1
|
Jun S, Kim M, Park H, Hwang E, Yamamoto Y, Tanaka-Yamamoto K. Organization of Purkinje cell development by neuronal MEGF11 in cerebellar granule cells. Cell Rep 2023; 42:113137. [PMID: 37708022 DOI: 10.1016/j.celrep.2023.113137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/24/2023] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
As cerebellar granule cells (GCs) coordinate the formation of regular cerebellar networks during postnatal development, molecules in GCs are expected to be involved. Here, we test the effects of the knockdown (KD) of multiple epidermal growth factor-like domains protein 11 (MEGF11), which is a homolog of proteins mediating astrocytic phagocytosis but is substantially increased at the later developmental stages of GCs on cerebellar development. MEGF11-KD in GCs of developing mice results in abnormal cerebellar structures, including extensively ectopic Purkinje cell (PC) somas, and in impaired motor functions. MEGF11-KD also causes abnormally asynchronous synaptic release from GC axons, parallel fibers, before the appearance of abnormal cerebellar structures. Interestingly, blockade of this abnormal synaptic release restores most of the cerebellar structures. Thus, apart from phagocytic functions of its related homologs in astrocytes, MEGF11 in GCs promotes proper PC development and cerebellar network formation by regulating immature synaptic transmission.
Collapse
Affiliation(s)
- Soyoung Jun
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Muwoong Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Heeyoun Park
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Eunmi Hwang
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea
| | - Yukio Yamamoto
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.
| | - Keiko Tanaka-Yamamoto
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea; Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology (UST), Seoul 02792, Republic of Korea.
| |
Collapse
|
2
|
Lyons LC, Vanrobaeys Y, Abel T. Sleep and memory: The impact of sleep deprivation on transcription, translational control, and protein synthesis in the brain. J Neurochem 2023; 166:24-46. [PMID: 36802068 PMCID: PMC10919414 DOI: 10.1111/jnc.15787] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/20/2023]
Abstract
In countries around the world, sleep deprivation represents a widespread problem affecting school-age children, teenagers, and adults. Acute sleep deprivation and more chronic sleep restriction adversely affect individual health, impairing memory and cognitive performance as well as increasing the risk and progression of numerous diseases. In mammals, the hippocampus and hippocampus-dependent memory are vulnerable to the effects of acute sleep deprivation. Sleep deprivation induces changes in molecular signaling, gene expression and may cause changes in dendritic structure in neurons. Genome wide studies have shown that acute sleep deprivation alters gene transcription, although the pool of genes affected varies between brain regions. More recently, advances in research have drawn attention to differences in gene regulation between the level of the transcriptome compared with the pool of mRNA associated with ribosomes for protein translation following sleep deprivation. Thus, in addition to transcriptional changes, sleep deprivation also affects downstream processes to alter protein translation. In this review, we focus on the multiple levels through which acute sleep deprivation impacts gene regulation, highlighting potential post-transcriptional and translational processes that may be affected by sleep deprivation. Understanding the multiple levels of gene regulation impacted by sleep deprivation is essential for future development of therapeutics that may mitigate the effects of sleep loss.
Collapse
Affiliation(s)
- Lisa C Lyons
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Iowa Neuroscience Institute, Iowa City, Iowa, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
- Iowa Neuroscience Institute, Iowa City, Iowa, USA
| |
Collapse
|
3
|
Whitworth GB, Watson FL. Translating Ribosome Affinity Purification (TRAP) and Bioinformatic RNA-Seq Analysis in Post-metamorphic Xenopus laevis. Methods Mol Biol 2023; 2636:279-310. [PMID: 36881307 DOI: 10.1007/978-1-0716-3012-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Recent technical advances provide the ability to isolate and purify mRNAs from genetically distinct cell types so as to provide a broader view of gene expression as they relate to gene networks. These tools allow the genome of organisms undergoing different developmental or diseased states and environmental or behavioral conditions to be compared. Translating ribosome affinity purification (TRAP), a method using transgenic animals expressing a ribosomal affinity tag (ribotag) that targets ribosome-bound mRNAs, allows for the rapid isolation of genetically distinct populations of cells. In this chapter, we provide stepwise methods for carrying out an updated protocol for using the TRAP method in the South African clawed frog Xenopus laevis. A discussion of the experimental design and necessary controls and their rationale, along with a description of the bioinformatic steps involved in analyzing the Xenopus laevis translatome using TRAP and RNA-Seq, is also provided.
