rasmus Moeller
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Skyler Uhl
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Arina D Omer
- Baylor Genetics, 2450 Holcombe Blvd, Houston, TX 77021, USA
| | - Max E Gottesman
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Stuart Firestein
- Department of Biological Sciences, Columbia University New York, NY 10027, USA
| | - Qizhi Gong
- Department of Cell Biology and Human Anatomy, School of Medicine, University of California at Davis, Davis, CA 95616, USA
| | - Peter D Canoll
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - James E Goldman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA.
| | - Jonathan B Overdevest
- Department of Otolaryngology, Head and Neck Surgery, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind, and Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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31
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Williams DL, Sikora VM, Hammer MA, Amin S, Brinjikji T, Brumley EK, Burrows CJ, Carrillo PM, Cromer K, Edwards SJ, Emri O, Fergle D, Jenkins MJ, Kaushik K, Maydan DD, Woodard W, Clowney EJ. May the Odds Be Ever in Your Favor: Non-deterministic Mechanisms Diversifying Cell Surface Molecule Expression. Front Cell Dev Biol 2022; 9:720798. [PMID: 35087825 PMCID: PMC8787164 DOI: 10.3389/fcell.2021.720798] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
How does the information in the genome program the functions of the wide variety of cells in the body? While the development of biological organisms appears to follow an explicit set of genomic instructions to generate the same outcome each time, many biological mechanisms harness molecular noise to produce variable outcomes. Non-deterministic variation is frequently observed in the diversification of cell surface molecules that give cells their functional properties, and is observed across eukaryotic clades, from single-celled protozoans to mammals. This is particularly evident in immune systems, where random recombination produces millions of antibodies from only a few genes; in nervous systems, where stochastic mechanisms vary the sensory receptors and synaptic matching molecules produced by different neurons; and in microbial antigenic variation. These systems employ overlapping molecular strategies including allelic exclusion, gene silencing by constitutive heterochromatin, targeted double-strand breaks, and competition for limiting enhancers. Here, we describe and compare five stochastic molecular mechanisms that produce variety in pathogen coat proteins and in the cell surface receptors of animal immune and neuronal cells, with an emphasis on the utility of non-deterministic variation.
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Affiliation(s)
- Donnell L. Williams
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Veronica Maria Sikora
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Max A. Hammer
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Sayali Amin
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Taema Brinjikji
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Emily K. Brumley
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Connor J. Burrows
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Paola Michelle Carrillo
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Kirin Cromer
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Summer J. Edwards
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Olivia Emri
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Fergle
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - M. Jamal Jenkins
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Krishangi Kaushik
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Daniella D. Maydan
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Wrenn Woodard
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - E. Josephine Clowney
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
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Tsukahara T, Brann DH, Pashkovski SL, Guitchounts G, Bozza T, Datta SR. A transcriptional rheostat couples past activity to future sensory responses. Cell 2021; 184:6326-6343.e32. [PMID: 34879231 PMCID: PMC8758202 DOI: 10.1016/j.cell.2021.11.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 10/07/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022]
Abstract
Animals traversing different environments encounter both stable background stimuli and novel cues, which are thought to be detected by primary sensory neurons and then distinguished by downstream brain circuits. Here, we show that each of the ∼1,000 olfactory sensory neuron (OSN) subtypes in the mouse harbors a distinct transcriptome whose content is precisely determined by interactions between its odorant receptor and the environment. This transcriptional variation is systematically organized to support sensory adaptation: expression levels of more than 70 genes relevant to transforming odors into spikes continuously vary across OSN subtypes, dynamically adjust to new environments over hours, and accurately predict acute OSN-specific odor responses. The sensory periphery therefore separates salient signals from predictable background via a transcriptional rheostat whose moment-to-moment state reflects the past and constrains the future; these findings suggest a general model in which structured transcriptional variation within a cell type reflects individual experience.
