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Characterization of an Eye Field-like State during Optic Vesicle Organoid Development [RNA-seq]

ABSTRACT: Specification of the eye field (EF) within the neural plate marks the earliest detectable stage of eye development. Experimental evidence, primarily from non-mammalian model systems, indicates that the stable formation of this group of cells requires the activation of a set of key transcription factors (TFs). This critical event is challenging to probe in mammals and, quantitatively, little is known regarding the regulation of the transition of cells to this ocular fate. Using optic vesicle organoids to model the onset of the EF, we generate timecourse transcriptomic data allowing us to identify dynamic gene-expression programs that characterise this cellular-state transition. Integrating this with chromatin accessibility data suggests a direct role of canonical EFTFs in regulating these gene-expression changes, and highlights candidate cis-regulatory elements through which these TFs act. Finally, we begin to test a subset of these candidate enhancer elements, within the organoid system, by perturbing the underlying DNA sequence and measuring transcriptomic changes during EF activation.

ORGANISM(S): Mus musculus

PROVIDER: GSE213272 | GEO | 2023/07/06

REPOSITORIES: GEO

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Characterization of an Eye Field-like State during Optic Vesicle Organoid Development [ATAC-seq]

Project description:Specification of the eye field (EF) within the neural plate marks the earliest detectable stage of eye development. Experimental evidence, primarily from non-mammalian model systems, indicates that the stable formation of this group of cells requires the activation of a set of key transcription factors (TFs). This critical event is challenging to probe in mammals and, quantitatively, little is known regarding the regulation of the transition of cells to this ocular fate. Using optic vesicle organoids to model the onset of the EF, we generate timecourse transcriptomic data allowing us to identify dynamic gene-expression programs that characterise this cellular-state transition. Integrating this with chromatin accessibility data suggests a direct role of canonical EFTFs in regulating these gene-expression changes, and highlights candidate cis-regulatory elements through which these TFs act. Finally, we begin to test a subset of these candidate enhancer elements, within the organoid system, by perturbing the underlying DNA sequence and measuring transcriptomic changes during EF activation.

2023-07-06 | GSE213271 | GEO

Expression data of Xrx1 gain and loss of function experiments from early Xenopus laevis embryos (stage 13)

2013-09-23 | GSE35918 | GEO

Expression data of Xrx1 gain and loss of function experiments from early Xenopus laevis embryos (stage 13)

Project description:Eye development is a multistep process that requires specific inductive signals and precise morphogenetic movements, starting early during development in the eye-field, a well-definite region of the anterior neural plate. It has been demonstrated that a gene network of eye field transcription factors (EFTFs) contributes to specify the neural and retinal fate of the eye field. Among these EFTFs, Xrx1 is involved in proliferation and neurogenesis in the eye field and is necessary for the correct development of the retina. By means of Affymetrix microarrays, a high throughput screening was performed, looking for genes that can mediate the function of Xrx1, by comparison of the expression profiles of whole embryos in which the Xrx1 function was either overexpressed or abolished by use of morpholino antisense oligonucleotides. Xenopus laevis embryos were harvested soon after fertilization. 50ng of capped Xrx1 mRNA or 0.5pmol of MoXrx1 antisense oligonucleotides were coinjected with 400ng of GFP synthetic mRNA as a tracer, in both dorsal blastomeres of 4-cells stage embryos. Embryos were let to develop until stage 13, in which the eye field induction steps are active, and selected for correct injection site by fluorescence topographic assessment. RNA was extracted from each single embryo and control PCRs were performed to assess the correct molecular signature of Xrx1 loss- and gain- of function.

