Publications – Novoa Lab

Publication highlights

Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing

April 2023

Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we introduce Nano-tRNAseq, a nanopore-based approach to sequence native tRNA populations that provides quantitative estimates of both tRNA abundances and modification dynamics in a single experiment. (…)

Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart

March 2023

The existence of naturally occurring ribosome heterogeneity is now a well-acknowledged phenomenon. However, whether this heterogeneity leads to functionally diverse ‘specialized ribosomes’ is still a controversial topic. Here, we explore the biological function of RPL3L (uL3L), a ribosomal protein (RP) paralogue of RPL3 (uL3) that is exclusively expressed in skeletal muscle and heart tissues, by generating a viable homozygous Rpl3l knockout mouse strain. (…)

Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing

December 2022

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 Nanopore 3′ end-capture sequencing (Nano3P-seq), a method that relies on nanopore cDNA sequencing to simultaneously quantify RNA abundance, tail composition, and tail length dynamics at per-read resolution. (…)

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing

October 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 other modifications, in particular pseudouridine (Ψ) and 2′-O-methylation (Nm), also result in characteristic base-calling ‘error’ signatures in the nanopore data. (…)

Accurate detection of m6A RNA modifications in native RNA sequences

September 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 RNA sequencing, N⁶-methyladenosine (m⁶A) RNA modifications can be detected with high accuracy, in the form of systematic errors and decreased base-calling qualities. (…)

Full list of publications

Timeline

For most updated list of publications, please see Google Scholar here.

2025

Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures.

Milenkovic I, Cruciani S, Llovera L, Lucas MC, Medina RM, Pauli C, Heid D, Muley T, Schneider MA, Klotz LV, Allgauer M, Lattuca R, LaFontaine D, Müller-Tidow C and Novoa EM^#. Molecular Cell, 2025, 85(1):177-190. doi: 10.1016/j.molcel.2024.11.014

Nano3P-seq: charting the coding and non-coding transcriptome at single molecule resolution.

Begik O*, Pryszcz LP*, Niazi AM, Valen E and Novoa EM^#. Nano3P-seq: charting the coding and non-coding transcriptome at single molecule resolution. Nat Protocols 2025, doi: 10.1038/s41596-025-01205-0

De novo basecalling of RNA modifications at single molecule and single nucleotide resolution.

Cruciani S*, Delgado-Tejedor A*, Pryszcz LP*^.#, Medina R, Llovera L and Novoa EM^#. Genome Biol 2025, doi: 10.1186/s13059-025-03498-6

Rapid and accurate tool to demultiplex direct RNA nanopore sequencing datasets with SeqTagger.

Pryszcz LP*, Diensthuber G*, Medina R, Llovera L, Delgado-Tejedor A, Cozzuto L, Ponomarenko J and Novoa EM^#. Genome Res 2025, doi: 10.1101/gr.279290.124

The new era of single-molecule RNA modification detection through nanopore basecalling models

Cruciani S and Novoa EM^#. Nat Rev Mol Cell Biol 2025, doi: 10.1038/s41580-025-00896-3

Toward the use of nanopore RNA sequencing technologies in the clinic: challenges and opportunities.

Katopodi XL, Begik O and Novoa EM^#. Nucleic Acids Res 2025, doi: https://doi.org/10.1093/nar/gkaf128

Ribosomal protein paralogues in ribosome specialization.

Milenkovic I and Novoa EM^#. Phil Trans R Soc B 2025 doi: https://doi.org/10.1098/rstb.2023.0387

Charting the epitranscriptomic landscape across RNA biotypes using native RNA nanopore sequencing

Diensthuber G and Novoa EM^#. Molecular Cell 2025, doi: https//doi.org/10.1016/j.molcel.2024.12.014

Disrupting tRNA modifications to target mitochondrial vulnerabilities in drug-resistant leukemia cells.