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Affiliation(s)
- Tatsuya Tsukahara
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - David H Brann
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Stan L Pashkovski
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Thomas Bozza
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
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Ypsilanti AR, Pattabiraman K, Catta-Preta R, Golonzhka O, Lindtner S, Tang K, Jones IR, Abnousi A, Juric I, Hu M, Shen Y, Dickel DE, Visel A, Pennachio LA, Hawrylycz M, Thompson CL, Zeng H, Barozzi I, Nord AS, Rubenstein JL. Transcriptional network orchestrating regional patterning of cortical progenitors. Proc Natl Acad Sci U S A 2021; 118:e2024795118. [PMID: 34921112 PMCID: PMC8713794 DOI: 10.1073/pnas.2024795118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2021] [Indexed: 12/23/2022] Open
Abstract
We uncovered a transcription factor (TF) network that regulates cortical regional patterning in radial glial stem cells. Screening the expression of hundreds of TFs in the developing mouse cortex identified 38 TFs that are expressed in gradients in the ventricular zone (VZ). We tested whether their cortical expression was altered in mutant mice with known patterning defects (Emx2, Nr2f1, and Pax6), which enabled us to define a cortical regionalization TF network (CRTFN). To identify genomic programming underlying this network, we performed TF ChIP-seq and chromatin-looping conformation to identify enhancer-gene interactions. To map enhancers involved in regional patterning of cortical progenitors, we performed assays for epigenomic marks and DNA accessibility in VZ cells purified from wild-type and patterning mutant mice. This integrated approach has identified a CRTFN and VZ enhancers involved in cortical regional patterning in the mouse.
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Affiliation(s)
- Athéna R Ypsilanti
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158;
| | - Kartik Pattabiraman
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Rinaldo Catta-Preta
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95618
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95618
| | - Olga Golonzhka
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158
| | - Ke Tang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Ian R Jones
- Institute for Human Genetics, University of California, San Francisco, CA 94143
- Department of Neurology, University of California, San Francisco, CA 94143
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Ivan Juric
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, CA 94143
- Department of Neurology, University of California, San Francisco, CA 94143
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- School of Natural Sciences, University of California, Merced, CA 95343
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720
| | - Len A Pennachio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720
- Comparative Biochemistry Program, University of California, Berkeley, CA 94720
| | | | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109
| | - Iros Barozzi
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College, London SW7 2AZ, United Kingdom
| | - Alex S Nord
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA 95618
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA 95618
| | - John L Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158;
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34
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Olfactory receptor choice: a case study for gene regulation in a multi-enhancer system. Curr Opin Genet Dev 2021; 72:101-109. [PMID: 34896807 DOI: 10.1016/j.gde.2021.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/25/2021] [Accepted: 11/11/2021] [Indexed: 12/14/2022]
Abstract
The mammalian genome possesses >2000 olfactory receptor (OR) alleles regulated by 63 known OR-Enhancer elements, yet each olfactory sensory neuron (OSN) expresses only a single OR allele. Choreographed changes to OSN nuclear architecture are evidently necessary for OR expression. Additionally, the insulated organization of OR-enhancers around an OR allele is a hallmark of the chosen OR. However, the biology guiding OR choice itself is unclear. Innovations in single-cell and biophysics-based analysis of nuclear architecture are revising previous models of the nucleus to include its dynamic and probabilistic nature. In this review, we ground current knowledge of OR gene regulation in these emerging theories to speculate on mechanisms that may give rise to diverse and singular OR expression.
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35
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Lin J, Huang L, Chen X, Zhang S, Wong KC. DeepMotifSyn: a deep learning approach to synthesize heterodimeric DNA motifs. Brief Bioinform 2021; 23:6370301. [PMID: 34524404 DOI: 10.1093/bib/bbab334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/21/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022] Open
Abstract
The cooperativity of transcription factors (TFs) is a widespread phenomenon in the gene regulation system. However, the interaction patterns between TF binding motifs remain elusive. The recent high-throughput assays, CAP-SELEX, have identified over 600 composite DNA sites (i.e. heterodimeric motifs) bound by cooperative TF pairs. However, there are over 25 000 inferentially effective heterodimeric TFs in the human cells. It is not practically feasible to validate all heterodimeric motifs due to cost and labor. We introduce DeepMotifSyn, a deep learning-based tool for synthesizing heterodimeric motifs from monomeric motif pairs. Specifically, DeepMotifSyn is composed of heterodimeric motif generator and evaluator. The generator is a U-Net-based neural network that can synthesize heterodimeric motifs from aligned motif pairs. The evaluator is a machine learning-based model that can score the generated heterodimeric motif candidates based on the motif sequence features. Systematic evaluations on CAP-SELEX data illustrate that DeepMotifSyn significantly outperforms the current state-of-the-art predictors. In addition, DeepMotifSyn can synthesize multiple heterodimeric motifs with different orientation and spacing settings. Such a feature can address the shortcomings of previous models. We believe DeepMotifSyn is a more practical and reliable model than current predictors on heterodimeric motif synthesis. Contact: kc.w@cityu.edu.hk.
