Searching journal content for articles similar to Zhou et al. 19 (1): 70.

Displaying results 1-10 of 11

For checked items

view abstracts
download to citation manager

Select this article
Research: Genome-wide mapping reveals R-loops associated with centromeric repeats in maize
- Yang Liu,
- Qian Liu,
- Handong Su,
- Kunpeng Liu,
- Xue Xiao,
- Wei Li,
- Qianwen Sun,
- James A. Birchler,
- and Fangpu Han
Genome Res. August 2021 31: 1409-1418; Published in Advance July 9, 2021, doi:10.1101/gr.275270.121
.... Different from the gene-body localization of sense R-loops in Arabidopsis and Oryza sativa, maize sense R-loops mainly formed in both promoters and transcription termination sites (TTSs), and relatively less formed in gene bodies, indicating a species-specific R-loop pattern (Fig. 1E). The antisense R...
Select this article
Method: Identification and dynamic quantification of regulatory elements using total RNA
- Sascha H. Duttke,
- Max W. Chang,
- Sven Heinz,
- and Christopher Benner
Genome Res. November 2019 29: 1836-1846; Published in Advance October 24, 2019, doi:10.1101/gr.253492.119
...for which total RNA can be extracted. To illustrate this, we profiled the starlet anemone Nematostella vectensis (metazoa), the fungus Neurospora crassa, rice plant leaves (Oryza sativa), and the protist Capsaspora owczarzaki (Sebé-Pedrós et al. 2016). These species were selected to broadly cover...
OPEN ACCESS ARTICLE
Select this article
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...
OPEN ACCESS ARTICLE
Select this article
Letter: Clusters and superclusters of phased small RNAs in the developing inflorescence of rice
- Cameron Johnson,
- Anna Kasprzewska,
- Kristin Tennessen,
- John Fernandes,
- Guo-Ling Nan,
- Virginia Walbot,
- Venkatesan Sundaresan,
- Vicki Vance,
- and Lewis H. Bowman
Genome Res. August 2009 19: 1429-1440; Published in Advance July 7, 2009, doi:10.1101/gr.089854.108
...that are targeted by the indicated small RNA. Figure 5. The genomic origins of the motif-targeting small RNAs, miR2118, and potential folding of transcripts containing these miRNAs. (A) The ;20-kb region that codes for most of the motif-targeting small RNAs. This region contains nine degenerate repeats each...
Select this article
LETTER: A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
- Qian-Hao Zhu,
- Andrew Spriggs,
- Louisa Matthew,
- Longjiang Fan,
- Gavin Kennedy,
- Frank Gubler,
- and Chris Helliwell
Genome Res. September 2008 18: 1456-1465; Published in Advance August 7, 2008, doi:10.1101/gr.075572.107
...sequencing sets. Duplicate sequences were tallied, then excised to form a nonredundant set of sequences. Sequences of &lt;18 nt were removed. To find the origins of the small RNAs, BLAST was used to search the Oryza sativa sequence (TIGR Rice Annotation Release 5.0, http://www.tigr.org/tdb/e2k1/osa1/overview...
Select this article
LETTER: Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs
- Hanhui Kuang,
- Chellappan Padmanabhan,
- Feng Li,
- Ayako Kamei,
- Pudota B. Bhaskar,
- Shu Ouyang,
- Jiming Jiang,
- C. Robin Buell,
- and Barbara Baker
Genome Res. January 2009 19: 42-56; Published in Advance November 26, 2008, doi:10.1101/gr.078196.108
...Northern blot hybridization analysis using probes for specific MiS families to analyze the low-molecular-weight RNA fractions isolated from Nicotiana benthamiana , N. tabacum SR1, N. tabacum SR1: NN , N. glutinosa , S. demissum , S. tuberosum Kennebec, S. lycopersicum , Oryza sativa , and Arabidopsis...
Select this article
Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...). Despite their inability to mobilize, degenerated TEs provide alternative DNA and RNA regulatory sequences (e.g., transcription factor binding sites, splicing information, transcriptional start or termination sites) or induce recombination owing to their repetitiveness (Ito et al. 2011; Kim and Zilberman...
OPEN ACCESS ARTICLE
Select this article
Resource: High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis
- Natalie W. Breakfield,
- David L. Corcoran,
- Jalean J. Petricka,
- Jeffrey Shen,
- Juthamas Sae-Seaw,
- Ignacio Rubio-Somoza,
- Detlef Weigel,
- Uwe Ohler,
- and Philip N. Benfey
Genome Res. January 2012 22: 163-176; Published in Advance September 22, 2011, doi:10.1101/gr.123547.111
...-confidence miRNAs using a computational pipeline, PIPmiR, specifically developed for the identification of plant miRNAs. PIPmiR uses a probabilistic model that combines RNA structure and expression information to identify miRNAs with high precision. Knockdown of three of the newly identified miRNAs results...
Select this article
Resource: An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
- Bernardo J. Clavijo,
- Luca Venturini,
- Christian Schudoma,
- Gonzalo Garcia Accinelli,
- Gemy Kaithakottil,
- Jonathan Wright,
- Philippa Borrill,
- George Kettleborough,
- Darren Heavens,
- Helen Chapman,
- James Lipscombe,
- Tom Barker,
- Fu-Hao Lu,
- Neil McKenzie,
- Dina Raats,
- Ricardo H. Ramirez-Gonzalez,
- Aurore Coince,
- Ned Peel,
- Lawrence Percival-Alwyn,
- Owen Duncan,
- Josua Trösch,
- Guotai Yu,
- Dan M. Bolser,
- Guy Namaati,
- Arnaud Kerhornou,
- Manuel Spannagl,
- Heidrun Gundlach,
- Georg Haberer,
- Robert P. Davey,
- Christine Fosker,
- Federica Di Palma,
- Andrew L. Phillips,
- A. Harvey Millar,
- Paul J. Kersey,
- Cristobal Uauy,
- Ksenia V. Krasileva,
- David Swarbreck,
- Michael W. Bevan,
- and Matthew D. Clark
Genome Res. May 2017 27: 885-896; Published in Advance April 18, 2017, doi:10.1101/gr.217117.116
..., Oryza sativa, Sorghum bicolor, Setaria italica, and Zea mays. A single orthologous wheat gene was identified for 2686 (99.22%) of these, with 2665 (98.45%) Figure 2. Comparative alignment of TGACv1 scaffolds with the 3B BAC-based pseudomolecule. (A,C) Dot plots between TGACv1 scaffolds and 3B show...
OPEN ACCESS ARTICLE
Select this article
RESOURCE: Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications
- Pierre Hilson,
- Joke Allemeersch,
- Thomas Altmann,
- Sébastien Aubourg,
- Alexandra Avon,
- Jim Beynon,
- Rishikesh P. Bhalerao,
- Frédérique Bitton,
- Michel Caboche,
- Bernard Cannoot,
- Vasil Chardakov,
- Cécile Cognet-Holliger,
- Vincent Colot,
- Mark Crowe,
- Caroline Darimont,
- Steffen Durinck,
- Holger Eickhoff,
- Andéol Falcon de Longevialle,
- Edward E. Farmer,
- Murray Grant,
- Martin T.R. Kuiper,
- Hans Lehrach,
- Céline Léon,
- Antonio Leyva,
- Joakim Lundeberg,
- Claire Lurin,
- Yves Moreau,
- Wilfried Nietfeld,
- Javier Paz-Ares,
- Philippe Reymond,
- Pierre Rouzé,
- Goran Sandberg,
- Maria Dolores Segura,
- Carine Serizet,
- Alexandra Tabrett,
- Ludivine Taconnat,
- Vincent Thareau,
- Paul Van Hummelen,
- Steven Vercruysse,
- Marnik Vuylsteke,
- Magdalena Weingartner,
- Peter J. Weisbeek,
- Valtteri Wirta,
- Floyd R.A. Wittink,
- Marc Zabeau,
- and Ian Small
Genome Res. October 15, 2004 14: 2176-2189; doi:10.1101/gr.2544504
...Department of Molecular Genetics, University Utrecht, NL-3584 CH Utrecht, The Netherlands Abstract Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Zhou et al. 19 (1): 70.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: