Browsing by Author "Liu, Huanle"

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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 ...
  • EpiNano: detection of m6A RNA modifications using Oxford nanopore direct RNA sequencing
    Liu, Huanle; Begik, Oguzhan; Novoa, Eva Maria (Springer, 2021)
    RNA modifications play pivotal roles in the RNA life cycle and RNA fate, and are now appreciated as a major posttranscriptional regulatory layer in the cell. In the last few years, direct RNA nanopore sequencing (dRNA-seq) ...
  • 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 ...
  • MasterOfPores: A workflow for the analysis of Oxford nanopore direct RNA sequencing datasets
    Cozzuto, Luca; Liu, Huanle; Pryszcz, Leszek Piotr, 1985-; Hermoso Pulido, Antonio; Delgado-Tejedor, Anna; Ponomarenko, Julia; Novoa, Eva Maria (Frontiers Media, 2020)
    The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA, fragmentation or amplification. As such, it is ...
  • Molecular barcoding of native RNAs using nanopore sequencing and deep learning
    Smith, Martin A.; Ersavas, Tansel; Ferguson, James M.; Liu, Huanle; Lucas, Morghan C.; Begik, Oguzhan; Bojarski, Lilly; Barton, Kirston; Novoa, Eva Maria (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)
    Nanopore sequencing enables direct measurement of RNA molecules without conversion to cDNA, thus opening the gates to a new era for RNA biology. However, the lack of molecular barcoding of direct RNA nanopore sequencing ...
  • 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 ...
  • Phenotypic and genotypic parallel evolution in parapatric ecotypes of Senecio
    James, Maddie E.; Wilkinson, Melanie J.; Bernal, Diana M.; Liu, Huanle; North, Henry L.; Engelstädter, Jan; Ortiz-Barrientos, Daniel (Wiley, 2021)
    The independent and repeated adaptation of populations to similar environments often results in the evolution of similar forms. This phenomenon creates a strong correlation between phenotype and environment and is referred ...
  • 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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