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Affiliation(s)
- Jiecong Lin
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR
| | - Lei Huang
- Hong Kong Institute for Data Science, City University of Hong Kong, Kowloon, Hong Kong SAR
| | - Xingjian Chen
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Shixiong Zhang
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR
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36
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37
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Hobert O. Homeobox genes and the specification of neuronal identity. Nat Rev Neurosci 2021; 22:627-636. [PMID: 34446866 DOI: 10.1038/s41583-021-00497-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2021] [Indexed: 12/27/2022]
Abstract
The enormous diversity of cell types that characterizes any animal nervous system is defined by neuron-type-specific gene batteries that endow cells with distinct anatomical and functional properties. To understand how such cellular diversity is genetically specified, one needs to understand the gene regulatory programmes that control the expression of cell-type-specific gene batteries. The small nervous system of the nematode Caenorhabditis elegans has been comprehensively mapped at the cellular and molecular levels, which has enabled extensive, nervous system-wide explorations into whether there are common underlying mechanisms that specify neuronal cell-type diversity. One principle that emerged from these studies is that transcription factors termed 'terminal selectors' coordinate the expression of individual members of neuron-type-specific gene batteries, thereby assigning unique identities to individual neuron types. Systematic mutant analyses and recent nervous system-wide expression analyses have revealed that one transcription factor family, the homeobox gene family, is broadly used throughout the entire C. elegans nervous system to specify neuronal identity as terminal selectors. I propose that the preponderance of homeobox genes in neuronal identity control is a reflection of an evolutionary trajectory in which an ancestral neuron type was specified by one or more ancestral homeobox genes, and that this functional linkage then duplicated and diversified to generate distinct cell types in an evolving nervous system.
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Affiliation(s)
- Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, NY, USA.
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38
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Lattke M, Goldstone R, Ellis JK, Boeing S, Jurado-Arjona J, Marichal N, MacRae JI, Berninger B, Guillemot F. Extensive transcriptional and chromatin changes underlie astrocyte maturation in vivo and in culture. Nat Commun 2021; 12:4335. [PMID: 34267208 PMCID: PMC8282848 DOI: 10.1038/s41467-021-24624-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/16/2021] [Indexed: 11/08/2022] Open
Abstract
Astrocytes have essential functions in brain homeostasis that are established late in differentiation, but the mechanisms underlying the functional maturation of astrocytes are not well understood. Here we identify extensive transcriptional changes that occur during murine astrocyte maturation in vivo that are accompanied by chromatin remodelling at enhancer elements. Investigating astrocyte maturation in a cell culture model revealed that in vitro-differentiated astrocytes lack expression of many mature astrocyte-specific genes, including genes for the transcription factors Rorb, Dbx2, Lhx2 and Fezf2. Forced expression of these factors in vitro induces distinct sets of mature astrocyte-specific transcripts. Culturing astrocytes in a three-dimensional matrix containing FGF2 induces expression of Rorb, Dbx2 and Lhx2 and improves astrocyte maturity based on transcriptional and chromatin profiles. Therefore, extrinsic signals orchestrate the expression of multiple intrinsic regulators, which in turn induce in a modular manner the transcriptional and chromatin changes underlying astrocyte maturation.
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Affiliation(s)
- Michael Lattke
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, London, UK
| | - Robert Goldstone
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - James K Ellis
- Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Stefan Boeing
- Software Development & Machine Learning Team, The Francis Crick Institute, London, UK
- Bioinformatics & Biostatistics, The Francis Crick Institute, London, UK
| | - Jerónimo Jurado-Arjona
- Institute of Psychiatry, Psychology & Neuroscience, Centre for Developmental Neurobiology, King's College London, London, UK
| | - Nicolás Marichal
- Institute of Psychiatry, Psychology & Neuroscience, Centre for Developmental Neurobiology, King's College London, London, UK
| | - James I MacRae
- Metabolomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Benedikt Berninger
- Institute of Psychiatry, Psychology & Neuroscience, Centre for Developmental Neurobiology, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
- The Francis Crick Institute, London, UK
| | - Francois Guillemot
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, London, UK.
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39
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Glenwinkel L, Taylor SR, Langebeck-Jensen K, Pereira L, Reilly MB, Basavaraju M, Rafi I, Yemini E, Pocock R, Sestan N, Hammarlund M, Miller DM, Hobert O. In silico analysis of the transcriptional regulatory logic of neuronal identity specification throughout the C. elegans nervous system. eLife 2021; 10:e64906. [PMID: 34165430 PMCID: PMC8225391 DOI: 10.7554/elife.64906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 05/07/2021] [Indexed: 12/11/2022] Open
Abstract
The generation of the enormous diversity of neuronal cell types in a differentiating nervous system entails the activation of neuron type-specific gene batteries. To examine the regulatory logic that controls the expression of neuron type-specific gene batteries, we interrogate single cell expression profiles of all 118 neuron classes of the Caenorhabditis elegans nervous system for the presence of DNA binding motifs of 136 neuronally expressed C. elegans transcription factors. Using a phylogenetic footprinting pipeline, we identify cis-regulatory motif enrichments among neuron class-specific gene batteries and we identify cognate transcription factors for 117 of the 118 neuron classes. In addition to predicting novel regulators of neuronal identities, our nervous system-wide analysis at single cell resolution supports the hypothesis that many transcription factors directly co-regulate the cohort of effector genes that define a neuron type, thereby corroborating the concept of so-called terminal selectors of neuronal identity. Our analysis provides a blueprint for how individual components of an entire nervous system are genetically specified.
