Neev, a novel long non-coding RNA, is expressed in chaetoblasts during regeneration of Eisenia fetida

Abstract

Eisenia fetida, the common vermicomposting earthworm, shows robust regeneration of posterior segments removed by amputation. During the period of regeneration, the newly formed tissue initially contains only undifferentiated cells but subsequently differentiates into a variety of cell types including muscle, nerve and vasculature. Transcriptomics analysis, reported previously, provided a number of candidate non-coding RNAs that were induced during regeneration. We found that one such long non-coding RNA (lncRNA) is expressed in the skin, only at the base of newly formed chaetae. The spatial organization and precise arrangement of the regenerating chaetae and the cells expressing the lncRNA on the ventral side clearly support a model wherein the regenerating tissue contains a zone of growth and cell division at the tip and a zone of differentiation at the site of amputation. The temporal expression pattern of the lncRNA, christened Neev, closely resembled the pattern of chitin synthase genes, implicated in chaetae formation. We found that the lncRNA harbours 49 sites for binding a set of four miRNAs while the Chitin Synthase 8 mRNA comprises 478 sites. The over-representation of shared miRNA sites suggests that lncRNA Neev may act as a miRNA sponge to transiently de-repress chitin synthase 8 during formation of new chaetae in the regenerating segments of Eisenia fetida.

Comparative Aspects of Annelid Regeneration: Towards Understanding the Mechanisms of Regeneration

“…The differences in the stages of regeneration used in different works also decrease the value of the published results for comparative transcriptomics (see Table 1). [24], Pristina leidyi [25], Eisenia fetida [26,27], Sphaerosyllis hystrix and Syllis gracilis [22], Eisenia andrei [28], Eudrilus eugeniae [29], and Lumbriculus variegatus [30] have lent support to the idea that a large and diverse repertoire of genes are up-regulated or down-regulated during regeneration in annelids. Many studies have shown the activation of, not only housekeeping genes and components of signaling pathways (FGF, MAPK, BMP, WNT, Hedgehog, Notch), but also genes that have specific functions in development, including homeobox genes (Hox, homothorax, even-skipped, msx), brachyury, factors related to nervous system development (gs, elav, slit), and stem-cellness [22,26,29,30].…”

“…The diameter of giant axons and the abundance of gap junctions, as well as the The molecular basis of neural regeneration has been poorly investigated. Works on the unbiased analysis have identified both conservative and novel potential drivers of reparative neurogenesis [22,23,[26][27][28]98,99]. Among the NS-associated genes, the strongest differential expression was noted for such neurodifferentiation markers as glutamine synthetase, slit, elav, neurofilament NF70, and Nerve Growth Factor [22,23,26,28,39,100].…”

“…So far, no targeted molecular genetic studies of muscle regeneration in annelids have been published. RNA-seq data on the earthworms Eisenia and Eudrilus indicate the presence of a large proportion of cells and genes associated with muscle differentiation in the regenerate [27,28]. Such marker genes with an enriched expression in the regenerative tissues are myosin heavy chains (paralogs of MHC, Myosin-10), tropomyosin (TPM), and obscurin (UNC-89).…”

Sex-biased gene expression precedes sexual dimorphism in the agonadal annelidPlatynereis dumerilii

“…lncRNAs can act as a decoy for miRNA that binds to specific mRNA targets, leading to increased expression of the mRNA targets (Ebert and Sharp, 2010). In the annelid Eisenia fetida , neev , a lncRNA has been related to the process of chaetogenesis acting as miRNA decoy (Patel et al, 2020). We identified numerous miRNAs that might interact with both id13944 and id3252 lncRNAs in P. dumerilii (Supplementary Materials 9 and 10), hinting at a role as a miRNA decoy.…”

It Cuts Both Ways: An Annelid Model System for the Study of Regeneration in the Laboratory and in the Classroom

“…Epigenetic regulation of regeneration is achieved by three main mechanisms: DNA methylation, histone modification and noncoding RNAs ( Rouhana and Tasaki, 2015 ). There are already reports of the relevance of epigenetic regulation for development and regeneration of annelids ( Giani et al, 2011 ; Niwa et al, 2013 ; Kozin and Kostyuchenko, 2015 ; Bhambri et al, 2018 ; Bicho et al, 2020 ; Singh Patel et al, 2020 ; Planques et al, 2021 ). An analysis of the regeneration transcriptome of Lumbriculus variegatus ( Tellez-Garcia et al, 2021 ) in search for transcripts encoding for writers and erasers of DNA methylation revealed genes encoding for DNA methyltransferases and several ten-eleven translocation proteins, as well as histone acetyltransferases, histone deacetylase, histone methyltransferases, and histone demethylases.…”