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Wade AA, van den Ameele J, Cheetham SW, Yakob R, Brand AH, Nord AS. In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain. iScience 2021; 24:103234. [PMID: 34746699 PMCID: PMC8551073 DOI: 10.1016/j.isci.2021.103234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/11/2021] [Accepted: 10/04/2021] [Indexed: 01/15/2023] Open
Abstract
Genetic studies of autism have revealed causal roles for chromatin remodeling gene mutations. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeler with significant de novo mutation rates in sporadic autism. However, relationships between CHD8 genomic function and autism-relevant biology remain poorly elucidated. Published studies utilizing ChIP-seq to map CHD8 protein-DNA interactions have high variability, consistent with technical challenges and limitations associated with this method. Thus, complementary approaches are needed to establish CHD8 genomic targets and regulatory functions in developing brain. We used in utero CHD8 Targeted DamID followed by sequencing (TaDa-seq) to characterize CHD8 binding in embryonic mouse cortex. CHD8 TaDa-seq reproduced interaction patterns observed from ChIP-seq and further highlighted CHD8 distal interactions associated with neuronal loci. This study establishes TaDa-seq as a useful alternative for mapping protein-DNA interactions in vivo and provides insights into the regulatory targets of CHD8 and autism-relevant pathophysiology associated with CHD8 mutations.
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Affiliation(s)
- A. Ayanna Wade
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95616, USA
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Jelle van den Ameele
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Seth W. Cheetham
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Rebecca Yakob
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Andrea H. Brand
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Alex S. Nord
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95616, USA
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, USA
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Mika K, Benton R. Olfactory Receptor Gene Regulation in Insects: Multiple Mechanisms for Singular Expression. Front Neurosci 2021; 15:738088. [PMID: 34602974 PMCID: PMC8481607 DOI: 10.3389/fnins.2021.738088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/24/2021] [Indexed: 12/25/2022] Open
Abstract
The singular expression of insect olfactory receptors in specific populations of olfactory sensory neurons is fundamental to the encoding of odors in patterns of neuronal activity in the brain. How a receptor gene is selected, from among a large repertoire in the genome, to be expressed in a particular neuron is an outstanding question. Focusing on Drosophila melanogaster, where most investigations have been performed, but incorporating recent insights from other insect species, we review the multilevel regulatory mechanisms of olfactory receptor expression. We discuss how cis-regulatory elements, trans-acting factors, chromatin modifications, and feedback pathways collaborate to activate and maintain expression of the chosen receptor (and to suppress others), highlighting similarities and differences with the mechanisms underlying singular receptor expression in mammals. We also consider the plasticity of receptor regulation in response to environmental cues and internal state during the lifetime of an individual, as well as the evolution of novel expression patterns over longer timescales. Finally, we describe the mechanisms and potential significance of examples of receptor co-expression.
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Affiliation(s)
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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The Serine Protease Homolog, Scarface, Is Sensitive to Nutrient Availability and Modulates the Development of the Drosophila Blood-Brain Barrier. J Neurosci 2021; 41:6430-6448. [PMID: 34210781 PMCID: PMC8318086 DOI: 10.1523/jneurosci.0452-20.2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 02/08/2021] [Accepted: 03/14/2021] [Indexed: 01/21/2023] Open
Abstract
The adaptable transcriptional response to changes in food availability not only ensures animal survival but also lets embryonic development progress. Interestingly, the CNS is preferentially protected from periods of malnutrition, a phenomenon known as “brain sparing.” However, the mechanisms that mediate this response remain poorly understood. To get a better understanding of this, we used Drosophila melanogaster as a model, analyzing the transcriptional response of neural stem cells (neuroblasts) and glia of the blood–brain barrier (BBB) from larvae of both sexes during nutrient restriction using targeted DamID. We found differentially expressed genes in both neuroblasts and glia of the BBB, although the effect of nutrient deficiency was primarily observed in the BBB. We characterized the function of a nutritional sensitive gene expressed in the BBB, the serine protease homolog, scarface (scaf). Scaf is expressed in subperineurial glia in the BBB in response to nutrition. Tissue-specific knockdown of scaf increases subperineurial glia endoreplication and proliferation of perineurial glia in the blood–brain barrier. Furthermore, neuroblast proliferation is diminished on scaf knockdown in subperineurial glia. Interestingly, reexpression of Scaf in subperineurial glia is able to enhance neuroblast proliferation and brain growth of animals in starvation. Finally, we show that loss of scaf in the blood–brain barrier increases sensitivity to drugs in adulthood, suggesting a physiological impairment. We propose that Scaf integrates the nutrient status to modulate the balance between neurogenesis and growth of the BBB, preserving the proper equilibrium between the size of the barrier and the brain. SIGNIFICANCE STATEMENT The Drosophila BBB separates the CNS from the open circulatory system. The BBB glia are not only acting as a physical segregation of tissues but participate in the regulation of the metabolism and neurogenesis during development. Here we analyze the transcriptional response of the BBB glia to nutrient deprivation during larval development, a condition in which protective mechanisms are switched on in the brain. Our findings show that the gene scarface reduces growth in the BBB while promoting the proliferation of neural stem, assuring the balanced growth of the larval brain. Thus, Scarface would link animal nutrition with brain development, coordinating neurogenesis with the growth of the BBB.
