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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
...in five mammals. Genome Res 22: 1173–1183. Fu Y, Sun Y, Li Y, Li J, Rao X, Chen C, Xu A. 2011. Differential -wide profiling of tandem 3′ UTRs among human breast cancer and normal cells by high-throughput sequencing. Genome Res 21: 741–747. Hunt AG, Xu R, Addepalli B, Rao S, Forbes KP, Meeks LR, Xing D, Mo...
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Research: Dynamic landscape of tandem 3′ UTRs during zebrafish development
- Yuxin Li,
- Yu Sun,
- Yonggui Fu,
- Mengzhen Li,
- Guangrui Huang,
- Chenxu Zhang,
- Jiahui Liang,
- Shengfeng Huang,
- Gaoyang Shen,
- Shaochun Yuan,
- Liangfu Chen,
- Shangwu Chen,
- and Anlong Xu
Genome Res. October 2012 22: 1899-1906; Published in Advance September 5, 2012, doi:10.1101/gr.128488.111
...). Based on integrative analysis of EST, SAGE, and microarray data, tandem 39 UTR lengthening has been observed during mouse embryogenesis ( Ji et al. 2009). However, the specific genes directly regulated by APA during vertebrate development remain unknown. Several high-throughput sequencing methods have...
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Research: Transcriptional consequences of genomic structural aberrations in breast cancer
- Koichiro Inaki,
- Axel M. Hillmer,
- Leena Ukil,
- Fei Yao,
- Xing Yi Woo,
- Leah A. Vardy,
- Kelson Folkvard Braaten Zawack,
- Charlie Wah Heng Lee,
- Pramila Nuwantha Ariyaratne,
- Yang Sun Chan,
- Kartiki Vasant Desai,
- Jonas Bergh,
- Per Hall,
- Thomas Choudary Putti,
- Wai Loon Ong,
- Atif Shahab,
- Valere Cacheux-Rataboul,
- Radha Krishna Murthy Karuturi,
- Wing-Kin Sung,
- Xiaoan Ruan,
- Guillaume Bourque,
- Yijun Ruan,
- and Edison T. Liu
Genome Res. May 2011 21: 676-687; Published in Advance April 5, 2011, doi:10.1101/gr.113225.110
...were ligated to the library DNA. High-throughput sequencing of the 2325 bp was performed on SOLiD sequencers according to the manufacturer’s recommendations (Applied Biosystems). Sequence tags were mapped to the human reference sequence (NCBI Build Fusion genes in breast cancer Genome Research 683 www...
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Research: Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events
- Jinfeng Liu,
- William Lee,
- Zhaoshi Jiang,
- Zhongqiang Chen,
- Suchit Jhunjhunwala,
- Peter M. Haverty,
- Florian Gnad,
- Yinghui Guan,
- Houston N. Gilbert,
- Jeremy Stinson,
- Christiaan Klijn,
- Joseph Guillory,
- Deepali Bhatt,
- Steffan Vartanian,
- Kimberly Walter,
- Jocelyn Chan,
- Thomas Holcomb,
- Peter Dijkgraaf,
- Stephanie Johnson,
- Julie Koeman,
- John D. Minna,
- Adi F. Gazdar,
- Howard M. Stern,
- Klaus P. Hoeflich,
- Thomas D. Wu,
- Jeff Settleman,
- Frederic J. de Sauvage,
- Robert C. Gentleman,
- Richard M. Neve,
- David Stokoe,
- Zora Modrusan,
- Somasekar Seshagiri,
- David S. Shames,
- and Zemin Zhang
Genome Res. December 2012 22: 2315-2327; Published in Advance October 2, 2012, doi:10.1101/gr.140988.112
.... A more comprehensive understanding of genomic alterations in lung cancers is critical for identifying new therapeutic targets as well as for identifying suitable patients who might respond to a given targeted agent. Recent advances in high-throughput sequencing have enabled the systematic analysis...
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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
...selection. Neuron 60: 1022–1038. ↵Fu Y, Sun Y, Li Y, Li J, Rao X, Chen C, Xu A. 2011. Differential -wide profiling of tandem 3′ UTRs among human breast cancer and normal cells by high-throughput sequencing. Genome Res 21: 741–747. ↵Fu Y, Ge Y, Sun Y, Liang J, Wan L, Wu X, Xu A. 2015. IVT-SAPAS: low...
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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
.... Analysis of expressed sequence tags (ESTs) suggests that a majority of mammalian genes contain multiple cleavage and polyadenylation sites (Tian et al. 2005), either in ‘‘tandem UTRs,’’ for which choice of an earlier site by the cleavage and polyadenylation machinery precludes use of later sites...
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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
.... Genome Biol 13: R59. ↵Elkon R, Ugalde AP, Agami R. 2013. Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet 14: 496–506. ↵Fu Y, Sun Y, Li Y, Li J, Rao X, Chen C, Xu A. 2011. Differential -wide profiling of tandem 3′ UTRs among human breast cancer and normal cells...
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Resource: A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers
- Christopher L. Plaisier,
- Min Pan,
- and Nitin S. Baliga
Genome Res. November 2012 22: 2302-2314; Published in Advance June 28, 2012, doi:10.1101/gr.133991.111
...to identify miRNAs driving coexpression of transcripts. Quantitative assays of the transcriptome are used to identify gene-coexpression signatures comprised of genes with significantly similar gene-expression profiles. The 39 UTR sequences for the coexpressed genes are then extracted from the and used...
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Research: DDX54 regulates transcriptome dynamics during DNA damage response
- Miha Milek,
- Koshi Imami,
- Neelanjan Mukherjee,
- Francesca De Bortoli,
- Ulrike Zinnall,
- Orsalia Hazapis,
- Christian Trahan,
- Marlene Oeffinger,
- Florian Heyd,
- Uwe Ohler,
- Matthias Selbach,
- and Markus Landthaler
Genome Res. August 2017 27: 1344-1359; Published in Advance June 8, 2017, doi:10.1101/gr.218438.116
...by a well-characterized network of DNA surveillance pathways. The contribution of post-transcriptional gene regulatory networks to the DNAdamage response (DDR) has not been extensively studied. Here, we systematically identified RNA-binding proteins differentially interacting with polyadenylated transcripts...
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Method: Long-read single-molecule maps of the functional methylome
- Hila Sharim,
- Assaf Grunwald,
- Tslil Gabrieli,
- Yael Michaeli,
- Sapir Margalit,
- Dmitry Torchinsky,
- Rani Arielly,
- Gil Nifker,
- Matyas Juhasz,
- Felix Gularek,
- Miguel Almalvez,
- Brandon Dufault,
- Sreetama Sen Chandra,
- Alexander Liu,
- Surajit Bhattacharya,
- Yi-Wen Chen,
- Eric Vilain,
- Kathryn R. Wagner,
- Jonathan Pevsner,
- Jeff Reifenberger,
- Ernest T. Lam,
- Alex R. Hastie,
- Han Cao,
- Hayk Barseghyan,
- Elmar Weinhold,
- and Yuval Ebenstein
Genome Res. April 2019 29: 646-656; Published in Advance March 7, 2019, doi:10.1101/gr.240739.118
...the at regions dense in CCGG sites. RRBS captures ∼60% of gene promoters, thus producing crucial regulatory information while requiring very little input sample (Gu et al. 2011). The low input implies that fewer reads are necessary for accurate sequencing, allowing for high-throughput, low-cost methylation...
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