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

Area of Science:

• Molecular Biology
• Genetics
• RNA Biology

Background:

• Germline homeostasis relies on intricate small RNA pathways and RNA processing in C. elegans.
• The interplay between RNA processing and small RNA pathways in the germline is not fully understood.

Purpose of the Study:

• To investigate the role of the conserved intron binding protein EMB-4 in germline small RNA pathways.
• To determine how EMB-4 interacts with the CSR-1 and HRDE-1 nuclear 22G-RNA pathways.

Main Methods:

• Transcriptome-wide analysis of small RNA and mRNA.
• Analysis of EMB-4 enrichment on pre-mRNAs.
• Comparison of EMB-4 binding to targets of CSR-1 and HRDE-1 pathways.

Main Results:

• Loss of emb-4 causes distinct changes in CSR-1 and HRDE-1 associated small RNA and mRNA.
• EMB-4 is associated with pre-mRNAs of approximately 8,000 transcripts.
• EMB-4 complexes bind intronic and exonic sequences of HRDE-1 targets, but only intronic sequences of CSR-1 targets.

Conclusions:

• EMB-4 plays a role in regulating germline small RNA pathways.
• EMB-4 may provide a molecular signature to differentiate targets of the CSR-1 and HRDE-1 pathways.