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Article ; Online: Long-read sequencing in the era of epigenomics and epitranscriptomics.

Lucas, Morghan C / Novoa, Eva Maria

2023 Volume 20, Issue 1, Page(s) 25–29

MeSH term(s)	Humans ; Epigenomics ; RNA/genetics ; Transcriptome ; High-Throughput Nucleotide Sequencing
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2023-01-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2169522-2
ISSN	1548-7105 ; 1548-7091
ISSN (online)	1548-7105
ISSN	1548-7091
DOI	10.1038/s41592-022-01724-8
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Article ; Online: ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data.

Pryszcz, Leszek P / Novoa, Eva Maria

Bioinformatics (Oxford, England)

2021 Volume 38, Issue 1, Page(s) 257–260

Abstract: Motivation: DNA and RNA modifications can now be identified using nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data.: Results: Here, we present ... ...

Abstract	Motivation: DNA and RNA modifications can now be identified using nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data. Results: Here, we present ModPhred, a versatile toolkit that facilitates DNA and RNA modification analysis from nanopore sequencing reads in a user-friendly manner. ModPhred integrates probabilistic DNA and RNA modification information within the FASTQ and BAM file formats, can be used to encode multiple types of modifications simultaneously, and its output can be easily coupled to genomic track viewers, facilitating the visualization and analysis of DNA and RNA modification information in individual reads in a simple and computationally efficient manner. Availability and implementation: ModPhred is available at https://github.com/novoalab/modPhred, is implemented in Python3, and is released under an MIT license. Docker images with all dependencies preinstalled are also provided. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Nanopore Sequencing ; Sequence Analysis, DNA/methods ; Nanopores ; Software ; DNA ; RNA ; High-Throughput Nucleotide Sequencing
Chemical Substances	DNA (9007-49-2) ; RNA (63231-63-0)
Language	English
Publishing date	2021-07-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btab539
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Article ; Online: Spectral libraries from nucleobases and deoxyribonucleosides facilitate the identification of ribonucleosides by nano-flow liquid chromatography-tandem mass spectrometry.

Espadas, Guadalupe / Llovera, Laia / Ollivier, Alexane / Tuorto, Francesca / Novoa, Eva Maria / Sabidó, Eduard

Rapid communications in mass spectrometry : RCM

2024 Volume 38, Issue 13, Page(s) e9759

Abstract: Rationale: The study addresses the challenge of identifying RNA post-transcriptional modifications when commercial standards are not available to generate reference spectral libraries. It proposes employing homologous nucleobases and ... ...

Abstract	Rationale: The study addresses the challenge of identifying RNA post-transcriptional modifications when commercial standards are not available to generate reference spectral libraries. It proposes employing homologous nucleobases and deoxyribonucleosides as alternative reference spectral libraries to aid in identifying modified ribonucleosides and distinguishing them from their positional isomers when the standards are unavailable. Methods: Complete sets of ribonucleoside, deoxyribonucleoside and nucleobase standards were analyzed using high-performance nano-flow liquid chromatography coupled to an Orbitrap Eclipse Tribrid mass spectrometer. Spectral libraries were constructed from homologous nucleobases and deoxyribonucleosides using targeted MS2 and neutral-loss-triggered MS3 methods, and collision energies were optimized. The feasibility of using these libraries for identifying modified ribonucleosides and their positional isomers was assessed through comparison of spectral fragmentation patterns. Results: Our analysis reveals that both MS2 and neutral-loss-triggered MS3 methods yielded rich spectra with similar fragmentation patterns across ribonucleosides, deoxyribonucleosides and nucleobases. Moreover, we demonstrate that spectra from nucleobases and deoxyribonucleosides, generated at optimized collision energies, exhibited sufficient similarity to those of modified ribonucleosides to enable their use as reference spectra for accurate identification of positional isomers within ribonucleoside families. Conclusions: The study demonstrates the efficacy of utilizing homologous nucleobases and deoxyribonucleosides as interchangeable reference spectral libraries for identifying modified ribonucleosides and their positional isomers. This approach offers a valuable solution for overcoming limitations posed by the unavailability of commercial standards, enhancing the analysis of RNA post-transcriptional modifications via mass spectrometry.
MeSH term(s)	Tandem Mass Spectrometry/methods ; Ribonucleosides/chemistry ; Ribonucleosides/analysis ; Deoxyribonucleosides/chemistry ; Chromatography, High Pressure Liquid/methods ; Nanotechnology/methods ; Chromatography, Liquid/methods
Chemical Substances	Ribonucleosides ; Deoxyribonucleosides
Language	English
Publishing date	2024-04-25
Publishing country	England
Document type	Journal Article
ZDB-ID	58731-x
ISSN	1097-0231 ; 0951-4198
ISSN (online)	1097-0231
ISSN	0951-4198
DOI	10.1002/rcm.9759
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Article ; Online: Exploring the epitranscriptome by native RNA sequencing.

