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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...map spl-TRs in a -wide manner across tissues throughout the whole body by using the Genotype-Tissue expression (GTEx) v8 data set, a population-scale resource of whole- sequencing (WGS) and RNA sequencing (RNA-seq).ResultsGenome-wide identification of spl-TRs across 49 tissuesWe discovered cis spl...
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Research: RNA Pol II–dependent transcription efficiency fine-tunes A-to-I editing levels
- Brigitta Szabo,
- Therese C. Mandl,
- Bernhard Woldrich,
- Gregor Diensthuber,
- David Martin,
- Michael F. Jantsch,
- and Konstantin Licht
Genome Res. February 2024 34: 231-242; Published in Advance March 12, 2024, doi:10.1101/gr.277686.123
...between pre-mRNA and mRNA editing levels, we next tested if differential splicing can explain the differences in editing levels. We had previously shown that ADARB1-mediated editing of Flna causes intron retention, presumably because editing reduces U1 snRNA base-pairing efficiency (Kapoor et al. 2020...
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Research: A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations
- Te-Lun Mai and
- Trees-Juen Chuang
Genome Res. November 2019 29: 1766-1776; Published in Advance September 12, 2019, doi:10.1101/gr.246033.118
...Te-Lun Mai and Trees-Juen Chuang Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan Corresponding author: trees@gate.sinica.edu.twAbstractAdenosine-to-inosine (A-to-I) RNA editing is a very common co-/posttranscriptional modification that can lead to A-to-G changes at the RNA level...
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Method: Allele-specific RNA N⁶-methyladenosine modifications reveal functional genetic variants in human tissues
- Shuo Cao,
- Haoran Zhu,
- Jinru Cui,
- Sun Liu,
- Yuhe Li,
- Junfang Shi,
- Junyuan Mo,
- Zihan Wang,
- Hailan Wang,
- Jiaxin Hu,
- Lizhi Chen,
- Yuan Li,
- Laixin Xia,
- and Shan Xiao
Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
...differentiation, artery development, and heart morphogenesis (Supplemental Fig. S5C) and that, in the brain, they were enriched in axonogenesis (Supplemental Fig. S5C), suggesting that ASm6As may affect diseases or traits by impacting the genes in which they are located. It is known that m6A can affect the RNA...
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Research: A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing
- Konstantin Licht,
- Utkarsh Kapoor,
- Fabian Amman,
- Ernesto Picardi,
- David Martin,
- Prajakta Bajad,
- and Michael F. Jantsch
Genome Res. September 2019 29: 1453-1463; Published in Advance August 19, 2019, doi:10.1101/gr.242636.118
...and 520 editing sites, respectively, were differentially edited as compared to wild type (P-value < 0.05) (Fig. 5A). Depending on the location of the NOVA-binding motif in the pre-mRNA, NOVA proteins can act as silencers or enhancers of splicing (Ule et al. 2006). Consequently, the overall level...
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PERSPECTIVE: Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
- W. Brad Barbazuk,
- Yan Fu,
- and Karen M. McGinnis
Genome Res. September 2008 18: 1381-1392; Published in Advance July 30, 2008, doi:10.1101/gr.053678.106
...et al. 2004 ). Combining microarrays with protein–RNA cross-linking and immunoprecipitation (CLIP) provides the opportunity to discover those mRNAs associated with specific SR proteins or other trans -acting protein factors involved in splice-site recognition. Genome-wide RNA-binding analysis of Nova...
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Research: RNA–DNA sequence differences in Saccharomyces cerevisiae
- Isabel X. Wang,
- Christopher Grunseich,
- Youree G. Chung,
- Hojoong Kwak,
- Girish Ramrattan,
- Zhengwei Zhu,
- and Vivian G. Cheung
Genome Res. November 2016 26: 1544-1554; Published in Advance September 16, 2016, doi:10.1101/gr.207878.116
...@umich.edu Abstract Alterations of RNA sequences and structures, such as those from editing and alternative splicing, result in two or more RNA transcripts from a DNA template. It was thought that in yeast, RNA editing only occurs in tRNAs. Here, we found that Saccharomyces cerevisiae have all 12 types of RNA...
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Research: Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs
- Cornelia Vesely,
- Stefanie Tauber,
- Fritz J. Sedlazeck,
- Arndt von Haeseler,
- and Michael F. Jantsch
Genome Res. August 2012 22: 1468-1476; Published in Advance February 6, 2012, doi:10.1101/gr.133025.111
.... Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol 22: 1001–1005. Li J, Levanon E, Yoon J, Aach J, Xie B, Leproust E, Zhang K, Gao Y, Church G. 2009. Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324...
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Method: Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach
- Fabien Wehbe,
- Levi Adams,
- Jordan Babadoudou,
- Samantha Yuen,
- Yoon-Seong Kim,
- and Yoshiaki Tanaka
Genome Res. January 2025 35: 135-146; Published in Advance December 2, 2024, doi:10.1101/gr.278812.123
...(blue; left) and cell types (right) in scRNA-seq of epilepsy patients and healthy donors. (G) UMAP plot of single cells colored by epileptogenic (red) and nonepileptogenic cells (blue; left) and clusters (right) in scRNA-seq of GBM patients. (H) Representative GO terms of differentially expressed genes...
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Research: Coexpression enrichment analysis at the single-cell level reveals convergent defects in neural progenitor cells and their cell-type transitions in neurodevelopmental disorders
- Kaifang Pang,
- Li Wang,
- Wei Wang,
- Jian Zhou,
- Chao Cheng,
- Kihoon Han,
- Huda Y. Zoghbi,
- and Zhandong Liu
Genome Res. June 2020 30: 835-848; Published in Advance June 18, 2020, doi:10.1101/gr.254987.119
...types and developmental stages at both cell-autonomous and cell–cell interaction levels, as larger scRNA-seq data sets covering later developmental stages become available.MethodsHigh-confidence NDD gene setsWe downloaded de novo mutation data for four NDDs: ASD, epilepsy, ID, and DD from the denovo...

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