Katopodi XL, Begik O and Novoa EM^#. Nucleic Acids Res 2025, doi: https://doi.org/10.1093/nar/gkaf128

2024

N6-methyladenosine modification is not a general trait of viral RNA genomes.

Baquero-Perez B*, Yonchev I*, Delgado-Tejedor A*, Medina R, Puig-Torrents M, Sudbery I, Begik O, Wilson S^#, Novoa EM^#, Diez J^#. Nat Comm 2024 (accepted). Preprint available at: doi.org/10.1101/2023.10.13.561839

The lncRNA Sngh11, a new candidate contributing to neurogenesis, plasticity and memory deficits in Down syndrome

Sierra C, Sabariego M, Fernandez-Blanco A, Cruciani S, Zamora-Moratalla A, Novoa EM and Dierssen M. Mol Psychiatry 2024. Preprint available at: DOI doi.org/10.21203/rs.3.rs-3184329/v1

2023

De novo basecalling of m6A modifications at single molecule and single nucleotide resolution.

Cruciani S*, Delgado-Tejedor A*, Pryszcz LP*, Medina R, Llovera L and Novoa EM. bioRxiv 2023. DOI: doi.org/10.1101/2023.11.13.566801 (under review)

Enhanced detection of RNA modifications and mappability with high-accuracy nanopore RNA basecalling models.

Diensthuber G*, Pryszcz LP*, Llovera L, Lucas MC, Delgado-Tejedor A, Cruciani C, Roignant JY, Begik O

and Novoa EM. bioRxiv 2023, DOI: doi.org/10.1101/2023.11.28.568965v1 (under review)

Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites

Anna Delgado-Tejedor, Rebeca Medina, Oguzhan Begik, Luca Cozzuto, Julia Ponomarenko, Eva Maria Novoa. Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites. bioRxiv. 2023. DOI: doi.org/10.1101/2023.03.21.533606 (under review)

Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster

Athena Sklias, Sonia Cruciani,Virginie Marchand, Mariangela Spagnuolo, Guillaume Lavergne, Valérie Bourguignon, René Dreos, Eva Maria Novoa, Yuri Motorin, Jean-Yves Roignant. Comprehensive map of ribosomal 2′-O-methylation and C/D box snoRNAs in Drosophila melanogaster. bioRxiv. 2023. DOI: 10.1101/2023.05.25.542231v1 (accepted in Nucl Acids Res)

Quantitative analysis of native tRNAs using direct RNA nanopore sequencing

Morghan C Lucas*, Leszek P Pryszcz*, Rebeca Medina, Ivan Milenkovic, Noelia Camacho, Virginie Marchand, Yuri Motorin, Lluís Ribas de Pouplana, Eva Maria Novoa. Quantitative analysis of native tRNAs using direct RNA nanopore sequencing. Nature Biotech. 2023. DOI: 10.1038/s41587-023-01743-6

Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart

Ivan Milenkovic, Helaine Graziele Santos Vieira, Morghan C Lucas, Jorge Ruiz-Orera, Giannino Patone, Scott Kesteven, Jianxin Wu, Michael Feneley, Guadalupe Espadas, Eduard Sabidó, Norbert Hübner, Sebastiaan van Heesch, Mirko Völkers, Eva Maria Novoa. Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart. Nucleic Acids Res, 2023. DOI: /10.1093/nar/gkad121

Long-read sequencing in the era of epigenomics and epitranscriptomics.

Morghan C. Lucas, Eva Maria Novoa. Long-read sequencing in the era of epigenomics and epitranscriptomics. Nature Methods, 2023. DOI: 10.1038/s41592-022-01724-8

2022

Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing

Oguzhan Begik, Gregor Diensthuber, Huanle Liu, Anna Delgado-Tejedor, Cassandra Kontur, Adnan Muhammad Niazi, Eivind Valen, Antonio J. Giraldez, Jean-Denis Beaudoin, John S. Mattick, Eva Maria Novoa. Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing. Nature Methods. 2022. DOI: 10.1038/s41592-022-01714-w

