Identification of neoblast- and regeneration-specific miRNAs in the planarian Schmidtea mediterranea

Abstract

In recent years, the planarian Schmidtea mediterranea has emerged as a tractable model system to study stem cell biology and regeneration. MicroRNAs are small RNA species that control gene expression by modulating translational repression and mRNA stability and have been implicated in the regulation of various cellular processes. Though recent studies have identified several miRNAs in S. mediterranea, their expression in neoblast subpopulations and during regeneration has not been examined. Here, we identify several miRNAs whose expression is enriched in different neoblast subpopulations and in regenerating tissue at different time points in S. mediterranea. Some of these miRNAs were enriched within 3 h postamputation and may, therefore, play a role in wound healing and/or neoblast migration. Our results also revealed miRNAs, such as sme-miR-2d-3p and the sme-miR-124 family, whose expression is enriched in the cephalic ganglia, are also expressed in the brain primordium during CNS regeneration. These results provide new insight into the potential biological functions of miRNAs in neoblasts and regeneration in planarians.

Analysis of extracellular vesicles produced in the biofilm by the dimorphic yeast Pichia fermentans

“…In P. fermentans EV the protein profile appeared to be conserved in both growth media considering the main known EV core components reported in literature for other yeasts (Lourenço et al, 2013;Zhu et al, 2016), except for two high molecular weight bands present only in YCU, which will require further investigation. snRNA (Wu, Xiao, Yang, & Yu, 2011), snR 17a (U3), essential for eukaryotic growth (Reichow, Hamma, Ferre-D'Amare, & Varani, 2007) and sme-mir-2152, highly expressed during regeneration of animal tissues (Sasidharan et al, 2013), were more highly expressed in EV from YCM. The increased expression of these miRNAs could be in keeping with findings in actively organizing tissues (Nolte-'t Hoen et al, 2015).…”

“…snR61, which controls site‐specific O‐methylation of RNAs (Watkins & Bohnsack, ) was more expressed in EV from YCU. Nevertheless, LSR1, a component of the stress‐induced spliceosome equivalent to mammalian U2 snRNA (Wu, Xiao, Yang, & Yu, ), snR 17a (U3), essential for eukaryotic growth (Reichow, Hamma, Ferre‐D'Amare, & Varani, ) and sme‐mir‐2152, highly expressed during regeneration of animal tissues (Sasidharan et al, ), were more highly expressed in EV from YCM. The increased expression of these miRNAs could be in keeping with findings in actively organizing tissues (Nolte‐'t Hoen et al, ).…”

Girardia dorotocephala transcriptome sequence, assembly, and validation through characterization of piwi homologs and stem cell progeny markers

“…The development of research tools to study gene expression and function in planarians, which include genome (Nishimura et al, 2015; Robb et al, 2015, 2008) and transcriptome (Brandl et al, 2016; Ishizuka et al, 2007; Nishimura et al, 2012; Sanchez Alvarado et al, 2002; Sasidharan et al, 2013; Zayas et al, 2005) sequences, as well as protocols for whole-mount in situ hybridization (King and Newmark, 2013; Pearson et al, 2009; Umesono et al, 1997) and RNA-interference (RNAi) (Newmark et al, 2003; Orii et al, 2003; Rouhana et al, 2013; Sanchez Alvarado and Newmark, 1999), have revitalized the use planarians as a model for molecular studies of stem cell-driven developmental processes (reviewed by Elliott and Sanchez Alvarado (2013), Newmark and Sanchez Alvarado (2002), Reddien and Sanchez Alvarado (2004), Rink (2013), Salo et al (2009) and Shibata et al (2010)). Planarians have also been the subject of recent work in toxicology, as well as behavioral, ecological, and evolutionary biology research (Alvarez-Presas et al, 2008; Hagstrom et al, 2016, 2015; Hicks et al, 2006; Inoue et al, 2015; Levin et al, 2016; Lombardo et al, 2011; Majdi et al, 2014; Shomrat and Levin, 2013), broadening their use as a model beyond fields related to developmental biology.…”

The novel microRNAs hsa-miR-nov7 and hsa-miR-nov3 are over-expressed in locally advanced breast cancer

“…The raw sequencing files (fastq) were processed using the novel miRNA prediction algorithm mirdeep v2.0.0.5 [10]. Potential novel miRNAs were identified using the human reference genome (hg19) and already identified miRNAs from humans and other hominids from miRbase 20 [28]. In the mirdeep2 algorithm, filtering parameters randfold P-value less than 0.05 and scores greater than or equal to 10 were applied.…”