https://github.com/starostikm/SNPC-1.3
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README.md

# Code associated with "SNPC-1.3 is a sex-specific transcription factor that drives male piRNA expression in _C. elegans_"

<font size="6">https://www.biorxiv.org/content/10.1101/2020.08.06.240200v1</font>

<font size="6">**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.</font>

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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.

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## Getting Started
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.

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## Resources
Please refer to our publication for a detailed description of how these analyses were performed.
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