Searching journal content for articles similar to Choquet et al. 35 (4): 712.

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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...direct RNA-seq method can potentially overcome these issues while also identifying RNA modifications in the native molecule. However, sequencing throughput from current direct RNA protocols is still relatively low compared to cDNA-based protocols (∼20 M reads in direct RNA protocols [Oxford Nanopore...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...fall in introns; thus, these reads likely represent mature mRNA molecules rather than DNA contamination, and 5′ truncation may occur during library preparation, sequencing, or processing of the data. The presence of truncation is also supported by the relatively shorter reads generated by ONT directRNA...
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Method: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
- Alexander J. Ritter,
- Jolene M. Draper,
- Christopher Vollmers,
- and Jeremy R. Sanford
Genome Res. November 2024 34: 2000-2011; Published in Advance June 5, 2024, doi:10.1101/gr.279170.124
...and ligates the exon sequences together to generate translation-competent mRNA (Wang et al. 2015). Conserved sequences at exon–intron boundaries (splice sites) direct spliceosome assembly on each newly synthesized intron. The spliceosome can assemble different combinations of exon sequences to generate mRNA...
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Method: Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms
- Kerstin C. Maier,
- Saskia Gressel,
- Patrick Cramer,
- and Björn Schwalb
Genome Res. September 2020 30: 1332-1344; Published in Advance September 4, 2020, doi:10.1101/gr.257857.119
...probability assessment using the direct RNA nanopore sequencing of the 5EU-containing synthetic RNAs showed that RNAs are recognizable as 5EU containing with a probability of 0.75 once a minimum length of 500 nt is reached (Supplemental Fig. S1C). This covers the vast majority (93%) of all mature RNAs...
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Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
- Mattia Furlan,
- Eugenia Galeota,
- Nunzio Del Gaudio,
- Erik Dassi,
- Michele Caselle,
- Stefano de Pretis,
- and Mattia Pelizzola
Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
...based on the integrative analysis of total and nascent transcription, the latter being quantified through RNA metabolic labeling. We developed INSPEcT−, a computational method based on the mathematical modeling of premature and mature RNA expression that is able to quantify kinetic rates from steady...
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Research: The asymmetric distribution of RNA polymerase II and nucleosomes on replicated daughter genomes is caused by differences in replication timing between the lagging and the leading strand
- Rahima Ziane,
- Alain Camasses,
- and Marta Radman-Livaja
Genome Res. February 2022 32: 337-356; Published in Advance January 18, 2022, doi:10.1101/gr.275387.121
...). This effectively means that, for the entire duration of S phase, two copies of a gene that replicated early produce as much mRNA as one copy had been producing before replication. Our findings on the kinetics of nucleosome positioning maturation, which suggest that one replicated gene copy is more expressed than...
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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...leverage mutants that ablate NMD, the sensitivity of short-read RNA sequencing, and the unique information captured by long-read, nanopore direct RNA sequencing. Using a modified nanopore sequencing protocol, we capture isoform, decapping/cleavage site, and poly(A) tail information for individual, native mRNA...
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Research: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
- Marcin P. Sajek,
- Danielle Y. Bilodeau,
- Michael A. Beer,
- Emma Horton,
- Yukiko Miyamoto,
- Katrina B. Velle,
- Lars Eckmann,
- Lillian Fritz-Laylin,
- Olivia S. Rissland,
- and Neelanjan Mukherjee
Genome Res. October 2024 34: 1570-1581; Published in Advance September 26, 2024, doi:10.1101/gr.279526.124
...(A) signal evolved in eukaryotes, we explored poly(A) signals in other eukaryotic species. Although our initial experiments with G. lamblia assemblage A used both short and long-read sequences to identify poly(A) signals (Bilodeau et al. 2022), we reasoned that direct RNA Oxford Nanopore Technology would...
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Research: Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome
- Christoph D. Treiber and
- Scott Waddell
Genome Res. November 2020 30: 1559-1569; Published in Advance September 24, 2020, doi:10.1101/gr.259200.119
...transposons introduce cryptic splice sites into the nascent transcript and thereby significantly expand the neural transcript repertoire. Some genes exclusively produce chimeric mRNAs with transposon sequence; on average, 11.6% of the mRNAs produced from a given gene are chimeric. Conversely, most transposon...
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Research: Systematic identification and characterization of exon–intron circRNAs
- Yinchun Zhong,
- Yan Yang,
- Xiaolin Wang,
- Bingbing Ren,
- Xueren Wang,
- Ge Shan,
- and Liang Chen
Genome Res. March 2024 34: 376-393; Published in Advance April 12, 2024, doi:10.1101/gr.278590.123
...of circRNAs, can be used to identify exonic, intronic, and intergenic circRNAs (Zheng et al. 2019). CYCLeR constructs a splice graph based on the alignment and can also capture the full-length sequences of circRNAs (Stefanov and Meyer 2023). Oxford Nanopore Technology (ONT) sequencing has also been...
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