This set of data confirms that PARP3 does specifically bind developmental genes and in particular some crucial for neuronal specification.
An in vivo analysis of the expression of PARP3-bound developmental genes in the context of reduced PARP3 expression in zebrafish embryos reveals that it regulates the expression of several developmental genes critical for the specification of neural crest cells at the neural plate border of zebrafish embryos.
These deregulated bivalently marked Ring1b bound genes included mostly developmental genes, such as Bin1, Bmi1, Bmp7, Col4a2, Ccnd2, En1, Gata3, Lmx1a and Wnt6, and were predominantly derepressed in absence of Ring1b (86%; 75/87; Figure 6H, 6I).
Moreover, GO terms of genes in the vicinity of the 2305 Tip60 bound enhancers are associated with developmental processes (Fig. 6d).
As shown previously (Hoogenkamp et al, 2009), Csf1r cannot be bound by RUNX1 at this developmental stage (Supplementary Figure 6D).
Nonetheless, we do not generally detect an obvious change in droplet-bound dynein levels as a function of developmental stage (Fig. 4C), suggesting there are likely not dramatic changes in the amount of dynein bound to the droplets in different developmental phases (though these measurements are not sensitive enough to detect subtle changes).
This is consistent with earlier reports, which show a role for PcG proteins in repressing a set of developmental genes that are bound by Oct4 and Nanog in ES cells [25], [51].
First, developmental PRC targets are bound by unproductive RNAPII (S5p+S7p−S2p−) genome-wide.
We analyzed developmental profiles of the genomic regions bound by each FruM isoform and relationships to neighboring genes.
Canonical Wnt signaling is mitogenic in a variety of developmental contexts, and its transcriptional effector Tcf/Lef bound to β-catenin has been shown to interact with Runx proteins [24].
The identified Tip60 bound genes belong to gene sets with housekeeping and developmental functions.
