title: AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling.
abstract: 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.
authors.affiliation: Functional Genomics Center Zurich, ETH and University of Zurich, CH-8057 Zurich, Switzerland.
authors.forename: Hubert
authors.initials: H
authors.lastname: Rehrauer
authors.forename: Catharine
authors.initials: C
authors.lastname: Aquino
authors.forename: Wilhelm
authors.initials: W
authors.lastname: Gruissem
authors.forename: Stefan R
authors.initials: SR
authors.lastname: Henz
authors.forename: Pierre
authors.initials: P
authors.lastname: Hilson
authors.forename: Sascha
authors.initials: S
authors.lastname: Laubinger
authors.forename: Naira
authors.initials: N
authors.lastname: Naouar
authors.forename: Andrea
authors.initials: A
authors.lastname: Patrignani
authors.forename: Stephane
authors.initials: S
authors.lastname: Rombauts
authors.forename: Huan
authors.initials: H
authors.lastname: Shu
authors.forename: Yves
authors.initials: Y
authors.lastname: Van de Peer
authors.forename: Marnik
authors.initials: M
authors.lastname: Vuylsteke
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
authors.forename: Georg
authors.initials: G
authors.lastname: Zeller
authors.forename: Lars
authors.initials: L
authors.lastname: Hennig
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology; D015342:DNA Probes; D020869:Gene Expression Profiling / Q000379:methods*; D017343:Genes, Plant; D023281:Genomics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D018749:RNA, Plant / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D015342:DNA Probes; D018749:RNA, Plant