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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...no correlation (Fig. 4F). These data indicate that while mCG and many mC readers are enriched in exons, mCG does not appear to direct splicing inclusion of events in Arabidopsis seedlings, and mC readers do not direct alternative splicing.Identification of mC reader protein interactionsTo gain insights...
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Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
- Fu-Yuan Zhu,
- Xin Chen,
- Yu-Chen Song,
- Lydia Pui Ying Lam,
- Yuki Tobimatsu,
- Bei Gao,
- Mo-Xian Chen,
- and Fu-Liang Cao
Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
...Laboratory of Ecological Security and Sustainable Development in Arid Areas, Urumqi, Xinjiang 830054, China ↵6 These authors contributed equally to this work. Corresponding authors: cmx2009920734@gmail.com, fuliangcaonjfu@163.comAbstractAlternative splicing (AS) regulates gene expression and increases...
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Research: Genome-wide analysis of plant miRNA action clarifies levels of regulatory dynamics across developmental contexts
- Xiaoli Ma,
- Tom Denyer,
- Marie Javelle,
- Antje Feller,
- and Marja C.P. Timmermans
Genome Res. May 2021 31: 811-822; Published in Advance April 16, 2021, doi:10.1101/gr.270918.120
...tissues. Alternatively, or concurrently, the lower than expected levels of miR156k, miR169c, and miR172c are perhaps driven by miRNA mobility. The movement of miRNAs is a carefully regulated process (Rosas-Diaz et al. 2018; Skopelitis et al. 2018), and within the vasculature, regulatory mechanisms...
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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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Method: Genome-wide dynamics of RNA synthesis, processing, and degradation without RNA metabolic labeling
- Mattia Furlan,
- Eugenia Galeota,
- Nunzio Del Gaudio,
- Erik Dassi,
- Michele Caselle,
- Stefano de Pretis,
- and Mattia Pelizzola
Genome Res. October 2020 30: 1492-1507; Published in Advance September 25, 2020, doi:10.1101/gr.260984.120
...affected in either processing or degradation (Fig. 5D).Second, we quantified for the first time all kinetic rates in plants, focusing on the temporal response to ethylene in Arabidopsis thaliana (Chang et al. 2013). Ethylene causes growth inhibition, which is initially independent and then dependent...
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Resource: Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms
- José Carlos Montañés,
- Marta Huertas,
- Simone G. Moro,
- William R. Blevins,
- Mercè Carmona,
- José Ayté,
- Elena Hidalgo,
- and M. Mar Albà
Genome Res. June 2022 32: 1215-1227; Published in Advance May 26, 2022, doi:10.1101/gr.276516.121
...(fission yeast) retains many of the splicing features observed in humans and is thus an excellent model to study the basic mechanisms of splicing. Nearly half the genes contain introns, but the impact of alternative splicing in gene regulation and proteome diversification remains largely unexplored. Here...
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Method: Genome-wide CRISPR screening reveals genes essential for cell viability and resistance to abiotic and biotic stresses in Bombyx mori
- Jiasong Chang,
- Ruolin Wang,
- Kai Yu,
- Tong Zhang,
- Xiaoxu Chen,
- Yue Liu,
- Run Shi,
- Xiaogang Wang,
- Qingyou Xia,
- and Sanyuan Ma
Genome Res. May 2020 30: 757-767; Published in Advance May 18, 2020, doi:10.1101/gr.249045.119
...and diverse eukaryotic species (Homo sapiens, Mus musculus, Drosophila melanogaster, Saccharomyces cerevisiae, Danio rerio, Caenorhabditis elegans, and Arabidopsis thaliana), and a prokaryotic species (Bacillus thuringiensis). (Asterisks) The intersection of 1006 essential genes with B. mori orthologs...
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Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
- Stefan Oberlin,
- Alexis Sarazin,
- Clément Chevalier,
- Olivier Voinnet,
- and Arturo Marí-Ordóñez
Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
...and transcriptionally active transposons in A. thaliana is illustrated by our comprehensive analysis of the cotranscriptional and translational features of Ty1/Copia elements, a family of young and active retroelements in plant s, and how such features impact their biology. Genome-wide transcript profiling revealed...
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Research: Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis
- Huan Wang,
- Pil Joong Chung,
- Jun Liu,
- In-Cheol Jang,
- Michelle J. Kean,
- Jun Xu,
- and Nam-Hai Chua
Genome Res. March 2014 24: 444-453; Published in Advance January 8, 2014, doi:10.1101/gr.165555.113
...Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis Huan Wang 1 , 4 , Pil Joong Chung 1 , 2 , 4 , Jun Liu 1 , In-Cheol Jang 1 , 3 , Michelle J. Kean 1 , Jun Xu...
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Research: Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana
- Eric J. Belfield,
- Xiangchao Gan,
- Aziz Mithani,
- Carly Brown,
- Caifu Jiang,
- Keara Franklin,
- Elizabeth Alvey,
- Anjar Wibowo,
- Marko Jung,
- Kit Bailey,
- Sharan Kalwani,
- Jiannis Ragoussis,
- Richard Mott,
- and Nicholas P. Harberd
Genome Res. July 2012 22: 1306-1315; Published in Advance April 12, 2012, doi:10.1101/gr.131474.111
...Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana Eric J. Belfield 1 , Xiangchao Gan 1 , 2 , Aziz Mithani 1 , 8 , Carly Brown 1 , Caifu Jiang 1...

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