The implementation of distinct gene expression profiles is essential for organismal development, physiological responses to external stimuli and pathogens, and defines a primary cause for disease. We are fascinated by the molecular events that control these processes at the post-transcriptional level, referred to as post-transcriptional gene silencing (PTGS). To this end we develop and implement state-of-the-art biochemical, genetic, molecular and computational tools to study RNA silencing pathways in vitro and in vivo in flies and mammals:

– We developed and implemented high-throughput sequencing protocols and bioinformatics pipelines to quantitatively and globally characterize small RNAs, long non-coding RNAs and mRNAs and their post-transcriptional modifications.

– We established in vitro systems to study the molecular basis for small RNA biogenesis, function and turnover in lysate and reconstituted from purified components.

– We developed novel high-throughput-compatible biochemical methods to dissect the molecular features, substrate specificities, and functional interactions of RNA-modifying and degrading enzymes.

– We implemented reverse genetics tools and endogenous tagging/mutagenesis approaches (based on CRISPR/Cas9 genome engineering and RNAi) in mammalian and Drosophila cultured cells and in vivo in flies to study the biological function of (small) RNA-modifying and degrading enzymes.

– We developed a novel metabolic labeling-based RNA sequencing strategy to globally monitor the intracellular kinetics of RNA biogenesis and turnover in living cells (SLAM-seq).

– We invented a chemogenetic small RNA-tagging approach that uncovers tissue- and cell type-specific miRNA profiles in model organisms at high spatiotemporal resolution.

Muhar M, Ebert A, Neumann T, Umkehrer C, Jude J, Wieshofer C, Rescheneder P, Lipp JJ, Herzog VA, Reichholf B, Cisneros DA, Hoffmann T, Schlapansky MF, Bhat P, von Haeseler A, Köcher T, Obenauf AC, Popow J, Ameres SL*, Zuber J*. 2018. SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. Science. 360(6390):800-805, doi: 10.1126/science.aao2793.

Herzog, VA., Reichholf, B., Neumann, T., Rescheneder, P., Bhat, P., Burkard, TR., Wlotzka, W., von Haeseler, A., Zuber, J., Ameres, SL. Thiol-linked alkylation of RNA to assess expression dynamics. Nature Methods, 2017 Dec, 14(12):1198-1204. doi: 10.1038/nmeth.4435

Alberti, C., Manzenreither, R.A., Sowemimo, I, Burkard, T.R., Wang, J., Mahofsky, K., Ameres,S.L.*, Cochella, L.*. Cell-type specific sequencing of microRNAs from complex animal tissues.Nature Methods, Epub 2018 Apr, 15(4):283-289. doi: 10.1038/nmeth.4610

Hayashi, R., Schnabl, J., Handler, D., Ameres, S.L.*, Brennecke, J.* Genetic and mechanistic diversity of piRNA 3 ́ end formation. Nature, 2016 Nov 24, 539: 588-92. doi: 10.1038/ nature20162

Reimão-Pinto, M.M., Ignatova, V., Burkard, T.R., Hung, J.-H., Manzenreither, R. A., Sowemimo, I., Herzog, V. A., Reichholf, B., Fariña-Lopez, S., and Ameres, S.L. Uridylation of RNA-hairpins by Tailor confines the emergence of microRNAs in Drosophila. Molecular Cell, 2015 Jul 16, 59(2):203-16. doi: 10.1016/j.molcel.2015.05.033

Ameres, S.L., Horwich, M.D., Hung, J.-H., Xu, J., Ghildiyal, M., Weng, Z., Zamore, P.D. Target RNA-directed trimming and tailing of small silencing RNAs. Science, 2010 Jun 18, 328 (5985), 1534-39. doi: 10.1126/science.1187058

Ameres, S.L., Martinez, J., Schroeder, R. Molecular basis for target-RNA recognition and cleavage by human RISC. Cell, 2007 Jul 13, 130 (1), 101-12. doi: 10.1016/j.cell.2007.04.037