Collapse
Affiliation(s)
- Gregg B Whitworth
- Department of Biology, Washington and Lee University, Lexington, VA, USA
| | - Fiona L Watson
- Department of Biology, Washington and Lee University, Lexington, VA, USA.
| |
Collapse
|
4
|
Yan M, Li J, Yan L, Li X, Chen JG. Transcription factor Foxp1 is essential for the induction of choroidal neovascularization. EYE AND VISION 2022; 9:10. [PMID: 35248156 PMCID: PMC8898411 DOI: 10.1186/s40662-022-00281-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/13/2022] [Indexed: 12/04/2022]
Abstract
Background The exudative form of age-related macular degeneration (AMD) is characterized by abnormal blood vessel growth, which is stimulated by vascular endothelial growth factor (VEGF) released from retinal pigment epithelium (RPE). The angiogenic behaviors of vascular endothelial cells in vitro depend on forkhead box protein P1 (Foxp1), a transcription repressor widely expressed in human and murine tissues during development. In this study, we aimed to determine whether loss of Foxp1 affects laser-induced choroidal neovascularization (CNV) in mouse. Methods Eye-selective deletion of Foxp1 was obtained by crossing Foxp1flox/flox with Six3-Cre mice. Laser photocoagulation was delivered to six- to eight-week-old mice to induce CNV. The expression of Foxp1 and Cre was determined by immunofluorescence in cryostat sections of the eyes. Fundus fluorescein angiography (FFA), optical coherence tomography (OCT), and B4 isolectin staining were applied to analyze the leakage, bulge height, and area of CNV lesions, respectively. RPE-choroid tissues were isolated for the determination of VEGF and pigment epithelium derived factor (PEDF) by Western blotting. Results Foxp1 was expressed in retinal ganglion cells, RPE, and the choroidal endothelial cells. Laser photocoagulation increased the number of Foxp1+-endothelial cells and induced CNV. Six3-Cre reduced Foxp1 expression in RPE but not the endothelium, leading to a lower level of VEGF in the RPE-choroid. Foxp1 knockout inhibited pathological angiogenesis and vascular leakage of the laser-induced CNV lesions. Conclusions Foxp1 regulates the expression of VEGF in the RPE, and inhibition of Foxp1 could potentially be a novel strategy for the prevention and therapy of neovascularization related to AMD.
Collapse
|
5
|
Chucair-Elliott AJ, Ocañas SR, Pham K, Van Der Veldt M, Cheyney A, Stanford D, Gurley J, Elliott MH, Freeman WM. Translatomic response of retinal Müller glia to acute and chronic stress. Neurobiol Dis 2022; 175:105931. [PMID: 36423879 PMCID: PMC9875566 DOI: 10.1016/j.nbd.2022.105931] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 11/14/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Analysis of retina cell type-specific epigenetic and transcriptomic signatures is crucial to understanding the pathophysiology of retinal degenerations such as age-related macular degeneration (AMD) and delineating cell autonomous and cell-non-autonomous mechanisms. We have discovered that Aldh1l1 is specifically expressed in the major macroglia of the retina, Müller glia, and, unlike the brain, is not expressed in retinal astrocytes. This allows use of Aldh1l1 cre drivers and Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) constructs for temporally controlled labeling and paired analysis of Müller glia epigenomes and translatomes. As validated through a variety of approaches, the Aldh1l1cre/ERT2-NuTRAP model provides Müller glia specific translatomic and epigenomic profiles without the need to isolate whole cells. Application of this approach to models of acute injury (optic nerve crush) and chronic stress (aging) uncovered few common Müller glia-specific transcriptome changes in inflammatory pathways, and mostly differential signatures for each stimulus. The expression of members of the IL-6 and integrin-linked kinase signaling pathways was enhanced in Müller glia in response to optic nerve crush but not aging. Unique changes in neuroinflammation and fibrosis signaling pathways were observed in response to aging but not with optic nerve crush. The Aldh1l1cre/ERT2-NuTRAP model allows focused molecular analyses of a single, minority cell type within the retina, providing more substantial effect sizes than whole tissue analyses. The NuTRAP model, nucleic acid isolation, and validation approaches presented here can be applied to any retina cell type for which a cell type-specific cre is available.
Collapse
Affiliation(s)
- Ana J. Chucair-Elliott
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Corresponding authors at: Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA. (A.J. Chucair-Elliott), (W.M. Freeman)
| | - Sarah R. Ocañas
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Kevin Pham
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Michael Van Der Veldt
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Ashley Cheyney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - David Stanford
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Jami Gurley
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael H. Elliott
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA,Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M. Freeman
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA,Oklahoma City Veterans Affairs Medical Center, Oklahoma City, OK, USA,Corresponding authors at: Genes & Human Disease Program, Oklahoma Medical Research Foundation, 825 NE 13th Street, Oklahoma City, OK 73104, USA. (A.J. Chucair-Elliott), (W.M. Freeman)
| |
Collapse
|
6
|
von Ziegler LM, Floriou-Servou A, Waag R, Das Gupta RR, Sturman O, Gapp K, Maat CA, Kockmann T, Lin HY, Duss SN, Privitera M, Hinte L, von Meyenn F, Zeilhofer HU, Germain PL, Bohacek J. Multiomic profiling of the acute stress response in the mouse hippocampus. Nat Commun 2022; 13:1824. [PMID: 35383160 PMCID: PMC8983670 DOI: 10.1038/s41467-022-29367-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 03/11/2022] [Indexed: 12/26/2022] Open
Abstract
The acute stress response mobilizes energy to meet situational demands and re-establish homeostasis. However, the underlying molecular cascades are unclear. Here, we use a brief swim exposure to trigger an acute stress response in mice, which transiently increases anxiety, without leading to lasting maladaptive changes. Using multiomic profiling, such as proteomics, phospho-proteomics, bulk mRNA-, single-nuclei mRNA-, small RNA-, and TRAP-sequencing, we characterize the acute stress-induced molecular events in the mouse hippocampus over time. Our results show the complexity and specificity of the response to acute stress, highlighting both the widespread changes in protein phosphorylation and gene transcription, and tightly regulated protein translation. The observed molecular events resolve efficiently within four hours after initiation of stress. We include an interactive app to explore the data, providing a molecular resource that can help us understand how acute stress impacts brain function in response to stress. Acute stress can help individuals to respond to challenging events, although chronic stress leads to maladaptive changes. Here, the authors present a multi omic analysis profiling acute stress-induced changes in the mouse hippocampus, providing a resource for the scientific community.
