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 of ten superfamilies of DNA transposon-derived conserved TF families (ZBED, CENPB, FHY3, HTH-Psq, THAP, and FLYWCH) were identified across nine phyla encompassing the entire metazoan phylogeny. The most extensive convergent domestication of potentially 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.

The highly repetitive genome of Myxobolus sp., a myxozoan parasite of fathead minnows

“…A good example of this is the expansion in proteins with the FLYWCH domains identified in M. rasmusseni . A recent analysis of DNA transposon-derived transcription factors in animals found that FLYWCH-domain containing transcription factors are rare in animals but have undergone expansion in one phylum of non-bilaterian animals – Ctenophora (Mukherjee & Moroz, 2023). This study did not include myxozoans in their comparisons.…”

Convergent evolution of type I antifreeze proteins from four different progenitors in response to global cooling

“…Despite the myriad detrimental effects that TEs have on the genome, they also have positive effects and their regulatory sequences have been co-opted by a number of genes (71, 72). In addition, numerous genes have arisen through ‘domestication’ of TEs, including proteins involved in the function of the brain and placenta (72), as well as a large number of transcription factors (73). They can also act as drivers of gene duplication, even after they have lost the ability to transpose on their own (72).…”

DOMESTICATION IS THE PROPRIETARY CASE OF EVOLUTION: ABOUT THE UNIVERSALITY OF PRINCIPLES AND ELEMENTS (review)

“…В геномах животных среди ТЕ доминируют короткие неавтономные ретротранспозоны, у растений -эндогенные ретровирусы (54); у животных, по крайней мере позвоночных, ключевым элементом в архитектонике интерфазного ядра, по-видимому, служит мотив посадки TF CTCF, у растений -сложный комплекс мотивов, вовлекаемых в межбелковые взаимодействия (77). Существенно различаются и семейства ТЕ, последовательности которых составляют основу для формирования факторов регуляции транскрипции TF у многоклеточных (78). Один из ярких примеров участия TE в приобретении новых признаков у животных -формирование и эволюция плаценты млекопитающих, связанные с активностью эндогенных ретровирусов, многие семейства которых были одомашнены с последующей генерацией новых регуляторных генов или регуляторных элементов (79).…”