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RNA-Seq and ChIP-Seq gene profiling of retinal ganglion cells in Math5Cre-driven Knockout of Ezh2 and G9a in murine retinal ganglion cells at P0

ABSTRACT: Epigenetic mark deposition during embryonic development contribute to postnatal homeostasis and tissue stability. Previously, we found out that Ezh2 contributes critically to the function and postnatal cell survival in bipolar cells but not in retinal ganglion cells in the retina. (Yan et al. Postnatal onset of retinal degeneration by loss of embryonic Ezh2 repression of Six1. Sci Report. doi:10.1038/srep33887; (Cheng L, Wong LJ, Yan N, Han RC et al. Ezh2 does not mediate retinal ganglion cell homeostasis or their susceptibility to injury. PLoS One 2018;13(2):e0191853.). In this study, we used RNA-seq to define up- and down regulated genes in both Ezh2 and G9a deficient (Math5Cre; Ezh2f/fG9af/+; dKO) retinal ganglion cells (RGC) to evaluate the hypothesis of Ezh2 and G9a interaction that has been discussed in other tissues but in the retina. ChIP-Seq was applied to evaluate H3K27me3 histone marks in retinal ganglion cells in wild type (WT), Ezh2 (Math5Cre; Ezh2-/-, sKO) and combined G9a-Ezh2 (Math5Cre; G9a+/-Ezh2-/-, dKO) knockout mutant mice at P1.

ORGANISM(S): Mus musculus

PROVIDER: GSE136360 | GEO | 2022/07/26

REPOSITORIES: GEO

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RNA-Seq gene profiling of retinal ganglion cells in Math5Cre-driven Knockout of Ezh2 in mice at P0

Project description:Epigenetic mark deposition during embryonic development contribute to postnatal homeostasis and tissue stability. Previously, we found out that Ezh2 contributes critically to the function and postnatal cell survival in bipolar cells in the retina. (Yan et al. Postnatal onset of retinal degeneration by loss of embryonic Ezh2 repression of Six1. Sci Report. doi:10.1038/srep33887) In this study, we used RNA-seq to define up- and down regulated genes in Math5CreEzh2f/f mice which express a selective deletion of Ezh2 in retinal ganglion cells (RGC). Gene expression was compared to wild type murine retinal cells.

2018-02-13 | GSE93674 | GEO

Combined double knockout of Ezh2 and G9a leads to expression change in murine retinal ganglion cells

Project description:Purpose: The goal of this study is to evaluate H3K27me3 histone marks in retinal ganglion cells in Ezh2 (Math5Cre, Ezh2-/-) and combined G9a-Ezh2 (Math5Cre; G9a+/-Ezh2-/-) knockout mutant mice at P1. Both Ezh2 and G9a are major epigenetic silencing machineries. Ezh2 mediates the trimethylation of lysine 27 on histone 3. Emerging evidences show an interdependence between Ezh2 and G9a to facilitate K27 trimethylation. Methods: P1 retinal ganglion cells were collected and chromatin immunoprecipitation was performed with EZ- CHIP kit from Millipore. Library preparation was done with Rubicon Genomics Thruplex DNAseq. Results: Here, we find a pool of common K27me3 target genes of Ezh2 and G9a in double knockout that leads to dysfunction in double mutant RGCs. Conclusion: This study provides the first Chip-seq analysis of K27me3 in murine RGCs. Our data supports that an interaction between Ezh2 and G9a is also evident in murine retinal ganglion cells. This work should be a framework for further study of retinal ganglion cells and retinal diseases.

2022-07-29 | GSE118011 | GEO

Direct induction of retinal ganglion cell-like neurons

Project description:Retinal ganglion cells (RGCs) are the projection neurons in the retina that connect the visual sensing tissue to the brain. We found that Ascl1/Brn3b/Isl1 transcription factor combination can quickly and efficiently reprogramming mouse embryonic fibroblasts (MEFs) into retinal ganglion cell-like neurons (iRGCs). Using RNA-seq, we analyzed the transcriptomes of MEFs infected with Ascl1/Brn3b/Isl1-overexpressing viruses on day 2 or day 7 of reprogramming, or the final iRGCs on day 13 of reprogramming.

2020-09-30 | GSE140689 | GEO

Transcription profiling of mouse developing retinal ganglion and amacrine cells reveals molecular heterogeneity of

Project description:During development of the central nervous system (CNS), cycling uncommitted progenitor cells give rise to a variety of distinct neuronal and glial cell types. As these different cell types are born, they progress from newly specified cells to fully differentiated neurons and glia. In order to define the developmental processes of individual cell types, single cell expression profiling was carried out on developing ganglion and amacrine cells of the murine retina. Individual cells from multiple developmental stages were isolated and profiled on Affymetrix oligonucleotide arrays. These experiments have yielded an expanded view of the processes underway in developing retinal ganglion and amacrine cells, as well as several hundred new marker genes for these cell types. In addition, this study has allowed for the definition of some of the molecular heterogeneity both between developing ganglion and amacrine cells and among subclasses of each cell type. Experiment Overall Design: Single retinal cells were isolated in tubes containing lysis buffer, their mRNAs were reverse transcribed, and the resulting cDNAs were PCR amplified for 35 cycles. Labeled cDNA samples were hybridized to Affymetrix 430 2.0 microarrays and the data was normalized using MAS5.0 software. Cells were identified post hoc as either developing retinal ganglion cells, amacrine cells or rod photoreceptor cells.

