3' UTRs are the primary regulators of gene expression in the C. elegans germline

Merritt et al. (2008). Curr Biol DOI: 10.1016/j.cub.2008.08.013 Citations: 422

Whether promoters or 3'UTRs drive C. elegans germline expression was unclear. This paper compared promoter and 3'UTR fusions for 30 genes and found 3'UTRs reproduce most patterns. 24 of 30 fusions matched patterns, and promoters were permissive except during spermatogenesis.

Parts used

EGFPmCherryPIE-1 Promoter

Key findings

  • Systematic analysis of 30 transgenic constructs pairing gene-specific 3' UTRs with the permissive pie-1 promoter demonstrated that 3' UTR sequences alone reproduced endogenous expression patterns for 24/30 genes across all germline developmental stages. The fusions generated 17 distinct cell-type-specific patterns from progenitors through oocytes, with quantitative boundaries matching reported protein distributions in 80% of cases.

  • Promoter fusions with a permissive 3' UTR (tbb-2) revealed that non-sperm promoters drove ubiquitous germline expression rather than cell-type specificity. Only spe-11 and msp-56 promoters maintained sperm-restricted patterns, while oocyte-specific promoters (spn-4, mex-5, pie-1) and progenitor-enriched promoters (fbf-1) showed activity in all germ cell types including early L2 larval progenitors, demonstrating promoter permissivity throughout germline development except during spermatogenesis.

  • Operon-based experiments confirmed 3' UTRs function posttranscriptionally by showing independent regulation of bicistronically transcribed reporters. RNAi depletion revealed that PUF domain proteins FBF-1 and FBF-2 mediate repression of gld-1 and fog-1 3' UTR fusions in the distal germline, while KH domain proteins MEX-3 and GLD-1 repress rme-2, pal-1, mex-5, and puf-5 fusions in progenitors, with mutation of FBF-binding elements in the gld-1 3' UTR eliminating distal repression.

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Abstract

How genes are regulated to produce the correct assortment of proteins for every cell type is a fundamental question in biology. For many genes, regulation begins at the DNA level with the use of promoter sequences to control transcription. Regulation can also occur after transcription using sequences in the 3′ untranslated region (UTR) of the mRNA to affect mRNA stability and/or translation. The C. elegans gonad is an excellent tissue to study gene regulation during development: In the adult, germ cells are arranged in order of differentiation, with undifferentiated progenitors at one end of the gonad, cells in meiotic prophase in the middle, and gametes at the other end. Using a transgenic assay, we have compared the contribution of promoters and 3′ UTRs to gene regulation during germline development. We find that for most genes tested, 3′ UTRs are sufficient for regulation. With the exception of promoters activated during spermatogenesis, promoters are permissive for expression in all germ cell types (from progenitors to oocytes and sperm). In progenitors, 3′ UTRs inhibit the production of meiotic and oocyte proteins by posttranscriptional mechanisms involving PUF- and KH-domain RNA-binding proteins. Our findings indicate that many genes rely primarily on 3′ UTRs, not promoters, for regulation during germline development.