Microgenomics: Genome-scale, cell-specific monitoring of multiple gene regulation tiers

Annual Review of Plant Biology

Volumn 64, Issue , 2013, Pages 293-325

  Bailey Serres, J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Epigenetic; Gene expression; Gene regulatory network; Posttranscriptional; Transcription; Translation

Indexed keywords

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HIGH THROUGHPUT SEQUENCING; METABOLISM; PLANT; PLANT CELL; PLANT GENOME; REVIEW;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; PLANT CELLS; PLANTS;

EID: 84873550025     PISSN: 15435008     EISSN: 15452123     Source Type: Book Series    
DOI: 10.1146/annurev-arplant-050312-120035     Document Type: Review

References (153)

1. Abbott E, Hall D, Hamberger B, Bohlmann J. 2010. Laser microdissection of conifer stem tissues: isolation and analysis of high quality RNA, terpene synthase enzyme activity and terpenoid metabolites from resin ducts and cambial zone tissue of white spruce (Picea glauca). BMC Plant Biol. 10:106
2. Alatorre-Cobos F, Cruz-Ramirez A, Hayden CA, Perez-Torres CA, Chauvin AL, et al. 2012. Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30. J. Exp. Bot. 63:5203-21
3. An G, Jeong DH, Jung KH, Lee S. 2005. Reverse genetic approaches for functional genomics of rice. Plant Mol. Biol. 59:111-23
4. Atares A, Moyano E, Morales B, Schleicher P, Garcia-Abellan JO, et al. 2011. An insertionalmutagenesis programme with an enhancer trap for the identification and tagging of genes involved in abiotic stress tolerance in the tomato wild-related species Solanum pennellii. Plant Cell Rep. 30:1865-79
5. Atkins CA, Smith PM, Rodriguez-Medina C. 2011. Macromolecules in phloem exudates - a review. Protoplasma 248:165-72
6. Autran D, Baroux C, Raissig MT, Lenormand T, Wittig M, et al. 2011. Maternal epigenetic pathways control parental contributions to Arabidopsis early embryogenesis. Cell 145:707-19
7. Aviv H, Leder P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Natl. Acad. Sci. USA 69:1408-12
8. Bailey-Serres J, Sorenson R, Juntawong P. 2009. Getting the message across: cytoplasmic ribonucleoprotein complexes. Trends Plant Sci. 14:443-53
9. Barcala M, Garcia A, Cabrera J, Casson S, Lindsey K, et al. 2010. Early transcriptomic events in microdissected Arabidopsis nematode-induced giant cells. Plant J. 61:698-712
10. Bargmann BO, Birnbaum KD. 2009. Positive fluorescent selection permits precise, rapid, and in-depth overexpression analysis in plant protoplasts. Plant Physiol. 149:1231-39
11. Bargmann BO, Birnbaum KD. 2010. Fluorescence activated cell sorting of plant protoplasts. J. Vis. Exp. 36:e1673
12. Barkan A. 2009. Genome-wide analysis of RNA-protein interactions in plants. MethodsMol. Biol. 553:13-37
13. Baroux C, Blanvillain R, Betts H, Batoko H, Craft J, et al. 2005. Predictable activation of tissue-specific expression from a single gene locus using the pOp/LhG4 transactivation system in Arabidopsis. Plant Biotechnol. J. 3:91-101
14. Bazzini AA, Lee MT, Giraldez AJ. 2012. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336:233-37
15. Belostotsky DA, Rose AB. 2005. Plant gene expression in the age of systems biology: integrating transcriptional and post-transcriptional events. Trends Plant Sci. 10:347-53
16. Birnbaum K, Jung JW, Wang JY, Lambert GM, Hirst JA, et al. 2005. Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines. Nat. Methods 2:615-19
17. Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, et al. 2003. A gene expression map of the Arabidopsis root. Science 302:1956-60
