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Research: Global regulatory features of alternative splicing across tissues and within the nervous system of C. elegans
- Bina Koterniak,
- Pallavi P. Pilaka,
- Xicotencatl Gracida,
- Lisa-Marie Schneider,
- Iva Pritišanac,
- Yun Zhang,
- and John A. Calarco
Genome Res. December 2020 30: 1766-1780; Published in Advance October 30, 2020, doi:10.1101/gr.267328.120
...RNA-seq compendium of reproducibly expressed splice junctions in C. elegans, assembled from 1682 publicly available RNA-seq experiments (Tourasse et al. 2017). Each splice junction has an associated percent spliced in (PSI) value, which is a measure of the frequency of each splice junction relative...
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Resource: The C. elegans embryonic transcriptome with tissue, time, and alternative splicing resolution
- Adam D. Warner,
- Louis Gevirtzman,
- LaDeana W. Hillier,
- Brent Ewing,
- and Robert H. Waterston
Genome Res. June 2019 29: 1036-1045; Published in Advance May 23, 2019, doi:10.1101/gr.243394.118
...Adam D. Warner, Louis Gevirtzman, LaDeana W. Hillier, Brent Ewing and Robert H. Waterston Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA Corresponding author: watersto@uw.eduAbstractWe have used RNA-seq in Caenorhabditis elegans...
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Research: Systematic transcriptome analysis associated with physiological and chronological aging in Caenorhabditis elegans
- Seokjin Ham,
- Sieun S. Kim,
- Sangsoon Park,
- Eun Ji E. Kim,
- Sujeong Kwon,
- Hae-Eun H. Park,
- Yoonji Jung,
- and Seung-Jae V. Lee
Genome Res. November/December 2022 32: 2003-2014; Published in Advance November 9, 2022, doi:10.1101/gr.276515.121
...of DAF-2-mediated development and longevity. Cell 154: 676–690. doi:10.1016/j.cell.2013.07.006 ↵Tourasse NJ, Millet JRM, Dupuy D. 2017. Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans. Genome Res 27: 2120–2128. doi:10.1101/gr.224626.117 ↵Weigelt CM, Sehgal R, Tain LS, Cheng J...
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Resource: Direct full-length RNA sequencing reveals unexpected transcriptome complexity during Caenorhabditis elegans development
- Runsheng Li,
- Xiaoliang Ren,
- Qiutao Ding,
- Yu Bi,
- Dongying Xie,
- and Zhongying Zhao
Genome Res. February 2020 30: 287-298; Published in Advance February 5, 2020, doi:10.1101/gr.251512.119
...,639 out of 52,846) identified using the long reads were also identified by meta-analysis of RNA-seq data (Tourasse et al. 2017) or were currently annotated in WormBase (Supplemental Fig. S1; Supplemental Table S1). Approximately half of the long reads were defined as full-length ones with these criteria...
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Resource: The full-length transcriptome of C. elegans using direct RNA sequencing
- Nathan P. Roach,
- Norah Sadowski,
- Amelia F. Alessi,
- Winston Timp,
- James Taylor,
- and John K. Kim
Genome Res. February 2020 30: 299-312; Published in Advance February 5, 2020, doi:10.1101/gr.251314.119
...error rates and the relative lack of bioinformatics tools and analysis pipelines designed for long, error-rich reads.In this study, we have generated an atlas of postembryonic transcript structure using dRNA-seq to sequence RNA extracted from the major stages of the C. elegans developmental life cycle...
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Resource: The C. elegans 3′ UTRome v2 resource for studying mRNA cleavage and polyadenylation, 3′-UTR biology, and miRNA targeting
- Hannah S. Steber,
- Christina Gallante,
- Shannon O'Brien,
- Po-Lin Chiu,
- and Marco Mangone
Genome Res. December 2019 29: 2104-2116; Published in Advance November 19, 2019, doi:10.1101/gr.254839.119
.... 2011).Alternative polyadenylation is widespread in C. elegans, with ∼42% of genes possessing at least two 3′-UTR isoforms (Fig. 3A). The PAS usage is still most commonly the hexamer “AAUAAA,” which is used to process ∼58% of all C. elegans 3′ UTRs (Fig. 3B). We found that the remaining 42% possess...
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Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
- Jonathan M. Mudge,
- Irwin Jungreis,
- Toby Hunt,
- Jose Manuel Gonzalez,
- James C. Wright,
- Mike Kay,
- Claire Davidson,
- Stephen Fitzgerald,
- Ruth Seal,
- Susan Tweedie,
- Liang He,
- Robert M. Waterhouse,
- Yue Li,
- Elspeth Bruford,
- Jyoti S. Choudhary,
- Adam Frankish,
- and Manolis Kellis
Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
...experiments (Nesvizhskii 2014).View larger version: In this window In a new window Figure 2. Novel protein-coding loci. Browser images show CDSs (open green rectangles), UTRs (pink), supporting PCCRs (red), top rank (black), cDNA evidence (brown), and RNA-seq–supported introns (blue rectangles). Additional...
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Research: Genome wide analysis of 3′ UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish
- Charles E. Vejnar,
- Mario Abdel Messih,
- Carter M. Takacs,
- Valeria Yartseva,
- Panos Oikonomou,
- Romain Christiano,
- Marlon Stoeckius,
- Stephanie Lau,
- Miler T. Lee,
- Jean-Denis Beaudoin,
- Damir Musaev,
- Hiba Darwich-Codore,
- Tobias C. Walther,
- Saeed Tavazoie,
- Daniel Cifuentes,
- and Antonio J. Giraldez
Genome Res. July 2019 29: 1100-1114; Published in Advance June 21, 2019, doi:10.1101/gr.245159.118
...regulate the dynamics of mRNA stability during MZT (Yartseva and Giraldez 2015). To identify which pathways regulate each mRNA, we analyzed transcript levels during the first 8 h postfertilization (hpf), at 30- to 60-min intervals in wild-type zebrafish embryos using mRNA-seq (Supplemental Table S1). We...

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