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Affiliation(s)
- Lori Glenwinkel
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Seth R Taylor
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | | | - Laura Pereira
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Manasa Basavaraju
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Ibnul Rafi
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Eviatar Yemini
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
| | - Roger Pocock
- Biotech Research and Innovation Centre, University of CopenhagenCopenhagenDenmark
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash UniversityMelbourneAustralia
| | - Nenad Sestan
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - Marc Hammarlund
- Department of Neurobiology, Yale University School of MedicineNew HavenUnited States
- Department of Genetics, Yale University School of MedicineNew HavenUnited States
| | - David M Miller
- Department of Cell and Developmental Biology, Vanderbilt University School of MedicineNashvilleUnited States
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical InstituteNew YorkUnited States
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40
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Shah A, Ratkowski M, Rosa A, Feinstein P, Bozza T. Olfactory expression of trace amine-associated receptors requires cooperative cis-acting enhancers. Nat Commun 2021; 12:3797. [PMID: 34145232 PMCID: PMC8213819 DOI: 10.1038/s41467-021-23824-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 05/18/2021] [Indexed: 11/28/2022] Open
Abstract
Olfactory sensory neurons express a large family of odorant receptors (ORs) and a small family of trace amine-associated receptors (TAARs). While both families are subject to so-called singular expression (expression of one allele of one gene), the mechanisms underlying TAAR gene choice remain obscure. Here, we report the identification of two conserved sequence elements in the mouse TAAR cluster (T-elements) that are required for TAAR gene expression. We observed that cell-type-specific expression of a TAAR-derived transgene required either T-element. Moreover, deleting either element reduced or abolished expression of a subset of TAAR genes, while deleting both elements abolished olfactory expression of all TAARs in cis with the mutation. The T-elements exhibit several features of known OR enhancers but also contain highly conserved, unique sequence motifs. Our data demonstrate that TAAR gene expression requires two cooperative cis-acting enhancers and suggest that ORs and TAARs share similar mechanisms of singular expression.
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Affiliation(s)
- Ami Shah
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Madison Ratkowski
- Department of Neurobiology, Northwestern University, Evanston, IL, USA
| | - Alessandro Rosa
- The Graduate Center Programs in Biochemistry, Biology and CUNY Neuroscience Collaborative, New York, NY, USA
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Paul Feinstein
- The Graduate Center Programs in Biochemistry, Biology and CUNY Neuroscience Collaborative, New York, NY, USA
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Thomas Bozza
- Department of Neurobiology, Northwestern University, Evanston, IL, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
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41
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Fei A, Wu W, Tan L, Tang C, Xu Z, Huo X, Bao H, Kong Y, Johnson M, Hartmann G, Talay M, Yang C, Riegler C, Herrera KJ, Engert F, Xie XS, Barnea G, Liberles SD, Yang H, Li Q. Coordination of two enhancers drives expression of olfactory trace amine-associated receptors. Nat Commun 2021; 12:3798. [PMID: 34145235 PMCID: PMC8213717 DOI: 10.1038/s41467-021-23823-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 05/18/2021] [Indexed: 02/05/2023] Open
Abstract
Olfactory sensory neurons (OSNs) are functionally defined by their expression of a unique odorant receptor (OR). Mechanisms underlying singular OR expression are well studied, and involve a massive cross-chromosomal enhancer interaction network. Trace amine-associated receptors (TAARs) form a distinct family of olfactory receptors, and here we find that mechanisms regulating Taar gene choice display many unique features. The epigenetic signature of Taar genes in TAAR OSNs is different from that in OR OSNs. We further identify that two TAAR enhancers conserved across placental mammals are absolutely required for expression of the entire Taar gene repertoire. Deletion of either enhancer dramatically decreases the expression probabilities of different Taar genes, while deletion of both enhancers completely eliminates the TAAR OSN populations. In addition, both of the enhancers are sufficient to drive transgene expression in the partially overlapped TAAR OSNs. We also show that the TAAR enhancers operate in cis to regulate Taar gene expression. Our findings reveal a coordinated control of Taar gene choice in OSNs by two remote enhancers, and provide an excellent model to study molecular mechanisms underlying formation of an olfactory subsystem.
