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Method: Kinetic measurement of gene-specific RNA polymerase II transcription elongation rates
- Haiyue Liu and
- Lea H. Gregersen
Genome Res. November 2025 35: 2550-2562; Published in Advance October 22, 2025, doi:10.1101/gr.280852.125
.... Whereas much research has focused on the initiation of transcription, regulation of elongation plays an important role not only in transcription dynamics but also in cotranscriptional RNA processing and stability. Despite advances in high-throughput approaches for global quantification of RNA polymerase...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...robust KCl-dependent transcript abundance changes in primary neurons, yet few have globally examined alternative splicing (West et al. 2001; Kim et al. 2010). We analyzed alternative splicing in five public RNA sequencing data sets of mouse primary neurons following KCl treatment (Fig. 1A; Maze et al...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...(RNA-seq), and Iso-Seq have uncovered many low-frequency alternative isoforms (Bitton et al. 2015a; Stepankiw et al. 2015; Kuang et al. 2017), suggesting that splicing fidelity in the species is relatively low.Little is known about the impact of alternative splicing (AS) in generating functional...
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Method: Assessing conservation of alternative splicing with evolutionary splicing graphs
- Diego Javier Zea,
- Sofya Laskina,
- Alexis Baudin,
- Hugues Richard,
- and Elodie Laine
Genome Res. August 2021 31: 1462-1473; Published in Advance June 15, 2021, doi:10.1101/gr.274696.120
...AS eventsWe tested ThorAxe on a curated set of 50 genes representing 16 families (Supplemental Table S1; Supplemental Methods), in which several splice variants have been associated with diverse protein functions. ThorAxe detected 448 alternative splicing, initiation, and termination events. RNA-seq splice...
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Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
- Fu-Yuan Zhu,
- Xin Chen,
- Yu-Chen Song,
- Lydia Pui Ying Lam,
- Yuki Tobimatsu,
- Bei Gao,
- Mo-Xian Chen,
- and Fu-Liang Cao
Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
....Transcription factor (TF)–SF synchronization in poplar in response to Pb stressSplicing factors (SFs) and TFs are typical factors that regulate AS. SF directly mediates the AS pattern, whereas TF influences pre-mRNA synthesis, including RNA polymerase II (RNAPII) elongation, which is known to impact cotranscriptional...
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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
...′-end occurs cotranscriptionally, after RNA polymerase II has transcribed through the poly(A) cleavage site, and is rapidly followed by polyadenylation, which consists of the addition of 200–250 adenines to the 3′-end of pre-mRNAs (Nicholson and Pasquinelli 2019). Alternative splicing (AS...
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Research: RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing
- Heidi Dvinge,
- Jamie Guenthoer,
- Peggy L. Porter,
- and Robert K. Bradley
Genome Res. October 2019 29: 1591-1604; Published in Advance August 21, 2019, doi:10.1101/gr.246678.118
...of the spliceosome are not merely basal factors, as has long been assumed. Instead, these noncoding RNAs constitute a previously uncharacterized layer of regulation of alternative splicing, and contribute to the establishment of global splicing programs in both healthy and malignant cells.Alternative pre-mRNA...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...reported (Fig. 2E; Supplemental Figs. S13, S14; Harkess et al. 2024).Thus, reduced 24 nt siRNA and mCHH levels in Spirodela can be explained by the combined reduction in RdDM composition and expression in addition to the absence of CMT2. However, it does not account for the global decrease in mCG and m...
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Research: Global variability in gene expression and alternative splicing is modulated by mitochondrial content
- Raul Guantes,
- Alberto Rastrojo,
- Ricardo Neves,
- Ana Lima,
- Begoña Aguado,
- and Francisco J. Iborra
Genome Res. May 2015 25: 633-644; Published in Advance March 23, 2015, doi:10.1101/gr.178426.114
.... 2A). This suggests that mitochondria have a positive impact on chromatin activation globally. A second level of gene expression control is the regulation of the transcription machinery. In order to study the influence of mitochondria on the transcription apparatus content, we focus on RNA Pol II...
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Research: Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation
- Jonathan Neve,
- Kaspar Burger,
- Wencheng Li,
- Mainul Hoque,
- Radhika Patel,
- Bin Tian,
- Monika Gullerova,
- and Andre Furger
Genome Res. January 2016 26: 24-35; Published in Advance November 6, 2015, doi:10.1101/gr.193995.115
..., triggered a flurry of investigations to annotate APA profiles in different tissues and cellular states (Ozsolak et al. 2010; Derti et al. 2012; Lin et al. 2012; You et al. 2015). RNA-seq–based global analysis extended the proportion of human genes that contain multiple CPA sites to ∼70% and demonstrated...
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