Collapse
Affiliation(s)
- Lukas M von Ziegler
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Amalia Floriou-Servou
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Rebecca Waag
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Rebecca R Das Gupta
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.,Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Oliver Sturman
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Katharina Gapp
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Christina A Maat
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Tobias Kockmann
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Han-Yu Lin
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Sian N Duss
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Mattia Privitera
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Laura Hinte
- Laboratory of Nutrition and Metabolic Epigenetics, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Hanns U Zeilhofer
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.,Institute of Pharmaceutical Sciences, ETH Zurich, Zurich, Switzerland
| | - Pierre-Luc Germain
- Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.,Computational Neurogenomics, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland.,Laboratory of Statistical Bioinformatics, Department for Molecular Life Sciences, University of Zürich, Zurich, Switzerland
| | - Johannes Bohacek
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland. .,Neuroscience Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland.
| |
Collapse
|
7
|
Jiang C, Liu P, La CM, Guan D. In silico integrative analysis of multi-omics reveals regulatory layers for diurnal gene expression in mouse liver. Front Endocrinol (Lausanne) 2022; 13:955070. [PMID: 35937828 PMCID: PMC9353712 DOI: 10.3389/fendo.2022.955070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 06/27/2022] [Indexed: 11/25/2022] Open
Abstract
Diurnal oscillation persists throughout the body and plays an essential role in maintaining physiological homeostasis. Disruption of diurnal rhythm contributes to many diseases including type 2 diabetes. The regulatory mechanism of the transcription-translation feedback loop (TTFL) of core clock genes is well-established, while a systematic study across all regulatory layers of gene expression, including gene transcription, RNA translation, and DNA binding protein (DBP) activities, is still lacking. We comprehensively bioinformatics analyzed the rhythmicity of gene transcription, mature RNA abundance, protein abundance and DBP activity using publicly available omic-datasets from mouse livers. We found that the core clock genes, Bmal1 and Rev-erbα, persistently retained rhythmicity in all stages, which supported the essential rhythmic function along with the TTFL. Interestingly, there were many layer-specific rhythmic genes playing layer-specific rhythmic functions. The systematic analysis of gene transcription rate, RNA translation efficiency, and post-translation modification of DBP were incorporated to determine the potential mechanisms for layer-specific rhythmic genes. We observed the gene with rhythmic expression in both mature RNA and protein layers were largely due to relatively consistent translation rate. In addition, rhythmic translation rate induced the rhythms of protein whose mature RNA levels were not rhythmic. Further analysis revealed a phosphorylation-mediated and an enhancer RNA-mediated cycling regulation between the corresponding layers. This study presents a global view of the oscillating genes in multiple layers via a systematical analysis and indicates the complexity of regulatory mechanisms across different layers for further functional study.
Collapse
|
8
|
Dalal JS, Winden KD, Salussolia CL, Sundberg M, Singh A, Pham TT, Zhou P, Pu WT, Miller MT, Sahin M. Loss of Tsc1 in cerebellar Purkinje cells induces transcriptional and translation changes in FMRP target transcripts. eLife 2021; 10:e67399. [PMID: 34259631 PMCID: PMC8279760 DOI: 10.7554/elife.67399] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/29/2021] [Indexed: 12/19/2022] Open
Abstract
Tuberous sclerosis complex (TSC) is a genetic disorder that is associated with multiple neurological manifestations. Previously, we demonstrated that Tsc1 loss in cerebellar Purkinje cells (PCs) can cause altered social behavior in mice. Here, we performed detailed transcriptional and translational analyses of Tsc1-deficient PCs to understand the molecular alterations in these cells. We found that target transcripts of the Fragile X Mental Retardation Protein (FMRP) are reduced in mutant PCs with evidence of increased degradation. Surprisingly, we observed unchanged ribosomal binding for many of these genes using translating ribosome affinity purification. Finally, we found that multiple FMRP targets, including SHANK2, were reduced, suggesting that compensatory increases in ribosomal binding efficiency may be unable to overcome reduced transcript levels. These data further implicate dysfunction of FMRP and its targets in TSC and suggest that treatments aimed at restoring the function of these pathways may be beneficial.
