14 papers · ranked by Valyu relevance
Tamer Butto, Stefan Pastore, Max Müller, Kaushik Viswanathan Iyer + 6 more
Nanopore technology offers real-time sequencing opportunities, providing rapid access to sequenced data and allowing researchers to manage the sequencing process efficiently, resulting in cost-effective strategies. Here, we present focused case studies demonstrating the versatility of real-time transcriptomics analysis…
Adam D Hargreaves, John F Mulley
Portable DNA sequencers such as the Oxford Nanopore MinION device have the potential to be truly disruptive technologies, facilitating new approaches and analyses and, in some cases, taking sequencing out of the lab and into the field. However, the capabilities of these technologies are still being revealed. Here we…
Thidathip Wongsurawat, Piroon Jenjaroenpun, Trudy M. Wassenaar, Taylor D Wadley + 6 more
Sequencing of native RNA and corresponding cDNA was performed using Oxford Nanopore Technology. The % Error of Specific Bases (%ESB) was higher for native RNA than for cDNA, which enabled detection of ribonucleotide modification sites. Based on %ESB differences of the two templates, a bioinformatic tool ELIGOS was…
Jonathan S. Abebe, Yasmine Alwie, Erik Fuhrmann, Jonas Leins + 5 more
High-resolution annotations of transcriptomes from all domains of life are essential for many sequencing-based RNA analyses, including Nanopore direct RNA sequencing (DRS), which would otherwise be hindered by misalignments and other analysis artefacts. DRS allows the capture and full-length sequencing of native RNAs…
Wen Jiang, Zhanyong Guo, Nuno Lages, W. Jim Zheng + 3 more
To understand cellular coordination of multiple transcriptome regulation mechanisms, we simultaneously measured three parameters – transcription rate (TR), mRNA abundance (RA) and translation activity (TA) – and assessed mRNA stability with the RA to TR ratio. This revealed multiple quantitative insights. First, the…
Ya-Hui Lin, Jennifer E. Dodd, Luisa Cutillo, Lydia M. Castelli + 14 more
Transcriptomes and translatomes measure genome-wide levels of total and ribosome-associated RNAs. A few hundred translatomes were reported over >250,000 transcriptomes highlighting the challenges of identifying translating RNAs. Here, we used a human isogenic inducible model of TDP-43-linked amyotrophic lateral…
Balázs Kakuk, Dóra Tombácz, Zsolt Balázs, Norbert Moldován + 5 more
Long-read sequencing (LRS), a powerful novel approach, is able to read full-length transcripts and confers a major advantage over the earlier gold standard short-read sequencing in the efficiency of identifying for example polycistronic transcripts and transcript isoforms, including transcript length- and splice…
Lorenzo Calviello, Antje Hirsekorn, Uwe Ohler
At the center of the gene expression cascade, translation is fundamental in defining the fate of much of the transcribed genome. RNA sequencing enables the quantification of complex transcript mixtures, often detecting several splice isoforms of unknown functions for one gene. We have developed ORFquant, a new approach…
Gloria M. Sheynkman, Katharine S. Tuttle, Elizabeth Tseng, Jason G. Underwood + 8 more
Most human protein-coding genes are expressed as multiple isoforms. This in turn greatly expands the functional repertoire of the encoded proteome. While at least one reliable open reading frame (ORF) model has been assigned for every gene, the majority of alternative isoforms remains uncharacterized experimentally.…
V Vern Lee, Louise M. Judd, Aaron R. Jex, Kathryn E. Holt + 2 more
Alternative splicing is a widespread phenomenon in metazoans by which single genes are able to produce multiple isoforms of the gene product. However, this has been poorly characterised in apicomplexans, a major phylum of some of the most important global parasites. Efforts have been hampered by atypical transcriptomic…
Vighnesh Ghatpande, Uma Paul, MacKenzie A Howard, Can Cenik
In the last decade, an unexpectedly large number of translated regions (translons) have been discovered using ribosome profiling and proteomics. Translons can regulate mRNA translation and encode micropeptides that contribute to multiprotein complex formation, Ca^2+^ regulation in muscle, and signaling during embryonic…
Jorge Ruiz-Orera, Pol Verdaguer-Grau, José Luis Villanueva-Cañas, Xavier Messeguer + 1 more
Cells express thousands of transcripts that show weak coding potential. Known as long non-coding RNAs (lncRNAs), they typically contain short open reading frames (ORFs) having no homology with known proteins. Recent studies show that a significant proportion of lncRNAs are translated, challenging the view that they are…
D. Paulet, A. David, E. Rivals
RNA translation has long been thought as a stable and uniform process by which a ribosome produces a protein encoded by the main Open Reading Frame (ORF) of an mRNA. Recently, growing evidence support incomplete correlation between RNA and protein abundance levels, the existence of alternative ORFs in numerous…
Laura Fancello, Thomas Burger
Proteogenomics aims at identifying variant or unknown proteins in bottom-up proteomics, searching transcriptome- or genome-derived custom protein databases. However, empirical observations reported that the large size of these proteogenomic databases is associated to lower sensitivity of peptide identifications.…