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Gracjan Michlewski


Nila Roy Choudhury, Gregory Heikel, Santosh Kumar, Jakub Stanislaw Nowak, Angela Downie Ruiz Velasco
Michlewski lab website

Regulation of MicroRNA Processing and Function

Regulation of RNA processing and function by RNA-binding proteins (RNA-BPs) plays an essential role in cell biology. RNA-binding proteins mediate and control gene expression by regulating mRNA splicing, localisation, translation and decay as well as miRNA maturation and function. Consequently, they contribute to the normal development and cellular homeostasis. Finally, changes in the levels of RNA-BPs and their RNA targets via epigenetic mechanisms and/or genetic mutations often contribute to human pathological states, including cancer.

Recent high-throughput studies on RNA-BPs are supplying an increasing catalogue of novel RNA-protein interactions. Importantly, new classes of RNA-binding proteins such as E3 ubiquitin ligases, kinases and metabolic enzymes, which we collectively describe as RNA-binding protein-modifying (RBPM) enzymes, have recently been discovered by highthroughput proteomics analysis and are awaiting functional characterisation.
My overall goal is to study the link between signaling pathways, RNA biology and gene expression. My group has focused on elucidating the cis and trans-acting factors of tissuespecific miRNA biogenesis in mammalian cells. We have identified proteins that regulate the production of brain-enriched and brain-specific miRNAs, as well as novel RNA-binding protein, responsible for the selective uridylation and degradation of miRNA precursors in embryonic cells. More recently my team discovered that the E3 ubiquitin ligase Trim25 could recognise specific RNAs and positively regulate the activity of cognate RNP complexes in cis.

We have discovered that the RNA-binding E3 ubiquitin ligase Trim25 regulates the Lin28- mediated uridylation of miRNA precursors (Choudhury et al., 2014). This offers novel insights into mechanisms that regulate RNA processing and function. To date, only a few E3
ubiquitin ligases, including Mex3b and Dizip3, have been shown to use RNA as a scaffold to mediate ubiquitination of their substrates. However, it is largely unknown if and how their ubiquitinating activity is involved in the regulation of RNA metabolism. We hypothesise that RBPM enzymes, including the Trim25 E3 ligase, provide an additional layer of control over canonical RNA-binding proteins and can dictate and define their function in cis. Our working model is that, when an RBPM enzyme binds RNA in the vicinity of a canonical RNABP, it will modify it, thereby altering or acting to fine-tune its molecular function. This model could explain a long-standing conundrum of why some RNA-BPs are multifunctional and, depending on the substrate they recognise, have positive, negative or passive effects on the related RNA processing event. Our research has the potential to open up new avenues to study other RBPM enzymes that control RNA processing, viral RNA-induced innate immunity, gene expression regulation and cellular homeostasis.

Selected publications:

Choudhury, N.R., Nowak, J.S., Zou, J., Rappsilber, J., Spoel, S.H., and Michlewski, G. (2014). Trim25 Is an RNA-Specific Activator of Lin28a/TuT4-Mediated Uridylation. Cell reports 9, 1265-1272.
Nowak, J.S., Choudhury, N.R., de Lima Alves, F., Rappsilber, J., and Michlewski, G. (2014). Lin28a regulates neuronal differentiation and controls miR-9 production. Nature communications 5, 3687.
Choudhury, N.R., de Lima Alves, F., de Andres-Aguayo, L., Graf, T., Caceres, J.F., Rappsilber, J., and Michlewski, G. (2013). Tissue-specific control of brainenriched miR-7 biogenesis. Genes & development 27, 24-38.

1. What is the Trim25 E3 ubiquitin ligase role in regulating RNA processing? Trim25 Co-IP shows its association with a number of RNA-binding proteins. GO term analysis of Trim25 Co-IP is shown.
2. CLIP-seq of Trim25 in HeLa cells reveals novel Trim25 mRNA targets. (Left panel) The distribution of Trim25 CLIP tags in total RNA and in protein coding genes shows binding specificity. (Right panel) The ab initio-derived Trim25- binding motif. T is representative of U in the RNA.