18. Borges F, Gomes G, Gardner R, Moreno N, McCormick S, et al. 2008. Comparative transcriptomics of Arabidopsis sperm cells. Plant Physiol. 148:1168-81
19. Bradnam KR, Korf I. 2008. Longer first introns are a general property of eukaryotic gene structure. PLoS ONE 3:e3093
20. Brady SM, Orlando DA, Lee JY, Wang JY, Koch J, et al. 2007. A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318:801-6
21. Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, et al. 2011. A stele-enriched gene regulatory network in the Arabidopsis root. Mol. Syst. Biol. 7:459
22. Branco-Price C, Kaiser KA, Jang CJ, Larive CK, Bailey-Serres J. 2008. Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana. Plant J. 56:743-55
23. Branco-Price C, Kawaguchi R, Ferreira RB, Bailey-Serres J. 2005. Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation. Ann. Bot. 96:647-60
24. Brandt SP. 2005. Microgenomics: gene expression analysis at the tissue-specific and single-cell levels. J. Exp. Bot. 56:495-505
25. BreakfieldNW, Corcoran DL, Petricka JJ, Shen J, Sae-Seaw J, et al. 2012. High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis. Genome Res. 22:163-76
26. Brooks L III, Strable J, Zhang X, Ohtsu K, Zhou R, et al. 2009. Microdissection of shoot meristem functional domains. PLoS Genet. 5:e1000476
27. Bruex A,Kainkaryam RM,Wieckowski Y,Kang YH, BernhardtC, et al. 2012. A gene regulatory network for root epidermis cell differentiation in Arabidopsis. PLoS Genet. 8:e1002446
28. Buchan JR, ParkerR. 2009. Eukaryotic stress granules: the ins and outs of translation. Mol. Cell 36:932-41
29. Calarco JP, Borges F, Donoghue MT, Van Ex F, Jullien PE, et al. 2012. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151:194-205
30. Cano-Delgado A, Lee JY, Demura T. 2010. Regulatory mechanisms for specification and patterning of plant vascular tissues. Annu. Rev. Cell Dev. Biol. 26:605-37
31. Castiglioni P, Warner D, Bensen RJ, Anstrom DC, Harrison J, et al. 2008. Bacterial RNA chaperones confer abiotic stress tolerance in plants and improved grain yield inmaize underwater-limited conditions. Plant Physiol. 147:446-55
32. Chandran D, Inada N, Hather G, Kleindt CK, Wildermuth MC. 2010. Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators. Proc. Natl. Acad. Sci. USA 107:460-65
33. Chen C, Farmer AD, Langley RJ, Mudge J, Crow JA, et al. 2010. Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes. BMC Plant Biol. 10:280
34. Chen X. 2012. Small RNAs in development - insights from plants. Curr. Opin. Genet. Dev. 22:361-67
35. Conn SJ, Gilliham M, Athman A, Schreiber AW, Baumann U, et al. 2011. Cell-specific vacuolar calcium storage mediated by CAX1 regulates apoplastic calcium concentration, gas exchange, and plant productivity in Arabidopsis. Plant Cell 23:240-57
36. Darnell RB. 2010. HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip. Rev. RNA 1:266-86
37. Day RC, GrossniklausU,Macknight RC. 2005. Be more specific! Laser-assisted microdissection of plant cells. Trends Plant Sci. 10:397-406
38. Deal RB, Henikoff S. 2010. A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev. Cell 18:1030-40
39. Deal RB, Henikoff S. 2011. Histone variants and modifications in plant gene regulation. Curr. Opin. Plant Biol. 14:116-22
40. Deal RB, Henikoff S. 2011. The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat. Protoc. 6:56-68
41. Deeken R, Ache P, Kajahn I, Klinkenberg J, Bringmann G, Hedrich R. 2008. Identification of Arabidopsis thaliana phloem RNAs provides a search criterion for phloem-based transcripts hidden in complex datasets of microarray experiments. Plant J. 55:746-59