2013-09-23 | E-GEOD-35918 | biostudies-arrayexpress

R-spondin 2 is required for optic vesicle morphogenesis and neuroretina specification in vivo and in vitro

Project description:Using stem cell–based therapies to treat retinal abnormalities is becoming a likely possibility; therefore, identifying the key factors and the relevant mechanisms controlling optic vesicle morphogenesis and neuroretina (NR) differentiation is important. Recent advances in self-organizing, 3-dimensional (3D) tissue cultures of embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) provided a valuable in vitro model for characterizing regulatory cascades and signaling pathways controlling mammalian retinal development. Using Rx-GFP expressing ESCs and Six3–/– iPSCs we identified R-spondin 2 (Rspo2)-mediated repression of Wnt signaling as a novel required step during optic vesicle morphogenesis and NR differentiation. Furthermore, we also show that transient ectopic expression of Rspo2 in the anterior neural plate of transgenic mouse embryos was sufficient to arrest NR differentiation. ChIP assays identified Six3-responsive elements in the Rspo2-promoter region, indicating that Six3-mediated repression of Rspo2 is required to restrict Wnt signaling in the developing anterior neuroectoderm and allow eye development to proceed.

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Expression data from mouse optic nerve head after optic nerve crush

Project description:Reactive gliosis is a complex process that involves profound changes in gene expression. We used microarray to indentify differentially expressed genes and to investigate the molecular mechanisms of reactive gliosis in optic nerve head in response to optic nerve crush injury. C57Bl/6 female mice were 6-8 weeks old at the time of optic nerve crush surgery. The optic nerve in the left eye was crush 1 mm behind the globe for 10 seconds and the right eye served as contralateral control. The animals were allowed to recover for 1 day, 3 day, 1 week, 3 weeks and 3 months before the optic nerve heads were collected. The naive control mice did not receive any surgery in either eye. Due to the small tissue size of the mouse optic nerve head, two optic nerve heads were pooled together for each microarray chip. The left eyes and the right eyes of two mice were combined respectively to form one pair of experiment and control samples. There were five biological replicates (10 mice) for each condition.

2013-07-15 | E-GEOD-40857 | biostudies-arrayexpress

Single-cell transcriptional analysis reveals developmental stage-dependent changes in retinal progenitors in the murine early optic vesicle

Project description:The optic vesicle in the developing embryonic eye contains a multitude of neuroepithelial progenitors that subsequently differentiate into functionally distinct domains of the optic cup, such as the neural retina, pigment epithelium, and optic stalk. To investigate cell-type diversity across early optic vesicles before regionalization of the optic cup, we performed single-cell RNA-sequencing (scRNA-seq) using 7,989 cells from the presumptive eye area in mouse embryos at the 12–26-somite stages at five developmental time points. We demonstrated the presence of seven optic vesicle populations, including three unique cell types located in the ventricular surface or dorsoventral areas of the optic vesicle structure. Moreover, the remaining four populations of retinal progenitor cells could be classified according to their stage-dependent time point, and these cells exhibited altered expression of several structural and metabolic key genes, such as Col9a1 and Ckb, just before regionalization of the optic cup. From these data, we provide the first report on stage-dependent transcriptional profiles during initial retinal specification at single-cell resolution and highlight the unexpected developmental heterogeneity of the murine optic vesicle structure.

2021-02-08 | GSE148063 | GEO

Identification of genes expressed preferentially in the developing peripheral margin of the optic cup

Project description:Identification of genes expressed in a preferential manner in the developing ciliary body/iris will provide a starting point for future functional analyses. To identify candidate genes expressed in a variety of ocular tissues during development, we have profiled single cells from the developing eye. Post hoc identification of the origin of these cells showed that they included cells from the periphery of the developing optic cup. By comparing the expression profiles of these cells to many retinal cell types, candidate genes for preferential expression in the periphery were identified.

2009-05-01 | GSE15566 | GEO

Optic vesicle morphogenesis requires primary cilia.

Project description: Not available

| S-EPMC8167498 | biostudies-literature

A SIX6 reporter for studies of early optic development

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2021-08-31 | GSE179260 | GEO

Multi-species single-cell transcriptomic analysis of ocular compartment regulons

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