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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
...–associated RNA-binding protein signatures. Taken together, our data demonstrate that alternative mRNA processing within the CDS and UTRs impacts the translational control of mRNA isoforms during stem cell differentiation, and highlight the utility of using a novel long-read sequencing–based method to study...
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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
...characterization of individual exons toward studying alternative RNA processing events in the isoform context. Therefore, LRS provides an attractive approach for studying full-length RNA molecules.Challenges of terminal end identification with long-read RNA sequencingShort-read sequencing (SRS) technologies...
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Research: Genetic regulation of nascent RNA maturation revealed by direct RNA nanopore sequencing
- Karine Choquet,
- Louis-Philippe Chaumont,
- Simon Bache,
- Autum R. Baxter-Koenigs,
- and L. Stirling Churchman
Genome Res. April 2025 35: 712-724; Published in Advance February 14, 2025, doi:10.1101/gr.279203.124
...) demonstrated that introns are not always removed in the order in which they appear in the nascent transcript. Our recent work extended these results by studying posttranscriptional splicing order for three to six consecutive introns (Choquet et al. 2023) using long-read direct RNA nanopore sequencing (Garalde...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...al. 2017. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 14: 959–962. doi:10.1038/nmeth.4396 ↵Core LJ, Waterfall JJ, Lis JT. 2008. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 322...
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Research: Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad
- Siyu Xie,
- Jun Li,
- Wanyan Chen,
- Lydia J.M. Fong,
- Chunhua Huang,
- Yan Feng,
- Qingbo Ai,
- Mian Zhao,
- Judith E. Mank,
- and Hua Wu
Genome Res. June 2025 35: 1325-1336; Published in Advance April 24, 2025, doi:10.1101/gr.280161.124
...Fi library construction. Whole- resequencing involved 40 individuals and one full-sib family. Transcriptomic sequencing used gonads at four developmental stages and adult somatic tissues. All procedures complied with CCNU-IACUC-2022-010 and relevant ethical regulations. Details for DNA/RNA extraction...
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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: 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
...depth of long-read sequencing.In the cases of rps-15A and rpl-30, the splicing event that creates the PTC enabled the unique assignment of unadapted and adapted mRNA molecules to either the NMD isoform or the non-NMD isoform (Fig. 2B). By assigning reads to isoforms, we observed that the vast majority...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...investigations in this field.Throughout their life cycle, RNAs undergo numerous processing events. Among these activities are RNA modifications, which describe changes to the chemical composition of individual nucleotides. Over 150 types of RNA modifications, also referred to as epitranscriptomic events or marks...
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Research: ADAR-deficiency perturbs the global splicing landscape in mouse tissues
- Utkarsh Kapoor,
- Konstantin Licht,
- Fabian Amman,
- Tobias Jakobi,
- David Martin,
- Christoph Dieterich,
- and Michael F. Jantsch
Genome Res. August 2020 30: 1107-1118; Published in Advance July 29, 2020, doi:10.1101/gr.256933.119
.... Moreover, catalytically dead ADAR also impacts splicing, demonstrating that RNA binding of ADAR affects splicing. In contrast, ADARB1 editing sites are found enriched 5′ of differentially spliced regions. Several of these ADARB1-mediated editing events change splice consensus sequences, therefore strongly...
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Resource: The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting
- Lishi Li,
- Yulong Song,
- Xinrui Shi,
- Jianheng Liu,
- Shaolei Xiong,
- Wanying Chen,
- Qiang Fu,
- Zichao Huang,
- Nannan Gu,
- and Rui Zhang
Genome Res. January 2018 28: 132-143; Published in Advance December 12, 2017, doi:10.1101/gr.224386.117
...levels (Fig. 2D). These data reveal the -wide pattern of complementary sequence preference in miRNA editing.To compare the conservation of miRNA editing among animal species, we analyzed both the miRNA and the editing site conservation. We found that within about 270 miRNAs conserved between human...

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