42. Dembinsky D, Woll K, Saleem M, Liu Y, Fu Y, et al. 2007. Transcriptomic and proteomic analyses of pericycle cells of the maize primary root. Plant Physiol. 145:575-88
43. Demura T, TashiroG,Horiguchi G, KishimotoN,Kubo M, et al. 2002. Visualization by comprehensive microarray analysis of gene expression programs during transdifferentiation ofmesophyll cells into xylem cells. Proc. Natl. Acad. Sci. USA 99:15794-99
44. De Veylder L, Larkin JC, Schnittger A. 2011. Molecular control and function of endoreplication in development and physiology. Trends Plant Sci. 16:624-34
45. Dinneny JR, Long TA, Wang JY, Jung JW, Mace D, et al. 2008. Cell identity mediates the response of Arabidopsis roots to abiotic stress. Science 320:942-45
46. Djuranovic S, Nahvi A, Green R. 2012. miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336:237-40
47. Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, et al. 2012. Widespread dynamic DNA methylation in response to biotic stress. Proc. Natl. Acad. Sci. USA 109:E2183-91
48. Doyle JP, Dougherty JD, Heiman M, Schmidt EF, Stevens TR, et al. 2008. Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell 135:749-62
49. Dupeux F, Antoni R, Betz K, Santiago J, Gonzalez-Guzman M, et al. 2011. Modulation of abscisic acid signaling in vivo by an engineered receptor-insensitive protein phosphatase type 2C allele. Plant Physiol. 156:106-16
50. Ebert B, Zoller D, Erban A, Fehrle I, Hartmann J, et al. 2010. Metabolic profiling of Arabidopsis thaliana epidermal cells. J. Exp. Bot. 61:1321-35
51. Filichkin SA, PriestHD,Givan SA, ShenR,BryantDW,et al. 2010. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res. 20:45-58
52. Fiorilli V, Catoni M, Miozzi L, Novero M, Accotto GP, Lanfranco L. 2009. Global and cell-type gene expression profiles in tomato plants colonized by an arbuscular mycorrhizal fungus. New Phytol. 184:975-87
53. Fox S, Filichkin S, Mockler TC. 2009. Applications of ultra-high-throughput sequencing. Methods Mol. Biol. 553:79-108
54. Galbraith DW, Birnbaum K. 2006. Global studies of cell type-specific gene expression in plants. Annu. Rev. Plant Biol. 57:451-75
55. Galbraith DW, Janda J, Lambert GM. 2011. Multiparametric analysis, sorting, and transcriptional profiling of plant protoplasts and nuclei according to cell type. Methods Mol. Biol. 699:407-29
56. GiffordML, Dean A, Gutierrez RA, Coruzzi GM, Birnbaum KD. 2008. Cell-specific nitrogen responses mediate developmental plasticity. Proc. Natl. Acad. Sci. USA 105:803-8
57. Goldberg RB, Hoschek G, Kamalay JC, Timberlake WE. 1978. Sequence complexity of nuclear and polysomal RNA in leaves of the tobacco plant. Cell 14:123-31
58. Goue N, Lesage-Descauses MC, Mellerowicz EJ, Magel E, Label P, Sundberg B. 2008. Microgenomic analysis reveals cell type-specific gene expression patterns between ray and fusiform initials within the cambial meristem of Populus. New Phytol. 180:45-56
59. Gregory BD, Belostotsky DA. 2009. Whole-genome microarrays: applications and technical issues. Methods Mol. Biol. 553:39-56
60. Guo H, Ingolia NT, Weissman JS, Bartel DP. 2010. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466:835-40
61. Halbeisen RE, Gerber AP. 2009. Stress-dependent coordination of transcriptome and translatome in yeast. PLoS Biol. 7:e1000105
62. Heiman M, Schaefer A, Gong S, Peterson JD, DayM, et al. 2008. A translational profiling approach for the molecular characterization of CNS cell types. Cell 135:738-48
