Small silencing RNAs regulate gene expression in nearly all eukaryotes and have enormous biotechnological and therapeutic potential. Among these, microRNAs belong to the larges family of trans-acting gene regulatory molecules in multicellular organisms. In flies and mammals, they control more than half of the protein-coding transcriptome, and act as key regulators of organismal development, physiology, and disease. We are interested in molecular mechanisms that govern small RNA silencing pathways in flies and mammals. Our focus lies on processes that regulate the production of small RNAs, their assembly into functional ribonucleoprotein complexes, and the disassembly thereof in response to synthetic and natural triggers. Our goal is to unravel mechanistic principles of small RNA-mediated gene regulation, a phenomenon that impacts virtually every aspect of metazoan biology.
For RNA to fulfil its essential function within the cellular environment, numerous chemical modifications have evolved to sculpt its physical and functional interactions. Although more than hundred types of RNA modifications have built the descriptive foundation of what is referred to as the epitranscriptome, their mode of action remains largely unknown. We are studying the function of chemical RNA modifications, at the intersection of small RNA silencing pathways and general RNA metabolism. Our focus lies on the post-transcriptional addition of nucleotides to the 3´ end of RNA (i.e. tailing) by the only rudimentary characterized enzyme family of terminal nucleotidyltransferases to dissect the regulation of microRNA biogenesis and function; and the role of small RNA ribose methylation to gain insights into the antiviral immune response through the RNAi pathway in insects. The emerging concepts will inevitable impact our view on more general functions of post-transcriptional modifications in RNA metabolism. And we are applying our mechanistic insights to the development of novel epitranscriptomics technologies to probe post-transcriptional gene regulatory networks at the transcriptome-wide level.
Drosophila melanogaster provides a unique combination of in vitro biochemical methods, cell culture experiments, and in vivo genetics to dissect the mechanisms and biological implications of RNA silencing. We are combining the strength of this model organism with the power of modern deep-sequencing technology and bioinformatics. The hypotheses that emerge from our fly studies are directly tested in human cell extracts and in cultured mammalian cell lines to determine the conservation and divergence of key principles in small RNA-mediated gene regulation and RNA metabolism in flies and mammals.
Overall, our goal is to determine fundamental biological mechanisms of post-transcriptional gene regulation through pathways with enormous biological, biomedical, and technological impact.
Alberti, C., Manzenreither, RA., Sowemimo, I., Burkard, TR., Wang, J., Mahofsky, K., Ameres, SL., Cochella, L. (2018). Cell-type specific sequencing of microRNAs from complex animal tissues. Nat Methods. 15(4):283-289
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
Reimão-Pinto, MM., Ignatova, V., Burkard, TR., Hung, JH., Manzenreither, RA., Sowemimo, I., Herzog, VA., Reichholf, B., Fariña-Lopez, S., Ameres, SL. (2015). Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila. Mol Cell. 59(2):203-16
Xie, J., Ameres, SL., Friedline, R., Hung, JH., Zhang, Y., Xie, Q., Zhong, L., Su, Q., He, R., Li, M., Li, H., Mu, X., Zhang, H., Broderick, JA., Kim, JK., Weng, Z., Flotte, TR., Zamore, PD., Gao, G. (2012). Long-term, efficient inhibition of microRNA function in mice using rAAV vectors. Nat Methods. 9(4):403-9
Ameres, SL., Horwich, MD., Hung, JH., Xu, J., Ghildiyal, M., Weng, Z., Zamore, PD. (2010). Target RNA-directed trimming and tailing of small silencing RNAs. Science. 328(5985):1534-9
Tafer, H., Ameres, SL., Obernosterer, G., Gebeshuber, CA., Schroeder, R., Martinez, J., Hofacker, IL. (2008). The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol. 26(5):578-83
Ameres, SL., Martinez, J., Schroeder, R. (2007). Molecular basis for target RNA recognition and cleavage by human RISC. Cell. 130(1):101-12