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Palmateer CM, Moseley SC, Ray S, Brovero SG, Arbeitman MN. Analysis of cell-type-specific chromatin modifications and gene expression in Drosophila neurons that direct reproductive behavior. PLoS Genet 2021; 17:e1009240. [PMID: 33901168 PMCID: PMC8102012 DOI: 10.1371/journal.pgen.1009240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 05/06/2021] [Accepted: 04/05/2021] [Indexed: 02/06/2023] Open
Abstract
Examining the role of chromatin modifications and gene expression in neurons is critical for understanding how the potential for behaviors are established and maintained. We investigate this question by examining Drosophila melanogaster fru P1 neurons that underlie reproductive behaviors in both sexes. We developed a method to purify cell-type-specific chromatin (Chromatag), using a tagged histone H2B variant that is expressed using the versatile Gal4/UAS gene expression system. Here, we use Chromatag to evaluate five chromatin modifications, at three life stages in both sexes. We find substantial changes in chromatin modification profiles across development and fewer differences between males and females. Additionally, we find chromatin modifications that persist in different sets of genes from pupal to adult stages, which may point to genes important for cell fate determination in fru P1 neurons. We generated cell-type-specific RNA-seq data sets, using translating ribosome affinity purification (TRAP). We identify actively translated genes in fru P1 neurons, revealing novel stage- and sex-differences in gene expression. We also find chromatin modification enrichment patterns that are associated with gene expression. Next, we use the chromatin modification data to identify cell-type-specific super-enhancer-containing genes. We show that genes with super-enhancers in fru P1 neurons differ across development and between the sexes. We validated that a set of genes are expressed in fru P1 neurons, which were chosen based on having a super-enhancer and TRAP-enriched expression in fru P1 neurons.
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Affiliation(s)
- Colleen M. Palmateer
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, Florida, United States of America
| | - Shawn C. Moseley
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, Florida, United States of America
| | - Surjyendu Ray
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, Florida, United States of America
| | - Savannah G. Brovero
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, Florida, United States of America
| | - Michelle N. Arbeitman
- Department of Biomedical Sciences, Florida State University, College of Medicine, Tallahassee, Florida, United States of America
- Program of Neuroscience, Florida State University, Tallahassee, Florida, United States of America
- * E-mail:
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Arguello JR, Abuin L, Armida J, Mika K, Chai PC, Benton R. Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants. eLife 2021; 10:63036. [PMID: 33666172 PMCID: PMC7993999 DOI: 10.7554/elife.63036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
Determining the molecular properties of neurons is essential to understand their development, function and evolution. Using Targeted DamID (TaDa), we characterize RNA polymerase II occupancy and chromatin accessibility in selected Ionotropic receptor (Ir)-expressing olfactory sensory neurons in Drosophila. Although individual populations represent a minute fraction of cells, TaDa is sufficiently sensitive and specific to identify the expected receptor genes. Unique Ir expression is not consistently associated with differences in chromatin accessibility, but rather to distinct transcription factor profiles. Genes that are heterogeneously expressed across populations are enriched for neurodevelopmental factors, and we identify functions for the POU-domain protein Pdm3 as a genetic switch of Ir neuron fate, and the atypical cadherin Flamingo in segregation of neurons into discrete glomeruli. Together this study reveals the effectiveness of TaDa in profiling rare neural populations, identifies new roles for a transcription factor and a neuronal guidance molecule, and provides valuable datasets for future exploration.