Begik, Oguzhan / Mattick, John S / Novoa, Eva Maria

RNA (New York, N.Y.)

2022 Volume 28, Issue 11, Page(s) 1430–1439

Abstract: 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 due to the advent of high- ... ...

Abstract	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 due to the advent of high-throughput sequencing methodologies, which typically consist of coupling modification-specific reagents, such as antibodies or enzymes, to next-generation sequencing. Recently, it also became possible to map RNA modifications directly by sequencing native RNAs using nanopore technologies, which has been applied for the detection of a number of RNA modifications, such as N6-methyladenosine (m
MeSH term(s)	Sequence Analysis, RNA ; Pseudouridine/genetics ; Pseudouridine/metabolism ; RNA/genetics ; RNA/metabolism ; High-Throughput Nucleotide Sequencing ; RNA Processing, Post-Transcriptional ; Transcriptome
Chemical Substances	Pseudouridine (1445-07-4) ; RNA (63231-63-0)
Language	English
Publishing date	2022-09-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.079404.122
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Article ; Online: The lncRNA Snhg11, a new candidate contributing to neurogenesis, plasticity, and memory deficits in Down syndrome.

Sierra, Cesar / Sabariego-Navarro, Miguel / Fernández-Blanco, Álvaro / Cruciani, Sonia / Zamora-Moratalla, Alfonsa / Novoa, Eva Maria / Dierssen, Mara

Molecular psychiatry

2024

Abstract: Down syndrome (DS) stands as the prevalent genetic cause of intellectual disability, yet comprehensive understanding of its cellular and molecular underpinnings remains limited. In this study, we explore the cellular landscape of the hippocampus in a DS ... ...

Abstract	Down syndrome (DS) stands as the prevalent genetic cause of intellectual disability, yet comprehensive understanding of its cellular and molecular underpinnings remains limited. In this study, we explore the cellular landscape of the hippocampus in a DS mouse model, the Ts65Dn, through single-nuclei transcriptional profiling. Our findings demonstrate that trisomy manifests as a highly specific modification of the transcriptome within distinct cell types. Remarkably, we observed a significant shift in the transcriptomic profile of granule cells in the dentate gyrus (DG) associated with trisomy. We identified the downregulation of a specific small nucleolar RNA host gene, Snhg11, as the primary driver behind this observed shift in the trisomic DG. Notably, reduced levels of Snhg11 in this region were also observed in a distinct DS mouse model, the Dp(16)1Yey, as well as in human postmortem brain tissue, indicating its relevance in Down syndrome. To elucidate the function of this long non-coding RNA (lncRNA), we knocked down Snhg11 in the DG of wild-type mice. Intriguingly, this intervention alone was sufficient to impair synaptic plasticity and adult neurogenesis, resembling the cognitive phenotypes associated with trisomy in the hippocampus. Our study uncovers the functional role of Snhg11 in the DG and underscores the significance of this lncRNA in intellectual disability. Furthermore, our findings highlight the importance of DG in the memory deficits observed in Down syndrome.
Language	English
Publishing date	2024-02-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1330655-8
ISSN	1476-5578 ; 1359-4184
ISSN (online)	1476-5578
ISSN	1359-4184
DOI	10.1038/s41380-024-02440-9
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Article ; Online: Nanopore Direct RNA Sequencing Data Processing and Analysis Using MasterOfPores.

Cozzuto, Luca / Delgado-Tejedor, Anna / Hermoso Pulido, Toni / Novoa, Eva Maria / Ponomarenko, Julia

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2624, Page(s) 185–205

Abstract: This chapter describes MasterOfPores v.2 (MoP2), an open-source suite of pipelines for processing and analyzing direct RNA Oxford Nanopore sequencing data. The MoP2 relies on the Nextflow DSL2 framework and Linux containers, thus enabling reproducible ... ...

