AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling    

Abstract

R., Y.V.d.P., M.V.)Transcriptome profiling has become a routine tool in biology. For Arabidopsis (Arabidopsis thaliana), the Affymetrix ATH1 expression array is most commonly used, but it lacks about one-third of all annotated genes present in the reference strain. An alternative are tiling arrays, but previous designs have not allowed the simultaneous analysis of both strands on a single array. We introduce AGRONOMICS1, a new Affymetrix Arabidopsis microarray that contains the complete paths of both genome strands, with on average one 25mer probe per 35-bp genome sequence window. In addition, the new AGRONOMICS1 array contains all perfect match probes from the original ATH1 array, allowing for seamless integration of the very large existing ATH1 knowledge base. The AGRONOMICS1 array can be used for diverse functional genomics applications such as reliable expression profiling of more than 30,000 genes, detection of alternative splicing, and chromatin immunoprecipitation coupled to microarrays (ChIP-chip). Here, we describe the design of the array and compare its performance with that of the ATH1 array. We find results from both microarrays to be of similar quality, but AGRONOMICS1 arrays yield robust expression information for many more genes, as expected. Analysis of the ATH1 probes on AGRONOMICS1 arrays produces results that closely mirror those of ATH1 arrays. Finally, the AGRONOMICS1 array is shown to be useful for ChIP-chip experiments. We show that heterochromatic H3K9me2 is strongly confined to the gene body of target genes in euchromatic chromosome regions, suggesting that spreading of heterochromatin is limited outside of pericentromeric regions.Microarrays have revolutionized experimental biology and are an essential source of data for systems biology approaches. While the first microarrays for plant research were developed only 10 years ago, they already have become routine tools for model and crop plants such as Arabidopsis (Arabidopsis thaliana), poplar (Populus spp.), rice (Oryza sativa), and barley (Hordeum vulgare;

Plastid Proteome Assembly without Toc159: Photosynthetic Protein Import and Accumulation of N-Acetylated Plastid Precursor Proteins

“…After RNA hybridization to AGRONOMICS1 genome tiling arrays (Rehrauer et al, 2010), signals above background in at least one of the samples were detected for 24,639 of the ;30,000 probe sets corresponding to 24,378 genes. Of these genes, 1998 (8.2%) were significantly upregulated in the wild type and 2268 (9.3%) in ppi2 ( Figure 3A; see Supplemental Data Set 4 online).…”

“…The experiment was performed with three biological replicates, and Affymetrix Arabidopsis AGRO-NOMICS1 microarrays were used. Labeling of samples, hybridizations, and measurements were performed as described (Hennig et al, 2004;Rehrauer et al, 2010). Signal values were derived using the robust multiarray analysis algorithm implemented in the statistical language R (R Development Core Team, 2010) using probe sets comprising exonic probes based on the TAIR9 genome annotation.…”

“…Signal values were derived using the robust multiarray analysis algorithm implemented in the statistical language R (R Development Core Team, 2010) using probe sets comprising exonic probes based on the TAIR9 genome annotation. For details of probe set definition and low-level data analysis, see Rehrauer et al (2010). Differentially expressed genes were selected using LIMMA (Smyth, 2004) followed by multiple testing correction according to Storey and Tibshirani (2003).…”

Measuring Arabidopsis Chromatin Accessibility Using DNase I-Polymerase Chain Reaction and DNase I-Chip Assays

“…The extracted DNA was amplified and labeled with biotin using the BioPrime DNA Labeling System (Invitrogen). Labeled DNA was hybridized to Affymetrix AGRONOMICS1 Arabidopsis tiling arrays as recommended by the manufacturer and as described previously (Rehrauer et al, 2010;Shu et al, 2012). Data analysis using freely available R packages has been described (Shu et al, 2012).…”

Gene co-expression analyses: an overview from microarray collections inArabidopsis thaliana

“…Because Arabidopsis thaliana is well established as a reference in plant biology, with a genome completely sequenced since the year 2000, its transcriptome has been extensively studied using different microarray technologies [18][19][20][21], offering useful collections for gene co-expression analyses. Indeed, an overwhelming number of experiments comes from the Affymetrix platform (ATH1).…”