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Research: Thermal stress accelerates Arabidopsis thaliana mutation rate
- Eric J. Belfield,
- Carly Brown,
- Zhong Jie Ding,
- Lottie Chapman,
- Mengqian Luo,
- Eleanor Hinde,
- Sam W. van Es,
- Sophie Johnson,
- Youzheng Ning,
- Shao Jian Zheng,
- Aziz Mithani,
- and Nicholas P. Harberd
Genome Res. January 2021 31: 40-50; Published in Advance December 17, 2020, doi:10.1101/gr.259853.119
...of these observations are considered further in Discussion. With most HT-induced indels being located in homopolymeric stretch/microsatellite regions, and most such regions being located in non-protein-encoding regions of the A. thaliana , we determined the specific genomic locations of HT-induced indels. All 138 HT...
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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
...transcription regulation and the generation of cellular complexity. Depending on their genomic origins, lncRNAs can be transcribed from intergenic or intragenic regions or from introns of protein-coding genes. We have recently reported more than 6000 intergenic lncRNAs in Arabidopsis . Here, we systematically...
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LETTER: Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
- Takeshi Itoh,
- Tsuyoshi Tanaka,
- Roberto A. Barrero,
- Chisato Yamasaki,
- Yasuyuki Fujii,
- Phillip B. Hilton,
- Baltazar A. Antonio,
- Hideo Aono,
- Rolf Apweiler,
- Richard Bruskiewich,
- Thomas Bureau,
- Frances Burr,
- Antonio Costa de Oliveira,
- Galina Fuks,
- Takuya Habara,
- Georg Haberer,
- Bin Han,
- Erimi Harada,
- Aiko T. Hiraki,
- Hirohiko Hirochika,
- Douglas Hoen,
- Hiroki Hokari,
- Satomi Hosokawa,
- Yue Hsing,
- Hiroshi Ikawa,
- Kazuho Ikeo,
- Tadashi Imanishi,
- Yukiyo Ito,
- Pankaj Jaiswal,
- Masako Kanno,
- Yoshihiro Kawahara,
- Toshiyuki Kawamura,
- Hiroaki Kawashima,
- Jitendra P. Khurana,
- Shoshi Kikuchi,
- Setsuko Komatsu,
- Kanako O. Koyanagi,
- Hiromi Kubooka,
- Damien Lieberherr,
- Yao-Cheng Lin,
- David Lonsdale,
- Takashi Matsumoto,
- Akihiro Matsuya,
- W. Richard McCombie,
- Joachim Messing,
- Akio Miyao,
- Nicola Mulder,
- Yoshiaki Nagamura,
- Jongmin Nam,
- Nobukazu Namiki,
- Hisataka Numa,
- Shin Nurimoto,
- Claire O’Donovan,
- Hajime Ohyanagi,
- Toshihisa Okido,
- Satoshi OOta,
- Naoki Osato,
- Lance E. Palmer,
- Francis Quetier,
- Saurabh Raghuvanshi,
- Naomi Saichi,
- Hiroaki Sakai,
- Yasumichi Sakai,
- Katsumi Sakata,
- Tetsuya Sakurai,
- Fumihiko Sato,
- Yoshiharu Sato,
- Heiko Schoof,
- Motoaki Seki,
- Michie Shibata,
- Yuji Shimizu,
- Kazuo Shinozaki,
- Yuji Shinso,
- Nagendra K. Singh,
- Brian Smith-White,
- Jun-ichi Takeda,
- Motohiko Tanino,
- Tatiana Tatusova,
- Supat Thongjuea,
- Fusano Todokoro,
- Mika Tsugane,
- Akhilesh K. Tyagi,
- Apichart Vanavichit,
- Aihui Wang,
- Rod A. Wing,
- Kaori Yamaguchi,
- Mayu Yamamoto,
- Naoyuki Yamamoto,
- Yeisoo Yu,
- Hao Zhang,
- Qiang Zhao,
- Kenichi Higo,
- Benjamin Burr,
- Takashi Gojobori,
- Takuji Sasaki,
- and for the Rice Annotation Project
Genome Res. February 2007 17: 175-183; Published in Advance January 8, 2007, doi:10.1101/gr.5509507
...; 39 Bio-Oriented Technology Research Advancement Institution, Minato-ku, Tokyo 105-0001, Japan. Abstract We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA...
