Finally finished with the epigenetic machinery analysis for the Deep Dive Expression manuscript!
After compiling a list of ~90 proteins/genes involved in ncRNA biogenesis and function, and then manually curating fastas (primarily cnidarian) for those proteins, I’ve now identified miRNA targets in all 3 of our study species that correspond to these ncRNA machinery proteins. I also searched for targets that match other epigenetic machinery (e.g., histone modifier, chromatin signaling, etc.), from an epigenetic machinery fasta compiled by Hollie/Steven.
Code for annotating ncRNA machinery in A. pulchra, P. evermanni, and P. tuahiniensis
Code for annotating miRNA targets in all 3 species for both my curated ncRNA machinery and Hollie’s epigenetic machinery.
Results summary
Generally, the protein machinery that are putatively targeted by our coral miRNAs is extremely diverse, covering all major “branches” of epigenetic regulation
Plot
Four functional categories were represented across all three species: ncRNA biogenesis, ubiquitin signaling, DNA methylation and reading, and histone modification. A. pulchra has both the largest and most diverse repertoire of miRNA-targeted epimachinery (potentially related to A.pulchra being more completely annotated?).
This pattern is largely preserved when considering only the miRNA-target pairs that are negatively coexpressed (as expected under canonical miRNA function) (though, note the shorter scale):
Some differences do arise. ADP-ribosylation, for example, is no longer represented at all, and Apul no longer exhibits any functional association with histone modification machinery,