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Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
- Qiuhui Li,
- Ayse G. Keskus,
- Justin Wagner,
- Michal B. Izydorczyk,
- Winston Timp,
- Fritz J. Sedlazeck,
- Alison P. Klein,
- Justin M. Zook,
- Mikhail Kolmogorov,
- and Michael C. Schatz
Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
...exon 1 of the APC gene (Fig. 2D). RNA-seq analysis revealed a substantial decrease in APC expression in the tumor sample (tumor fragments per kilobase of transcript per million fragments mapped (FPKM): 0.296 vs. normal FPKM: 2.262). The SV was not detected by short-read sequencing, likely because...
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Method: System-wide analyses of the fission yeast poly(A)⁺ RNA interactome reveal insights into organization and function of RNA–protein complexes
- Cornelia Kilchert,
- Tea Kecman,
- Emily Priest,
- Svenja Hester,
- Ebru Aydin,
- Krzysztof Kus,
- Oliver Rossbach,
- Alfredo Castello,
- Shabaz Mohammed,
- and Lidia Vasiljeva
Genome Res. July 2020 30: 1012-1026; Published in Advance June 18, 2020, doi:10.1101/gr.257006.119
...in gene expression and orchestrate production, function, and turnover of mRNAs. The accuracy and dynamics of RNA–protein interactions within these molecular machines are essential for their function and are mediated by RNA-binding proteins (RBPs). Here, we show that fission yeast whole-cell poly(A)+ RNA...
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Research: Long-read sequencing of nascent RNA reveals coupling among RNA processing events
- Lydia Herzel,
- Korinna Straube,
- and Karla M. Neugebauer
Genome Res. July 2018 28: 1008-1019; Published in Advance June 14, 2018, doi:10.1101/gr.232025.117
...-read RNA sequencing of nascent, multi-intron transcripts in the fission yeast Schizosaccharomyces pombe. Most multi-intron transcripts were fully spliced, consistent with rapid cotranscriptional splicing. However, an unexpectedly high proportion of transcripts were either fully spliced or fully unspliced...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
...metabolism. Notably, SRSF1, initially identified as a splicing factor, regulates various aspects of the mRNA life cycle, including alternative splicing, transcription, nuclear export, and translation. Consistent with the role of RNA-binding proteins in R-loop prevention, in vivo depletion of SRSF1 leads...
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Resource: Large-scale analysis of branchpoint usage across species and cell lines
- Allison J. Taggart,
- Chien-Ling Lin,
- Barsha Shrestha,
- Claire Heintzelman,
- Seongwon Kim,
- and William G. Fairbrother
Genome Res. April 2017 27: 639-649; Published in Advance January 24, 2017, doi:10.1101/gr.202820.115
...(between 10 and 60 nt upstream of the 3′ss AG), but the fission yeast branchpoints were more proximal. The ENCODE RNA-seq data sets were used to test the relationship between branchpoint location and alternative splicing outcomes. Taggart et al. 640 Genome Research www..org this method to lariat data from...
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Research: U2AF1 mutations alter splice site recognition in hematological malignancies
- Janine O. Ilagan,
- Aravind Ramakrishnan,
- Brian Hayes,
- Michele E. Murphy,
- Ahmad S. Zebari,
- Philip Bradley,
- and Robert K. Bradley
Genome Res. January 2015 25: 14-26; Published in Advance September 29, 2014, doi:10.1101/gr.181016.114
...-exome sequencing studies have identified common mutations affecting genes encoding components of the RNA splicing machinery in hematological malignancies. Here, we sought to determine how mutations affecting the 39 splice site recognition factor U2AF1 alter its normal role in RNA splicing. We find that U2AF1...
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Research: Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation
- Michael S. Werner,
- Bogdan Sieriebriennikov,
- Neel Prabh,
- Tobias Loschko,
- Christa Lanz,
- and Ralf J. Sommer
Genome Res. November 2018 28: 1675-1687; Published in Advance September 19, 2018, doi:10.1101/gr.234872.118
...Supplemental Fig. S1G).View larger version: In this window In a new window Figure 2. Long-read RNA sequencing (Iso-Seq) improves gene annotation, identifies alternative splicing, and can distinguish different evolutionary gene classes by gene structure. (A) Density distribution of cDNA gene lengths between...
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Article: Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing
- Jung-Hyun Kim,
- Thomas Ebersole,
- Natalay Kouprina,
- Vladimir N. Noskov,
- Jun-Ichirou Ohzeki,
- Hiroshi Masumoto,
- Brankica Mravinac,
- Beth A. Sullivan,
- Adam Pavlicek,
- Sinisa Dovat,
- Svetlana D. Pack,
- Yoo-Wook Kwon,
- Patrick T. Flanagan,
- Dmitri Loukinov,
- Victor Lobanenkov,
- and Vladimir Larionov
Genome Res. April 2009 19: 533-544; Published in Advance January 13, 2009, doi:10.1101/gr.086496.108
...of pericentromeric heterochromatin beyond its normal boundary into centromeric chromatin, which leads to defective chromosome segregation during meiosis. Interestingly, this barrier activity is encoded by functional tRNA genes. In some cells, insulators establish separate domains that isolate transcription enhancer...

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