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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...or are trafficked into mature oocytes (Chalvet et al. 1999; Wang et al. 2018). Alternatively, it may be that somatic expression is only mildly deleterious to the zebrafish host and, therefore, occasionally arises with little functional consequence for either the host or the TEs. This may be the case...
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Resource: Genome-wide dynamics of alternative polyadenylation in rice
- Haihui Fu,
- Dewei Yang,
- Wenyue Su,
- Liuyin Ma,
- Yingjia Shen,
- Guoli Ji,
- Xinfu Ye,
- Xiaohui Wu,
- and Qingshun Q. Li
Genome Res. December 2016 26: 1753-1760; Published in Advance October 12, 2016, doi:10.1101/gr.210757.116
..., Shkumatava A, Jan CH, Subtelny AO, Koppstein D, Bell GW, Sive H, Bartel DP. 2012. Extensive alternative polyadenylation during zebrafish development. Genome Res 22: 2054–2066. WuX, LiuM, Downie B, Liang C, Ji G, Li QQ, Hunt AG. 2011. Genome-wide landscape of polyadenylation in Arabidopsis provides evidence...
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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
...al. 2007). Additional long-read sequencing of transcriptomes will help clarify how extensive alternative transcripts are among taxa.Sex chromosomes evolve sex-biased gene content owing to different selection pressures in males and females (Rice 1984). The X Chromosome is transmitted two...
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Research: A compendium of conserved cleavage and polyadenylation events in mammalian genes
- Ruijia Wang,
- Dinghai Zheng,
- Ghassan Yehia,
- and Bin Tian
Genome Res. October 2018 28: 1427-1441; Published in Advance August 24, 2018, doi:10.1101/gr.237826.118
..., Rutgers University, New Brunswick, New Jersey 08901, USA Corresponding author: btian@rutgers.eduAbstractCleavage and polyadenylation is essential for 3′ end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to m...
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Research: Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants
- Ya-Ru Li and
- Ming-Jung Liu
Genome Res. October 2020 30: 1418-1433; Published in Advance September 24, 2020, doi:10.1101/gr.261834.120
...protein synthesis. Studies have uncovered a number of alternative translation initiation sites (TISs) in mammalian mRNAs and showed their roles in reshaping the proteome. However, the extent to which alternative TISs affect gene expression across plants remains largely unclear. Here, by profiling...
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Resource: Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns
- Jamie C. Kwasnieski,
- Terry L. Orr-Weaver,
- and David P. Bartel
Genome Res. July 2019 29: 1188-1197; Published in Advance June 24, 2019, doi:10.1101/gr.242164.118
...Early activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained introns Jamie C. Kwasnieski1,2,3, Terry L. Orr-Weaver2,3 and David P. Bartel1,2,3 1Howard Hughes Medical Institute, Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142...
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Resource: A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation
- Andreas J. Gruber,
- Ralf Schmidt,
- Andreas R. Gruber,
- Georges Martin,
- Souvik Ghosh,
- Manuel Belmadani,
- Walter Keller,
- and Mihaela Zavolan
Genome Res. August 2016 26: 1145-1159; Published in Advance July 5, 2016, doi:10.1101/gr.202432.115
...Andreas J. Gruber,1 Ralf Schmidt,1 Andreas R. Gruber,1 Georges Martin,1 Souvik Ghosh,1 Manuel Belmadani,1,2 Walter Keller,1 and Mihaela Zavolan1 1Computational and Systems Biology, Biozentrum, University of Basel, 4056 Basel, Switzerland Alternative polyadenylation (APA) is a general mechanism...
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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
...cytoplasmic polyadenylation, which would increase mRNA translation efficiency early in embryonic development (Subtelny et al. 2014). We find a strong correspondence between the motifs identified by RESA and those recently reported in zebrafish by Rabani et al. (2017). We further characterized the sequence...
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Research: Extensive relationship between antisense transcription and alternative splicing in the human genome
- A. Sorana Morrissy,
- Malachi Griffith,
- and Marco A. Marra
Genome Res. August 2011 21: 1203-1212; Published in Advance June 30, 2011, doi:10.1101/gr.113431.110
...Extensive relationship between antisense transcription and alternative splicing in the human genome A. Sorana Morrissy , Malachi Griffith and Marco A. Marra 1 British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, British Columbia V5Z...
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Research: Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition
- Vladimir Despic,
- Mario Dejung,
- Mengting Gu,
- Jayanth Krishnan,
- Jing Zhang,
- Lydia Herzel,
- Korinna Straube,
- Mark B. Gerstein,
- Falk Butter,
- and Karla M. Neugebauer
Genome Res. July 2017 27: 1184-1194; Published in Advance April 5, 2017, doi:10.1101/gr.215954.116
...established mRNA reporters into one-cell-stage embryos along with HA-tagged Renilla luciferase RNA (Rluc-HA RNA, injection control) and measured polyadenylation and translation 2 h after injection. To measure poly(A) tail length, we implemented the extension poly(A) test (ePAT) (Supplemental Fig. S3A; Janicke...

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