The role of circular RNAs in gene regulation

Summary of the work

The Focus Group covered several different relevant omics levels: (1) Genomics: With a new tool called NeEDL, we uncovered interactions between single-nucleotide genetic variations (SNPs) that could contribute to complex diseases. (2) Epigenomics: We created TF-Prioritizer, a tool that identifies transcription factors (TFs) controlling RNA production from DNA in specific biological conditions. (3) Transcriptomics: The group developed two tools, spongEffects and circRNA-sponging, to explore regulatory networks within the transcriptomics layer. 4) CircRNA detection: As part of an Anna-Boyksen Fellowship (Fellow Prof. Priscilla Furth), the Focus Group has sought to better understand how circRNA expression is regulated by estrogen. CircRNA transcripts have a unique circular shape, making them more resistant to degradation, and they hold promise as stable biomarkers.

The work builds on our published circRNA [1] detection pipeline that pioneered the integrative analysis of circRNA and microRNAs for their regulatory interactions. Here, the group then worked toward integrating our work into the nf-core project [2], where we developed a uniform pipeline, merging the best features of our pipeline and the previously published [3] one (Fig. 1). This refined pipeline formed the basis for benchmarking circRNA detection across tools and data sets, particularly where both polyA-enriched and total RNA-sequencing were performed. Since polyA enrichment should, in theory, deplete most if not all circRNAs, we considered a direct comparison of such data sets a unique opportunity to establish the robustness and false positive rate of circRNA detection tools.

We then turned to the specific application of understanding how estrogen signaling might alter expression patterns of circRNAs in the mammary gland, as this question had not yet been explored. The estrogen pathway is critical to both normal mammary gland development – including puberty, pregnancy, lactation and involution with menopause (reproductive senescence) – and the onset of breast cancer. Here, utilizing mammary gland-specific sequencing data derived from two unique genetically engineered mouse models (GEMMs) of estrogen pathway-induced breast cancer, we investigated the hypothesis that expression of specific circRNAs is regulated by the estrogen pathway. The GEMMs were part of a time-course experiment that followed normal and cancerous mammary gland development with age through natural reproductive senescence, when levels of ovarian estrogens fall, as well as before and after exposure to the clinically employed anti-estrogens tamoxifen and letrozole. Differentially expressed circular RNAs were identified in all three experimental settings: pharmacological down-regulation of the estrogen pathway using anti-estrogens, physiological down-regulation with reproductive senescence, and up-regulation of the pathway through ERalpha transgene over-expression (Fig. 2).

The Focus Group also addressed gender-related challenges in the daily lives of researchers. Prof. Furth and Prof. List co-organized the Life & Science Career Symposium with the Collaborative Research Center 1371 on 10/10/2024 in Freising, featuring a broad selection of speakers and role models, covering opportunities, challenges, and obstacles in their career paths. The event culminated in a lively exchange with the audience, mostly young researchers who were eager to talk about how family can be fostered during an academic career and also had questions on sometimes overlooked topics such as taking care of elderly family members.