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https://www.readbyqxmd.com/read/29777220/re-evaluating-microglia-expression-profiles-using-ribotag-and-cell-isolation-strategies
#1
Zhana Haimon, Alon Volaski, Johannes Orthgiess, Sigalit Boura-Halfon, Diana Varol, Anat Shemer, Simon Yona, Binyamin Zuckerman, Eyal David, Louise Chappell-Maor, Ingo Bechmann, Martin Gericke, Igor Ulitsky, Steffen Jung
Transcriptome profiling is widely used to infer functional states of specific cell types, as well as their responses to stimuli, to define contributions to physiology and pathophysiology. Focusing on microglia, the brain's macrophages, we report here a side-by-side comparison of classical cell-sorting-based transcriptome sequencing and the 'RiboTag' method, which avoids cell retrieval from tissue context and yields translatome sequencing information. Conventional whole-cell microglial transcriptomes were found to be significantly tainted by artifacts introduced by tissue dissociation, cargo contamination and transcripts sequestered from ribosomes...
May 18, 2018: Nature Immunology
https://www.readbyqxmd.com/read/29765956/transcriptomic-profiling-of-zebrafish-hair-cells-using-ribotag
#2
Maggie S Matern, Alisha Beirl, Yoko Ogawa, Yang Song, Nikhil Paladugu, Katie S Kindt, Ronna Hertzano
The zebrafish inner ear organs and lateral line neuromasts are comprised of a variety of cell types, including mechanosensitive hair cells. Zebrafish hair cells are evolutionarily homologous to mammalian hair cells, and have been particularly useful for studying normal hair cell development and function. However, the relative scarcity of hair cells within these complex organs, as well as the difficulty of fine dissection at early developmental time points, makes hair cell-specific gene expression profiling technically challenging...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29408990/leydig-cell-genes-change-their-expression-and-association-with-polysomes-in-a-stage-specific-manner-in-the-adult-mouse-testis
#3
Estela J Jauregui, Debra Mitchell, Savanna M Garza, Traci Topping, Cathryn A Hogarth, Michael D Griswold
Spermatogenesis in mammals occurs in a very highly organized manner within the seminiferous epithelium regulated by different cell types in the testis. Testosterone produced by Leydig cells regulates blood-testis barrier formation, meiosis, spermiogenesis, and spermiation. However, it is unknown whether Leydig cell function changes with the different stages of the seminiferous epithelium. This study utilized the WIN 18,446 and retinoic acid (RA) treatment regime combined with the RiboTag mouse methodology to synchronize male germ cell development and allow for the in vivo mapping of the Leydig cell translatome across the different stages of one cycle of the seminiferous epithelium...
May 1, 2018: Biology of Reproduction
https://www.readbyqxmd.com/read/29279367/cell-specific-and-region-specific-transcriptomics-in-the-multiple-sclerosis-model-focus-on-astrocytes
#4
Noriko Itoh, Yuichiro Itoh, Alessia Tassoni, Emily Ren, Max Kaito, Ai Ohno, Yan Ao, Vista Farkhondeh, Hadley Johnsonbaugh, Josh Burda, Michael V Sofroniew, Rhonda R Voskuhl
Changes in gene expression that occur across the central nervous system (CNS) during neurological diseases do not address the heterogeneity of cell types from one CNS region to another and are complicated by alterations in cellular composition during disease. Multiple sclerosis (MS) is multifocal by definition. Here, a cell-specific and region-specific transcriptomics approach was used to determine gene expression changes in astrocytes in the most widely used MS model, experimental autoimmune encephalomyelitis (EAE)...
