NvERTx: A gene expression database to compare Embryogenesis and Regeneration in the sea anemoneNematostella vectensis

Abstract

For more than a century researchers have been comparing embryogenesis and regeneration hoping that lessons learned from embryonic development will unlock hidden regenerative potential. This problem has historically been a difficult one to investigate since the best regenerative model systems are poor embryonic models and vice versa. Recently however, the comparison of embryogenesis and regeneration has seen renewed interest as emerging models including the sea anemone Nematostella vectensis have allowed researchers to investigate these processes in the same organism. This interest has been further fueled by the advent of high-throughput transcriptomic analyses that provide virtual mountains of data. Unfortunately much of this data remains in raw unanalyzed formats that are difficult to access or browse. Here we present Nematostella vectensis Embryogenesis and Regeneration Transcriptomics -NvERTx, the first platform for comparing gene expression during embryogenesis and regeneration. NvERTx is comprised of close to 50 RNAseq datasets spanning embryogenesis and regeneration in Nematostella. These data were used to perform a robust de novo transcriptome assembly which users can search, BLAST and plot expression of multiple genes during these two developmental processes. The site is also home to the results of gene clustering analyses, to further mine the data and identify groups of co-expressed genes. The site can be accessed at http://nvertx.kahikai.org. Introduction:

Whole body regeneration deploys a rewired embryonic gene regulatory network logic

“…To compare embryogenesis and regeneration on a global transcriptome-wide scale we employed four RNAseq datasets, one spanning 16 time points of regeneration (Warner et al, 2018) and three spanning a total of 34 embryonic time points (Helm et al 2013;Fischer and Smith 2014;Warner et al 2018). In order to directly compare the data, raw sequencing reads were processed, mapped and quantified using the same workflow for all datasets (see materials and methods for quantification details).…”

“…The approach used to identify these genetic programs, comparative transcriptional profiling, highlights the utility in considering not just individual gene use but how those genes are arranged into co-expression modules. Here we investigated one module and the role apoptosis plays in regeneration but we anticipate further studies on gene module use during embryogenesis and regeneration as the community continues to investigate expression dynamics during these two processes thanks in part to a database containing all of the data from this study (Warner et al 2018). Further studies, especially those comparing regeneration activation across species, will provide novel insight into our understanding of why certain organisms can regenerate while others can't and could unlock hidden regenerative potential in poorly regenerating organisms.…”

“…Detailed methods of the RNAseq methodology can be found in (Warner et al 2018) and are described briefly here. For regeneration experiments, six week old juveniles were bisected below the pharynx and incubated in the dark 22°C in 1/3 strength ASW.…”

FGF signalling plays similar roles in development and regeneration of the skeleton in the brittle starAmphiura filiformis

“…However, these studies were limited to a comparison of only one or a few 11 genes. Most recently, the transcriptomes of the embryo and regenerating 12 stages of the sea anemone, Nematostella vectensis, have provided the first 13 large-scale resource for comparing those two processes (7). It is thus of great 14…”

“…However, few studies have 22 been carried out thus far, and these mostly compare the expression of a 23 single gene between development and regeneration in the same organism. A 24 new transcriptomic database has recently been published which will provide a 25 platform for whole-transcriptome comparison of development and 1 regeneration in the sea anemone, however no direct functional comparison of 2 specific molecular networks is yet available (7). 3…”