CHIKV infection reprograms codon optimality to favor viral RNA translation by altering the tRNA epitranscriptome

Jennifer Jungfleisch, René Böttcher, Marc Talló-Parra, Gemma Pérez-Vilaró, Andres Merits, Eva Maria Novoa, Juana Díez. CHIKV infection reprograms codon optimality to favor viral RNA translation by altering the tRNA epitranscriptome. Nature Comm. 2022. DOI: 10.1038/s41467-022-31835-x

High performance nano-flow liquid chromatography column combined with high- and low-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry

Guadalupe Espadas, Julia Morales-Sanfrutos, Rebeca Medina, Morghan C Lucas, Eva Maria Novoa, Eduard Sabidó. High performance nano-flow liquid chromatography column combined with high- and low-collision energy data-independent acquisition enables targeted and discovery identification of modified ribonucleotides by mass spectrometry. Journal of Chromatography A. 2022. DOI: 10.1016/j.chroma.2022.462803

Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores

Luca Cozzuto, Anna Delgado-Tejedor, Toni Hermoso Pulido, Eva Maria Novoa, Julia Ponomarenko. Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores. Methods Mol Biol. 2022. DOI: 10.1007/978-1-0716-2962-8_13

Exploring the epitranscriptome by native RNA sequencing

Oguzhan Begik, John S. Mattick, Eva Maria Novoa. Exploring the epitranscriptome by native RNA sequencing. RNA. 2022. DOI: 10.1261/rna.079404.122

2021

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing

Oguzhan Begik, Morghan C Lucas, Leszek P Pryszcz, Jose Miguel Ramirez, Rebeca Medina, Ivan Milenkovic, Sonia Cruciani, Huanle Liu, Helaine Graziele Santos Vieira, Aldema Sas-Chen, John S Mattick, Schraga Schwartz, Eva Maria Novoa. Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing. Nature Biotech. 2021. DOI: 10.1038/s41587-021-00915-6

Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation

Nicky Jonkhout, Sonia Cruciani, Helaine Graziele Santos Vieira, Julia Tran, Huanle Liu, Ganqiang Liu, Russell Pickford, Dominik Kaczorowski, Gloria R Franco, Franz Vauti, Noelia Camacho, Seyedeh Sedigheh Abedini, Hossein Najmabadi, Lluís Ribas de Pouplana, Daniel Christ, Nicole Schonrock, John S Mattick, Eva Maria Novoa. Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation. RNA Biol. 2021. DOI: 10.1080/15476286.2021.1881291

ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data

Leszek P Pryszcz, Eva Maria Novoa. ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data. Bioinformatics. 2021. DOI: 10.1093/bioinformatics/btab539

Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins

Adrian Gabriel Torres, Marta Rodríguez-Escribà, Marina Marcet-Houben, Helaine Graziele Santos Vieira, Noelia Camacho, Helena Catena, Marina Murillo Recio, Àlbert Rafels-Ybern, Oscar Reina, Francisco Miguel Torres, Ana Pardo-Saganta, Toni Gabaldón, Eva Maria Novoa, Lluís Ribas de Pouplana. Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins. Nucl Acids Res. 2021. DOI: 10.1093/nar/gkab461

High-throughput 5′ UTR engineering for enhanced protein production in non-viral gene therapies

Jicong Cao, Eva Maria Novoa, Zhizhuo Zhang, William C W Chen, Dianbo Liu, Gigi C G Choi, Alan S L Wong, Claudia Wehrspaun, Manolis Kellis, Timothy K Lu. High-throughput 5′ UTR engineering for enhanced protein production in non-viral gene therapies. Nature Communications. 2021. DOI: 10.1038/s41467-021-24436-7

EpiNano: Detection of m6A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing

Huanle Liu, Oguzhan Begik, Eva Maria Novoa. EpiNano: Detection of m⁶A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing. RNA Modifications. Humana, New York, NY. 2021. DOI: 10.1038/s41467-021-24436-7

