Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

Plant Methods

Sean T May²  Philip J White¹  Henrik J Townsend²  Zoe F Emmerson²  Janet Higgins²  David J Craigon²  Martin R Broadley³  John P Hammond¹ 

[1] Warwick HRI, University of Warwick, Wellesbourne, Warwick, CV35 9EF, UK;Nottingham Arabidopsis Stock Centre, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK;Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK

关键词: transcriptomics;    probe masking;    plant nutrition;    phosphorus;    phosphate;    oligonucleotide;    microarray;    cross-species;    Brassicaceae;    Brassica oleracea;    Arabidopsis thaliana;   

Others  :  823153
DOI  :  10.1186/1746-4811-1-10

 received in 2005-08-03, accepted in 2005-11-09,  发布年份 2005

【 摘 要 】

High-density oligonucleotide (oligo) arrays are a powerful tool for transcript profiling. Arrays based on GeneChip^® technology are amongst the most widely used, although GeneChip^® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip^® array is available, using a GeneChip^® array designed for Arabidopsis thaliana (L.) Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip^® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM) probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P) stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip^® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ webcite and may be used to facilitate transcriptomic analyses of a wide range of plant and animal species in the absence of custom arrays.

【 授权许可】

   
2005 Hammond et al; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 3.

Figure 4.

【 参考文献 】

• [1]Lipshutz RJ, Fodor SPA, Gingeras TR, Lockhart DJ: High density synthetic oligonucleotide arrays. Nature Genet 1999, 21:20-24.
• [2]Harmer SL, Hogenesch LB, Straume M, Chang HS, Han B, Zhu T, Wang X, Kreps JA, Kay SA: Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 2000, 290:2110-2113.
• [3]Zhu T, Wang X: Large scale profiling of the Arabidopsis transcriptome. Plant Physiol 2000, 124:1472-1476.
• [4]Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S: NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res 2004, 32:D575-D577.
• [5]Chismar JD, Mondala T, Fox HS, Roberts E, Langford D, Masliah E, Salomon DR, Head SR: Analysis of results variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridisations. Biotechniques 2002, 33:516-524.
• [6]Enard W, Khaitovich P, Klose J, Zöllner S, Heissig F, Giavalisco P, Nieselt-Struwe K, Muchmore E, Varki A, Ravid R, Doxiadis GM, Bontrop RE, Pääbo S: Intra-and interspecific variation in primate gene expression patterns. Science 2002, 296:340-343.
• [7]Caceres M, Lachuer J, Zapala MA, Redmond JC, Kudo L, Geschwind DH, Lockhart DJ, Preuss TM, Barlow C: Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci USA 2003, 100:13030-13035.
• [8]Higgins MA, Berridge BR, Mills BJ, Schultze AE, Gao H, Searfoss GH, Baker TK, Ryan TP: Gene Expression analysis of the acute phase response using a canine microarray. Toxicol Sci 2003, 74:470-484.
• [9]Becher M, Talke IN, Krall L, Krämer U: Cross-species microarray transcript profiling reveals high constitutive expression of metal homeostasis genes in shoots of the zinc hyperaccumulator Arabidopsis halleri. Plant J 2004, 37:251-268.
• [10]Khaitovich P, Weiss G, Lachmann M, Hellmann I, Enard W, Muetzel B, Wirkner U, Ansorge W, Pääbo S: A neutral model of transcriptome evolution. PLo S Biol 2004, 2:682-689.
• [11]Uddin M, Wildman DE, Liu GZ, Xu WB, Johnson RM, Hof PR, Kapatos G, Grossman LI, Goodman M: Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. Proc Natl Acad Sci USA 2004, 101:2957-2962.
• [12]Weber M, Harada E, Vess C, v. Roepenack-Lahaye E, Clemens S: Comparative microarray analysis of Arabidopsis thaliana and Arabidopsis halleri roots identifies nicotianamine synthase, a ZIP transporter and other genes as potential metal hyperaccumulation factors. Plant J 2004, 37:269-281.
• [13]Ji W, Zhou W, Gregg K, Yu N, Davis S, Davis S: A method for cross-species gene expression analysis with high-density oligonucleotide arrays. Nucleic Acids Res 2004, 32:e93. doi:10.1093/nar/gnh084.
• [14]AGI (The Arabidopsis Genome Initiative): Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 2000, 408:796-815.
• [15]Hammond JP, Bennett MJ, Bowen HC, Broadley MR, Eastwood DC, May ST, Rahn C, Swarup R, Woolaway KE, White PJ: Changes in gene expression in Arabidopsis shoots during phosphate starvation and the potential for developing smart plants. Plant Physiol 2003, 132:578-596.
• [16]Hammond JP, Broadley MR, White PJ: Genetic responses to phosphorus deficiency. Ann Bot 2004, 94:323-332.
• [17]Wu P, Ma L, Hou X, Wang M, Wu Y, Liu F, Deng XW: Phosphate starvation triggers distinct alterations of genome expression in arabidopsis roots and leaves. Plant Physiol 2003, 132:1260-1271.
• [18]Ticconi CA, Abel S: Short on phosphate: plant surveillance and countermeasures. Trends in Plant Science 2004, 9:548-555.
• [19]Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264.
• [20]Essigmann B, Güler S, Narang RA, Linke D, Benning C: Phosphate availability affects the thylakoid lipid composition and the expression of SQD1, a gene required for sulfolipid biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci USA 1998, 95:1950-1955.
• [21]Yu B, Xu C, Benning C: Arabidopsis disrupted in SQD2 encoding sulfolipid synthase is impaired in phosphate-limited growth. Proc Natl Acad Sci USA 2002, 99:5732-5737.
• [22]Kobayashi K, Awai K, Takamiya K-I, Ohta H: Arabidopsis type B monogalactosyldiacylglycerol synthase genes are expressed during pollen tube growth and induced by phosphate starvation. Plant Physiol 2004, 134:640-648.
• [23]Bariola PA, Howard CJ, Taylor CB, Verburg MT, Jaglan VD, Green PJ: The Arabidopsis ribonuclease gene RNS1 is tightly controlled in response to phosphate limitation. Plant J 1994, 6:673-685.
• [24]van der Rest B, Boisson A-M, Gout E, Bligny R, Douce R: Glycerophosphocholine metabolism in higher plant cells. Evidence of a new glyceryl-phosphodiester phosphodiesterase. Plant Physiol 2003, 130:244-255.