Epigenetic regulation of planarian stem cells by the SET1/MLL family of histone methyltransferases

Abstract

Chromatin regulation is a fundamental mechanism underlying stem cell pluripotency, differentiation, and the establishment of cell type-specific gene expression profiles. To examine the role of chromatin regulation in stem cells in vivo, we study regeneration in the freshwater planarian Schmidtea mediterranea. These animals possess a high concentration of pluripotent stem cells, which are capable of restoring any damaged or lost tissues after injury or amputation. Here, we identify the S. mediterranea homologs of the SET1/MLL family of histone methyltransferases and COMPASS and COMPASS-like complex proteins and investigate their role in stem cell function during regeneration. We identified six S. mediterranea homologs of the SET1/MLL family (set1, mll1/2, trr-1, trr-2, mll5–1 and mll5–2), characterized their patterns of expression in the animal, and examined their function by RNAi. All members of this family are expressed in the stem cell population and differentiated tissues. We show that set1, mll1/2, trr-1, and mll5–2 are required for regeneration and that set1, trr-1 and mll5–2 play roles in the regulation of mitosis. Most notably, knockdown of the planarian set1 homolog leads to stem cell depletion. A subset of planarian homologs of COMPASS and COMPASS-like complex proteins are also expressed in stem cells and implicated in regeneration, but the knockdown phenotypes suggest that some complex members also function in other aspects of planarian biology. This work characterizes the function of the SET1/MLL family in the context of planarian regeneration and provides insight into the role of these enzymes in adult stem cell regulation in vivo.

Genome-wide analysis of the bHLH gene family in planarians identifies factors required for adult neurogenesis and neuronal regeneration

“…For long-term experiments, animals were fed 12 times over 6 weeks before amputation; uninjured animals were fixed 1 week after the final feeding. Relative gene expression after RNAi was determined by real-time quantitative PCR as described previously (Hubert et al, 2013); primers are listed in supplementary material Table S2.…”

Trithorax regulates systemic signaling duringDrosophilaimaginal disc regeneration

“…Interestingly, specific chromatin modifiers are important for regeneration in several organisms, suggesting that chromatin modification regulates the expression of at least some regeneration genes. For example, pharmacological inhibition of histone deacetylases blocks Xenopus tail regeneration (Tseng et al, 2011), the H3K27me3 demethylase Kdm6b.1 is required for zebrafish fin regeneration (Stewart et al, 2009), the PRC1 component Bmi1 is required for a regenerative response to pancreatitis in mice (Fukuda et al, 2012), several members of the Set1/MLL family of histone methyltransferases are required for the stem cell-based regeneration that occurs in planaria (Hubert et al, 2014), the SWI/SNF component Brg1 (Smarca4 -Mouse Genome Informatics) is essential for mouse epidermal wound repair and hair regeneration (Xiong et al, 2013) and its Drosophila homolog, Brahma, is important for midgut regeneration (Jin et al, 2013). In most of these cases, however, the extent to which tissue damage induces chromatin modification and the genes regulated by these chromatin modifiers during regeneration remain unknown.…”

“…Indeed, chromatin modification could rapidly and efficiently alter the developmental program in damaged tissue to enable regeneration. Importantly, RNAi knockdown of the planarian homolog of trx, Smed-mll1/2, did not prevent formation of a regeneration blastema but did impair regeneration of particular cells (Hubert et al, 2014), suggesting that Trx and its homologs play specific roles in regeneration across species.…”

The NuRD complex componentp66suppresses photoreceptor neuron regeneration in planarians

“…2012) and set1 (Hubert et al. 2013; Duncan et al. 2015), histone methyl binding protein HP1 (Zeng et al.…”