63. Hogan DJ, Riordan DP, Gerber AP, Herschlag D, Brown PO. 2008. Diverse RNA-binding proteins interact with functionally related sets of RNAs, suggesting an extensive regulatory system. PLoS Biol. 6:e255
64. Holscher D, Shroff R, Knop K, Gottschaldt M, Crecelius A, et al. 2009. Matrix-free UV-laser desorption/ ionization (LDI) mass spectrometric imaging at the single-cell level: distribution of secondary metabolites of Arabidopsis thaliana and Hypericum species. Plant J. 60:907-18
65. HummelM, Cordewener JH, de Groot JC, Smeekens S, America AH,Hanson J. 2012. Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MSE proteomics. Proteomics 12:1024-38
66. HummelM, Rahmani F, Smeekens S,Hanson J. 2009. Sucrose-mediated translational control. Ann. Bot. 104:1-7
67. Hunt AG. 2011. RNA regulatory elements and polyadenylation in plants. Front. Plant Sci. 2:109
68. Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. 2012. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat. Protoc. 7:1534-50
69. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-23
70. Ivanov IP, Atkins JF, Michael AJ. 2010. A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation. Nucleic Acids Res. 38:353-59
71. Iyer-Pascuzzi AS, Jackson T, Cui H, Petricka JJ, Busch W, et al. 2011. Cell identity regulators link development and stress responses in the Arabidopsis root. Dev. Cell 21:770-82
72. Jefferson RA, Kavanagh TA, Bevan MW. 1987. GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J. 6:3901-7
73. Jiao Y, Meyerowitz EM. 2010. Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control. Mol. Syst. Biol. 6:419
74. Jiao Y, Riechmann JL, Meyerowitz EM. 2008. Transcriptome-wide analysis of uncapped mRNAs in Arabidopsis reveals regulation of mRNA degradation. Plant Cell 20:2571-85
75. Jiao Y, Tausta SL,Gandotra N, SunN, Liu T, et al. 2009. A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat. Genet. 41:258-63
76. Johnson AA, Hibberd JM,Gay C, Essah PA, Haseloff J, et al. 2005. Spatial control of transgene expression in rice (Oryza sativa L.) using the GAL4 enhancer trapping system. Plant J. 41:779-89
77. JouannetV,MorenoAB, ElmayanT, Vaucheret H, CrespiMD,MaizelA. 2012. CytoplasmicArabidopsis AGO7 accumulates in membrane-associated siRNA bodies and is required for ta-siRNA biogenesis. EMBO J. 31:1704-13
78. Juntawong P, Bailey-Serres J. 2012. Dynamic light regulation of translation status in Arabidopsis thaliana. Front. Plant Sci. 3:66
79. Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, et al. 2012. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res. 40:2454-69
80. Kamalay JC, Goldberg RB. 1984. Organ-specific nuclear RNAs in tobacco. Proc. Natl. Acad. Sci. USA 81:2801-5
81. Kaufmann K, Muino JM, Osteras M, Farinelli L, Krajewski P, AngenentGC. 2010. Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP). Nat. Protoc. 5:457-72
82. Kawaguchi R, Bailey-Serres J. 2002. Regulation of translational initiation in plants. Curr. Opin. Plant Biol. 5:460-65
83. Kawaguchi R, Bailey-Serres J. 2005. mRNA sequence features that contribute to translational regulation in Arabidopsis. Nucleic Acids Res. 33:955-65
84. Kerenyi Z, Merai Z, Hiripi L, Benkovics A, Gyula P, et al. 2008. Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay. EMBO J. 27:1585-95
85. Klink VP, Hosseini P, Matsye P, Alkharouf NW, Matthews BF. 2009. A gene expression analysis of syncytia laser microdissected from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode). Plant Mol. Biol. 71:525-67
86. Lauria M, Rossi V. 2011. Epigenetic control of gene regulation in plants. Biochim. Biophys. Acta 1809:369-78
87. Law JA, Jacobsen SE. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11:204-20
88. Lee JY, Colinas J, Wang JY, Mace D, OhlerU, Benfey PN. 2006. Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots. Proc. Natl. Acad. Sci. USA 103:6055-60
89. Leonhardt N, Kwak JM, Robert N, Waner D, Leonhardt G, Schroeder JI. 2004. Microarray expression analyses of Arabidopsis guard cells and isolation of a recessive abscisic acid hypersensitive protein phosphatase 2C mutant. Plant Cell 16:596-615
90. Levesque MP, Vernoux T, Busch W, Cui H, Wang JY, et al. 2006. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol. 4:e143
91. Li P, Ponnala L, Gandotra N, Wang L, Si Y, et al. 2010. The developmental dynamics of the maize leaf transcriptome. Nat. Genet. 42:1060-67
92. Li S, Pandey S, Gookin TE, Zhao Z,Wilson L, Assmann SM. 2012. Gene-sharing networks reveal organizing principles of transcriptomes in Arabidopsis and other multicellular organisms. Plant Cell 24:1362-78
93. Lister R, Ecker Jr. 2009. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res. 19:959-66
94. Long TA, Brady SM, Benfey PN. 2008. Systems approaches to identifying gene regulatory networks in plants. Annu. Rev. Cell Dev. Biol. 24:81-103
95. Long TA, Tsukagoshi H, Busch W, Lahner B, Salt DE, Benfey PN. 2010. The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots. Plant Cell 22:2219-36
96. Lorkovic ZJ. 2009. Role of plant RNA-binding proteins in development, stress response and genome organization. Trends Plant Sci. 14:229-36
97. Matas AJ, YeatsTH, Buda GJ, Zheng Y,Chatterjee S, et al. 2011. Tissue-and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. Plant Cell 23:3893-910
98. Meyers BC, Tej SS, Vu TH, Haudenschild CD, Agrawal V, et al. 2004. The use of MPSS for wholegenome transcriptional analysis in Arabidopsis. Genome Res. 14:1641-53
99. MocoS, Schneider B, Vervoort J. 2009. Plantmicrometabolomics: the analysis of endogenous metabolites present in a plant cell or tissue. J. Proteome Res. 8:1694-703
100. Molnar A, Melnyk C, Baulcombe DC. 2011. Silencing signals in plants: a long journey for small RNAs. Genome Biol. 12:215
101. Mustroph A, Bailey-Serres J. 2010. The Arabidopsis translatome cell-specific mRNA atlas: mining suberin and cutin lipid monomer biosynthesis genes as an example for data application. Plant Signal. Behav. 5:320-24
102. Mustroph A, Zanetti ME, Jang CJ, Holtan HE, Repetti PP, et al. 2009. Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis. Proc.Natl. Acad. Sci. USA 106:18843-48
103. Nawy T, Lee JY, Colinas J, Wang JY, Thongrod SC, et al. 2005. Transcriptional profile of the Arabidopsis root quiescent center. Plant Cell 17:1908-25
104. Nelson T, Gandotra N, Tausta SL. 2008. Plant cell types: reporting and sampling with new technologies. Curr. Opin. Plant Biol. 11:567-73
105. Nelson T, Tausta SL, Gandotra N, Liu T. 2006. Laser microdissection of plant tissue: what you see is what you get. Annu. Rev. Plant Biol. 57:181-201
106. Nobuta K, Venu RC, Lu C, Belo A, Vemaraju K, et al. 2007. An expression atlas of rice mRNAs and small RNAs. Nat. Biotechnol. 25:473-77
107. Nodine MD, Bartel DP. 2012. Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos. Nature 482:94-97
108. Ohtsu K, Smith MB, Emrich SJ, Borsuk LA, Zhou R, et al. 2007. Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.). Plant J. 52:391-404
109. Okumoto S, Jones A, FrommerWB. 2012. Quantitative imaging with fluorescent biosensors. Annu. Rev. Plant Biol. 63:663-706
110. Orlando DA, Brady SM, Koch JD, Dinneny JR, Benfey PN. 2009. Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. Methods Mol. Biol. 553:57-77