Collapse
Affiliation(s)
- Jasbir Singh Dalal
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Kellen Diamond Winden
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Catherine Lourdes Salussolia
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Maria Sundberg
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Achint Singh
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Truc Thanh Pham
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
| | - Pingzhu Zhou
- Department of Cardiology, Boston Children’s HospitalBostonUnited States
| | - William T Pu
- Department of Cardiology, Boston Children’s HospitalBostonUnited States
- Harvard Medical SchoolBostonUnited States
| | - Meghan T Miller
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases, Roche Innovation Center BaselBaselSwitzerland
| | - Mustafa Sahin
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, Kirby Neurobiology Center, Boston Children’s HospitalBostonUnited States
- Harvard Medical SchoolBostonUnited States
| |
Collapse
|
9
|
Han X, Burger LL, Garcia-Galiano D, Moenter SM, Myers MG, Olson DP, Elias CF. Protocol to extract actively translated mRNAs from mouse hypothalamus by translating ribosome affinity purification. STAR Protoc 2021; 2:100589. [PMID: 34159322 PMCID: PMC8196219 DOI: 10.1016/j.xpro.2021.100589] [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] [Indexed: 11/18/2022] Open
Abstract
Here, we present an in-depth protocol for extracting ribosome-bound mRNAs in low-abundance cells of hypothalamic nuclei. mRNAs are extracted from the micropunched tissue using refined translating ribosome affinity purification. Isolated RNAs can be used for sequencing or transcript quantification. This protocol enables the identification of actively translated mRNAs in varying physiological states and can be modified for use in any neuronal subpopulation labeled with a ribo-tag. We use leptin receptor-expressing neurons as an example to illustrate the protocol. For complete details on the use and execution of this protocol, please refer to Han et al. (2020).
Collapse
Affiliation(s)
- Xingfa Han
- Department of Molecular & integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
- Isotope Research Lab, Sichuan Agricultural University, Ya’an 625014, China
| | - Laura L. Burger
- Department of Molecular & integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David Garcia-Galiano
- Department of Molecular & integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Suzanne M. Moenter
- Department of Molecular & integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Martin G. Myers
- Department of Molecular & integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI 48109, USA
| | - David P. Olson
- Department of Molecular & integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carol F. Elias
- Department of Molecular & integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI 48109, USA
| |
Collapse
|
10
|
Pallos J, Jeng S, McWeeney S, Martin I. Dopamine neuron-specific LRRK2 G2019S effects on gene expression revealed by translatome profiling. Neurobiol Dis 2021; 155:105390. [PMID: 33984508 DOI: 10.1016/j.nbd.2021.105390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/05/2021] [Accepted: 05/06/2021] [Indexed: 12/13/2022] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) mutations are the most common genetic cause of late-onset Parkinson's disease. The pathogenic G2019S mutation enhances LRRK2 kinase activity and induces neurodegeneration in C. elegans, Drosophila and rodent models through unclear mechanisms. Gene expression profiling has the potential to provide detailed insight into the biological pathways modulated by LRRK2 kinase activity. Prior in vivo studies have surveyed the effects of LRRK2 G2019S on genome-wide mRNA expression in complex brain tissues with high cellular heterogeneity, limiting their power to detect more restricted gene expression changes occurring in a cell type-specific manner. Here, we used translating ribosome affinity purification (TRAP) coupled to RNA-seq to profile dopamine neuron-specific gene expression changes caused by LRRK2 G2019S in the Drosophila CNS. A number of genes were differentially expressed in the presence of mutant LRRK2 that represent a broad range of molecular functions including DNA repair (RfC3), mRNA metabolism and translation (Ddx1 and lin-28), calcium homeostasis (MCU), and other categories (Ugt37c1, disp, l(1)G0196, CG6602, CG1126 and CG11068). Further analysis on a subset of these genes revealed that LRRK2 G2019S did not alter their expression across the whole brain, consistent with dopamine neuron-specific effects uncovered by the TRAP approach that may yield insight into the neurodegenerative process. To our knowledge, this is the first study to profile the effects of LRRK2 G2019S specifically on DA neuron gene expression in vivo. Beyond providing a set of differentially expressed gene candidates relevant to LRRK2, we demonstrate the effective use of TRAP to perform high-resolution assessment of dopamine neuron gene expression for the study of PD.
Collapse
Affiliation(s)
- Judit Pallos
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - Sophia Jeng
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Shannon McWeeney
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA; Oregon Clinical and Translational Research Institute, Oregon Health and Science University, Portland, OR 97239, USA; Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Ian Martin
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, OR, USA.
| |
Collapse
|
11
|
Minehart JA, Speer CM. A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. Front Synaptic Neurosci 2021; 12:615059. [PMID: 33469427 PMCID: PMC7813761 DOI: 10.3389/fnsyn.2020.615059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
A key challenge in developmental neuroscience is identifying the local regulatory mechanisms that control neurite and synaptic refinement over large brain volumes. Innovative molecular techniques and high-resolution imaging tools are beginning to reshape our view of how local protein translation in subcellular compartments drives axonal, dendritic, and synaptic development and plasticity. Here we review recent progress in three areas of neurite and synaptic study in situ-compartment-specific transcriptomics/translatomics, targeted proteomics, and super-resolution imaging analysis of synaptic organization and development. We discuss synergies between sequencing and imaging techniques for the discovery and validation of local molecular signaling mechanisms regulating synaptic development, plasticity, and maintenance in circuits.
