Abstract

The control of translation is facilitated in many cases by trans acting factors that interact with the transcript in a regulated and dynamic manner. An interesting group of transcripts that show tight regulation in response to mitogenic and nutritional signals are mRNAs encoding for components of the mammalian protein synthesis machinery (ribosomal proteins and elongation factors). A unique sequence element, termed the 5' Terminal OligoPyrimidine tract (5'-TOP) characterizes this group of mRNAs. This motif comprises the core of a translational regulatory element in cis. The post transcriptional control of these so-called TOP mRNAs manifests by their selective and reversible shift from polysomes in dividing cells into subpolysomal mRNP particles in quiescent or starving cells. Several factors have been implicated in TOP mRNA regulation but it is still unclear how this is achieved at the mechanistic level and whether the TOP mRNP composition as a whole changes in response to nutritional conditions. We have established a new technique termed Grad-Seq that allows the systematic and comprehensive investigation of mRNP composition in cellular extracts. Using this technique along with traditional biochemical approaches we will investigate the biochemical composition of TOP mRNAs under normal conditions and upon starvation strategies. The identification of factors that selectively bind to TOP mRNAs under defined conditions will help to understand how the biosynthesis of the translational machinery is accomplished at the post-transcriptional level.

Project-related publications

Interaction of 7SK with the Smn complex modulates snRNP production. Ji C, Bader J, Ramanathan P, Hennlein L, Meissner F, Jablonka S, Mann M, Fischer U, Sendtner M, Briese M. Nat Commun. 2021 Feb 24;12(1):1278. doi: 10.1038/s41467-021-21529-1.

The SARS-CoV-2 RNA-protein interactome in infected human cells. Schmidt N, Lareau CA, Keshishian H, Ganskih S, Schneider C, Hennig T, Melanson R, Werner S, Wei Y, Zimmer M, Ade J, Kirschner L, Zielinski S, Dölken L, Lander ES, Caliskan N, Fischer U, Vogel J, Carr SA, Bodem J, Munschauer M. Nat Microbiol. 2021 Mar;6(3):339-353. doi: 10.1038/s41564-020-00846-z. Epub 2020 Dec 21.

Impaired Local Translation of β-actin mRNA in Ighmbp2-Deficient Motoneurons: Implications for Spinal Muscular Atrophy with respiratory Distress (SMARD1). Surrey V, Zöller C, Lork AA, Moradi M, Balk S, Dombert B, Saal-Bauernschubert L, Briese M, Appenzeller S, Fischer U, Jablonka S. Neuroscience. 2018 Aug 21;386:24-40. doi: 10.1016/j.neuroscience.2018.06.019.

Deciphering the mRNP code: RNA-bound determinants of post-transcriptional gene regulation. NH Gehring, E Wahle, U Fischer. TIBS. 2021. 42 (5), 369-382

The world of stable ribonucleoproteins and its mapping with Grad-seq and related approaches. Gerovac M, Vogel J, Smirnov A (2021) Frontiers in Molecular Biosciences in press

Analysis of the RNA and Protein Complexome by Grad-seq. Hör J, Vogel J (2021) Methods in Molecular Biology in press