RNA Biology

E-mail: stefan.ameres(at)imba.oeaw.ac.at, stefan.ameres@univie.ac.at
Phone: 0043 1 79044-4740
Research Group: www.imba.oeaw.ac.at/research/stefan-ameres

https://www.maxperutzlabs.ac.at/research/research-groups/ameres
Institution: IMBA, Max Perutz Labs

Full member of the DoktoratsKolleg (DK) RNA Biology since 2014 and of the Focus Regulatory RNA (SFB RNA Reg) since 2015.

PhD students within/associated to the DK:

Pooja Bhat
Moritz Staltner

DK RNA Biology alumni & their PhD theses:

Madalena Reimão-Pinto: “Molecular basis and biological functions of RNA 3′ end uridylation in Drosophila melanogaster”
Brian Reichholf: “Dissecting the kinetics of miRNA biogenesis and turnover in living cells”

For complete list of group members please visit the Ameres group website.

 

Mechanism and Biology of RNA Silencing

Small silencing RNAs regulate animal physiology and development, enhance target gene discovery in pharmacological industry and serve as next-generation therapy for human disease. In RNA silencing pathways, ~22 nucleotide small RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), guide ribonucleoprotein complexes to complementary sequences within messenger RNAs to mediate their post-transcriptional silencing.
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 ribonucleoprotein complexes, and the disassembly thereof in response to synthetic and natural triggers, such as target mRNAs. Our goal is to define the principles that establish and maintain small RNA profiles in a given tissue or cell type. To do so, we are using a combination of biochemical, genetic and bioinformatic approaches using Drosophila melanogaster as a model organism. The hypotheses emerging from our studies in flies are directly tested for their conservation in mammals.

 

Publications: (since 2014)

Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis.
Reichholf B, Herzog VA, Fasching N, Manzenreither RA, Sowemimo I, Ameres SL.
Mol Cell. 2019 Jul 9. pii: S1097-2765(19)30474-5. [Epub ahead of print]

Sequencing cell-type-specific transcriptomes with SLAM-ITseq. Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA.
Nat Protoc. 2019 Jun 26. doi: 10.1038/s41596-019-0179-x. [Epub ahead of print] Erratum in: Nat Protoc. 2019 Jul 11;:.

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets.
Neumann T, Herzog VA, Muhar M, von Haeseler A, Zuber J, Ameres SL, Rescheneder P.
BMC Bioinformatics. 2019 May 20;20(1):258.

Structural basis for acceptor RNA substrate selectivity of the 3′ terminal uridylyl transferase Tailor.
Kroupova A, Ivascu A, Reimão-Pinto MM, Ameres SL, Jinek M.
Nucleic Acids Res. 2019 Jan 25;47(2):1030-1042.

Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm.
Sharma U, Sun F, Conine CC, Reichholf B, Kukreja S, Herzog VA, Ameres SL, Rando OJ.
Dev Cell. 2018 Aug 20;46(4):481-494.e6.

Positioning Europe for the EPITRANSCRIPTOMICS challenge.
Jantsch MF, Quattrone A, O’Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R.
RNA Biol. 2018 May 9:1-3.

Analysis of 3′ End Modifications in microRNAs by High-Throughput Sequencing.
Reimão-Pinto MM, Rodrigues-Viana AM, Ameres SL.
Methods Mol Biol. 2018;1823:115-139.

SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting.
Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA.
Development. 2018 Jul 11;145(13).

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis.
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.
Science. 2018 May 18;360(6390):800-805.

Cell-type specific sequencing of microRNAs from complex animal tissues.
Alberti C, Manzenreither RA, Sowemimo I, Burkard TR, Wang J, Mahofsky K, Ameres SL, Cochella L.
Nat Methods. 2018 Apr;15(4):283-289.

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

Genetic and mechanistic diversity of piRNA 3′-end formation.
Hayashi R, Schnabl J, Handler D, Mohn F, Ameres SL, Brennecke J.
Nature. 2016 Nov 24;539(7630):588-592.

Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila.
Reimão-Pinto MM, Manzenreither RA, Burkard TR, Sledz P, Jinek M, Mechtler K, Ameres SL.
EMBO J. 2016 Nov 15;35(22):2417-2434.

Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila.
Reimão-Pinto MM, Ignatova V, Burkard TR, Hung JH, Manzenreither RA, Sowemimo I, Herzog VA, Reichholf B, Fariña-Lopez S, Ameres SL.
Mol Cell. 2015 Jul 16;59(2):203-16.

Selective Suppression of the Splicing-Mediated MicroRNA Pathway by the Terminal Uridyltransferase Tailor.
Bortolamiol-Becet D, Hu F, Jee D, Wen J, Okamura K, Lin CJ, Ameres SL, Lai EC.
Mol Cell. 2015 Jul 16;59(2):217-28.

Approaching the Golden Fleece a Molecule at a Time: Biophysical Insights into Argonaute-Instructed Nucleic Acid Interactions.
Herzog VA, Ameres SL.
Mol Cell. 2015 Jul 2;59(1):4-7.