Collapse
Affiliation(s)
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD, United States
| |
Collapse
|
12
|
Kim HD, Wei J, Call T, Quintus NT, Summers AJ, Carotenuto S, Johnson R, Ma X, Xu C, Park JG, Qiu S, Ferguson D. Shisa6 mediates cell-type specific regulation of depression in the nucleus accumbens. Mol Psychiatry 2021; 26:7316-7327. [PMID: 34253865 PMCID: PMC8752624 DOI: 10.1038/s41380-021-01217-8] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 06/15/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022]
Abstract
Depression is the leading cause of disability and produces enormous health and economic burdens. Current treatment approaches for depression are largely ineffective and leave more than 50% of patients symptomatic, mainly because of non-selective and broad action of antidepressants. Thus, there is an urgent need to design and develop novel therapeutics to treat depression. Given the heterogeneity and complexity of the brain, identification of molecular mechanisms within specific cell-types responsible for producing depression-like behaviors will advance development of therapies. In the reward circuitry, the nucleus accumbens (NAc) is a key brain region of depression pathophysiology, possibly based on differential activity of D1- or D2- medium spiny neurons (MSNs). Here we report a circuit- and cell-type specific molecular target for depression, Shisa6, recently defined as an AMPAR component, which is increased only in D1-MSNs in the NAc of susceptible mice. Using the Ribotag approach, we dissected the transcriptional profile of D1- and D2-MSNs by RNA sequencing following a mouse model of depression, chronic social defeat stress (CSDS). Bioinformatic analyses identified cell-type specific genes that may contribute to the pathogenesis of depression, including Shisa6. We found selective optogenetic activation of the ventral tegmental area (VTA) to NAc circuit increases Shisa6 expression in D1-MSNs. Shisa6 is specifically located in excitatory synapses of D1-MSNs and increases excitability of neurons, which promotes anxiety- and depression-like behaviors in mice. Cell-type and circuit-specific action of Shisa6, which directly modulates excitatory synapses that convey aversive information, identifies the protein as a potential rapid-antidepressant target for aberrant circuit function in depression.
Collapse
Affiliation(s)
- Hee-Dae Kim
- grid.134563.60000 0001 2168 186XDepartment of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ USA
| | - Jing Wei
- grid.134563.60000 0001 2168 186XDepartment of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ USA
| | - Tanessa Call
- grid.134563.60000 0001 2168 186XDepartment of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ USA
| | - Nicole Teru Quintus
- grid.134563.60000 0001 2168 186XDepartment of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ USA
| | - Alexander J. Summers
- grid.134563.60000 0001 2168 186XDepartment of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ USA
| | - Samantha Carotenuto
- grid.134563.60000 0001 2168 186XDepartment of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ USA
| | - Ross Johnson
- grid.134563.60000 0001 2168 186XDepartment of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ USA
| | - Xiaokuang Ma
- grid.134563.60000 0001 2168 186XDepartment of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ USA
| | - Chenxi Xu
- grid.215654.10000 0001 2151 2636Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Jin G. Park
- grid.215654.10000 0001 2151 2636Virginia G. Piper Biodesign Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ USA
| | - Shenfeng Qiu
- grid.134563.60000 0001 2168 186XDepartment of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ USA
| | - Deveroux Ferguson
- Department of Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA.
| |
Collapse
|
13
|
Lyons LC, Chatterjee S, Vanrobaeys Y, Gaine ME, Abel T. Translational changes induced by acute sleep deprivation uncovered by TRAP-Seq. Mol Brain 2020; 13:165. [PMID: 33272296 PMCID: PMC7713217 DOI: 10.1186/s13041-020-00702-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/17/2020] [Indexed: 12/14/2022] Open
Abstract
Sleep deprivation is a global health problem adversely affecting health as well as causing decrements in learning and performance. Sleep deprivation induces significant changes in gene transcription in many brain regions, with the hippocampus particularly susceptible to acute sleep deprivation. However, less is known about the impacts of sleep deprivation on post-transcriptional gene regulation. To identify the effects of sleep deprivation on the translatome, we took advantage of the RiboTag mouse line to express HA-labeled Rpl22 in CaMKIIα neurons to selectively isolate and sequence mRNA transcripts associated with ribosomes in excitatory neurons. We found 198 differentially expressed genes in the ribosome-associated mRNA subset after sleep deprivation. In comparison with previously published data on gene expression in the hippocampus after sleep deprivation, we found that the subset of genes affected by sleep deprivation was considerably different in the translatome compared with the transcriptome, with only 49 genes regulated similarly. Interestingly, we found 478 genes differentially regulated by sleep deprivation in the transcriptome that were not significantly regulated in the translatome of excitatory neurons. Conversely, there were 149 genes differentially regulated by sleep deprivation in the translatome but not in the whole transcriptome. Pathway analysis revealed differences in the biological functions of genes exclusively regulated in the transcriptome or translatome, with protein deacetylase activity and small GTPase binding regulated in the transcriptome and unfolded protein binding, kinase inhibitor activity, neurotransmitter receptors and circadian rhythms regulated in the translatome. These results indicate that sleep deprivation induces significant changes affecting the pool of actively translated mRNAs.
