From transposon to transcription factor: Genome-wide functional studies of the conserved primate CSB-PGBD3 fusion protein
Gray, Lucas Tucker
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The CSB-PGBD3 fusion protein arose over 43 million years ago when a 2.5 kb piggyBac 3 (PGBD3) transposon inserted into intron 5 of the Cockayne syndrome Group B (CSB) gene in the common ancestor of all higher primates. As a result, full length CSB is now coexpressed with an abundant CSB-PGBD3 fusion protein by alternative splicing of CSB exons 1-5 to the PGBD3 transposase. An internal deletion of the piggyBac transposase ORF also gave rise to 889 dispersed, 140 bp MER85 elements which were mobilized in trans by PGBD3 transposase. Here, we show that the CSB-PGBD3 fusion protein binds MER85s in vitro, and induces a strong interferon-like innate antiviral immune response when expressed in CSB-null UVSS1KO cells. To explore the connection between DNA binding and gene expression changes induced by CSB-PGBD3, we investigated the genome-wide DNA binding profile of the fusion protein. CSB-PGBD3 binds to 363 MER85 elements in vivo, but these sites do not correlate with gene expression changes induced by the fusion protein. Instead, CSB-PGBD3 is enriched at AP-1, TEAD1, and CTCF motifs, presumably through protein-protein interactions with the cognate transcription factors; moreover, recruitment of CSB-PGBD3 to AP-1 and TEAD1 motifs correlates with nearby genes regulated by CSB-PGBD3 expression in UVSS1KO cells and downregulated by CSB rescue of mutant CS1AN cells. We also examined close PGBD3 homologs in galago monkeys, which have no domesticated PGBD3, and the freshwater cnidarian Hydra magnipapillata to show that as many as 30 mutations lead to the domestication of PGBD3. We conclude that horizontal transfer of PGBD3 created the CSB-PGBD3 fusion protein, which substantially reshapes the transcriptome in CS patient CS1AN, and that continued expression of the CSB-PGBD3 fusion protein in the absence of functional CSB may affect the clinical presentation of CS patients by directly altering the transcriptional program.
- Biological chemistry