Satellite DNA-containing gigantic introns in a unique gene expression program during Drosophila spermatogenesis

Abstract

12Intron gigantism, where genes contain megabase-sized introns, is observed across 13 species, yet little is known about its purpose or regulation. Here we identify a unique gene 14 expression program utilized for the proper expression of genes with intron gigantism. We 15 find that two Drosophila genes with intron gigantism, kl-3 and kl-5, are transcribed in a 16 spatiotemporal manner over the course of spermatocyte differentiation, which spans ~90 17 hours. The introns of these genes contain megabases of simple satellite DNA repeats that 18 comprise over 99% of the gene loci, and these satellite-DNA containing introns are 19 transcribed. We identify two RNA-binding proteins that specifically localize to kl-3 and kl-5 20 transcripts and are needed for the successful transcription or processing of these genes. We 21 propose that genes with intron gigantism require a unique gene expression program, which 22 may serve as a platform to regulate gene expression during cellular differentiation. 23 24 25

A germline PAF1 paralog complex ensures cell type-specific gene expression

“…The mechanism underlying the observed requirement of tPAF for normal expression of the six male fertility factor genes remains unknown. However, we speculate that tPAF plays a role in the co-transcriptional regulation of these gigantic genes to facilitate their timely expression before the end of spermatocyte development 48,54 . For example, tPAF might enable timely RNA polymerase II transcription through the vast repetitive intronic sequences within the male fertility factor genes, or facilitate efficient splicing of these gigantic introns.…”

“…In fact, all six male fertility factor genes showed reduced expression in Leo1L and Paf1L mutants in RNA-seq from spermatocyte as well as bulk testis, while Ctr9L mutants showed a similar trend with small effect size (Figure 4G, Figure S14E). All six fertility factor genes harbor gigantic introns in the megabase-range 46,47 that require the full ~90 hours-duration of spermatocyte development to transcribe 48 . We therefore speculate that tPAF, through an unknown co-transcriptional mechanism, enables expression of these gigantic genes on the Y chromosome, which likely contributes to the observed fertility defect in tPAF-deficient male flies.…”