Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

被引:144
作者
Jiao, Yuling [1 ]
Meyerowitz, Elliot M. [1 ]
机构
[1] CALTECH, Div Biol, Pasadena, CA 91125 USA
关键词
Arabidopsis; flower; intron; transcriptome; translation; GENOME-WIDE ANALYSIS; FLORAL ORGAN IDENTITY; SHOOT APICAL MERISTEM; GENE-EXPRESSION MAP; ARABIDOPSIS-THALIANA; TRANSCRIPTION FACTORS; MESSENGER-RNAS; PLANT; SEQ; PROTEIN;
D O I
10.1038/msb.2010.76
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Determining both the expression levels of mRNA and the regulation of its translation is important in understanding specialized cell functions. In this study, we describe both the expression profiles of cells within spatiotemporal domains of the Arabidopsis thaliana flower and the post-transcriptional regulation of these mRNAs, at nucleotide resolution. We express a tagged ribosomal protein under the promoters of three master regulators of flower development. By precipitating tagged polysomes, we isolated cell type-specific mRNAs that are probably translating, and quantified those mRNAs through deep sequencing. Cell type comparisons identified known cell-specific transcripts and uncovered many new ones, from which we inferred cell type-specific hormone responses, promoter motifs and coexpressed cognate binding factor candidates, and splicing isoforms. By comparing translating mRNAs with steady-state overall transcripts, we found evidence for widespread post-transcriptional regulation at both the intron splicing and translational stages. Sequence analyses identified structural features associated with each step. Finally, we identified a new class of noncoding RNAs associated with polysomes. Findings from our profiling lead to new hypotheses in the understanding of flower development. Molecular Systems Biology 6: 419; published online 5 October 2010; doi: 10.1038/msb.2010.76
引用
收藏
页数:14
相关论文
共 72 条
[1]   Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae [J].
Arava, Y ;
Wang, YL ;
Storey, JD ;
Liu, CL ;
Brown, PO ;
Herschlag, D .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2003, 100 (07) :3889-3894
[2]   Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes [J].
Aukerman, MJ ;
Sakai, H .
PLANT CELL, 2003, 15 (11) :2730-2741
[3]   Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics [J].
Baerenfaller, Katja ;
Grossmann, Jonas ;
Grobei, Monica A. ;
Hull, Roger ;
Hirsch-Hoffmann, Matthias ;
Yalovsky, Shaul ;
Zimmermann, Philip ;
Grossniklaus, Ueli ;
Gruissem, Wilhelm ;
Baginsky, Sacha .
SCIENCE, 2008, 320 (5878) :938-941
[4]   Getting the message across: cytoplasmic ribonucleoprotein complexes [J].
Bailey-Serres, J. ;
Sorenson, Reed ;
Juntawong, Piyada .
TRENDS IN PLANT SCIENCE, 2009, 14 (08) :443-453
[5]   Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses [J].
Ben Amor, Besma ;
Wirth, Sonia ;
Merchan, Francisco ;
Laporte, Philippe ;
d'Aubenton-Carafa, Yves ;
Hirsch, Judith ;
Maizel, Alexis ;
Mallory, Allison ;
Lucas, Antoine ;
Deragon, Jean Marc ;
Vaucheret, Herve ;
Thermes, Claude ;
Crespi, Martin .
GENOME RESEARCH, 2009, 19 (01) :57-69
[6]   APL regulates vascular tissue identity in Arabidopsis [J].
Bonke, M ;
Thitamadee, S ;
Mähönen, AP ;
Hauser, MT ;
Helariutta, Y .
NATURE, 2003, 426 (6963) :181-186
[7]   A high-resolution root spatiotemporal map reveals dominant expression patterns [J].
Brady, Siobhan M. ;
Orlando, David A. ;
Lee, Ji-Young ;
Wang, Jean Y. ;
Koch, Jeremy ;
Dinneny, Jose R. ;
Mace, Daniel ;
Ohler, Uwe ;
Benfey, Philip N. .
SCIENCE, 2007, 318 (5851) :801-806
[8]   Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana [J].
Branco-Price, Cristina ;
Kaiser, Kayla A. ;
Jang, Charles J. H. ;
Larive, Cynthia K. ;
Bailey-Serres, Julia .
PLANT JOURNAL, 2008, 56 (05) :743-755
[9]   Jasmonate controls late development stages of petal growth in Arabidopsis thaliana [J].
Brioudes, Florian ;
Joly, Caroline ;
Szecsi, Judit ;
Varaud, Emilie ;
Leroux, Julie ;
Bellvert, Floriant ;
Bertrand, Cedric ;
Bendahmane, Mohammed .
PLANT JOURNAL, 2009, 60 (06) :1070-1080
[10]   Widespread translational inhibition by plant miRNAs and siRNAs [J].
Brodersen, Peter ;
Sakvarelidze-Achard, Lali ;
Bruun-Rasmussen, Marianne ;
Dunoyer, Patrice ;
Yamamoto, Yoshiharu Y. ;
Sieburth, Leslie ;
Voinnet, Olivier .
SCIENCE, 2008, 320 (5880) :1185-1190