January 9, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29130191/axon-trap-ribotag-affinity-purification-of-translated-mrnas-from-neuronal-axons-in-mouse-in-vivo
#5
Toshiaki Shigeoka, Jane Jung, Christine E Holt, Hosung Jung
Translating ribosome affinity purification (TRAP) is a widely used technique to analyze ribosome-bound mRNAs in particular target cells that express a tagged ribosomal protein. We developed axon-TRAP-RiboTag, a TRAP-based method that allows purification and identification of translated mRNAs from distal neuronal axons in mouse, and identified more than 2000 of translated mRNAs in retinal ganglion cell (RGC) axons in vivo. The use of Cre-negative littermate control to filter out false-positive signals allows unbiased detection, and combining TRAP with in vitro ribosome run-off enables identification of actively translated mRNAs...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29106571/retrieval-induced-upregulation-of-tet3-in-pyramidal-neurons-of-the-dorsal-hippocampus-mediates-cocaine-associated-memory-reconsolidation
#6
Cao Liu, Xue Sun, Zhilin Wang, Qiumin Le, Peipei Liu, Changyou Jiang, Feifei Wang, Lan Ma
Background: Memory retrieval refers to reexposure to information previously encoded and stored in the brain. Following retrieval, a once-consolidated memory destabilizes and undergoes reconsolidation, during which gene expression changes to restabilize memory. Investigating epigenetic regulation during reconsolidation could provide insights into normal memory formation and pathological memory associated with psychiatric disorders. Methods: We used cocaine-induced conditioned place preference to assess the cocaine-associated memory of mice and used chemogenetic methods to manipulate the activity of the pyramidal neurons in the dorsal hippocampus...
March 1, 2018: International Journal of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29104533/cell-type-specific-mrna-dysregulation-in-hippocampal-ca1-pyramidal-neurons-of-the-fragile-x-syndrome-mouse-model
#7
Laura Ceolin, Nathalie Bouquier, Jihane Vitre-Boubaker, Stéphanie Rialle, Dany Severac, Emmanuel Valjent, Julie Perroy, Emma Puighermanal
Fragile X syndrome (FXS) is a genetic disorder due to the silencing of the Fmr1 gene, causing intellectual disability, seizures, hyperactivity, and social anxiety. All these symptoms result from the loss of expression of the RNA binding protein fragile X mental retardation protein (FMRP), which alters the neurodevelopmental program to abnormal wiring of specific circuits. Aberrant mRNAs translation associated with the loss of Fmr1 product is widely suspected to be in part the cause of FXS. However, precise gene expression changes involved in this disorder have yet to be defined...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29074977/the-translation-of-cyclin-b1-and-b2-is-differentially-regulated-during-mouse-oocyte-reentry-into-the-meiotic-cell-cycle
#8
Seung Jin Han, João Pedro Sousa Martins, Ye Yang, Min Kook Kang, Enrico Maria Daldello, Marco Conti
Control of protein turnover is critical for meiotic progression. Using RiboTag immunoprecipitation, RNA binding protein immunoprecipitation, and luciferase reporter assay, we investigated how rates of mRNA translation, protein synthesis and degradation contribute to the steady state level of Cyclin B1 and B2 in mouse oocytes. Ribosome loading onto Ccnb1 and Mos mRNAs increases during cell cycle reentry, well after germinal vesicle breakdown (GVBD). This is followed by the translation of reporters containing 3' untranslated region of Mos or Ccnb1 and the accumulation of Mos and Cyclin B1 proteins...
October 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28155666/ribotagger-fast-and-unbiased-16s-18s-profiling-using-whole-community-shotgun-metagenomic-or-metatranscriptome-surveys
#9
Chao Xie, Chin Lui Wesley Goi, Daniel H Huson, Peter F R Little, Rohan B H Williams
BACKGROUND: Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis. RESULTS: Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion...
December 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28130359/macrophage-transcriptional-profile-identifies-lipid-catabolic-pathways-that-can-be-therapeutically-targeted-after-spinal-cord-injury
#10
Y Zhu, K Lyapichev, D H Lee, D Motti, N M Ferraro, Y Zhang, S Yahn, C Soderblom, J Zha, J R Bethea, K L Spiller, V P Lemmon, J K Lee
Although infiltrating macrophages influence many pathological processes after spinal cord injury (SCI), the intrinsic molecular mechanisms that regulate their function are poorly understood. A major hurdle has been dissecting macrophage-specific functions from those in other cell types as well as understanding how their functions change over time. Therefore, we used the RiboTag method to obtain macrophage-specific mRNA directly from the injured spinal cord in mice and performed RNA sequencing to investigate their transcriptional profile...
