Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Zebrafish eye populations transcriptomics

ABSTRACT: The zebrafish eye develops from a neuroepithelial layer of retinal progenitors, which then become postmitotic and differentiate into the mature retinal cell types. After 72hpf, the embryonic development of the retina is completed, since all major cell types are present and arranged in the characteristic lamination of the vertebrate retina. At this point, the cells located in the central retina have already exited the cell cycle and almost all growth comes from astem cell niche located at the periphery of the retina, called the ciliary marginal zone (CMZ). The CMZ is an heterogeneous region composed of stem cells, which continuously supply the CMZ with intermediate progenitors, that gradually proliferate and differentiate moving towards the central retina, a process that spatially recapitulates the temporal progression of embryonic development. The aim of this project is to characterise the transcriptome of the stem cells and the proliferative progenitors in order to build gene networks within each compartment, and subsequently characterise the mechanisms by which a stem cell gives rise to a differentiated cell in a post-embryonic retina This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Danio rerio

SUBMITTER:

PROVIDER: E-ERAD-441 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The early retinal progenitor-expressed gene Sox11 regulates the timing of the differentiation of retinal cells. Sry-related HMG box (Sox) proteins play diverse and critical roles in a variety of morphogenetic processes during embryonic development. Sox11 and Sox4 are members of the SoxC subtype, and we found that Sox11 was strongly expressed in early retinal progenitor cells, and that when expression of Sox11 subsided around birth, Sox4 expression began. To analyze the role of Sox11 and Sox4 in retinal development, we perturbed their expression pattern by expressing them ectopically in retinal explant culture. Overexpression of Sox11 or Sox4 in retinal progenitors resulted in similar phenotypes, that is, increased cone cells and decreased Muller glia. Sox11-knockout retinas showed delayed onset and progress of differentiation of early-born retinal cells during the embryonic period. After birth, retinal differentiation took place relatively normally, probably because of the redundant activity of Sox4, which starts to differentiate around birth. Neither overexpression nor loss-of-function analysis gave any evidence that Sox11 and Sox4 directly regulate transcription of genes critical to early-born retinal cells. However, histone H3 acetylation status of the early neurogenic genes was lowered in knockout retinas, suggesting that Sox11 regulates the timing of differentiation in early-born retinas by creating an epigenetic state that helps to establish the competency to differentiate. We also found that the unique expression patterns of Sox11 and Sox4 may be achieved by the Notch signaling pathway and by epigenetic regulation. Taking our findings together, we propose that the precise regulation of Sox11 and Sox4 expression during retinogenesis by multiple mechanisms leads to the fine adjustment of retinal differentiation. To delineate the molecular mechanisms underlying the retinal action of Sox11, we performed microarray analysis of E18 retinas from wild-type and Sox11 knockout mice. Total RNA was obtained from each one retina of Sox11 knockout and wild-type littermate embryos at E18.

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Zebrafish eye populations transcriptomics

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