Computational methods for RNA modification detection from nanopore direct RNA sequencing data

Mattia Furlan, Anna Delgado-Tejedor, Logan Mulroney, Mattia Pelizzola, Eva Maria Novoa, Tommaso Leonardi. Computational methods for RNA modification detection from nanopore direct RNA sequencing data. RNA Biol. 2021. DOI: 10.1080/15476286.2021.1978215

2020

Molecular barcoding of native RNAs using nanopore sequencing and deep learning

Martin A. Smith, Tansel Ersavas, James M. Ferguson, Huanle Liu, Morghan C. Lucas, Oguzhan Begik, Lilly Bojarski, Kirston Barton, Eva Maria Novoa. Molecular barcoding of native RNAs using nanopore sequencing and deep learning. Genome Research. 2020. DOI: 10.1101/gr.260836.120

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

Oguzhan Begik, Morghan C. Lucas, Huanle Liu, Jose Miguel Ramirez, John S. Mattick, Eva Maria Novoa. Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures. Genome Biology. 2020. DOI: 10.1186/s13059-020-02009-z

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets

Luca Cozzuto, Huanle Liu, Leszek P Pryszcz, Toni Hermoso Pulido, Anna Delgado-Tejedor, Julia Ponomarenko, Eva Maria Novoa. MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets. Front Genet. 2020. DOI: 10.3389/fgene.2020.00211

2019

Accurate detection of m6A RNA modifications in native RNA sequences

Huanle Liu, Oguzhan Begik, Morghan C. Lucas, Jose Miguel Ramirez, Christopher E. Mason, David Wiener, Schraga Schwartz, John S. Mattick, Martin A. Smith, Eva Maria Novoa. Accurate detection of m6A RNA modifications in native RNA sequences. Nature Communications. 2019. DOI: 10.1038/s41467-019-11713-9

Elucidation of Codon Usage Signatures across the Domains of Life

Eva Maria Novoa, Irwin Jungreis, Olivier Jaillon, Manolis Kellis. Elucidation of Codon Usage Signatures across the Domains of Life. Molecular Biology and Evolution. 2019. DOI: 10.1093/molbev/msz124

A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS)

Ming-Ru Wu, Lior Nissim, Doron Stupp, Erez Pery, Adina Binder-Nissim, Karen Weisinger, Casper Enghuus, Sebastian R. Palacios, Melissa Humphrey, Zhizhuo Zhang, Eva Maria Novoa, Manolis Kellis, Ron Weiss, Samuel D. Rabkin, Yuval Tabach, Timothy K. Lu. A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS). Nature Communication. 2019. DOI: 10.1038/s41467-019-10912-8

Mitochondrial Protein Synthesis and mtDNA Levels Coordinated through an Aminoacyl-tRNA Synthetase Subunit

Daria Picchioni, Albert Antolin-Fontes, Noelia Camacho, Claus Schmitz, Alba Pons-Pons, Marta Rodríguez-Escribà, Antigoni Machallekidou, Merve Nur Güler, Panagiota Siatra, Maria Carretero-Junquera, Alba Serrano, Stacy L Hovde, Philip A Knobel, Eva Maria Novoa, Maria Solà-Vilarrubias, Laurie S Kaguni, Travis H Stracker, Lluís Ribas de Pouplana. Mitochondrial Protein Synthesis and mtDNA Levels Coordinated through an Aminoacyl-tRNA Synthetase Subunit. Cell Reports. 2019. DOI: 10.1016/j.celrep.2019.03.022

2018

Analyses of mRNA structure dynamics identify the embryonic gene regulatory programs

Jean-Denis Beaudoin, Eva Maria Novoa, Charles E Vejnar, Valeria Yartseva, Carter M Takacs, Manolis Kellis, Antonio J Giraldez. Analyses of mRNA structure dynamics identify the embryonic gene regulatory programs. Nat Struct Mol Biol. 2018. DOI: 10.1038/s41594-018-0091-z