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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
...(fission yeast) retains many of the splicing features observed in humans and is thus an excellent model to study the basic mechanisms of splicing. Nearly half the genes contain introns, but the impact of alternative splicing in gene regulation and proteome diversification remains largely unexplored. Here...
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Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
- Hsin-Yen Larry Wu,
- Isaiah D. Kaufman,
- and Polly Yingshan Hsu
Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
...a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.References ↵Barrell BG, Air GM, Hutchison CA. 1976. Overlapping genes in bacteriophage phiX174. Nature 264: 34–41. doi:10.1038/264034a0 ↵Bazin J, Baerenfaller K, Gosai SJ...
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Research: Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids
- Benjamin D. Umans and
- Yoav Gilad
Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
...levels. We annotated cell clusters using fetal brain reference data (Polioudakis et al. 2019; Trevino et al. 2021) and known marker genes, finding a variety of cortical cell types, including radial glial progenitors, intermediate progenitors, excitatory neurons, and inhibitory neurons (Fig. 1B...
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Method: Deep profiling and custom databases improve detection of proteoforms generated by alternative splicing
- Laura M. Agosto,
- Matthew R. Gazzara,
- Caleb M. Radens,
- Simone Sidoli,
- Josue Baeza,
- Benjamin A. Garcia,
- and Kristen W. Lynch
Genome Res. December 2019 29: 2046-2055; Published in Advance November 14, 2019, doi:10.1101/gr.248435.119
...Seq databases to improve identification of splicing-derived proteoforms by 28% compared with use of the SWISS-PROT database alone. Altogether, we identified peptide evidence for 554 alternate proteoforms corresponding to 274 genes. Our increased depth and detection of proteins also allowed us to track changes...
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Research: RBFOX splicing factors contribute to a broad but selective recapitulation of peripheral tissue splicing patterns in the thymus
- Kathrin Jansen,
- Noriko Shikama-Dorn,
- Moustafa Attar,
- Stefano Maio,
- Maria Lopopolo,
- David Buck,
- Georg A. Holländer,
- and Stephen N. Sansom
Genome Res. November 2021 31: 2022-2034; Published in Advance October 14, 2021, doi:10.1101/gr.275245.121
...the generation of long “classical” transcripts (with 5′ and 3′ UTRs) but has only a limited impact on alternative splicing in mTEC. Comprehensive assessment of SF expression in mTEC identified a small set of nonpromiscuously expressed SF genes, among which we confirmed RBFOX to be present with AIRE in m...
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Research: Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs
- Marta Melé,
- Kaia Mattioli,
- William Mallard,
- David M. Shechner,
- Chiara Gerhardinger,
- and John L. Rinn
Genome Res. January 2017 27: 27-37; Published in Advance December 7, 2016, doi:10.1101/gr.214205.116
...upstream. 3′ splice sites We selected all annotated nonredundant 3′ splice sites in lincRNAs andmRNAs.We defined constitutive or alternative 3′ splice sites as those present in at least 75% or in <25% of all annotated isoforms of a gene, respectively. k-mer analyses To perform discriminative k...
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Methods: Improving gene annotation using peptide mass spectrometry
- Stephen Tanner,
- Zhouxin Shen,
- Julio Ng,
- Liliana Florea,
- Roderic Guigó,
- Steven P. Briggs,
- and Vineet Bafna
Genome Res. February 2007 17: 231-239; Published in Advance December 22, 2006, doi:10.1101/gr.5646507
..., prespliced mRNA, as well as untranslated regions. Thus it is hard to determine if every alternative splice form predicted from an EST is also expressed at the protein level. Alternative splicing and overlapping genes present particularly difficult annotation problems. Some estimates suggest that the majority...
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Resource: Phenotypic annotation of the mouse X chromosome
- Brian J. Cox,
- Marion Vollmer,
- Owen Tamplin,
- Mei Lu,
- Steffen Biechele,
- Marina Gertsenstein,
- Claude van Campenhout,
- Thomas Floss,
- Ralf Kühn,
- Wolfgang Wurst,
- Heiko Lickert,
- and Janet Rossant
Genome Res. August 2010 20: 1154-1164; Published in Advance June 14, 2010, doi:10.1101/gr.105106.110
..., Toronto, Ontario M5T 3H7, Canada ↵ 12 These authors contributed equally to this work. Abstract Mutational screens are an effective means used in the functional annotation of a genome. We present a method for a mutational screen of the mouse X chromosome using gene trap...
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Research: Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
- Hagen Tilgner,
- David G. Knowles,
- Rory Johnson,
- Carrie A. Davis,
- Sudipto Chakrabortty,
- Sarah Djebali,
- João Curado,
- Michael Snyder,
- Thomas R. Gingeras,
- and Roderic Guigó
Genome Res. September 2012 22: 1616-1625; doi:10.1101/gr.134445.111
...-Zwierz et al. 2009; Nahkuri et al. 2009; Schwartz et al. 2009; Spies et al. 2009; Tilgner et al. 2009). Intragenic histone modifications and chromatin structure influences on alternative splicing events have been documented in detail for the fibronectin and FGFR2 gene (Allo et al. 2009; Schor et al. 2009...
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Method: Predicting cell-type–specific gene expression from regions of open chromatin
- Anirudh Natarajan,
- Galip Gürkan Yardımcı,
- Nathan C. Sheffield,
- Gregory E. Crawford,
- and Uwe Ohler
Genome Res. September 2012 22: 1711-1722; doi:10.1101/gr.135129.111
...of TFs to predict cell-type–specific gene expression. Therefore, developing predictivemodels of gene expressionwithout relying on ChIP would facilitate our understanding of transcriptional regulation. A more widely applicable alternative to ChIP is to use known cognate binding preferences for TFs...
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