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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
...a detailed characterization of the genomic landscape and embryonic expression of zebrafish TEs. Our study highlights the staggering diversity of TEs in zebrafish, yields insights into the effect of selection on the genomic distribution of different TE types, and describes a wide diversity of transcriptional...
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Resource: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
- Qicheng Ma,
- Satyam P. Srivastav,
- Stephanie Gamez,
- Gargi Dayama,
- Fabiana Feitosa-Suntheimer,
- Edward I. Patterson,
- Rebecca M. Johnson,
- Erik M. Matson,
- Alexander S. Gold,
- Douglas E. Brackney,
- John H. Connor,
- Tonya M. Colpitts,
- Grant L. Hughes,
- Jason L. Rasgon,
- Tony Nolan,
- Omar S. Akbari,
- and Nelson C. Lau
Genome Res. March 2021 31: 512-528; Published in Advance January 8, 2021, doi:10.1101/gr.265157.120
...in the satellite tandem repeats within this MCpiRCL.A major genic piRCL is dynamically evolving yet syntenically conserved through mosquito phylogenyTo define other genic and intergenic piRCLs in mosquitoes (Supplemental Tables S2, S4–S6), we combined automated scanning with manual curation. The six top major Ae...
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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
...decay pathways during zebrafish MZT. By using a massively parallel reporter assay, we identified cis-regulatory sequences in the 3′ UTR, including U-rich motifs that are associated with increased mRNA stability. In contrast, miR-430 target sequences, UAUUUAUU AU-rich elements (ARE), CCUC, and CUGC...
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Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
- Tanner D. Jensen,
- Bohan Ni,
- Chloe M. Reuter,
- John E. Gorzynski,
- Sarah Fazal,
- Devon Bonner,
- Rachel A. Ungar,
- Pagé C. Goddard,
- Archana Raja,
- Euan A. Ashley,
- Jonathan A. Bernstein,
- Stephan Zuchner,
- Undiagnosed Diseases Network,
- Michael D. Greicius,
- Stephen B. Montgomery,
- Michael C. Schatz,
- Matthew T. Wheeler,
- and Alexis Battle
Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
...a Zebrafish model further supported that biallelic LOF mutations on FAM177A1 could potentially lead to neurodevelopmental problems via abnormal Golgi complex dynamics.DiscussionMultitechnology, high-sequencing-depth references have shown that there are roughly 22,000–27,000 rare SVs per (Audano et al. 2019...
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Research: 3′ UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts
- Noah Spies,
- Christopher B. Burge,
- and David P. Bartel
Genome Res. December 2013 23: 2078-2090; Published in Advance September 26, 2013, doi:10.1101/gr.156919.113
...global measurements of decay and translation rates for mRNAs with alternative 3′ untranslated regions (3′ UTRs) in murine 3T3 cells. Distal tandem isoforms had slightly but significantly lower mRNA stability and greater translational efficiency than proximal isoforms on average. The diversity...
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Research: Crosstalk between alternative polyadenylation and miRNAs in the regulation of protein translational efficiency
- Yonggui Fu,
- Liutao Chen,
- Chengyong Chen,
- Yutong Ge,
- Mingjing Kang,
- Zili Song,
- Jingwen Li,
- Yuchao Feng,
- Zhanfeng Huo,
- Guopei He,
- Mengmeng Hou,
- Shangwu Chen,
- and Anlong Xu
Genome Res. November 2018 28: 1656-1663; Published in Advance September 18, 2018, doi:10.1101/gr.231506.117
...-inhibition. J Cell Biochem 110: 1234–1243. ↵Li Y, Sun Y, Fu Y, Li M, Huang G, Zhang C, Liang J, Huang S, Shen G, Yuan S, et al. 2012. Dynamic landscape of tandem 3′ UTRs during zebrafish development. Genome Res 22: 1899–1906. ↵Lin Y, Li Z, Ozsolak F, Kim SW, Arango-Argoty G, Liu TT, Tenenbaum SA, Bailey T...
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Research: 3′ UTR lengthening as a novel mechanism in regulating cellular senescence
- Meng Chen,
- Guoliang Lyu,
- Miao Han,
- Hongbo Nie,
- Ting Shen,
- Wei Chen,
- Yichi Niu,
- Yifan Song,
- Xueping Li,
- Huan Li,
- Xinyu Chen,
- Ziyue Wang,
- Zheng Xia,
- Wei Li,
- Xiao-Li Tian,
- Chen Ding,
- Jun Gu,
- Yufang Zheng,
- Xinhua Liu,
- Jinfeng Hu,
- Gang Wei,
- Wei Tao,
- and Ting Ni
Genome Res. March 2018 28: 285-294; Published in Advance February 12, 2018, doi:10.1101/gr.224451.117
..., Seo YH, Kim YS, Park MH, Chung HY, Woo HG, Yoon G. 2013b. Implications of time-series gene expression profiles of replicative senescence. Aging Cell 12: 622–634. ↵Li Y, Sun Y, Fu Y, Li M, Huang G, Zhang C, Liang J, Huang S, Shen G, Yuan S, et al. 2012. Dynamic landscape of tandem 3′ UTRs during...
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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
...amounts, but again, dominant in pollen (Fig. 5D). In addition, upon investigating APA site switching dynamics in pollen compared to other tissues (Fig. 5B), results showed that pollen possesses longer 3′ UTRs compared with embryo, endosperm, and dry seed but used shorter 3′ UTRs when compared...
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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
.... Analysis of a conservative set of tandem poly(A) sites showed that among the poly(A) sites that were derepressed upon HNRNPC knockdown and that had at least one (U)5 motif within −200 to +100 nt, two-thirds (390 sites, 67.2%) were located distally, leading to longer 3′ UTRs, whereas the remaining one...
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Research: An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
- Ignacio Maeso,
- Manuel Irimia,
- Juan J. Tena,
- Esther González-Pérez,
- David Tran,
- Vydianathan Ravi,
- Byrappa Venkatesh,
- Sonsoles Campuzano,
- José Luis Gómez-Skarmeta,
- and Jordi Garcia-Fernàndez
Genome Res. April 2012 22: 642-655; Published in Advance January 10, 2012, doi:10.1101/gr.132233.111
..., and that many Iroquois –CRMs were ancestrally located within Sowah introns. Retroposition, gene, and genome duplication have allowed selective elimination of Sowah exons from the Iroquois regulatory landscape while keeping associated CRMs, resulting in large associated gene deserts. These results...

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