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Affiliation(s)
- Aimei Fei
- Center for Brain Science of Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wanqing Wu
- Center for Brain Science of Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Longzhi Tan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Cheng Tang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brian-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhengrong Xu
- Center for Brain Science of Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaona Huo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brian-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hongqiang Bao
- Center for Brain Science of Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yalei Kong
- Center for Brain Science of Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mark Johnson
- Department of Neuroscience, Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Griffin Hartmann
- Department of Neuroscience, Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Mustafa Talay
- Department of Neuroscience, Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Cheng Yang
- Center for Brain Science of Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Clemens Riegler
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Kristian J Herrera
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Florian Engert
- Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - X Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gilad Barnea
- Department of Neuroscience, Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Stephen D Liberles
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Research Center for Brain Science and Brian-Inspired Intelligence, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qian Li
- Center for Brain Science of Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, China.
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42
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Agelopoulos M, Foutadakis S, Thanos D. The Causes and Consequences of Spatial Organization of the Genome in Regulation of Gene Expression. Front Immunol 2021; 12:682397. [PMID: 34149720 PMCID: PMC8212036 DOI: 10.3389/fimmu.2021.682397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 01/05/2023] Open
Abstract
Regulation of gene expression in time, space and quantity is orchestrated by the functional interplay of cis-acting elements and trans-acting factors. Our current view postulates that transcription factors recognize enhancer DNA and read the transcriptional regulatory code by cooperative DNA binding to specific DNA motifs, thus instructing the recruitment of transcriptional regulatory complexes forming a plethora of higher-ordered multi-protein-DNA and protein-protein complexes. Here, we reviewed the formation of multi-dimensional chromatin assemblies implicated in gene expression with emphasis on the regulatory role of enhancer hubs as coordinators of stochastic gene expression. Enhancer hubs contain many interacting regulatory elements and represent a remarkably dynamic and heterogeneous network of multivalent interactions. A functional consequence of such complex interaction networks could be that individual enhancers function synergistically to ensure coordination, tight control and robustness in regulation of expression of spatially connected genes. In this review, we discuss fundamental paradigms of such inter- and intra- chromosomal associations both in the context of immune-related genes and beyond.
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Affiliation(s)
| | | | - Dimitris Thanos
- Biomedical Research Foundation, Academy of Athens, Athens, Greece
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43
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Abstract
The field of molecular embryology started around 1990 by identifying new genes and analyzing their functions in early vertebrate embryogenesis. Those genes encode transcription factors, signaling molecules, their regulators, etc. Most of those genes are relatively highly expressed in specific regions or exhibit dramatic phenotypes when ectopically expressed or mutated. This review focuses on one of those genes, Lim1/Lhx1, which encodes a transcription factor. Lim1/Lhx1 is a member of the LIM homeodomain (LIM-HD) protein family, and its intimate partner, Ldb1/NLI, binds to two tandem LIM domains of LIM-HDs. The most ancient LIM-HD protein and its partnership with Ldb1 were innovated in the metazoan ancestor by gene fusion combining LIM domains and a homeodomain and by creating the LIM domain-interacting domain (LID) in ancestral Ldb, respectively. The LIM domain has multiple interacting interphases, and Ldb1 has a dimerization domain (DD), the LID, and other interacting domains that bind to Ssbp2/3/4 and the boundary factor, CTCF. By means of these domains, LIM-HD-Ldb1 functions as a hub protein complex, enabling more intricate and elaborate gene regulation. The common, ancestral role of LIM-HD proteins is neuron cell-type specification. Additionally, Lim1/Lhx1 serves crucial roles in the gastrula organizer and in kidney development. Recent studies using Xenopus embryos have revealed Lim1/Lhx1 functions and regulatory mechanisms during development and regeneration, providing insight into evolutionary developmental biology, functional genomics, gene regulatory networks, and regenerative medicine. In this review, we also discuss recent progress at unraveling participation of Ldb1, Ssbp, and CTCF in enhanceosomes, long-distance enhancer-promoter interactions, and trans-interactions between chromosomes.
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Affiliation(s)
- Yuuri Yasuoka
- Laboratory for Comprehensive Genomic Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Masanori Taira
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Bunkyo-ku, Tokyo, Japan.
