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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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Resource: Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish
- Alice S. Naftaly,
- Shana Pau,
- and Michael A. White
Genome Res. August 2021 31: 1486-1497; Published in Advance June 15, 2021, doi:10.1101/gr.274282.120
...junctions, and correcting previous estimates of TSSs and TTSs. The modified splice junctions were highly accurate, verified through deep RNA-seq. TSSs and TTSs may still have some error in their exact location as the clustering algorithm used by Iso-Seq3 allows for 100 bp of variability at the 5′ end and 30...
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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
...modifying complexes to TEs through sequence complementarity (Malone and Hannon 2009; Moazed 2009). In flowering plants (angiosperms), TE silencing is mostly associated with DNA methylation and H3K9me2, and the mechanism by which sRNAs guide chromatin modifications is known as RNA-directed DNA methylation...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...” and “UACUCC” IRES elements, and novel short C/U-related sequences (such as “CCCUCUU” and “UUCCUU) that can base pair with 18S rRNAs within a scanning ribosome to enhance cap-independent translation (Weingarten-Gabbay et al. 2016). However, much less evidence is available for their regulatory roles in plant mRNA...
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Research: Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
- Tingting Lu,
- Guojun Lu,
- Danlin Fan,
- Chuanrang Zhu,
- Wei Li,
- Qiang Zhao,
- Qi Feng,
- Yan Zhao,
- Yunli Guo,
- Wenjun Li,
- Xuehui Huang,
- and Bin Han
Genome Res. September 2010 20: 1238-1249; Published in Advance July 13, 2010, doi:10.1101/gr.106120.110
...research, our study firstly focused on the identification of exon-splicing junctions by relying on the deep sequencing of the transcriptome at single-base resolution by RNA-seq. We developed SPSS (searching positions of 4These authors contributed equally to this work. 5Corresponding author. E-mail bhan...
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Resource: Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
- Yamile Marquez,
- John W.S. Brown,
- Craig Simpson,
- Andrea Barta,
- and Maria Kalyna
Genome Res. June 2012 22: 1184-1195; Published in Advance March 5, 2012, doi:10.1101/gr.134106.111
....] Alternative splicing (AS) is a widespread mechanism which increases transcriptome and proteome complexity and controls developmental programs and responses to the environment in higher eukaryotes. The splicing process, removal of introns and ligation of exons, is performed by a large RNA-protein complex...
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Perspective: Decrypting noncoding RNA interactions, structures, and functional networks
- Muller Fabbri,
- Leonard Girnita,
- Gabriele Varani,
- and George A. Calin
Genome Res. September 2019 29: 1377-1388; Published in Advance August 21, 2019, doi:10.1101/gr.247239.118
.... 2017). Over the last decade, advances in bioinformatics and deep sequencing technology have allowed the identification and annotation of tens of thousands of short and long ncRNAs (lncRNAs). These include endogenous microRNAs (miRNAs), small interfering RNAs (endo-siRNAs), PIWI-interacting RNAs (piRNAs...
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Research: Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency
- Chan-Shuo Wu,
- Chun-Ying Yu,
- Ching-Yu Chuang,
- Michael Hsiao,
- Cheng-Fu Kao,
- Hung-Chih Kuo,
- and Trees-Juen Chuang
Genome Res. January 2014 24: 25-36; Published in Advance October 16, 2013, doi:10.1101/gr.159483.113
...sequencing of different human embryonic stem cell (hESC) lines to effectively minimize false positives while detecting trans-splicing. Combining TSscan screening with multiple experimental validation steps revealed that most chimeric RNA products were platformdependent experimental artifacts of RNA...
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Research: Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents
- Anja Paschold,
- Yi Jia,
- Caroline Marcon,
- Steve Lund,
- Nick B. Larson,
- Cheng-Ting Yeh,
- Stephan Ossowski,
- Christa Lanz,
- Dan Nettleton,
- Patrick S. Schnable,
- and Frank Hochholdinger
Genome Res. December 2012 22: 2445-2454; Published in Advance October 19, 2012, doi:10.1101/gr.138461.112
...are actually expressed in such experiments. Finally, in microarray experiments, often arbitrarily introduced fold-change cut-offs such as Fc $ 2 are introduced. By contrast, RNA-seq experiments allow full quantification of gene expression. In addition, deep sequencing allows for the detection...
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LETTER: In-depth characterization of the microRNA transcriptome in a leukemia progression model
- Florian Kuchenbauer,
- Ryan D. Morin,
- Bob Argiropoulos,
- Oleh I. Petriv,
- Malachi Griffith,
- Michael Heuser,
- Eric Yung,
- Jessica Piper,
- Allen Delaney,
- Anna-Liisa Prabhu,
- Yongjun Zhao,
- Helen McDonald,
- Thomas Zeng,
- Martin Hirst,
- Carl L. Hansen,
- Marco A. Marra,
- and R. Keith Humphries
Genome Res. November 2008 18: 1787-1797; Published in Advance October 10, 2008, doi:10.1101/gr.077578.108
...this table: In this window In a new window Table 1. Overview about detected miRNA/miRNA* species, expression range and distribution View larger version: In this window In a new window Figure 1. Overview of small RNA and miRNA gene expression in a preleukemic and leukemic cell model obtained by deep...

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