March 1, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27974617/hermes-regulates-axon-sorting-in-the-optic-tract-by-post-trancriptional-regulation-of-neuropilin-1
#11
Hanna Hörnberg, Jean-Michel Cioni, William A Harris, Christine E Holt
The establishment of precise topographic maps during neural development is facilitated by the presorting of axons in the pathway before they reach their targets. In the vertebrate visual system, such topography is seen clearly in the optic tract (OT) and in the optic radiations. However, the molecular mechanisms involved in pretarget axon sorting are poorly understood. Here, we show in zebrafish that the RNA-binding protein Hermes, which is expressed exclusively in retinal ganglion cells (RGCs), is involved in this process...
December 14, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27939582/new-transgenic-mouse-lines-for-selectively-targeting-astrocytes-and-studying-calcium-signals-in-astrocyte-processes-in-situ-and-in-vivo
#12
Rahul Srinivasan, Tsai-Yi Lu, Hua Chai, Ji Xu, Ben S Huang, Peyman Golshani, Giovanni Coppola, Baljit S Khakh
Astrocytes exist throughout the nervous system and are proposed to affect neural circuits and behavior. However, studying astrocytes has proven difficult because of the lack of tools permitting astrocyte-selective genetic manipulations. Here, we report the generation of Aldh1l1-Cre/ERT2 transgenic mice to selectively target astrocytes in vivo. We characterized Aldh1l1-Cre/ERT2 mice using imaging, immunohistochemistry, AAV-FLEX-GFP microinjections, and crosses to RiboTag, Ai95, and new Cre-dependent membrane-tethered Lck-GCaMP6f knockin mice that we also generated...
December 21, 2016: Neuron
https://www.readbyqxmd.com/read/27939396/a-role-for-peroxisome-proliferator-activated-receptor-gamma-coactivator-1%C3%AE-in-nucleus-accumbens-neuron-subtypes-in-cocaine-action
#13
Ramesh Chandra, Michel Engeln, T Chase Francis, Prasad Konkalmatt, Dipal Patel, Mary Kay Lobo
BACKGROUND: Molecules critically involved in cocaine behavioral plasticity are known to regulate and interact with peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α). In addition, the PGC-1α promoter has binding sites for early growth response 3 (Egr3), which plays a dynamic role in cocaine action in nucleus accumbens (NAc) medium spiny neuron (MSN) subtypes, those enriched in dopamine receptor D1 (D1-MSN) versus D2 (D2-MSN). However, the role of PGC-1α in NAc in cocaine action is unknown...
April 1, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/27321671/dynamic-axonal-translation-in-developing-and-mature-visual-circuits
#14
Toshiaki Shigeoka, Hosung Jung, Jane Jung, Benita Turner-Bridger, Jiyeon Ohk, Julie Qiaojin Lin, Paul S Amieux, Christine E Holt
Local mRNA translation mediates the adaptive responses of axons to extrinsic signals, but direct evidence that it occurs in mammalian CNS axons in vivo is scant. We developed an axon-TRAP-RiboTag approach in mouse that allows deep-sequencing analysis of ribosome-bound mRNAs in the retinal ganglion cell axons of the developing and adult retinotectal projection in vivo. The embryonic-to-postnatal axonal translatome comprises an evolving subset of enriched genes with axon-specific roles, suggesting distinct steps in axon wiring, such as elongation, pruning, and synaptogenesis...
June 30, 2016: Cell
https://www.readbyqxmd.com/read/26657954/ribotag-not-lost-in-translation
#15
REVIEW
Adam J Lesiak, John F Neumaier
No abstract text is available yet for this article.