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44
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Jafari S, Henriksson J, Yan H, Alenius M. Stress and odorant receptor feedback during a critical period after hatching regulates olfactory sensory neuron differentiation in Drosophila. PLoS Biol 2021; 19:e3001101. [PMID: 33793547 PMCID: PMC8043390 DOI: 10.1371/journal.pbio.3001101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/13/2021] [Accepted: 03/02/2021] [Indexed: 11/19/2022] Open
Abstract
Here, we reveal that the regulation of Drosophila odorant receptor (OR) expression during the pupal stage is permissive and imprecise. We found that directly after hatching an OR feedback mechanism both directs and refines OR expression. We demonstrate that, as in mice, dLsd1 and Su(var)3-9 balance heterochromatin formation to direct OR expression. We show that the expressed OR induces dLsd1 and Su(var)3-9 expression, linking OR level and possibly function to OR expression. OR expression refinement shows a restricted duration, suggesting that a gene regulatory critical period brings olfactory sensory neuron differentiation to an end. Consistent with a change in differentiation, stress during the critical period represses dLsd1 and Su(var)3-9 expression and makes the early permissive OR expression permanent. This induced permissive gene regulatory state makes OR expression resilient to stress later in life. Hence, during a critical period OR feedback, similar to in mouse OR selection, defines adult OR expression in Drosophila.
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Affiliation(s)
- Shadi Jafari
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Johan Henriksson
- Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Hua Yan
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
| | - Mattias Alenius
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
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45
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Genetic and Non-Genetic Mechanisms Underlying Cancer Evolution. Cancers (Basel) 2021; 13:cancers13061380. [PMID: 33803675 PMCID: PMC8002988 DOI: 10.3390/cancers13061380] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/10/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Our manuscript summarizes the up-to-date data on the complex and dynamic nature of adaptation mechanisms and evolutionary processes taking place during cancer initiation, development and progression. Although for decades cancer has been viewed as a process governed by genetic mechanisms, it is becoming more and more clear that non-genetic mechanisms may play an equally important role in cancer evolution. In this review, we bring together these fundamental concepts and discuss how those tightly interconnected mechanisms lead to the establishment of highly adaptive quickly evolving cancers. Furthermore, we argue that in depth understanding of cancer progression from the evolutionary perspective may allow the prediction and direction of the evolutionary path of cancer populations towards drug sensitive phenotypes and thus facilitate the development of more effective anti-cancer approaches. Abstract Cancer development can be defined as a process of cellular and tissular microevolution ultimately leading to malignancy. Strikingly, though this concept has prevailed in the field for more than a century, the precise mechanisms underlying evolutionary processes occurring within tumours remain largely uncharacterized and rather cryptic. Nevertheless, although our current knowledge is fragmentary, data collected to date suggest that most tumours display features compatible with a diverse array of evolutionary paths, suggesting that most of the existing macro-evolutionary models find their avatar in cancer biology. Herein, we discuss an up-to-date view of the fundamental genetic and non-genetic mechanisms underlying tumour evolution with the aim of concurring into an integrated view of the evolutionary forces at play throughout the emergence and progression of the disease and into the acquisition of resistance to diverse therapeutic paradigms. Our ultimate goal is to delve into the intricacies of genetic and non-genetic networks underlying tumour evolution to build a framework where both core concepts are considered non-negligible and equally fundamental.
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46
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Bertero A. RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture. Front Genet 2021; 12:645863. [PMID: 33732290 PMCID: PMC7957078 DOI: 10.3389/fgene.2021.645863] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
Three-dimensional (3D) genome organization has emerged as an important layer of gene regulation in development and disease. The functional properties of chromatin folding within individual chromosomes (i.e., intra-chromosomal or in cis) have been studied extensively. On the other hand, interactions across different chromosomes (i.e., inter-chromosomal or in trans) have received less attention, being often regarded as background noise or technical artifacts. This viewpoint has been challenged by emerging evidence of functional relationships between specific trans chromatin interactions and epigenetic control, transcription, and splicing. Therefore, it is an intriguing possibility that the key processes involved in the biogenesis of RNAs may both shape and be in turn influenced by inter-chromosomal genome architecture. Here I present the rationale behind this hypothesis, and discuss a potential experimental framework aimed at its formal testing. I present a specific example in the cardiac myocyte, a well-studied post-mitotic cell whose development and response to stress are associated with marked rearrangements of chromatin topology both in cis and in trans. I argue that RNA polymerase II clusters (i.e., transcription factories) and foci of the cardiac-specific splicing regulator RBM20 (i.e., splicing factories) exemplify the existence of trans-interacting chromatin domains (TIDs) with important roles in cellular homeostasis. Overall, I propose that inter-molecular 3D proximity between co-regulated nucleic acids may be a pervasive functional mechanism in biology.
