A systems approach to understand shoot branching

Current Plant Biology - Tập 3-4 - Trang 13-19 - 2015
Caihuan Tian1, Yuling Jiao1
1State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China

Tóm tắt

Từ khóa


Tài liệu tham khảo

Graham, 2000, The origin of plants: body plan changes contributing to a major evolutionary radiation, Proc. Natl. Acad. Sci. U. S. A., 97, 4535, 10.1073/pnas.97.9.4535

Glasby, 2012, Branching out: a remarkable new branching syllid (Annelida) lixving in a Petrosia sponge (Porifera: Demospongiae), Zool. J. Linn. Soc., 164, 481, 10.1111/j.1096-3642.2011.00800.x

Hagemann, 1990, Comparative morphology of acrogenous branch systems and phylogenetic considerations, Acta Biotheor., 38, 207, 10.1007/BF00047241

Harrison, 2009, Local cues and asymmetric cell divisions underpin body plan transitions in the moss Physcomitrella patens, Curr. Biol., 19, 461, 10.1016/j.cub.2009.02.050

Hagemann, 1989, Acrogenous branchin pteridophytes, 245

Long, 2000, Initiation of axillary and floral meristems in Arabidopsis, Dev. Biol., 218, 341, 10.1006/dbio.1999.9572

Han, 2014, Regulation of inflorescence architecture by cytokinins, Front. Plant Sci., 5, 10.3389/fpls.2014.00669

Springer, 2010, Shaping a better rice plant, Nat. Genet., 42, 475, 10.1038/ng0610-475

Stirnberg, 2002, MAX1 and MAX2 control shoot lateral branching in Arabidopsis, Development, 129, 1131, 10.1242/dev.129.5.1131

Domagalska, 2011, Signal integration in the control of shoot branching, Nat. Rev. Mol. Cell Biol., 12, 211, 10.1038/nrm3088

Eshed, 2001, Establishment of polarity in lateral organs of plants, Curr. Biol., 11, 1251, 10.1016/S0960-9822(01)00392-X

Lynn, 1999, The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene, Development, 126, 469, 10.1242/dev.126.3.469

McConnell, 1998, Leaf polarity and meristem formation in Arabidopsis, Development, 125, 2935, 10.1242/dev.125.15.2935

Furner, 1996, Clonal analysis of the late flowering fca mutant of Arabidopsis thaliana: cell fate and cell autonomy, Development, 122, 1041, 10.1242/dev.122.3.1041

Schnittger, 1996, Epidermal fate map of the Arabidopsis shoot meristem, Dev. Biol., 175, 248, 10.1006/dbio.1996.0112

Schumacher, 1999, The Lateral suppressor (Ls) gene of tomato encodes a new member of the VHIID protein family, Proc. Natl. Acad. Sci. U. S. A., 96, 290, 10.1073/pnas.96.1.290

Greb, 2003, Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation, Genes Dev., 17, 1175, 10.1101/gad.260703

Li, 2003, Control of tillering in rice, Nature, 422, 618, 10.1038/nature01518

Schmitz, 2002, The tomato Blind gene encodes a MYB transcription factor that controls the formation of lateral meristems, Proc. Natl. Acad. Sci. U. S. A., 99, 1064, 10.1073/pnas.022516199

Keller, 2006, Arabidopsis REGULATOR OF AXILLARY MERISTEMS1 controls a leaf axil stem cell niche and modulates vegetative development, Plant Cell, 18, 598, 10.1105/tpc.105.038588

Muller, 2006, Blind homologous R2R3 Myb genes control the pattern of lateral meristem initiation in Arabidopsis, Plant Cell, 18, 586, 10.1105/tpc.105.038745

Komatsu, 2003, LAX and SPA: major regulators of shoot branching in rice, Proc. Natl. Acad. Sci. U. S. A., 100, 11765, 10.1073/pnas.1932414100

Gallavotti, 2004, The role of barren stalk1 in the architecture of maize, Nature, 432, 630, 10.1038/nature03148

Woods, 2011, Phylogenomic analyses of the BARREN STALK1/LAX PANICLE1 (BA1/LAX1) genes and evidence for their roles during axillary meristem development, Mol. Biol. Evol., 28, 2147, 10.1093/molbev/msr036

Yang, 2012, The bHLH protein ROX acts in concert with RAX1 and LAS to modulate axillary meristem formation in Arabidopsis, Plant J., 71, 61, 10.1111/j.1365-313X.2012.04970.x

Aida, 1997, Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant, Plant Cell, 9, 841, 10.1105/tpc.9.6.841

Hibara, 2006, Arabidopsis CUP-SHAPED COTYLEDON3 regulates postembryonic shoot meristem and organ boundary formation, Plant Cell, 18, 2946, 10.1105/tpc.106.045716

Raman, 2008, Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana, Plant J., 55, 65, 10.1111/j.1365-313X.2008.03483.x

Talbert, 1995, The REVOLUTA gene is necessary for apical meristem development and for limiting cell divisions in the leaves and stems of Arabidopsis thaliana, Development, 121, 2723, 10.1242/dev.121.9.2723

Otsuga, 2001, REVOLUTA regulates meristem initiation at lateral positions, Plant J., 25, 223, 10.1046/j.1365-313x.2001.00959.x

Zhu, 2011, Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development, Cell, 145, 242, 10.1016/j.cell.2011.03.024

Jiao, 2009, A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies, Nat. Genet., 41, 258, 10.1038/ng.282

Birnbaum, 2003, A gene expression map of the Arabidopsis root, Science, 302, 1956, 10.1126/science.1090022

Brady, 2007, A high-resolution root spatiotemporal map reveals dominant expression patterns, Science, 318, 801, 10.1126/science.1146265

Deal, 2010, A simple method for gene expression and chromatin profiling of individual cell types within a tissue, Dev. Cell, 18, 1030, 10.1016/j.devcel.2010.05.013

Deal, 2011, The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana, Nat. Protoc., 6, 56, 10.1038/nprot.2010.175

Doyle, 2008, Application of a translational profiling approach for the comparative analysis of CNS cell types, Cell, 135, 749, 10.1016/j.cell.2008.10.029

Mustroph, 2009, Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis, Proc. Natl. Acad. Sci. U. S. A., 106, 18843, 10.1073/pnas.0906131106

Jiao, 2010, Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control, Mol. Syst. Biol., 6, 419, 10.1038/msb.2010.76

Tian, 2014, An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation, Mol. Syst. Biol., 10, 755, 10.15252/msb.20145470

Zadnikova, 2014, How boundaries control plant development, Curr. Opin. Plant Biol., 17, 116, 10.1016/j.pbi.2013.11.013

Breuil-Broyer, 2004, High-resolution boundary analysis during Arabidopsis thaliana flower development, Plant J., 38, 182, 10.1111/j.1365-313X.2004.02026.x

Hamant, 2008, Developmental patterning by mechanical signals in Arabidopsis, Science, 322, 1650, 10.1126/science.1165594

Wang, 2014, The stem cell niche in leaf axils is established by auxin and cytokinin in Arabidopsis, Plant Cell, 26, 2055, 10.1105/tpc.114.123083

Sang, 2009, The stem cell–chromatin connection, Semi. Cell Dev. Biol., 20, 1143, 10.1016/j.semcdb.2009.09.006

Xu, 2008, Polycomb silencing of KNOX genes confines shoot stem cell niches in Arabidopsis, Curr. Biol., 18, 1966, 10.1016/j.cub.2008.11.019

Schaller, 2015, The Yin-Yang of hormones: cytokinin and auxin interactions in plant development, Plant Cell, 27, 44, 10.1105/tpc.114.133595

Heisler, 2005, Patterns of auxin transport and gene expression during primordium development revealed by live imaging of the Arabidopsis inflorescence meristem, Curr. Biol., 15, 1899, 10.1016/j.cub.2005.09.052

Reinhardt, 2003, Regulation of phyllotaxis by polar auxin transport, Nature, 426, 255, 10.1038/nature02081

Benkova, 2003, Local, efflux-dependent auxin gradients as a common module for plant organ formation, Cell, 115, 591, 10.1016/S0092-8674(03)00924-3

De Smet, 2007, Auxin-dependent regulation of lateral root positioning in the basal meristem of Arabidopsis, Development, 134, 681, 10.1242/dev.02753

Dubrovsky, 2008, Auxin acts as a local morphogenetic trigger to specify lateral root founder cells, Proc. Natl. Acad. Sci. U. S. A., 105, 8790, 10.1073/pnas.0712307105

