Maintenance of Tissue Pluripotency by Epigenetic Factors Acting at Multiple Levels

Abstract

Pluripotent stem cells often adopt a unique developmental program while retaining certain flexibility. The molecular basis of such properties remains unclear. Using differentiation of pluripotent Drosophila imaginal tissues as assays, we examined the contribution of epigenetic factors in ectopic activation of Hox genes. We found that over-expression of Trithorax H3K4 methyltransferase can induce ectopic adult appendages by selectively activating the Hox genes Ultrabithorax and Sex comb reduced in wing and leg discs, respectively. This tissue-specific inducibility correlates with the presence of paused RNA polymerase II in the promoter-proximal region of these genes. Although the Antennapedia promoter is paused in eye-antenna discs, it cannot be induced by Trx without a reduction in histone variants or their chaperones, suggesting additional control by the nucleosomal architecture. Lineage tracing and pulse-chase experiments revealed that the active state of Hox genes is maintained substantially longer in mutants deficient for HIRA, a chaperone for the H3.3 variant. In addition, both HIRA and H3.3 appeared to act cooperatively with the Polycomb group of epigenetic repressors. These results support the involvement of H3.3-mediated nucleosome turnover in restoring the repressed state. We propose a regulatory framework integrating transcriptional pausing, histone modification, nucleosome architecture and turnover for cell lineage maintenance.

Splice Variants of the SWR1-type Nucleosome Remodeling Factor Domino Have Distinct Functions duringDrosophila melanogasterOogenesis

“…Sequence similarity searches revealed only one SWR1 homolog in fruit flies, the Domino (DOM) protein (Ruhf et al, 2001). Phenotypes of mutant domino alleles suggest broad requirements for cell proliferation and differentiation, homeotic gene silencing, Notch signaling, hematopoiesis and oogenesis (Braun et al, 1998; Eissenberg et al, 2005; Ellis et al, 2015; Kwon et al, 2013; Lu et al, 2007; Ruhf et al, 2001; Sadasivam and Huang, 2016; Walker et al, 2011; Xi and Xie, 2005; Yan et al, 2014). These requirements are presumed to be due to a wide-spread involvement of Domino in transcription regulation.…”

“…Domino was characterized as a gene required for cell proliferation and viability, homeotic gene regulation and Notch signaling (Eissenberg et al, 2005; Ellis et al, 2015; Gause et al, 2006; Kwon et al, 2013; Lu et al, 2007; Ruhf et al, 2001; Sadasivam and Huang, 2016; Walker et al, 2011). Previous genetic analyses did not attempt to resolve distinct functions of the two isoforms, as the known dom mutant alleles affect both splice forms.…”

Splice variants of the SWR1-type nucleosome remodeling factor Domino have distinct functions during Drosophila melanogaster oogenesis

“…Previous genetic analyses characterized dom as required for cell proliferation and viability, homeotic gene regulation and Notch signaling (Eissenberg et al, 2005;Ellis et al, 2015;Gause et al, 2006;Kwon et al, 2013;Lu et al, 2007;Ruhf et al, 2001;Sadasivam and Huang, 2016;Walker et al, 2011), but did not attempt to resolve distinct functions of the two isoforms. dom is essential for fly development (Ruhf et al, 2001) and dom mutants die during pupariation (Braun et al, 1998;Ruhf et al, 2001).…”

Feedback regulation by antagonistic epigenetic factors potentially maintains developmental homeostasis in Drosophila

“…Several distinct activities have been described for trxG proteins, including histone methylation (Byrd and Shearn, 2003;Shilatifard, 2012), chromatin remodeling (Kingston and Tamkun, 2014) and modulation of transcription elongation (Yang et al, 2005;Devaiah et al, 2012). Importantly, the supply of extra dosages of trxG proteins by overexpression can disrupt the silenced state, resulting in the ectopic expression of Hox genes (Chang et al, 2007;Sadasivam and Huang, 2016). These activated Hox genes may return rapidly to the silenced state after Trx withdrawal, and the effective erasure of the active state is dependent upon PcG and other epigenetic factors (Sadasivam and Huang, 2016).…”

“…Importantly, the supply of extra dosages of trxG proteins by overexpression can disrupt the silenced state, resulting in the ectopic expression of Hox genes (Chang et al, 2007;Sadasivam and Huang, 2016). These activated Hox genes may return rapidly to the silenced state after Trx withdrawal, and the effective erasure of the active state is dependent upon PcG and other epigenetic factors (Sadasivam and Huang, 2016). Thus, a mechanism that can survey and restore the proper balance between PcG and trxG proteins seems to be necessary to ensure stable transmission of the silenced state.…”