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Affiliation(s)
- Alessandro Bertero
- Department of Laboratory Medicine and Pathology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, United States
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47
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Brovkina MV, Duffié R, Burtis AEC, Clowney EJ. Fruitless decommissions regulatory elements to implement cell-type-specific neuronal masculinization. PLoS Genet 2021; 17:e1009338. [PMID: 33600447 PMCID: PMC7924761 DOI: 10.1371/journal.pgen.1009338] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/02/2021] [Accepted: 01/04/2021] [Indexed: 01/12/2023] Open
Abstract
In the fruit fly Drosophila melanogaster, male-specific splicing and translation of the Fruitless transcription factor (FruM) alters the presence, anatomy, and/or connectivity of >60 types of central brain neurons that interconnect to generate male-typical behaviors. While the indispensable function of FruM in sex-specific behavior has been understood for decades, the molecular mechanisms underlying its activity remain unknown. Here, we take a genome-wide, brain-wide approach to identifying regulatory elements whose activity depends on the presence of FruM. We identify 436 high-confidence genomic regions differentially accessible in male fruitless neurons, validate candidate regions as bona fide, differentially regulated enhancers, and describe the particular cell types in which these enhancers are active. We find that individual enhancers are not activated universally but are dedicated to specific fru+ cell types. Aside from fru itself, genes are not dedicated to or common across the fru circuit; rather, FruM appears to masculinize each cell type differently, by tweaking expression of the same effector genes used in other circuits. Finally, we find FruM motifs enriched among regulatory elements that are open in the female but closed in the male. Together, these results suggest that FruM acts cell-type-specifically to decommission regulatory elements in male fruitless neurons. Courtship behavior in male Drosophila melanogaster is controlled by a well-defined neural circuit that is labeled by the male-specific transcription factor Fruitless (FruM). While FruM is known to change the number, anatomy and connectivity of neurons which comprise the circuit and has been suggested to repress the expression of a few gene targets, the mechanism of how FruM regulates genes across many different kinds of neurons is unknown. Using an approach to identify gene regulatory elements based on their chromatin accessibility states (ATAC-seq), we identified a large set of chromatin accessibility changes downstream of Fruitless. By examining the activity of these regulatory elements in vivo, we found that their activity was 1) sexually dimorphic and 2) specific to a single class of FruM neurons, suggesting that FruM acts on different chromatin targets in different neuron classes comprising the courtship circuit. Further, we found a known FruM-regulated enhancer of the FruM-repressed gene Lgr3 to have closed chromatin specifically in FruM neurons. Combined with an enrichment of FruM motifs in regions which are closed in FruM neurons, we present a mechanism where FruM directs the decommissioning of sex-shared regulatory elements to masculinize neurons in a cell-type specific manner.
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Affiliation(s)
- Margarita V. Brovkina
- Graduate Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Rachel Duffié
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, New York, United States of America
| | - Abbigayl E. C. Burtis
- Department of Molecular, Cellular, and Developmental Biology, The University of Michigan, Ann Arbor, Michigan, United States of America
| | - E. Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, The University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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48
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Bertero A, Rosa-Garrido M. Three-dimensional chromatin organization in cardiac development and disease. J Mol Cell Cardiol 2021; 151:89-105. [PMID: 33242466 PMCID: PMC11056610 DOI: 10.1016/j.yjmcc.2020.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Recent technological advancements in the field of chromatin biology have rewritten the textbook on nuclear organization. We now appreciate that the folding of chromatin in the three-dimensional space (i.e. its 3D "architecture") is non-random, hierarchical, and highly complex. While 3D chromatin structure is partially encoded in the primary sequence and thereby broadly conserved across cell types and states, a substantial portion of the genome seems to be dynamic during development or in disease. Moreover, there is growing evidence that at least some of the 3D structure of chromatin is functionally linked to gene regulation, both being modulated by and impacting on multiple nuclear processes (including DNA replication, transcription, and RNA splicing). In recent years, these new concepts have nourished several investigations about the functional role of 3D chromatin topology dynamics in the heart during development and disease. This review aims to provide a comprehensive overview of our current understanding in this field, and to discuss how this knowledge can inform further research as well as clinical practice.
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Affiliation(s)
- Alessandro Bertero
- Department of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA.
| | - Manuel Rosa-Garrido
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California, 650 Charles Young Dr, Los Angeles, CA 90095, USA.
