Search Results - "Ameres, Stefan L."

Diversifying microRNA sequence and function by Ameres, Stefan L., Zamore, Phillip D.

“…Key Points MicroRNAs (miRNAs) are small non-coding RNAs that guide post-transcriptional gene regulation to shape the rate at which genetic information is…”
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Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm by Sharma, Upasna, Sun, Fengyun, Conine, Colin C., Reichholf, Brian, Kukreja, Shweta, Herzog, Veronika A., Ameres, Stefan L., Rando, Oliver J.

“…The biogenesis of the RNA payload of mature sperm is of great interest, because RNAs delivered to the zygote at fertilization can affect early development…”
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Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets by Neumann, Tobias, Herzog, Veronika A, Muhar, Matthias, von Haeseler, Arndt, Zuber, Johannes, Ameres, Stefan L, Rescheneder, Philipp

“…Methods to read out naturally occurring or experimentally introduced nucleic acid modifications are emerging as powerful tools to study dynamic cellular…”
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Genetic and mechanistic diversity of piRNA 3′-end formation by Hayashi, Rippei, Schnabl, Jakob, Handler, Dominik, Mohn, Fabio, Ameres, Stefan L., Brennecke, Julius

“…Drosophila have two pathways for PIWI-interacting RNA (piRNA) 3′-end formation—depending on which pathway is used, piRNA biogenesis is directed towards either…”
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The 3′-to-5′ Exoribonuclease Nibbler Shapes the 3′ Ends of MicroRNAs Bound to Drosophila Argonaute1 by Han, Bo W., Hung, Jui-Hung, Weng, Zhiping, Zamore, Phillip D., Ameres, Stefan L.

“…MicroRNAs (miRNAs) are ∼22 nucleotide (nt) small RNAs that control development, physiology, and pathology in animals and plants. Production of miRNAs involves…”
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SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis by Muhar, Matthias, Ebert, Anja, Neumann, Tobias, Umkehrer, Christian, Jude, Julian, Wieshofer, Corinna, Rescheneder, Philipp, Lipp, Jesse J, Herzog, Veronika A, Reichholf, Brian, Cisneros, David A, Hoffmann, Thomas, Schlapansky, Moritz F, Bhat, Pooja, von Haeseler, Arndt, Köcher, Thomas, Obenauf, Anna C, Popow, Johannes, Ameres, Stefan L, Zuber, Johannes

“…Defining direct targets of transcription factors and regulatory pathways is key to understanding their roles in physiology and disease. We combined SLAM-seq…”
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Splice_sim: a nucleotide conversion-enabled RNA-seq simulation and evaluation framework by Popitsch, Niko, Neumann, Tobias, von Haeseler, Arndt, Ameres, Stefan L

“…Nucleotide conversion RNA sequencing techniques interrogate chemical RNA modifications in cellular transcripts, resulting in mismatch-containing reads. Biases…”
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Target RNA-Directed Trimming and Tailing of Small Silencing RNAs by Ameres, Stefan L, Horwich, Michael D, Hung, Jui-Hung, Xu, Jia, Ghildiyal, Megha, Weng, Zhiping, Zamore, Phillip D

“…In Drosophila, microRNAs (miRNAs) typically guide Argonaute1 to repress messenger RNA (mRNA), whereas small interfering RNAs (siRNAs) guide Argonaute2 to…”
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Hijacking of transcriptional condensates by endogenous retroviruses by Asimi, Vahid, Sampath Kumar, Abhishek, Niskanen, Henri, Riemenschneider, Christina, Hetzel, Sara, Naderi, Julian, Fasching, Nina, Popitsch, Niko, Du, Manyu, Kretzmer, Helene, Smith, Zachary D., Weigert, Raha, Walther, Maria, Mamde, Sainath, Meierhofer, David, Wittler, Lars, Buschow, René, Timmermann, Bernd, Cisse, Ibrahim I., Ameres, Stefan L., Meissner, Alexander, Hnisz, Denes

“…Most endogenous retroviruses (ERVs) in mammals are incapable of retrotransposition; therefore, why ERV derepression is associated with lethality during early…”
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Selective Suppression of the Splicing-Mediated MicroRNA Pathway by the Terminal Uridyltransferase Tailor by Bortolamiol-Becet, Diane, Hu, Fuqu, Jee, David, Wen, Jiayu, Okamura, Katsutomo, Lin, Ching-Jung, Ameres, Stefan L., Lai, Eric C.

“…Several terminal uridyltransferases (TUTases) are known to modulate small RNA biogenesis and/or function via diverse mechanisms. Here, we demonstrate that…”
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SLAMseq resolves the kinetics of maternal and zygotic gene expression during early zebrafish embryogenesis by Bhat, Pooja, Cabrera-Quio, Luis E., Herzog, Veronika A., Fasching, Nina, Pauli, Andrea, Ameres, Stefan L.