Collapse
Affiliation(s)
- Lisa C Lyons
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
- Program in Neuroscience, Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| | - Snehajyoti Chatterjee
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Yann Vanrobaeys
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Marie E Gaine
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
- Department of Pharmaceutical Sciences and Experimental Therapeutics (PSET), College of Pharmacy, University of Iowa, Iowa City, IA, USA
| | - Ted Abel
- Department of Neuroscience and Pharmacology, Iowa Neuroscience Institute, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| |
Collapse
|
14
|
Petelski AA, Slavov N. Analyzing Ribosome Remodeling in Health and Disease. Proteomics 2020; 20:e2000039. [PMID: 32820594 PMCID: PMC7501214 DOI: 10.1002/pmic.202000039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/01/2020] [Indexed: 12/24/2022]
Abstract
Increasing evidence suggests that ribosomes actively regulate protein synthesis. However, much of this evidence is indirect, leaving this layer of gene regulation largely unexplored, in part due to methodological limitations. Indeed, evidence is reviewed demonstrating that commonly used methods, such as transcriptomics, are inadequate because the variability in mRNAs coding for ribosomal proteins (RP) does not necessarily correspond to RP variability. Thus protein remodeling of ribosomes should be investigated by methods that allow direct quantification of RPs, ideally of isolated ribosomes. Such methods are reviewed, focusing on mass spectrometry and emphasizing method-specific biases and approaches to control these biases. It is argued that using multiple complementary methods can help reduce the danger of interpreting reproducible systematic biases as evidence for ribosome remodeling.
Collapse
Affiliation(s)
- Aleksandra A Petelski
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
- Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, MA, 02115, USA
- Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| |
Collapse
|
15
|
Fu O, Iwai Y, Kondoh K, Misaka T, Minokoshi Y, Nakajima KI. SatB2-Expressing Neurons in the Parabrachial Nucleus Encode Sweet Taste. Cell Rep 2020; 27:1650-1656.e4. [PMID: 31067452 DOI: 10.1016/j.celrep.2019.04.040] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 03/12/2019] [Accepted: 04/08/2019] [Indexed: 12/21/2022] Open
Abstract
The gustatory system plays an important role in sensing appetitive and aversive tastes for evaluating food quality. In mice, taste signals are relayed by multiple brain regions, including the parabrachial nucleus (PBN) of the pons, before reaching the gustatory cortex via the gustatory thalamus. Recent studies show that taste information at the periphery is encoded in a labeled-line manner, such that each taste modality has its own receptors and neuronal pathway. In contrast, the molecular identity of gustatory neurons in the CNS remains unknown. Here, we show that SatB2-expressing neurons in the PBN play a pivotal role in sweet taste transduction. With cell ablation, in vivo calcium imaging, and optogenetics, we reveal that SatB2PBN neurons encode positive valance and selectively transmit sweet taste signals to the gustatory thalamus.
Collapse
Affiliation(s)
- Ou Fu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Division of Endocrinology and Metabolism, National Institute for Physiological Sciences, Okazaki, Aichi, Japan
| | - Yuu Iwai
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kunio Kondoh
- Division of Endocrinology and Metabolism, National Institute for Physiological Sciences, Okazaki, Aichi, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasuhiko Minokoshi
- Division of Endocrinology and Metabolism, National Institute for Physiological Sciences, Okazaki, Aichi, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Ken-Ichiro Nakajima
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Division of Endocrinology and Metabolism, National Institute for Physiological Sciences, Okazaki, Aichi, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan.
| |
Collapse
|
16
|
Koltun B, Ironi S, Gershoni-Emek N, Barrera I, Hleihil M, Nanguneri S, Sasmal R, Agasti SS, Nair D, Rosenblum K. Measuring mRNA translation in neuronal processes and somata by tRNA-FRET. Nucleic Acids Res 2020; 48:e32. [PMID: 31974573 PMCID: PMC7102941 DOI: 10.1093/nar/gkaa042] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 12/04/2019] [Accepted: 01/15/2020] [Indexed: 01/12/2023] Open
Abstract
In neurons, the specific spatial and temporal localization of protein synthesis is of great importance for function and survival. Here, we visualized tRNA and protein synthesis events in fixed and live mouse primary cortical culture using fluorescently-labeled tRNAs. We were able to characterize the distribution and transport of tRNAs in different neuronal sub-compartments and to study their association with the ribosome. We found that tRNA mobility in neural processes is lower than in somata and corresponds to patterns of slow transport mechanisms, and that larger tRNA puncta co-localize with translational machinery components and are likely the functional fraction. Furthermore, chemical induction of long-term potentiation (LTP) in culture revealed up-regulation of mRNA translation with a similar effect in dendrites and somata, which appeared to be GluR-dependent 6 h post-activation. Importantly, measurement of protein synthesis in neurons with high resolutions offers new insights into neuronal function in health and disease states.