111. Pandey S, Wang RS,Wilson L, Li S, Zhao Z, et al. 2010. Booleanmodeling of transcriptome data reveals novel modes of heterotrimeric G-protein action. Mol. Syst. Biol. 6:372
112. Pant BD, Buhtz A, Kehr J, Scheible WR. 2008. MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. Plant J. 53:731-38
113. Petersson SV, Johansson AI, KowalczykM,Makoveychuk A, Wang JY, et al. 2009. An auxin gradient and maximum in the Arabidopsis root apex shown by high-resolution cell-specific analysis of IAA distribution and synthesis. Plant Cell 21:1659-68
114. Petricka JJ, SchauerMA, Megraw M, BreakfieldNW, Thompson JW, et al. 2012. The protein expression landscape of the Arabidopsis root. Proc. Natl. Acad. Sci. USA 109:6811-18
115. Plett D, Johnson A, Jacobs A, Tester M. 2010. Cell type-specific expression of sodium transporters improves salinity tolerance of rice. GM Crops 1:273-75
116. Plett D, Safwat G, Gilliham M, Skrumsager Moller I, Roy S, et al. 2010. Improved salinity tolerance of rice through cell type-specific expression of AtHKT1;1. PLoS ONE 5:e12571
117. Rahmani F, Hummel M, Schuurmans J, Wiese-Klinkenberg A, Smeekens S, Hanson J. 2009. Sucrose control of translation mediated by an upstream open reading frame-encoded peptide. Plant Physiol. 150:1356-67
118. Rajhi I, Yamauchi T, Takahashi H, Nishiuchi S, Shiono K, et al. 2011. Identification of genes expressed in maize root cortical cells during lysigenous aerenchyma formation using laser microdissection and microarray analyses. New Phytol. 190:351-68
119. Reddy AS, Rogers MF, Richardson DN, Hamilton M, Ben-Hur A. 2012. Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. Front. Plant Sci. 3:18
120. ReynosoMA, Blanco FA, Bailey-Serres J, CrespiM, Zanetti ME. 2013. Selective recruitment of mRNAs and miRNAs to polyribosomes in response to rhizobia infection in Medicago truncatula. Plant J. 73:289-301
121. Ribeiro DM, Araujo WL, Fernie AR, Schippers JH, Mueller-Roeber B. 2012. Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis. J. Exp. Bot. 63:2769-86
122. Roy B, Vaughn JN, Kim BH, Zhou F, Gilchrist MA, Von Arnim AG. 2010. The h subunit of eIF3 promotes reinitiation competence during translation of mRNAs harboring upstream open reading frames. RNA 16:748-61
123. Schena M, Heller RA, Theriault TP, Konrad K, Lachenmeier E,Davis RW. 1998. Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol. 16:301-6
124. Schiebold S, Tschiersch H, Borisjuk L, Heinzel N, Radchuk R, Rolletschek H. 2011. A novel procedure for the quantitative analysis of metabolites, storage products and transcripts of laser microdissected seed tissues of Brassica napus. Plant Methods 7:19
125. Schmid MW, Schmidt A, Klostermeier UC, BarannM, Rosenstiel P, Grossniklaus U. 2012. A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing. PLoS ONE 7:e29685
126. ShenY,VenuRC, NobutaK,WuX,Notibala V, et al. 2011. Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. Genome Res. 21:1478-86
127. Sozzani R, Cui H, Moreno-Risueno MA, Busch W, Van Norman JM, et al. 2010. Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature 466:128-32
128. Springer PS. 2000. Gene traps: tools for plant development and genomics. Plant Cell 12:1007-20
129. Steiner FA, Talbert PB, Kasinathan S, Deal RB, Henikoff S. 2012. Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. Genome Res. 22:766-77
130. Stern DB, Goldschmidt-Clermont M, Hanson MR. 2010. Chloroplast RNA metabolism. Annu. Rev. Plant Biol. 61:125-55
131. Strickler SR, Bombarely A, Mueller LA. 2012. Designing a transcriptome next-generation sequencing project for a nonmodel plant species. Am. J. Bot. 99:257-66