Abstract	This chapter describes MasterOfPores v.2 (MoP2), an open-source suite of pipelines for processing and analyzing direct RNA Oxford Nanopore sequencing data. The MoP2 relies on the Nextflow DSL2 framework and Linux containers, thus enabling reproducible data analysis in transcriptomic and epitranscriptomic studies. We introduce the key concepts of MoP2 and provide a step-by-step fully reproducible and complete example of how to use the workflow for the analysis of S. cerevisiae total RNA samples sequenced using MinION flowcells. The workflow starts with the pre-processing of raw FAST5 files, which includes basecalling, read quality control, demultiplexing, filtering, mapping, estimation of per-gene/transcript abundances, and transcriptome assembly, with support of the GPU computing for the basecalling and read demultiplexing steps. The secondary analyses of the workflow focus on the estimation of RNA poly(A) tail lengths and the identification of RNA modifications. The MoP2 code is available at https://github.com/biocorecrg/MOP2 and is distributed under the MIT license.
MeSH term(s)	Software ; Nanopore Sequencing ; Nanopores ; RNA/genetics ; Saccharomyces cerevisiae/genetics ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, RNA
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2023-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2962-8_13
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Article ; Online: EpiNano: Detection of m

Liu, Huanle / Begik, Oguzhan / Novoa, Eva Maria

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2298, Page(s) 31–52

Abstract: 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) has emerged as a promising ... ...

Abstract	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) has emerged as a promising technology that can provide single-molecule resolution maps of RNA modifications in their native RNA context. While native RNA can be successfully sequenced using this technology, the detection of RNA modifications is still challenging. Here, we provide an upgraded version of EpiNano (version 1.2), an algorithm to predict m
MeSH term(s)	Escherichia coli/genetics ; Nanopore Sequencing/methods ; Nanopores ; RNA/genetics ; RNA Processing, Post-Transcriptional/genetics ; Sequence Analysis, RNA/methods
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2021-06-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1374-0_3
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Article ; Online: 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.

Espadas, Guadalupe / Morales-Sanfrutos, Julia / Medina, Rebeca / Lucas, Morghan C / Novoa, Eva Maria / Sabidó, Eduard

Journal of chromatography. A

2022 Volume 1665, Page(s) 462803

Abstract: Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key ... ...

Abstract	Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their dysregulation in humans has been linked to several diseases such as cancer, metabolic diseases or neurological disorder. Nowadays, liquid chromatography-tandem mass spectrometry is considered the gold standard method for the identification and quantification of these modifications due to its sensitivity and accuracy. However, the analysis of modified ribonucleosides by mass spectrometry is complex due to the presence of positional isomers. In this scenario, optimal separation of these compounds by highly sensitive liquid chromatography combined with the generation of high-information spectra is critical to unequivocally identify them, especially in high-complex mixtures. Here we present an analytical method that comprises a new type of mixed-mode nano-flow liquid chromatography column combined with high- and low-collision energy data-independent mass spectrometric acquisition for the identification and quantitation of modified ribonucleosides. The method produces content-rich spectra and combines targeted and screening capabilities thus enabling the identification of a variety of modified nucleosides in biological matrices by single-shot liquid chromatographic analysis coupled to mass spectrometry.
Language	English
Publishing date	2022-01-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1171488-8
ISSN	1873-3778 ; 0021-9673
ISSN (online)	1873-3778
ISSN	0021-9673
DOI	10.1016/j.chroma.2022.462803
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Article: The lncRNA Snhg11, a new candidate contributing to neurogenesis, plasticity and memory deficits in Down syndrome.

Sierra, Cesar / Sabariego-Navarro, Miguel / Fernández-Blanco, Álvaro / Cruciani, Sonia / Zamora-Moratalla, Alfonsa / Novoa, Eva Maria / Dierssen, Mara

Research square

2023

Abstract	Down syndrome (DS) stands as the prevalent genetic cause of intellectual disability, yet comprehensive understanding of its cellular and molecular underpinnings remains limited. In this study, we explore the cellular landscape of the hippocampus in a DS mouse model through single-nuclei transcriptional profiling. Our findings demonstrate that trisomy manifests as a highly specific modification of the transcriptome within distinct cell types. Remarkably, we observed a significant shift in the transcriptomic profile of granule cells in the dentate gyrus (DG) associated with trisomy. We identified the downregulation of a specific small nucleolar RNA host gene,
Language	English
Publishing date	2023-09-25
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3184329/v1
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Article ; Online: N

Baquero-Pérez, Belinda / Yonchev, Ivaylo D / Delgado-Tejedor, Anna / Medina, Rebeca / Puig-Torrents, Mireia / Sudbery, Ian / Begik, Oguzhan / Wilson, Stuart A / Novoa, Eva Maria / Díez, Juana

Nature communications

2024 Volume 15, Issue 1, Page(s) 1964

Abstract: Despite the nuclear localization of the ... ...

Abstract	Despite the nuclear localization of the m
MeSH term(s)	Humans ; Chikungunya virus/genetics ; Dengue Virus/genetics ; Dengue ; RNA, Viral/genetics ; Chikungunya Fever ; Antibodies, Viral ; Adenosine/analogs & derivatives
Chemical Substances	RNA, Viral ; N-methyladenosine (CLE6G00625) ; Antibodies, Viral ; Adenosine (K72T3FS567)
Language	English
Publishing date	2024-03-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-46278-9
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