Collapse
Affiliation(s)
- Bella Koltun
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Sivan Ironi
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | | | - Iliana Barrera
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - Mohammad Hleihil
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | | | - Ranjan Sasmal
- New Chemistry Unit and Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka, India
| | - Sarit S Agasti
- New Chemistry Unit and Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka, India
| | - Deepak Nair
- Centre for Neuroscience, Indian Institute of Science, Bangalore, India
| | - Kobi Rosenblum
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel.,Center for Gene Manipulation in the Brain, University of Haifa, Haifa, Israel
| |
Collapse
|
17
|
The molecular and cellular mechanisms of depression: a focus on reward circuitry. Mol Psychiatry 2019; 24:1798-1815. [PMID: 30967681 PMCID: PMC6785351 DOI: 10.1038/s41380-019-0415-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/18/2019] [Accepted: 03/18/2019] [Indexed: 12/16/2022]
Abstract
Depression is a complex disorder that takes an enormous toll on individual health. As affected individuals display a wide variation in their clinical symptoms, the precise neural mechanisms underlying the development of depression remain elusive. Although it is impossible to phenocopy every symptom of human depression in rodents, the preclinical field has had great success in modeling some of the core affective and neurovegetative depressive symptoms, including social withdrawal, anhedonia, and weight loss. Adaptations in select cell populations may underlie these individual depressive symptoms and new tools have expanded our ability to monitor and manipulate specific cell types. This review outlines some of the most recent preclinical discoveries on the molecular and neurophysiological mechanisms in reward circuitry that underlie the expression of behavioral constructs relevant to depressive symptoms.
Collapse
|
18
|
Fernandez-Albert J, Lipinski M, Lopez-Cascales MT, Rowley MJ, Martin-Gonzalez AM, Del Blanco B, Corces VG, Barco A. Immediate and deferred epigenomic signatures of in vivo neuronal activation in mouse hippocampus. Nat Neurosci 2019; 22:1718-1730. [PMID: 31501571 PMCID: PMC6875776 DOI: 10.1038/s41593-019-0476-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 07/23/2019] [Indexed: 11/08/2022]
Abstract
Activity-driven transcription plays an important role in many brain processes, including those underlying memory and epilepsy. Here we combine genetic tagging of nuclei and ribosomes with RNA sequencing, chromatin immunoprecipitation with sequencing, assay for transposase-accessible chromatin using sequencing and Hi-C to investigate transcriptional and chromatin changes occurring in mouse hippocampal excitatory neurons at different time points after synchronous activation during seizure and sparse activation by novel context exploration. The transcriptional burst is associated with an increase in chromatin accessibility of activity-regulated genes and enhancers, de novo binding of activity-regulated transcription factors, augmented promoter-enhancer interactions and the formation of gene loops that bring together the transcription start site and transcription termination site of induced genes and may sustain the fast reloading of RNA polymerase complexes. Some chromatin occupancy changes and interactions, particularly those driven by AP1, remain long after neuronal activation and could underlie the changes in neuronal responsiveness and circuit connectivity observed in these neuroplasticity paradigms, perhaps thereby contributing to metaplasticity in the adult brain.
Collapse
Affiliation(s)
- Jordi Fernandez-Albert
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain
| | - Michal Lipinski
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain
| | - María T Lopez-Cascales
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain
| | - M Jordan Rowley
- Department of Biology, Emory University, Atlanta, GA, USA
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ana M Martin-Gonzalez
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain
- Nencki Institute of Experimental Biology PAS, Warsaw, Poland
| | - Beatriz Del Blanco
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain
| | | | - Angel Barco
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Sant Joan d'Alacant, Alicante, Spain.
| |
Collapse
|
19
|
Seimetz J, Arif W, Bangru S, Hernaez M, Kalsotra A. Cell-type specific polysome profiling from mammalian tissues. Methods 2018; 155:131-139. [PMID: 30500367 DOI: 10.1016/j.ymeth.2018.11.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/29/2018] [Accepted: 11/26/2018] [Indexed: 12/21/2022] Open
Abstract
The regulation of gene expression occurs through complex relationships between transcription, processing, turnover, and translation, which are only beginning to be elucidated. We know that at least for certain messenger (m) RNAs, processing, modifications, and sequence elements can greatly influence their translational output through recognition by translation and turn-over machinery. Recently, we and others have combined high-throughput sequencing technologies with traditional biochemical methods of studying translation to extend our understanding of these relationships. Additionally, there is growing importance given to how these processes may be regulated across varied cell types as a means to achieve tissue-specific expression of proteins. Here, we provide an in-depth methodology for polysome profiling to dissect the composition of mRNAs and proteins that make up the translatome from both whole tissues and a specific cell type isolated from mammalian tissue. Also, we provide a detailed computational workflow for the analysis of the next-generation sequencing data generated from these experiments.