132. Tang X, Zhang ZY, Zhang WJ, Zhao XM, Li X, et al. 2010. Global gene profiling of laser-captured pollen mother cells indicates molecular pathways and gene subfamilies involved in rice meiosis. Plant Physiol. 154:1855-70
133. Tauris B, Borg S, Gregersen PL, Holm PB. 2009. A roadmap for zinc trafficking in the developing barley grain based on laser capture microdissection and gene expression profiling. J. Exp. Bot. 60:1333-47
134. Taylor CG, Fuchs B, Collier R, Lutke WK. 2006. Generation of composite plants using Agrobacterium rhizogenes. Methods Mol. Biol. 343:155-67
135. Thiel J, Hollmann J, Rutten T,Weber H, Scholz U, WeschkeW. 2012. 454 transcriptome sequencing suggests a role for two-component signalling in cellularization and differentiation of barley endosperm transfer cells. PLoS ONE 7:e41867
136. Thomas A, Lee PJ, Dalton JE, Nomie KJ, Stoica L, et al. 2012. A versatile method for cell-specific profiling of translated mRNAs in Drosophila. PLoS ONE 7:e40276
137. Tissier A. 2012. Glandular trichomes:What comes after expressed sequence tags? Plant J. 70:51-68
138. Voinnet O. 2009. Fly antiviral RNA silencing and miRNA biogenesis claim ARS2. Cell Host Microbe 6:99-101
139. Voinnet O. 2009. Origin, biogenesis, and activity of plant microRNAs. Cell 136:669-87
140. Wang H, Zhang X, Liu J, Kiba T, Woo J, et al. 2011. Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant J. 67:292-304
141. Wang L, Si Y, Dedow LK, Shao Y, Liu P, Brutnell TP. 2011. A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq. PLoS ONE 6:e26426
142. Washida H, Sugino A, Doroshenk KA, Satoh-Cruz M, Nagamine A, et al. 2012. RNA targeting to a specific ER sub-domain is required for efficient transport and packaging of α-globulins to the protein storage vacuole in developing rice endosperm. Plant J. 70:471-79
143. Weber C,Nover L, FauthM. 2008. Plant stress granules and mRNA processing bodies are distinct from heat stress granules. Plant J. 56:517-30
144. Wolin SL, Walter P. 1988. Ribosome pausing and stacking during translation of a eukaryotic mRNA. EMBO J. 7:3559-69
145. Wu X, Liu M, Downie B, Liang C, Ji G, et al. 2011. Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc. Natl. Acad. Sci. USA 108:12533-38
146. Wuest SE, Vijverberg K, Schmidt A,Weiss M, Gheyselinck J, et al. 2010. Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes. Curr. Biol. 20:506-12
147. Xu J, Chua NH. 2012. Dehydration stress activates Arabidopsis MPK6 to signal DCP1 phosphorylation. EMBO J. 31:1975-84
148. Yadav RK, Girke T, Pasala S, Xie M, Reddy GV. 2009. Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proc. Natl. Acad. Sci. USA 106:4941-46
149. Zanetti ME, Chang IF, Gong F, Galbraith DW, Bailey-Serres J. 2005. Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol. 138:624-35
150. Zhang C, Barthelson RA, Lambert GM, Galbraith DW. 2008. Global characterization of cell-specific gene expression through fluorescence-activated sorting of nuclei. Plant Physiol. 147:30-40
151. Zhang C, Galbraith DW. 2012. RNA interference-mediated gene knockdown within specific cell types. Plant Mol. Biol. 80:169-76
152. Zhang C, Gong FC, Lambert GM, Galbraith DW. 2005. Cell type-specific characterization of nuclear DNA contents within complex tissues and organs. Plant Methods 1:7
153. Zhu JY, Sun Y, Wang ZY. 2012. Genome-wide identification of transcription factor-binding sites in plants using chromatin immunoprecipitation followed by microarray (ChIP-chip) or sequencing (ChIPseq). Methods Mol. Biol. 876:173-88