“…The maternal-to-zygotic transition (MZT) is a key developmental process in metazoan embryos that involves the activation of zygotic transcription (ZGA) and…”
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Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila by Reimão-Pinto, Madalena M., Ignatova, Valentina, Burkard, Thomas R., Hung, Jui-Hung, Manzenreither, Raphael A., Sowemimo, Ivica, Herzog, Veronika A., Reichholf, Brian, Fariña-Lopez, Sara, Ameres, Stefan L.

“…Uridylation of RNA species represents an emerging theme in post-transcriptional gene regulation. In the microRNA pathway, such modifications regulate small RNA…”
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Long-term, efficient inhibition of microRNA function in mice using rAAV vectors by Xie, Jun, Ameres, Stefan L, Friedline, Randall, Hung, Jui-Hung, Zhang, Yu, Xie, Qing, Zhong, Li, Su, Qin, He, Ran, Li, Mengxin, Li, Huapeng, Mu, Xin, Zhang, Hongwei, Broderick, Jennifer A, Kim, Jason K, Weng, Zhiping, Flotte, Terence R, Zamore, Phillip D, Gao, Guangping

“…Tough decoy microRNA inhibitor, shown to be the most effective of several designs, is packaged in recombinant adeno-associated virus and used for prolonged…”
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NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation by Huth, Michelle, Santini, Laura, Galimberti, Elena, Ramesmayer, Julia, Titz-Teixeira, Fabian, Sehlke, Robert, Oberhuemer, Michael, Stummer, Sarah, Herzog, Veronika, Garmhausen, Marius, Romeike, Merrit, Chugunova, Anastasia, Leesch, Friederike, Holcik, Laurenz, Weipoltshammer, Klara, Lackner, Andreas, Schoefer, Christian, von Haeseler, Arndt, Buecker, Christa, Pauli, Andrea, Ameres, Stefan L, Smith, Austin, Beyer, Andreas, Leeb, Martin

“…Cell fate transitions depend on balanced rewiring of transcription and translation programs to mediate ordered developmental progression. Components of the…”
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Structure-function analysis of microRNA 3′-end trimming by Nibbler by Xie, Wei, Sowemimo, Ivica, Hayashi, Rippei, Wang, Juncheng, Burkard, Thomas R., Brennecke, Julius, Ameres, Stefan L., Patel, Dinshaw J.

“…Nibbler (Nbr) is a 3′-to-5′ exoribonuclease whose catalytic 3′-end trimming activity impacts microRNA (miRNA) and PIWI-interacting RNA (piRNA) biogenesis…”
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SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting by Matsushima, Wayo, Herzog, Veronika A, Neumann, Tobias, Gapp, Katharina, Zuber, Johannes, Ameres, Stefan L, Miska, Eric A

“…Cell type-specific transcriptome analysis is an essential tool for understanding biological processes in which diverse types of cells are involved. Although…”
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Cleavage of the siRNA passenger strand during RISC assembly in human cells by Leuschner, Philipp J F, Ameres, Stefan L, Kueng, Stephanie, Martinez, Javier

“…A crucial step in the RNA interference (RNAi) pathway involves the assembly of RISC, the RNA‐induced silencing complex. RISC initially recognizes a…”
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The impact of target site accessibility on the design of effective siRNAs by Obernosterer, Gregor, Hofacker, Ivo L, Tafer, Hakim, Ameres, Stefan L, Gebeshuber, Christoph A, Schroeder, Renée, Martinez, Javier

“…Small-interfering RNAs (siRNAs) assemble into RISC, the RNA-induced silencing complex, which cleaves complementary mRNAs. Despite their fluctuating efficacy,…”
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Approaching the Golden Fleece a Molecule at a Time: Biophysical Insights into Argonaute-Instructed Nucleic Acid Interactions by Herzog, Veronika A., Ameres, Stefan L.

“…Argonaute proteins act at the core of nucleic acid-guided interference pathways that regulate gene expression and defend organisms against foreign genetic…”
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MicroRNA-regulated, Systemically Delivered rAAV9: A Step Closer to CNS-restricted Transgene Expression by Xie, Jun, Xie, Qing, Zhang, Hongwei, Ameres, Stefan L, Hung, Jui-Hung, Su, Qin, He, Ran, Mu, Xin, Seher Ahmed, Seemin, Park, Soyeon, Kato, Hiroki, Li, Chengjian, Mueller, Christian, Mello, Craig C, Weng, Zhiping, Flotte, Terence R, Zamore, Phillip D, Gao, Guangping

“…Recombinant adeno-associated viruses (rAAVs) that can cross the blood–brain-barrier and achieve efficient and stable transvascular gene transfer to the central…”
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