Retina Development in Vertebrates: Systems Biology Approaches to Understanding Genetic Programs

Buono, Lorena; Martı́nez-Morales, Juan Ramón

doi:10.1002/bies.201900187

Cited by 17 publications

(3 citation statements)

References 118 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Among them are the eye field transcription factors (Rx1, Pax6, Otx2, Optx2, Six3, Chx10, Prox1, Dlx1-2, Pitx1-2, etc.) that are activated in the retina at the early stage of embryogenesis and control retinal cell type specialization [42][43][44].…”

Section: Homeobox Transcription Factors Expressed In Retinamentioning

confidence: 99%

Inherited Eye Diseases with Retinal Manifestations through the Eyes of Homeobox Genes

Markitantova

Симирский

2020

IJMS

View full text Add to dashboard Cite

Retinal development is under the coordinated control of overlapping networks of signaling pathways and transcription factors. The paper was conceived as a review of the data and ideas that have been formed to date on homeobox genes mutations that lead to the disruption of eye organogenesis and result in inherited eye/retinal diseases. Many of these diseases are part of the same clinical spectrum and have high genetic heterogeneity with already identified associated genes. We summarize the known key regulators of eye development, with a focus on the homeobox genes associated with monogenic eye diseases showing retinal manifestations. Recent advances in the field of genetics and high-throughput next-generation sequencing technologies, including single-cell transcriptome analysis have allowed for deepening of knowledge of the genetic basis of inherited retinal diseases (IRDs), as well as improve their diagnostics. We highlight some promising avenues of research involving molecular-genetic and cell-technology approaches that can be effective for IRDs therapy. The most promising neuroprotective strategies are aimed at mobilizing the endogenous cellular reserve of the retina.

show abstract

Section: Homeobox Transcription Factors Expressed In Retinamentioning

confidence: 99%

Inherited Eye Diseases with Retinal Manifestations through the Eyes of Homeobox Genes

Markitantova

Симирский

2020

IJMS

View full text Add to dashboard Cite

show abstract

“…This is what is expected for TF that act predominantly as activators in the corresponding cell type. Reassuringly, the list of predicted activators includes several TF that are known to play key roles during retinal development such as Crx, Neurod1, Nr2e3, Nrl, Rora, Rorb, Rxrg, Sox9 and Thrb [30,[41][42][43].…”

Section: E Fmentioning

confidence: 99%

Evidence from combined analysis of single cell RNA-Seq and ATAC-Seq data of regulatory toggles operating in native and iPS-derived murine retina

Georges

Lavergne

Mandai³

et al. 2020

Preprint

View full text Add to dashboard Cite

17We herein report the generation and analysis of single-cell RNA Seq data (> 38,000 cells) from 18 native and iPSC-derived murine retina at four matched developmental stages spanning the 19 emergence of the major retinal cell types. We combine information from temporal sampling, 20 visualization of 3D UMAP manifolds in virtual reality, and RNA velocity analysis to show that 21 iPSC-derived 3D retinal aggregates broadly recapitulate the native developmental trajectories 22 with evidence supporting re-specification from amacrine cells to horizontal and 23 photoreceptor precursor cells, as well as a direct differentiation of Tbr1 + retinal ganglion cells 24 from neuro-epithelium cells. We show relaxation of spatial and temporal transcriptome 25 control, premature emergence and dominance of photoreceptor precursor cells, and 26 susceptibility of dynamically regulated pathways and transcription factors to culture 27 conditions in iPSC-derived retina. We generate bulk ATAC-Seq data for native and iPSC-28 derived murine retina at three of the four same developmental stages identifying ~125,000 29 peaks. The number of ATAC-Seq peaks increased with developmental stage in native but not 30 in iPSC-derived retina. We combine single-cell RNA Seq with ATAC-Seq information and 31demonstrate that approximately halve of the transcription factors that are dynamically 32 Georges et al.Page 2 of 46 regulated during retinal development act as repressors rather than activators. We provide 33 evidence that sets of activators and repressors with cell-type specific expression control 34

show abstract

“…Although the traditional RNA transcriptomics is often used to study the molecular mechanism of photoreceptor development at different stages in retinal development, the gene expression of single cell types cannot be accurately detected because of the cellular heterogeneity of retina [15]. With the rapid development of single-cell technologies, the development of each cell can be clearly observed, thus the molecule changes and regulation mechanism of retinal photoreceptor development can be detected more accurately.…”

Section: Introductionmentioning

confidence: 99%

Regulatory Mechanisms of Retinal Photoreceptors Development at Single Cell Resolution

Zhao

Peng

2021

IJMS

View full text Add to dashboard Cite

Photoreceptors are critical components of the retina and play a role in the first step of the conversion of light to electric signals. With the discovery of the intrinsically photosensitive retinal ganglion cells, which regulate non-image-forming visual processes, our knowledge of the photosensitive cell family in the retina has deepened. Photoreceptor development is regulated by specific genes and proteins and involves a series of molecular processes including DNA transcription, post-transcriptional modification, protein translation, and post-translational modification. Single-cell sequencing is a promising technology for the study of photoreceptor development. This review presents an overview of the types of human photoreceptors, summarizes recent discoveries in the regulatory mechanisms underlying their development at single-cell resolution, and outlines the prospects in this field.

show abstract

Retina Development in Vertebrates: Systems Biology Approaches to Understanding Genetic Programs

Cited by 17 publications

References 118 publications

Inherited Eye Diseases with Retinal Manifestations through the Eyes of Homeobox Genes

Inherited Eye Diseases with Retinal Manifestations through the Eyes of Homeobox Genes

Evidence from combined analysis of single cell RNA-Seq and ATAC-Seq data of regulatory toggles operating in native and iPS-derived murine retina

Regulatory Mechanisms of Retinal Photoreceptors Development at Single Cell Resolution

Contact Info

Product

Resources

About