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Duchamp-Viret P, Boyer J, La Villa F, Coureaud G. Brief olfactory learning drives perceptive sensitivity in newborn rabbits: New insights in peripheral processing of odor mixtures and induction. Physiol Behav 2021; 229:113217. [PMID: 33098882 DOI: 10.1016/j.physbeh.2020.113217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/29/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022]
Abstract
Perception of the wide, complex and moving odor world requires that the olfactory system engages processing mechanisms ensuring detection, discrimination and environment adaptation, as early as the peripheral stages. Odor items are mainly elicited by odorant mixtures which give rise to either elemental or configural perceptions. Here, we first explored the contribution of the peripheral olfactory system to configural and elemental perception through odorant interactions at the olfactory receptor (OR) level. This was done in newborn rabbits, which offer the opportunity to pair peripheral electrophysiology and well characterized behavioral responses to two binary mixtures, AB and A'B', which differ in their component ratio (A: ethyl isobutyrate, B: ethyl maltol), and that rabbit pups respectively perceived configurally and elementally. Second, we studied the influence on peripheral reactivity of the brief but powerful learning of one mixture component (odorant B), conditioned by association with the mammary pheromone (MP), which allowed us to assess the possible implication of the phenomenon called induction in neonatal odor learning. Induction is a plasticity mechanism expected to alter both the peripheral electrophysiological responses to, and perceptual detection threshold of, the conditioned stimulus. The results reveal that perceptual modes are partly rooted in differential peripheral processes, the AB configurally perceived mixture mirroring odorant antagonist interactions at OR level to a lesser extent than the A'B' elementally perceived mixture. Further, the results highlight that a single and brief MP-induced odor learning episode is sufficient to alter peripheral responses to the conditioned stimulus and mixtures including it, and shifts the conditioned stimulus detection threshold towards lower concentrations. Thus, MP-induced odor learning relies on induction phenomenon in newborn rabbits.
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Affiliation(s)
- Patricia Duchamp-Viret
- Lyon Neuroscience Research Center, CNRS UMR 5292 - INSERM U 1028 - Université Claude Bernard Lyon 1, Centre Hospitalier Le Vinatier - Bâtiment 462 - Neurocampus, 95 Boulevard Pinel, 69675 Bron Cedex, FRANCE.
| | - Jiasmine Boyer
- Lyon Neuroscience Research Center, CNRS UMR 5292 - INSERM U 1028 - Université Claude Bernard Lyon 1, Centre Hospitalier Le Vinatier - Bâtiment 462 - Neurocampus, 95 Boulevard Pinel, 69675 Bron Cedex, FRANCE
| | - Florian La Villa
- Lyon Neuroscience Research Center, CNRS UMR 5292 - INSERM U 1028 - Université Claude Bernard Lyon 1, Centre Hospitalier Le Vinatier - Bâtiment 462 - Neurocampus, 95 Boulevard Pinel, 69675 Bron Cedex, FRANCE
| | - Gérard Coureaud
- Lyon Neuroscience Research Center, CNRS UMR 5292 - INSERM U 1028 - Université Claude Bernard Lyon 1, Centre Hospitalier Le Vinatier - Bâtiment 462 - Neurocampus, 95 Boulevard Pinel, 69675 Bron Cedex, FRANCE.
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50
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Iwata T, Tomeoka S, Hirota J. A class I odorant receptor enhancer shares a functional motif with class II enhancers. Sci Rep 2021; 11:510. [PMID: 33436797 PMCID: PMC7804114 DOI: 10.1038/s41598-020-79980-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/15/2020] [Indexed: 11/09/2022] Open
Abstract
In the mouse, 129 functional class I odorant receptor (OR) genes reside in a ~ 3 megabase huge gene cluster on chromosome 7. The J element, a long-range cis-regulatory element governs the singular expression of class I OR genes by exerting its effect over the whole cluster. To elucidate the molecular mechanisms underlying class I-specific enhancer activity of the J element, we analyzed the J element sequence to determine the functional region and essential motif. The 430-bp core J element, that is highly conserved in mammalian species from the platypus to humans, contains a class I-specific conserved motif of AAACTTTTC, multiple homeodomain sites, and a neighboring O/E-like site, as in class II OR-enhancers. A series of transgenic reporter assays demonstrated that the class I-specific motif is not essential, but the 330-bp core J-H/O containing the homeodomain and O/E-like sites is necessary and sufficient for class I-specific enhancer activity. Further motif analysis revealed that one of homeodomain sequence is the Greek Islands composite motif of the adjacent homeodomain and O/E-like sequences, and mutations in the composite motif abolished or severely reduced class I-enhancer activity. Our results demonstrate that class I and class II enhancers share a functional motif for their enhancer activity.
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Affiliation(s)
- Tetsuo Iwata
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.,Biomaterial Analysis Division, Technical Department, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Satoshi Tomeoka
- Department of Life Science and Technology, Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Junji Hirota
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, 226-8501, Japan. .,Department of Life Science and Technology, Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
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