Browsing by Author "Mattick, John S."

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  • Accurate detection of m6A RNA modifications in native RNA sequences
    Liu, Huanle; Begik, Oguzhan; Lucas, Morghan C.; Ramirez, Jose Miguel; Mason, Christopher E.; Wiener, David; Schwartz, Schraga; Mattick, John S.; Smith, Martin A.; Novoa, Eva Maria (Nature Research, 2019)
    The epitranscriptomics field has undergone an enormous expansion in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here, we show that using direct ...
  • Exploring the epitranscriptome by native RNA sequencing
    Begik, Oguzhan; Mattick, John S.; Novoa, Eva Maria (Cold Spring Harbor Laboratory Press (CSHL Press), 2022)
    Chemical RNA modifications, collectively referred to as the "epitranscriptome," are essential players in fine-tuning gene expression. Our ability to analyze RNA modifications has improved rapidly in recent years, largely ...
  • Improved definition of the mouse transcriptome via targeted RNA sequencing
    Bussotti, Giovanni, 1983-; Leonardi, Tommaso; Clark, Michael B.; Mercer, Tim R.; Crawford, Joanna; Malquori, Lorenzo; Notredame, Cedric; Dinger, Marcel E.; Mattick, John S.; Enright, Anton J. (Cold Spring Harbor Laboratory Press (CSHL Press), 2016)
    Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied ...
  • Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures
    Begik, Oguzhan; Lucas, Morghan C.; Liu, Huanle; Ramírez, José Miguel; Mattick, John S.; Novoa, Eva Maria (BioMed Central, 2020)
    Background: RNA modifications play central roles in cellular fate and differentiation. However, the machinery responsible for placing, removing, and recognizing more than 170 RNA modifications remains largely uncharacterized ...
  • Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing
    Begik, Oguzhan; Diensthuber, Gregor; Liu, Huanle; Delgado-Tejedor, Anna; Kontur, Cassandra; Niazi, Adnan Muhammad; Valen, Eivind; Giraldez, Antonio J.; Beaudoin, Jean-Denis; Mattick, John S.; Novoa, Eva Maria (Nature Research, 2023)
    RNA polyadenylation plays a central role in RNA maturation, fate, and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translation efficiency and stability of mRNAs. Here we develop ...
  • Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing
    Begik, Oguzhan; Lucas, Morghan C.; Pryszcz, Leszek Piotr, 1985-; Ramirez, Jose Miguel; Medina, Rebeca; Milenkovic, Ivan; Cruciani, Sonia; Liu, Huanle; Santos Vieira, Helaine Graziele; Sas Chen, Aldema; Mattick, John S.; Schwartz, Schraga; Novoa, Eva Maria (Nature Research, 2021)
    Nanopore RNA sequencing shows promise as a method for discriminating and identifying different RNA modifications in native RNA. Expanding on the ability of nanopore sequencing to detect N6-methyladenosine, we show that ...
  • Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation
    Jonkhout, Nicky; Cruciani, Sonia; Santos Vieira, Helaine Graziele; Tran, Julian; Liu, Huanle; Liu, Ganqiang; Pickford, Russell; Kaczorowski, Dominic; Franco, Gloria R.; Vauti, Franz; Camacho, Noelia; Abedini, Seyedeh Sedigheh; Najmabadi, Hossein; Ribas de Pouplana, Lluís; Christ, Daniel; Schonrock, Nicole; Mattick, John S.; Novoa, Eva Maria (Taylor & Francis, 2021)
    RNA modifications are dynamic chemical entities that expand the RNA lexicon and regulate RNA fate. The most abundant modification present in mRNAs, N6-methyladenosine (m6A), has been implicated in neurogenesis and memory ...

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