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Perspective: Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship
- Marie A. Brunet,
- Sébastien A. Levesque,
- Darel J. Hunting,
- Alan A. Cohen,
- and Xavier Roucou
Genome Res. May 2018 28: 609-624; Published in Advance April 6, 2018, doi:10.1101/gr.230938.117
...-SLC35A4. The SLC35A4 mRNA encodes two ORFs. Under physiological conditions, the canonical ORF, SLC35A4, is weakly expressed. The uORF-encoded protein alt-SLC35A4 is suspected to be the major protein product. Under cellular stress, both proteins are expressed. The alt-SLC35A4 expression level remains...
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Method: Discovery and annotation of small proteins using genomics, proteomics, and computational approaches
- Xiaohan Yang,
- Timothy J. Tschaplinski,
- Gregory B. Hurst,
- Sara Jawdy,
- Paul E. Abraham,
- Patricia K. Lankford,
- Rachel M. Adams,
- Manesh B. Shah,
- Robert L. Hettich,
- Erika Lindquist,
- Udaya C. Kalluri,
- Lee E. Gunter,
- Christa Pennacchio,
- and Gerald A. Tuskan
Genome Res. April 2011 21: 634-641; Published in Advance March 2, 2011, doi:10.1101/gr.109280.110
...) gene family clustering within P. deltoides . As a result, a high-confidence sORF candidate set containing 1469 genes was obtained. Analysis of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein mass spectrometry data supported this high-confidence sORF set...
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ARTICLE: Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression
- Wei Deng,
- Xiaopeng Zhu,
- Geir Skogerbø,
- Yi Zhao,
- Zhuo Fu,
- Yudong Wang,
- Housheng He,
- Lun Cai,
- Hong Sun,
- Changning Liu,
- Biao Li,
- Baoyan Bai,
- Jie Wang,
- Dong Jia,
- Shiwei Sun,
- Hang He,
- Yan Cui,
- Yu Wang,
- Dongbo Bu,
- and Runsheng Chen
Genome Res. January 2006 16: 20-29; Published in Advance December 12, 2005, doi:10.1101/gr.4139206
...acting as regulatory elements in nematode development. Small non-protein-coding RNAs (ncRNAs) such as microRNAs (miRNAs) have received increasing attention as regulatory factors shaping cellular and organismal life. A catalog of reported miRNAs from various eukaryotes now covers 400 different RNA species...
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LETTER: Improvement of whole-genome annotation of cereals through comparative analyses
- Wei Zhu and
- C. Robin Buell
Genome Res. March 2007 17: 299-310; Published in Advance February 6, 2007, doi:10.1101/gr.5881807
...described above concentrated on the identification of protein coding regions; however, conservation is not restricted within protein coding regions but also exists in noncoding regions. In addition to the regular protein coding genes, there are numerous non-protein coding RNA (ncRNA) molecules encoded...
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Methods: Generic eukaryotic core promoter prediction using structural features of DNA
- Thomas Abeel,
- Yvan Saeys,
- Eric Bonnet,
- Pierre Rouzé,
- and Yves Van de Peer
Genome Res. February 2008 18: 310-323; Published in Advance December 20, 2007, doi:10.1101/gr.6991408
...be calculated for these analyses because the program will always predict all types of promoters and it will never give predictions specific for a single type of promoter. Therefore, we focus only on how many known noncoding RNA promoters we can identify with our approach. Although EP3 can identify non-protein...

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