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Affiliation(s)
- J Roman Arguello
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland.,Department of Ecology and Evolution Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Liliane Abuin
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Jan Armida
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Kaan Mika
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Phing Chian Chai
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
| | - Richard Benton
- Center for Integrative Genomics Faculty of Biology and Medicine University of Lausanne, Lausanne, Switzerland
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Aloia L. Epigenetic Regulation of Cell-Fate Changes That Determine Adult Liver Regeneration After Injury. Front Cell Dev Biol 2021; 9:643055. [PMID: 33732709 PMCID: PMC7957008 DOI: 10.3389/fcell.2021.643055] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
The adult liver has excellent regenerative potential following injury. In contrast to other organs of the body that have high cellular turnover during homeostasis (e.g., intestine, stomach, and skin), the adult liver is a slowly self-renewing organ and does not contain a defined stem-cell compartment that maintains homeostasis. However, tissue damage induces significant proliferation across the liver and can trigger cell-fate changes, such as trans-differentiation and de-differentiation into liver progenitors, which contribute to efficient tissue regeneration and restoration of liver functions. Epigenetic mechanisms have been shown to regulate cell-fate decisions in both embryonic and adult tissues in response to environmental cues. Underlying their relevance in liver biology, expression levels and epigenetic activity of chromatin modifiers are often altered in chronic liver disease and liver cancer. In this review, I examine the role of several chromatin modifiers in the regulation of cell-fate changes that determine efficient adult liver epithelial regeneration in response to tissue injury in mouse models. Specifically, I focus on epigenetic mechanisms such as chromatin remodelling, DNA methylation and hydroxymethylation, and histone methylation and deacetylation. Finally, I address how altered epigenetic mechanisms and the interplay between epigenetics and metabolism may contribute to the initiation and progression of liver disease and cancer.
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Affiliation(s)
- Luigi Aloia
- MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
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Askjaer P, Harr JC. Genetic approaches to revealing the principles of nuclear architecture. Curr Opin Genet Dev 2020; 67:52-60. [PMID: 33338753 DOI: 10.1016/j.gde.2020.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022]
Abstract
The spatial organization of chromosomes inside the eukaryotic nucleus is important for DNA replication, repair and gene expression. During development of multicellular organisms, different compendiums of genes are either repressed or activated to produce specific cell types. Genetic manipulation of tractable organisms is invaluable to elucidate chromosome configuration and the underlying mechanisms. Systematic inhibition of genes through RNA interference and, more recently, CRISPR/Cas9-based screens have identified new proteins with significant roles in nuclear organization. Coupling this with advances in imaging techniques, such as multiplexed DNA fluorescence in situ hybridization, and with tissue-specific genome profiling by DNA adenine methylation identification has increased our knowledge about the immense complexity and dynamics of the nucleus.
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Affiliation(s)
- Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville 41013, Spain.
| | - Jennifer C Harr
- Department of Biological Sciences, St. Mary's University, One Camino Santa Maria, San Antonio, TX, 78228, USA.
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A viral toolkit for recording transcription factor-DNA interactions in live mouse tissues. Proc Natl Acad Sci U S A 2020; 117:10003-10014. [PMID: 32300008 DOI: 10.1073/pnas.1918241117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Transcription factors (TFs) enact precise regulation of gene expression through site-specific, genome-wide binding. Common methods for TF-occupancy profiling, such as chromatin immunoprecipitation, are limited by requirement of TF-specific antibodies and provide only end-point snapshots of TF binding. Alternatively, TF-tagging techniques, in which a TF is fused to a DNA-modifying enzyme that marks TF-binding events across the genome as they occur, do not require TF-specific antibodies and offer the potential for unique applications, such as recording of TF occupancy over time and cell type specificity through conditional expression of the TF-enzyme fusion. Here, we create a viral toolkit for one such method, calling cards, and demonstrate that these reagents can be delivered to the live mouse brain and used to report TF occupancy. Further, we establish a Cre-dependent calling cards system and, in proof-of-principle experiments, show utility in defining cell type-specific TF profiles and recording and integrating TF-binding events across time. This versatile approach will enable unique studies of TF-mediated gene regulation in live animal models.
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