January 2016: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/26054767/ribotag-is-a-flexible-tool-for-measuring-the-translational-state-of-targeted-cells-in-heterogeneous-cell-cultures
#16
Adam J Lesiak, Matthew Brodsky, John F Neumaier
Primary neuronal cultures are a useful tool for measuring pharmacological- and transgene-regulated gene expression; however, accurate measurements can be confounded by heterogeneous cell types and inconsistent transfection efficiency. Here we describe our adaptation of a ribosomal capture strategy that was designed to be used in transgenic mice expressing tagged ribosomal subunits (RiboTag) in specific cell types, thereby allowing measurement of translating RNAs from desired cell types within complex tissues...
June 2015: BioTechniques
https://www.readbyqxmd.com/read/25995477/opposing-role-for-egr3-in-nucleus-accumbens-cell-subtypes-in-cocaine-action
#17
Ramesh Chandra, T Chase Francis, Prasad Konkalmatt, Ariunzaya Amgalan, Amy M Gancarz, David M Dietz, Mary Kay Lobo
An imbalance in molecular signaling cascades and transcriptional regulation in nucleus accumbens (NAc) medium spiny neuron (MSN) subtypes, those enriched in dopamine D1 versus D2 receptors, is implicated in the behavioral responses to psychostimulants. To provide further insight into the molecular mechanisms occurring in MSN subtypes by cocaine, we examined the transcription factor early growth response 3 (Egr3). We evaluated Egr3 because it is a target of critical cocaine-mediated signaling pathways and because Egr3-binding sites are found on promoters of key cocaine-associated molecules...
May 20, 2015: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/25603796/cell-type-specific-gene-expression-profiling-in-brain-tissue-comparison-between-trap-lcm-and-rna-seq
#18
COMPARATIVE STUDY
TaeHyun Kim, Chae-Seok Lim, Bong-Kiun Kaang
The brain is an organ that consists of various cell types. As our knowledge of the structure and function of the brain progresses, cell type-specific research is gaining importance. Together with advances in sequencing technology and bioinformatics, cell type-specific transcriptome studies are providing important insights into brain cell function. In this review, we discuss 3 different cell type-specific transcriptome analyses i.e., Laser Capture Microdissection (LCM), Translating Ribosome Affinity Purification (TRAP)/RiboTag, and single cell RNA-Seq, that are widely used in the field of neuroscience...
July 2015: BMB Reports
https://www.readbyqxmd.com/read/25545461/drd2-cre-ribotag-mouse-line-unravels-the-possible-diversity-of-dopamine-d2-receptor-expressing-cells-of-the-dorsal-mouse-hippocampus
#19
Emma Puighermanal, Anne Biever, Julie Espallergues, Giuseppe Gangarossa, Dimitri De Bundel, Emmanuel Valjent
Increasing evidences suggest that dopamine facilitates the encoding of novel memories by the hippocampus. However, the role of dopamine D2 receptors (D2R) in such regulations remains elusive due to the lack of the precise identification of hippocampal D2R-expressing cells. To address this issue, mice expressing the ribosomal protein Rpl22 tagged with the hemagglutinin (HA) epitope were crossed with Drd2-Cre mice allowing the selective expression of HA in D2R-containing cells (Drd2-Cre:RiboTag mice). This new transgenic model revealed a more widespread pattern of D2R-expressing cells identified by HA immunoreactivity than the one initially reported in Drd2-EGFP mice, in which the hilar mossy cells were the main neuronal population detectable...
July 2015: Hippocampus
https://www.readbyqxmd.com/read/25486063/quantitative-profiling-of-initiating-ribosomes-in-vivo
#20
Xiangwei Gao, Ji Wan, Botao Liu, Ming Ma, Ben Shen, Shu-Bing Qian
Cells have evolved exquisite mechanisms to fine-tune the rate of protein synthesis in response to stress. Systemic mapping of start-codon positions and precise measurement of the corresponding initiation rate would transform our understanding of translational control. Here we present quantitative translation initiation sequencing (QTI-seq), with which the initiating ribosomes can be profiled in real time at single-nucleotide resolution. Resultant initiation maps not only delineated variations of start-codon selection but also highlighted a dynamic range of initiation rates in response to nutrient starvation...
February 2015: Nature Methods
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