Nucleome Dynamics during Retinal Development

Norrie, Jacqueline L.; Lupo, Marybeth; Xu, Beisi; Diri, Issam Al; Valentine, Marc; Putnam, Daniel K.; Griffiths, Lyra; Zhang, Jiakun; Johnson, Dianna A.; Easton, John; Shao, Ying; Honnell, Victoria; Frase, Sharon; Miller, Shondra; Stewart, Victoria; Zhou, Xin; Chen, Xiang; Dyer, Michael A.

doi:10.1016/j.neuron.2019.08.002

Cited by 77 publications

(110 citation statements)

References 65 publications

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“…This combined strategy identified a Vsx2 super‐enhancer with a specific activity in bipolar cells. In mouse, the deletions of this Vsx2 super‐enhancer resulted in the total absence of bipolar neurons, with no impairment of RPCs or Müller glia, where Vsx2 expression is also required for a proper development of the retina (Figure D) . These data have set a new milestone remarking the importance of single‐cell analyses to spot critical cis‐regulatory interactions in retina differentiation.…”

Section: Rare Cell Types and Neuron‐specific Enhancers Can Be Identifmentioning

confidence: 82%

“…Furthermore, model's predictions need to be eventually validated by genetic experiments in which key nodes (TF), and particularly central edges (cis‐regulatory elements) are tested. Although CRISPR/Cas9 editing has allowed investigating the precise role of a few cis‐regulatory modules in retina development, these are still isolated examples . Systems biology approaches need to be developed also for functional analyses in order to progress in our understanding of the retina GRNs, and to identify potential therapeutic targets for sight diseases.…”

Section: Conclusion Challenges and Future Directionsmentioning

confidence: 99%

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

Buono

Martı́nez-Morales

2020

BioEssays

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The ontogeny of the vertebrate retina has been a topic of interest to developmental biologists and human geneticists for many decades. Understanding the unfolding of the genetic program that transforms a field of progenitors cells into a functionally complex and multi‐layered sensory organ is a formidable challenge. Although classical genetic studies succeeded in identifying the key regulators of retina specification, understanding the architecture of their gene network and predicting their behavior are still a distant hope. The emergence of next‐generation sequencing platforms revolutionized the field unlocking the access to genome‐wide datasets. Emerging techniques such as RNA‐seq, ChIP‐seq, ATAC‐seq, or single cell RNA‐seq are used to characterize eye developmental programs. These studies provide valuable information on the transcriptional and cis‐regulatory profiles of precursors and differentiated cells, outlining the trajectories that connect each intermediate state. Here, recent systems biology efforts are reviewed to understand the genetic programs shaping the vertebrate retina.

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Section: Rare Cell Types and Neuron‐specific Enhancers Can Be Identifmentioning

confidence: 82%

Section: Conclusion Challenges and Future Directionsmentioning

confidence: 99%

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

Buono

Martı́nez-Morales

2020

BioEssays

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“…However, HiC libraries may have a high level of trans-interactions when samples (such as tissues) are harder to process. For example, the published mouse retina dataset that we selected possesses a high level of trans-interactions [30]. Whether we include these interactions or not in calculating the resolution would have a significant impact on the final result.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, the 20 th percentile of coverage can be considered as a linear function of the window size for a given number of reads, as well as a linear function of the number of valid reads for a given window size. To validate our model, we used several subsamples of high-resolution HiC datasets that were publicly available (see methods) [6,30]. We predicted the resolution versus the number of valid read pairs using a 100M sequenced read pairs subsample of the library.…”

Section: Elucidation Of Relationship Between the Resolution And The Qmentioning

confidence: 99%

“…). Similarly, we tested HiCRes on postmitotic cell types including HiC libraries from MboI digested chromatin of mouse retina[30] (Figure 3 B) and those performed using a kit from Arima technology on purified mouse rod photoreceptors generated in our Laboratory(Figure 3 C). For all these various samples, the predictions perfectly corroborated the observed resolution intervals.…”

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confidence: 99%

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HiCRes: a computational method to estimate and predict the resolution of HiC libraries

Marchal

Singh

Corso-Díaz

et al. 2020

Preprint

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Three-dimensional (3D) conformation of the chromatin is crucial to stringently regulate gene expression patterns and DNA replication in a cell-type specific manner. HiC is a key technique for measuring 3D chromatin interactions genome wide. Estimating and predicting the resolution of a library is an essential step in any HiC experimental design. Here, we present the mathematical concepts to estimate the resolution of a library and predict whether deeper sequencing would enhance the resolution. We have developed HiCRes, a docker pipeline, by applying these concepts to human and mouse HiC libraries.

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Single‐cell RNA sequencing: A new opportunity for retinal research

et al. 2021

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Single-cell RNA sequencing (scRNA-seq) is a technology for single-cell transcriptome analysis that can be used to characterize complex dynamics of various retinal cell types. It provides deep scrutiny into the gene expression character of diverse cell types, lending insight into all the biological processes being carried out. The scRNA-seq is an alternative to regular RNA-seq, which does not achieve cellular heterogeneity. The retina, is a part of the central nervous system (CNS) and consists of six types of neurons and several types of glial cells. Studying retinal cell heterogeneity is important for understanding retinal diseases. Currently, scRNA-seq is employed to assess retina development and retinal disease pathogenesis and has improved our understanding of the relationship between the retina, its visual pathways, and the brain. Moreover, this technology provides new ideas on the sensitivity and molecular mechanisms of cell subtypes involved in retinal-related diseases. The application of scRNA-seq technology has given us a deeper understanding of the latest advancements and challenges in retinal development and diseases. We advocate scRNA-seq as one of the important tools for developing novel therapies for retinal diseases. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA in Disease and Development > RNA in Development RNA in Disease and Development > RNA in Disease K E Y W O R D S data analysis, retina development, retina disease, retina neuron, single-cell RNA sequencing | INTRODUCTIONCells are the basic components of living things, with each cell type being unique (Wagner et al., 2016). Regular RNA sequencing (RNA-seq) often fails to capture this uniqueness. Single-cell RNA sequencing (scRNA-seq) is the emerging technology that can overcome this challenge (Macosko et al., 2015;Ramskold et al., 2012). The scRNA-seq is a method of profiling individual cell transcriptomes. This approach allows for the classification of different cell types and identification of novel biomarkers. scRNA-seq is also used to reveal the mechanisms underlying retinal development, function,

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Nucleome Dynamics during Retinal Development

Cited by 77 publications

References 65 publications

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

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

HiCRes: a computational method to estimate and predict the resolution of HiC libraries

Single‐cell RNA sequencing: A new opportunity for retinal research

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