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Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon

ABSTRACT: Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon

PROVIDER: PRJEB48872 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR7384910_1.fastq.gz	Fastqsanger.gz
	ERR7384910_2.fastq.gz	Fastqsanger.gz
	ERR7384920_1.fastq.gz	Fastqsanger.gz
	ERR7384920_2.fastq.gz	Fastqsanger.gz
	ERR7384911_1.fastq.gz	Fastqsanger.gz

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Comparative transcriptome analysis of the three different stages of the regenerating zebrafish telencephalon

Project description:Adult zebrafish can completely regenerate a wide range of injured organs including the CNS. RNA sequencing (RNA-Seq) is a high-throughput sequencing method facilitating quantification of gene expression in a precisely manner. Development of RNA-Seq technologies and their extensive data-analysis methods make investigation of regulatory genes and functional gene annotations possible under specific conditions. In this study, we reveal the whole transcriptome profiles of the lesioned hemispheres of the zebrafish telencephalon at early wound healing (1 day post-lesion), early proliferative (3 day post-lesion) and differentiation (14 day post-lesion) stages of regeneration.

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Comparative transcriptome analysis of the regenerating zebrafish telencephalon unravels a key regulatory role for Wnt/β-catenin signaling at the early wound healing stage

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Project description:Teleost fish have the remarkable ability to regenerate their body parts including heart, spinal cord, and the caudal fin, while many higher vertebrates including us humans have only a limited ability. To facilitate molecular and genetic approaches for regeneration, we previously established an assay using the fin fold of early stage larvae, which regenerate their caudal fin folds as in adult regeneration. Here, we performed transcriptional profiling of regenerating larval fin folds and identified genes with differential expression during regeneration. Gene expression profiling of zebrafish larval fin-fold regeneration was performed by comparing amputated fin fold and uncut control. Keywords: Stress response, injury response. Two time points, 18-24 hours post amputation (hpa) and 48 hpa, of regenerating fin fold were analyzed. We performed one replicate per each time point. For microarray expression profiling, total RNA was extracted from regenerating and uncut caudal fin folds of AB strain larvae. Tail tissues of 16-24 hpa, 48 hpa, and uncut siblings of the respective stages including 3-5 posterior somite segments were collected on ice. Total RNA was extracted by using TRIzol reagent (Invitrogen, Carlsbad, California, United States) according to the manufacturerâs instruction. The quantity and quality of total RNA were assessed by absorbance at 260 nm and 280 nm and by gel electrophoresis. Approx. 9 Î¼g of total RNA was recovered from ~250 tail tissues at 16-24 hpa or uncut control tissues; and approx. 5 Î¼g, from ~130 tail tissues at 48 hpa or uncut control tissues. Probes for microarray analysis were labeled with cy3 (amputated fin fold at 16-24 hpa and uncut control at 48 hpa) or cy5 (uncut control at 16-24 hpa and amputated fin fold at 48 hpa), and used for hybridization.

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Comparative Transcriptome Analysis of the Regenerating Zebrafish Telencephalon Unravels a Resource With Key Pathways During Two Early Stages and Activation of Wnt/β-Catenin Signaling at the Early Wound Healing Stage.

Project description:Owing to its pronounced regenerative capacity in many tissues and organs, the zebrafish brain represents an ideal platform to understand the endogenous regeneration mechanisms that restore tissue integrity and function upon injury or disease. Although radial glial and neuronal cell populations have been characterized with respect to specific marker genes, comprehensive transcriptomic profiling of the regenerating telencephalon has not been conducted so far. Here, by processing the lesioned and unlesioned hemispheres of the telencephalon separately, we reveal the differentially expressed genes (DEGs) at the early wound healing and early proliferative stages of regeneration, i.e., 20 h post-lesion (hpl) and 3 days post-lesion (dpl), respectively. At 20 hpl, we detect a far higher number of DEGs in the lesioned hemisphere than in the unlesioned half and only 7% of all DEGs in both halves. However, this difference disappears at 3 dpl, where the lesioned and unlesioned hemispheres share 40% of all DEGs. By performing an extensive comparison of the gene expression profiles in these stages, we unravel that the lesioned hemispheres at 20 hpl and 3 dpl exhibit distinct transcriptional profiles. We further unveil a prominent activation of Wnt/β-catenin signaling at 20 hpl, returning to control level in the lesioned site at 3 dpl. Wnt/β-catenin signaling indeed appears to control a large number of genes associated primarily with the p53, apoptosis, forkhead box O (FoxO), mitogen-activated protein kinase (MAPK), and mammalian target of rapamycin (mTOR) signaling pathways specifically at 20 hpl. Based on these results, we propose that the lesioned and unlesioned hemispheres react to injury dynamically during telencephalon regeneration and that the activation of Wnt/β-catenin signaling at the early wound healing stage plays a key role in the regulation of cellular and molecular events.

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