Code associated with "SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in C. elegans"
https://www.biorxiv.org/content/10.1101/2020.08.06.240200v1
Authors: Charlotte P. Choi, Rebecca J. Tay, Margaret R. Starostik, Suhua Feng, James J. Moresco, Brooke E. Montgomery, Emily Xu, Maya A. Hammonds, Michael C. Schatz, Taiowa A. Montgomery, John R. Yates III, Steven E. Jacobsen, John K. Kim.
Piwi-interacting RNAs (piRNAs) play essential roles in silencing repetitive elements to promote fertility in metazoans. Studies in worms, flies, and mammals reveal that piRNAs are expressed in a sex-specific manner. However, the mechanisms underlying this sex-specific regulation are unknown. Here we identify SNPC-1.3, a male germline-enriched variant of a conserved subunit of the small nuclear RNA activating protein complex, as a male-specific piRNA transcription factor in Caenorhabditis elegans. SNPC-1.3 colocalizes with the core piRNA transcription factor, SNPC-4, in nuclear foci of the male germline. Binding of SNPC-1.3 at male piRNA loci drives spermatogenic piRNA transcription and requires SNPC-4. Loss of snpc-1.3 leads to depletion of male piRNAs and defects in male-dependent fertility. Furthermore, TRA-1, a master regulator of sex determination, binds to the snpc-1.3 promoter and represses its expression during oogenesis. Loss of TRA-1 targeting causes ectopic expression of snpc-1.3 and male piRNAs during oogenesis. Thus, sexually dimorphic regulation of snpc-1.3 expression coordinates male and female piRNA expression during germline development.
The scripts directory contains code to run small RNA-seq and ChIP-seq analysis to reproduce all results and figures.
The data directory contains metadata tables.
Please refer to our publication for a detailed description of how these analyses were performed.