A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies.

Nature Genetics
Yuling JiaoTimothy Nelson

Abstract

The functions of the plant body rely on interactions among distinct and nonequivalent cell types. The comparison of transcriptomes from different cell types should expose the transcriptional networks that underlie cellular attributes and contributions. Using laser microdissection and microarray profiling, we have produced a cell type transcriptome atlas that includes 40 cell types from rice (Oryza sativa) shoot, root and germinating seed at several developmental stages, providing patterns of cell specificity for individual genes and gene classes. Cell type comparisons uncovered previously unrecognized properties, including cell-specific promoter motifs and coexpressed cognate binding factor candidates, interaction partner candidates and hormone response centers. We inferred developmental regulatory hierarchies of gene expression in specific cell types by comparison of several stages within root, shoot and embryo.

References

Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Nov 28, 2002·Nature Genetics·Gary A Churchill
Dec 13, 2003·Science·Kenneth BirnbaumPhilip N Benfey
Feb 14, 2004·Bioinformatics·Tim Beissbarth, Terence P Speed
Mar 19, 2004·Molecular Genetics and Genomics : MGG·G-X YangS Komatsu
May 8, 2004·Nature Reviews. Genetics·Laurence D HurstMartin J Lercher
Jun 8, 2004·Bioinformatics·Alok J Saldanha
Oct 4, 2005·Functional & Integrative Genomics·Mukesh JainJitendra P Khurana
Jan 18, 2006·The Plant Journal : for Cell and Molecular Biology·Shuhua ZhanLewis N Lukens
Jan 20, 2006·Nature·Fawzi A RazemRobert D Hill
May 4, 2006·Annual Review of Plant Biology·Timothy NelsonTie Liu
Oct 20, 2006·Nature·Yuan-Yue ShenDa-Peng Zhang
Mar 21, 2007·Plant Physiology·Jalean Joyanne Petricka, Timothy Mark Nelson
Nov 3, 2007·Science·Siobhan M BradyPhilip N Benfey
Jul 26, 2008·Current Opinion in Plant Biology·Timothy NelsonS Lori Tausta

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Citations

Mar 12, 2010·Journal of Plant Research·Hirokazu TakahashiMikio Nakazono
Jun 25, 2013·Photosynthesis Research·Sarah CovshoffBritta M C Kümpers
Nov 1, 2011·Nature Methods·Allison GaudinierSiobhan M Brady
Oct 22, 2009·Proceedings of the National Academy of Sciences of the United States of America·Angelika MustrophJulia Bailey-Serres
Apr 14, 2010·Proceedings of the National Academy of Sciences of the United States of America·Brandon H LeRobert B Goldberg
Nov 2, 2011·Proceedings of the National Academy of Sciences of the United States of America·Insuk LeePamela C Ronald
Jul 18, 2009·Bioinformatics·Dustin A CartwrightPhilip N Benfey
Dec 8, 2010·Bioinformatics·M MiquelC M Vicient
Jul 29, 2011·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Kuaifei XiaMingyong Zhang
Dec 22, 2010·Journal of Experimental Botany·Stéphanie M SwarbreckDimah Z Habash
Feb 22, 2011·Journal of Experimental Botany·Kaisa KajalaWilliam P Quick
Oct 19, 2012·Journal of Experimental Botany·Sarah CovshoffJulian M Hibberd
Nov 28, 2012·Nucleic Acids Research·Yutaka SatoYoshiaki Nagamura
Nov 28, 2012·Nucleic Acids Research·Yutaka SatoYoshiaki Nagamura
May 21, 2013·Nucleic Acids Research·Eiru KimInsuk Lee
Mar 9, 2010·Plant & Cell Physiology·Keiichi Mochida, Kazuo Shinozaki
Nov 11, 2010·Plant & Cell Physiology·Masahiro FujitaNori Kurata
May 31, 2011·Plant & Cell Physiology·Takayuki OhnishiTetsu Kinoshita
Oct 6, 2010·Plant Physiology·Jen Sheen
Oct 14, 2010·Plant Physiology·Udo Gowik, Peter Westhoff
Jan 6, 2011·Plant Physiology·Madana M R AmbavaramAndy Pereira
Feb 8, 2013·Plant Physiology·Gregory S DownsLewis N Lukens
Apr 30, 2009·The Plant Cell·Siobhan M Brady, Nicholas J Provart
Jan 1, 2013·The Plant Cell·Katia PetroniRoberto Mantovani
Aug 18, 2012·BMC Bioinformatics·Ross E CurtisEric P Xing
Nov 11, 2009·PloS One·Antoine DissetRabary Rajerison

❮ Previous
Next ❯

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