The Conserved Intron Binding Protein EMB-4 Plays Differential Roles in Germline Small RNA Pathways of C. elegans

Publication date: 7 August 2017
Source:Developmental Cell, Volume 42, Issue 3
Author(s): Katarzyna M. Tyc, Amena Nabih, Monica Z. Wu, Christopher J. Wedeles, Julia A. Sobotka, Julie M. Claycomb
Proper regulation of the germline transcriptome is essential for fertility. In C. elegans, germline homeostasis hinges on a complex repertoire of both silencing and activating small RNA pathways, along with RNA processing. However, our understanding of how fundamental RNA processing steps intersect with small RNA machineries in the germline remains limited. Here, we link the conserved intron binding protein, EMB-4/AQR/IBP160, to the CSR-1 and HRDE-1 nuclear 22G-RNA pathways in the C. elegans germline. Loss of emb-4 leads to distinct alterations in CSR-1- versus HRDE-1-associated small RNA and mRNA transcriptomes. Our transcriptome-wide analysis shows that EMB-4 is enriched along pre-mRNAs of nearly 8,000 transcripts. While EMB-4 complexes are enriched for both intronic and exonic sequences of HRDE-1 targets, CSR-1 pathway targets are enriched for intronic, but not exonic, sequences. These data suggest that EMB-4 could contribute to a molecular signature that distinguishes the targets of these two germline small RNA pathways.

Graphical abstract

Teaser

The CSR-1 and HRDE-1 nuclear small RNA pathways maintain germline transcriptome homeostasis and fertility in C. elegans. Tyc, Nabih, Wu et al. implicate conserved intron binding protein EMB-4/AQR/IBP160 in these pathways. EMB-4 differentially binds to CSR-1 versus HRDE-1 targets, possibly contributing to a molecular signature that distinguishes transcripts between pathways.


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