Swarup, 2008, The auxin influx carrier LAX3 promotes lateral root emergence, Nat. Cell Biol., 10, 946, 10.1038/ncb1754

Bielach, 2012, Spatiotemporal regulation of lateral root organogenesis in Arabidopsis by cytokinin, Plant Cell, 24, 3967, 10.1105/tpc.112.103044

Laplaze, 2007, Cytokinins act directly on lateral root founder cells to inhibit root initiation, Plant Cell, 19, 3889, 10.1105/tpc.107.055863

Ruzicka, 2009, Cytokinin regulates root meristem activity via modulation of the polar auxin transport, Proc. Natl. Acad. Sci. U. S. A., 106, 4284, 10.1073/pnas.0900060106

Li, 2006, Cytokinin-mediated cell cycling arrest of pericycle founder cells in lateral root initiation of Arabidopsis, Plant Cell Physiol., 47, 1112, 10.1093/pcp/pcj082

Werner, 2003, Cytokinin-deficient transgenic Arabidopsis plants show multiple developmental alterations indicating opposite functions of cytokinins in the regulation of shoot and root meristem activity, Plant Cell, 15, 2532, 10.1105/tpc.014928

Murray, 2012, Systems analysis of shoot apical meristem growth and development: integrating hormonal and mechanical signaling, Plant Cell, 24, 3907, 10.1105/tpc.112.102194

Perilli, 2012, Growth and development of the root apical meristem, Curr. Opin. Plant Biol., 15, 17, 10.1016/j.pbi.2011.10.006

Wang, 2014, Auxin depletion from the leaf axil conditions competence for axillary meristem formation in Arabidopsis and tomato, Plant Cell, 26, 2068, 10.1105/tpc.114.123059

Vernoux, 2011, The auxin signalling network translates dynamic input into robust patterning at the shoot apex, Mol. Syst. Biol., 7, 508, 10.1038/msb.2011.39

Qi, 2014, Auxin depletion from leaf primordia contributes to organ patterning, Proc. Natl. Acad. Sci. U. S. A., 111, 18769, 10.1073/pnas.1421878112

Bardou, 2014, Long noncoding RNA modulates alternative splicing regulators in Arabidopsis, Dev. Cell, 30, 166, 10.1016/j.devcel.2014.06.017

Müller, 2015, Cytokinin is required for escape but not release from auxin mediated apical dominance, Plant J., 82, 874, 10.1111/tpj.12862

Venglat, 1996, Benzylaminopurine induces phenocopies of floral meristem and organ identity mutants in wild-type Arabidopsis plants, Planta, 198, 480, 10.1007/BF00620066

Irish, 1990, Function of the apetala-1 gene during Arabidopsis floral development, Plant Cell, 2, 741, 10.1105/tpc.2.8.741

Kempin, 1995, Molecular basis of the cauliflower phenotype in Arabidopsis, Science, 267, 522, 10.1126/science.7824951

Wang, 2015, Epigenome profiling of specific plant cell types using a streamlined INTACT protocol and ChIP-seq, Methods Mol. Biol., 1284, 3, 10.1007/978-1-4939-2444-8_1

Brady, 2011, A stele-enriched gene regulatory network in the Arabidopsis root, Mol. Syst. Biol., 7, 459, 10.1038/msb.2010.114

Barabasi, 2004, Network biology: understanding the cell’s functional organization, Nat. Rev. Genet., 5, 101, 10.1038/nrg1272

Deplancke, 2006, A gene-centered C. elegans protein–DNA interaction network, Cell, 125, 1193, 10.1016/j.cell.2006.04.038

Vermeirssen, 2007, Transcription factor modularity in a gene-centered C. elegans core neuronal protein–DNA interaction network, Genome Res., 17, 1061, 10.1101/gr.6148107

Ma, 2013, Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways, PLoS Genet., 9, e1003840, 10.1371/journal.pgen.1003840

Ideker, 2001, A new approach to decoding life: systems biology, Annu. Rev. Genomics Hum. Genet., 2, 343, 10.1146/annurev.genom.2.1.343

Long, 2008, Systems approaches to identifying gene regulatory networks in plants, Annu. Rev. Cell Dev. Biol., 24, 81, 10.1146/annurev.cellbio.24.110707.175408