How is RNA localization and local translation regulated?

 

Targeting of RNAs to specific cellular compartments has emerged as a powerful and wide-spread mechanism to establish cell asymmetry. It is particularly important for highly polarized cells, such as oocytes, migrating cells, and neurons. Translation of localized mRNAs can be activated in response to specific stimuli, for example, upon synaptic activation. To study these processes in neurons, we developed neurite/soma separation scheme in combinationation with RNA-seq, Ribo-seq, mass spectrometry and bioinformatics analyses to identify local neuronal proteome, transcriptome and translatome.

Using this approach, we identified hundreds of neurite-localized and locally translated mRNAs and proteins and demonstrated that mRNA localization is the primary mechanism for protein localization, accounting for more than a half of the neurite-localized proteome (Zappulo et al. 2017). Moreover, we have identified multiple neurite-targeted non-coding RNAs and RNA-binding proteins with potential regulatory roles. Using a combination of PAR-CLIP, RIP, and CRISPR/Cas-mediated knockouts, we are dissecting the roles of selected neurite-targeted RBPs and miRNAs in establishment of neuronal polarity (DFG-funded projects).

RNA localization is mediated by specific cis-regulatory elements, so called zipcodes. So far our knowledge is restricted to only a few examples of zipcodes. We are working to identify these elements on a genome-wide scale and dissect biochemical mechanisms underlying their function (GIF-funded project).

Local transcriptome, proteome and translatome across Motor Neuron Disorders

Motor neuron disorders (MNDs) are a group of neurodegenerative diseases affecting motor neurons, i.e. neurons that control skeletal muscle contraction to produce motion. Degeneration of motor neurons leads to progressive paralysis and severe disability and no curative treatment exists. Despite their heterogeneity, MNDs share common pathogenic pathways, including abnormalities in RNA splicing and transport. To identify common players (mRNAs, proteins, lncRNAs) that change their expression and/or localization pattern in multiple MND models, we are applying our neurite/soma separation scheme to motor neurons and their MNDs models. This work is a collaborative effort of several international partners (EU-JPND-funded consortium), contributing different expertise to the project, including computational analysis, in vivo MND models and clinical research.

Methods

RNA biology and omics (Riboseq, PAR-CLIP, RIP, transcriptomic data analysis, polysome profiling, in vitro translation systems), neuronal differentiation systems, primary cortical neuron cultures, Crspr/CAS, imaging

Education

2013

group leader, Berlin Institute for Medical Systems biology (BIMSB/MDC)

studies on intracellular RNA localization and roles of non-coding RNAs and RBPs in this process

2006 - 2012

joint postdoc, Friedrich Miescher Institute (Basel, Switzerland)/University of Arizona (USA)

studies on the mechanism of miRNA silencing

2001 - 2005

PhD student, EMBL (Heidelberg, Germany)

studies on the mechanisms of oskar mRNA localization and local translation in Drosophila oocyte

© 2015 by Chekulaeva

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