PS Webinar Series: The ALBAnian RNA-binding landscape
Abstract - RNA-binding proteins (RBPs) are critical regulators of gene expression, but have been poorly studied relative to other classes of gene regulators. Recently, mRNA-interactome capture identified many Arabidopsis RBPs of unknown function, including a family of ALBA domain containing proteins. Arabidopsis has three short-form ALBA homologues (ALBA1-3) and three long-form ALBA homologues (ALBA4-6), both of which are conserved throughout the plant kingdom and are preferentially expressed in young, rapidly dividing tissues. Focusing on the long-form ALBA family members, we set out to globally determine the in vivo target transcripts of ALBA4 via individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP). Using seven-day-old ALBA4-GFP seedlings, iCLIP identified 7687 transcripts with significantly enriched crosslink sites compared to plants expressing GFP alone. The majority of these crosslink sites were located in the 3′ untranslated region of target transcripts and enriched in U-rich motifs. Moreover, ALBA4 binds to many transcripts containing m6A RNA methylation, which is in line with IP-MS data showing an interaction with m6A reader proteins. Additionally, we performed RNA-sequencing analysis of alba456 triple mutants to identify the direct effects of ALBA4, ALBA5 and ALBA6 loss-of-function. Comparing iCLIP and RNA-seq data, we found that differentially expressed ALBA4 targets were enriched in genes related to stress response and were mostly downregulated upon loss of ALBA4/5/6 function, suggesting that ALBA4 positively regulates its targets.
Biography - Marlene completed her PhD at the ANU in 2016 characterising plant microRNAs and RNA-binding proteins with Associate Professor Tony Millar. She is currently an Alexander von Humboldt fellow at Bielefeld university, working with Professor Dorothee Staiger investigating post-transcriptional regulation via RNA-binding proteins.