Transposon-derived transcription factors across metazoans

Abstract

Transposable elements (TE) could serve as sources of new transcription factors (TFs) in plants and some other model species, but such evidence is lacking for most animal lineages. Here, we discovered multiple independent co-options of TEs to generate 788 TFs across Metazoa, including all early-branching animal lineages. Six out of ten super-families of known TEs (ZBED, CENPB, FHY3, HTH-Psq, THAP, and FLYWCH) were recruited as representatives of nine phyla. The most extensive convergent domestication of TE-derived TFs occurred in the hydroid polyps, polychaete worms, cephalopods, oysters, and sea slugs. Phylogenetic reconstructions showed species-specific clustering and lineage-specific expansion; none of the identified TE-derived TFs revealed homologs in their closest neighbors. Together, our study established a framework for categorizing TE-derived TFs and informing the origins of novel genes across phyla.

Evolution of homology: From archetype towards a holistic concept of cell type

“…Therefore, the structural and functional complexity of metazoans must have been shaped concurrently by other evolutionary processes, particularly, the expansion of distal cis ‐regulators (e.g., Sebé‐Pedrós et al, 2016; Sebé‐Pedrós, Chomsky, et al, 2018; Sebé‐Pedrós, Saudemont, et al, 2018) and gain/change of cell function via the mechanisms of creating multidomain proteins, including exon shuffling (e.g., Patthy, 2021). It is the matter of future discovery to understand how cell phenotype stability is supported by the underlying gene expression, if and how regulatory factor specificity or the end function of regulated genes can be affected by engaging new specific distal enhancers (Gaiti et al, 2017; Schwaiger et al, 2014; Sebé‐Pedrós et al, 2016), promoter types (Lenhard et al, 2012), regulatory RNAs and their binding sites (Gaiti et al, 2018) or other emerging sources of genetic regulation and enrichment, such as transposable elements (Mukherjee & Moroz, 2022).…”