The Chekulaeva lab is interested in understanding the molecular mechanisms that regulate intracellular RNA localization and translation in neurons and roles of RNA-binding proteins (RBPs) in these processes. We developed neurite/soma separation scheme in combination with mass spectrometry, RNAseq, Riboseq and bioinformatics analyses to identify proteins and RNAs that are differentially localized and translated between neurites and soma of neuronal cells (Zappulo et al 2017; Ciolli Mattioli et al. 2019; Ludwik et al. 2019). As test systems, we use mESC- and hiPSC-based neuronal differentiation systems and primary cortical neuron cultures. We participate in the FOR2333 Research Unit with the following projects:
Project 1: Identification and functional analysis of Cdc42 zipcodes. Our prior analysis showed that alternative and functionally diverse isoforms of the cell polarity gene Cdc42 are differentially localized between neurites and soma (Ciolli Mattioli et al. 2019). We are dissecting the mechanisms mediating differential localization of Cdc42 isoforms, by identifying the Cdc42 zipcodes and their bound RBPs.
Project 2: We also contribute to several collaborative projects within FOR2333. By combining cell separation scheme with RNA bio-ID (collaboration with Jansen lab), we are identifying trans-acting factors bound to localized mRNAs using beta-actin. We also study how mutations of two RBPs - PUM2 (collaboration with Niessing lab) and RBM3 (collaboration with Feldbrügge lab) – affect RNA localization and local translation in neurons, using neurite/soma separation scheme in combination with omics analyses.