Project description:The mature mammalian retina results from a complex series of developmental events. A lot of work now exists on the organization, function, and development of mouse retina, and the high-throughput technologies for gene expression analyses have helped us to obtain deep insight into the mechanism about the genes that control the retinal neurogenesis and vasculogenesis. MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs that inhibit protein translation through binding to target mRNAs. miRNAs have been reported to be involved in regulating multiple physiological and pathological activities, such as ontogenesis, organogenesis, immunoprotection, and tumorigenesis. To identify miRNAs that are specifically regulated in retinal development, total RNAs isolated from retinas isolated from mice in different developmental periods were used for high-throughput sequencing. The data presented here reveals the spatiotemporal miRNA expression patterns which occur during mice retina development and provides a foundation to further investigate how miRNAs contribute to retinal neurogenesis and vasculogenesis.
Project description:Ten-eleven translocation (Tet) hydroxylases (Tet1-3) oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). In neurons increased 5hmC levels within gene bodies correlate positively with gene expression. Here, we studied 5hmC profiles (hMeDIP) during retinal maturation between postnatal week 2 and postnatal week 3 using HiSeq 2000 instrument. Study of retinal 5hmC profile dynamics in 2-week old and 3-week old wild type (WT) mouse.
Project description:The nuclei of rod photoreceptors in mice and other nocturnal species have an unusual inverted chromatin structure with centrally located heterochromatin that helps to focus light and improve photosensitivity. To gain a deeper understanding of this unique nuclear organization of rod photoreceptors, we have carried out Hi-C on retina at 3 stages of development and on purified rod photoreceptors. Predicted looping interactions from the Hi-C data were validated with fluorescent in situ hybridization (FISH). We discovered that a subset of genes important for retinal development, cancer and stress response in the retina are localized to the facultative heterochromatin domain in a developmental stage– and cell type–specific manner. We used machine learning to develop an algorithm based on our chromatin Hidden Markov Modeling (chromHMM) of retinal development to predict heterochromatin domains and study their dynamics during retinogenesis. FISH data for 264 genomic loci were used to train and validate the algorithm. These integrated data (https://pecan.stjude.cloud/retinalnucleome) were used to identify a developmental stage- and cell type-specific core regulatory circuit super-enhancer (CRC-SE) upstream of the Vsx2 gene that is required for bipolar neuron expression. Deletion of the Vsx2 CRC-SE in mice led to the loss of bipolar neurons in the retina.
Project description:We used parallel ribosome profiling and RNA sequencing to investigate the relationship between RNA editing and translation. Through systematically profiling mouse tissues from different developmental stages, we found dynamic changes in A-to-I RNA editome during retinal development. Further analysis revealed that altered translational efficiency in retinal development correlates with dynamics of A-to-I RNA editome.