Collapse
Affiliation(s)
- Joseph Seimetz
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA
| | - Waqar Arif
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA
| | - Mikel Hernaez
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois, Urbana-Champaign, IL, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA; Cancer Center@ Illinois, University of Illinois, Urbana-Champaign, IL, USA.
| |
Collapse
|
20
|
Ouwenga R, Lake AM, Aryal S, Lagunas T, Dougherty JD. The Differences in Local Translatome across Distinct Neuron Types Is Mediated by Both Baseline Cellular Differences and Post-transcriptional Mechanisms. eNeuro 2018; 5:ENEURO.0320-18.2018. [PMID: 30723792 PMCID: PMC6361723 DOI: 10.1523/eneuro.0320-18.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 12/05/2018] [Accepted: 12/12/2018] [Indexed: 12/13/2022] Open
Abstract
Local translation in neurites is a phenomenon that enhances the spatial segregation of proteins and their functions away from the cell body, yet it is unclear how local translation varies across neuronal cell types. Further, it is unclear whether differences in local translation across cell types simply reflect differences in transcription or whether there is also a cell type-specific post-transcriptional regulation of the location and translation of specific mRNAs. Most of the mRNAs discovered as being locally translated have been identified from hippocampal neurons because their laminar organization facilitates neurite-specific dissection and microscopy methods. Given the diversity of neurons across the brain, studies have not yet analyzed how locally translated mRNAs differ across cell types. Here, we used the SynapTRAP method to harvest two broad cell types in the mouse forebrain: GABAergic neurons and layer 5 projection neurons. While some transcripts overlap, the majority of the local translatome is not shared across these cell types. In addition to differences driven by baseline expression levels, some transcripts also exhibit cell type-specific post-transcriptional regulation. Finally, we provide evidence that GABAergic neurons specifically localize mRNAs for peptide neurotransmitters, including somatostatin and cortistatin, suggesting localized production of these key signaling molecules in the neurites of GABAergic neurons. Overall, this work suggests that differences in local translation in neurites across neuronal cell types are poised to contribute substantially to the heterogeneity in neuronal phenotypes.
Collapse
Affiliation(s)
- Rebecca Ouwenga
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Allison M. Lake
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Shivani Aryal
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Tomas Lagunas
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Joseph D. Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110
| |
Collapse
|
21
|
Burger LL, Vanacker C, Phumsatitpong C, Wagenmaker ER, Wang L, Olson DP, Moenter SM. Identification of Genes Enriched in GnRH Neurons by Translating Ribosome Affinity Purification and RNAseq in Mice. Endocrinology 2018; 159. [PMID: 29522155 PMCID: PMC6287592 DOI: 10.1210/en.2018-00001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Gonadotropin-releasing hormone (GnRH) neurons are a nexus of fertility regulation. We used translating ribosome affinity purification coupled with RNA sequencing to examine messenger RNAs of GnRH neurons in adult intact and gonadectomized (GDX) male and female mice. GnRH neuron ribosomes were tagged with green fluorescent protein (GFP) and GFP-labeled polysomes isolated by immunoprecipitation, producing one RNA fraction enhanced for GnRH neuron transcripts and one RNA fraction depleted. Complementary DNA libraries were created from each fraction and 50-base, paired-end sequencing done and differential expression (enhanced fraction/depleted fraction) determined with a threshold of >1.5- or <0.66-fold (false discovery rate P ≤ 0.05). A core of ∼840 genes was differentially expressed in GnRH neurons in all treatments, including enrichment for Gnrh1 (∼40-fold), and genes critical for GnRH neuron and/or gonadotrope development. In contrast, non-neuronal transcripts were not enriched or were de-enriched. Several epithelial markers were also enriched, consistent with the olfactory epithelial origins of GnRH neurons. Interestingly, many synaptic transmission pathways were de-enriched, in accordance with relatively low innervation of GnRH neurons. The most striking difference between intact and GDX mice of both sexes was a marked downregulation of genes associated with oxidative phosphorylation and upregulation of glucose transporters in GnRH neurons from GDX mice. This may suggest that GnRH neurons switch to an alternate fuel to increase adenosine triphosphate production in the absence of negative feedback when GnRH release is elevated. Knowledge of the GnRH neuron translatome and its regulation can guide functional studies and can be extended to disease states, such as polycystic ovary syndrome.
Collapse
Affiliation(s)
- Laura L Burger
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
| | - Charlotte Vanacker
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
| | | | - Elizabeth R Wagenmaker
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
| | - Luhong Wang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
| | - David P Olson
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Suzanne M Moenter
- Department of Molecular and Integrative Physiology, University of Michigan, Ann
Arbor, Michigan
- Department of Internal Medicine, University of Michigan, Ann Arbor,
Michigan
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor,
Michigan
- Correspondence: Laura L. Burger, PhD, University of Michigan, 7725 Med Sci II, 1137 E. Catherine
Street, Ann Arbor, Michigan 48109-5622. E-mail:
| |
Collapse
|