2008-06-16 | E-GEOD-9812 | biostudies-arrayexpress

Molecular heterogeneity of developing retinal ganglion and amacrine cells

Project description:During development of the central nervous system (CNS), cycling uncommitted progenitor cells give rise to a variety of distinct neuronal and glial cell types. As these different cell types are born, they progress from newly specified cells to fully differentiated neurons and glia. In order to define the developmental processes of individual cell types, single cell expression profiling was carried out on developing ganglion and amacrine cells of the murine retina. Individual cells from multiple developmental stages were isolated and profiled on Affymetrix oligonucleotide arrays. These experiments have yielded an expanded view of the processes underway in developing retinal ganglion and amacrine cells, as well as several hundred new marker genes for these cell types. In addition, this study has allowed for the definition of some of the molecular heterogeneity both between developing ganglion and amacrine cells and among subclasses of each cell type. Keywords: Single retinal cell gene expression profiling across multiple mouse developmental stages

2007-12-31 | GSE9812 | GEO

Molecular Profiling of Small and Large Retinal Ganglion Cells

2008-05-17 | GSE11468 | GEO

RNA-seq analysis of RNA from DBA/2J retinal ganglion cells

Project description:RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells

2017-03-07 | GSE90654 | GEO

Transcription profiling of rat small and large retinal ganglion cells

Project description:Different sub-types of ganglion cells existing in mammalian retinas possessing distinct function in processing the visual information. In primates, RGC are commonly divided into midget cells, which are relatively small, and parasol cells, with a larger soma size. Rodents also possess morphologically distinct populations, but their physiological properties are less characterized. The two types of mammalian RGCs differ in their response to pathological conditions such as retinal ischemia, diabetic retinopathy and glaucoma. In this work, we compared gene expression profiles of large (LRGCs) and small (SRGCs) ganglion cells isolated from rat retina in attempt to identify molecular determinants underlying differences in function and tolerance to stress. Experiment Overall Design: Rat RGCs retrogradely labeled with 4DI-10ASP were purified from freshly dissected retinas and subjected to fluorescent-activated cell sorting (FACS) in order to separate the SRGC and LRGC sub-populations. Actinomycin D was added to prevent new transcription during experimental procedures. Purified cells were used for RNA isolation. Following two rounds of linear amplification aRNA probes were hybridized with two-color Agilent Rat Genomic Oligo Arrays. We utilized the dye swap experimental design to eliminate the dye bias effects and make data from different experiments available for the cross-comparison.

2008-06-20 | E-GEOD-11468 | biostudies-arrayexpress

Subcellular expression profiling of the growth cones of retinal ganglion cells (RGC)

Project description:Cue-directed axon guidance depends partly on local translation in growth cones. Many mRNA transcripts are known to reside in developing axons yet little is known about their subcellular distribution or, specifically, which transcripts are in growth cones. Laser capture microdissection (LCM) was used to isolate the growth cones of retinal ganglion cell (RGC) axons of two vertebrate species, mouse and Xenopus, coupled with unbiased genome-wide microarray profiling. Localized mRNA from the isolated growth cones of Xenopus laevis and Mus musculus retinal ganglion cells were subjected to microarray analysis

2010-11-23 | E-GEOD-25166 | biostudies-arrayexpress

SARS-CoV-2 infects and replicates in photoreceptor and retinal ganglion cells of human retinal organoids

Project description:Recent data suggests that COVID-19 is a systemic disease affecting multiple organs including the central nervous system. Retinal involvement in COVID-19 has been indicated by several studies, yet many questions remain regarding the ability of SARS-CoV-2 to infect and replicate retinal cells and its effect on the retina. Here we have used human stem cell derived retinal organoids to study retinal infection by SARS-CoV-2. Indeed, SARS-CoV-2 can infect and replicate in retinal organoids, as it is shown to be able to infect different retinal lineages, including retinal ganglion cells and photoreceptors which are the targets of many retinal diseases leading to blindness. SARS-CoV-2 infection of retinal organoids also induces the expression of several inflammatory genes, including Interleukin 33, which is known to be associated with acute COVID-19 disease and with retinal degeneration. Finally, we show that blocking the ACE2 receptor using antibody treatment significantly reduces retinal organoid infection, indicating that SARS-CoV-2 infects retinal cells in an ACE2 dependent manner. These results suggest a direct retinal involvement in COVID-19, and emphasize the need to monitor retinal pathologies as a possible element of “long COVID”.

2022-01-01 | GSE174843 | GEO

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