Identification of genes required for cellulose synthesis by regression analysis of public microarray data sets

Abstract

Coexpression patterns of gene expression across many microarray data sets may reveal networks of genes involved in linked processes. To identify factors involved in cellulose biosynthesis, we used a regression method to analyze 408 publicly available Affymetrix Arabidopsis microarrays. Expression of genes previously implicated in cellulose synthesis, as well as several uncharacterized genes, was highly coregulated with expression of cellulose synthase (CESA) genes. Four candidate genes, which were coexpressed with CESA genes implicated in secondary cell wall synthesis, were investigated by mutant analysis. Two mutants exhibited irregular xylem phenotypes similar to those observed in mutants with defects in secondary cellulose synthesis and were designated irx8 and irx13. Thus, the general approach developed here is useful for identification of elements of multicomponent processes.Arabidopsis ͉ cell wall ͉ xylem ͉ coexpression

Pattern of Deposition of Cell Wall Polysaccharides and Transcript Abundance of Related Cell Wall Synthesis Genes during Differentiation in Barley Endosperm

“…We have examined the monosaccharide composition of the endosperm over the course of development, applied the recently generated xyloglucan antibody to early endosperm development, and modified our approach to studying arabino-(1→4)-b-D-xylan using the LM11 antibody. Previous studies identifying genes involved in the synthesis of cell wall polysaccharides have shown that transcript accumulation correlates with the time of polysaccharide synthesis and deposition (Pear et al, 1996;Doblin et al, 2001;Dhugga et al, 2004;Brown et al, 2005;Persson et al, 2005;Cocuron et al, 2007;Mitchell et al, 2007). By coupling our immuno-EM observations with transcript profiles of candidate cell wall synthesis genes, we can now infer which subfamily members of these gene families is functional during key stages of endosperm development.…”

Molecular characterization, expression pattern, and function analysis of the OsBC1L family in rice

“…In addition to COBRA, five other members of this superfamily have been identified and characterized in plants. AtCOBL4 is required for cellulose biosynthesis in the secondary cell wall in Arabidopsis (Brown et al 2005;Persson et al 2005). AtCOBL9 is required for tip-directed growth in root hair development in Arabidopsis (Parker et al 2000;Jones et al 2006).…”

“…Further, additional research tools of functional genomics in rice, such as full-length cDNA collection and whole genome expression profiling, have been established and have enhanced the pace for elucidating gene function throughout the genome . The combination of expression profiling and insertional mutagenesis strategies has been successful in assigning functions to several COBRA-like genes, such as AtCOBL4 and AtCOBL9 (Brown et al 2005;Persson et al 2005;Parker et al 2000;Jones et al 2006). As for COBRA-like genes in rice, only BC1 has been characterized and the functions of the other OsBC1Ls remain to be elucidated.…”

LASSO modeling of the Arabidopsis thaliana seed/seedling transcriptome: a model case for detection of novel mucilage and pectin metabolism genes

“…Indeed, several new genes were found to be co-expressed with these CESAs and characterized as displaying cellulose synthesis deficiencies. 14,15 Further examples where these databases and/or methods have been used for candidate gene discovery encompass different processes such as starch metabolism, 16,17 seed germination 18 and shade avoidance. 19 However, many of these approaches rely primarily on simple Pearson correlation, sometimes coupled with network clustering approaches 20 or sequence analysis.…”