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Browse MaizePLEX Experiment Data

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Expression profiling of zmet2-m1 mutants relative to wild-type
Nathan,M,Springer, University of Minnesota, Saint Paul, Minnesota (springer@umn.edu)
Experiment design (18 hybridizations)
genetic line
•B73 •Mo17
genotype
•wildtype •zmet2-m1

This experiment has been imported by PLEXdb from NCBI GEO (GSE8188)

Series_summary:
The contribution of epigenetic alterations to nat...[complete overview]

Experiment     Expression     Hybridizations & Samples     Quality Control     Compare Treatments     Downloads    

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Experiment Name: Expression profiling of zmet2-m1 mutants relative to wild-type
Accession No: ZM26
Microarray: maize18k
Visibility: public
Experiment Type:
Experiment Factor(s):
genetic line
•B73   •Mo17
genotype
•wildtype   •zmet2-m1
Quality Control: biological replicates
Treatment summary:
 genetic line  genotype  # replicates
 B73  wildtype  6
 B73  zmet2-m1  6
 Mo17  wildtype  3
 Mo17  zmet2-m1  3
Total hybridizations: 18
Description: This experiment has been imported by PLEXdb from NCBI GEO (GSE8188)

Series_summary:
The contribution of epigenetic alterations to natural variation for gene transcription levels remains unclear. In this study, we investigated the functional targets of the maize chromomethylase ZMET2 in multiple inbred lines to determine whether epigenetic changes conditioned by this chromomethylase are conserved or variable within the species. Gene expression microarrays were hybridized with RNA samples from the inbred lines B73 and Mo17, and from near-isogenic derivatives containing the loss-of-function allele zmet2-m1. A set of 126 genes that displayed statistically significant differential expression in zmet2 mutants relative to wild-type plants in at least one of the two genetic backgrounds were identified. Analysis of the transcript levels in both wild-type and mutant individuals revealed that only 10% of these genes were affected in zmet2 mutants in both B73 and Mo17 genetic backgrounds. Over 80% of the genes with expression patterns affected by zmet2 mutations display variation for gene expression between wild-type B73 and Mo17 plants. Further analysis was performed for seven genes that were transcriptionally silent in wild-type B73, but expressed in B73 zmet2-m1, wild-type Mo17 and Mo17 zmet2-m1 lines. Mapping experiments confirmed that the expression differences in wild-type B73 relative to Mo17 inbreds for these genes were caused by cis-acting regulatory variation. Methylation-sensitive PCR and bisulphite sequencing demonstrated that for five of these genes the CpNpG methylation in the wild-type B73 genetic background was substantially decreased in the B73 zmet2-m1 mutant and in wild-type Mo17. A survey of eight maize inbreds reveals that each of these five genes exhibit transcriptionally silent and methylated states in some inbred lines and unmethylated, expressed states in other inbreds, providing evidence for natural variation in epigenetic states for some maize genes.

Keywords: mutant versus wild-type comparison in two inbred genotypes

Series_overall_design:
The zmet2-m1 mutant allele was backcrossed into two inbred backgrounds, B73 and Mo17. RNA was isolated from 6 biological replicates of B73 wild-type plants, 6 biological replicates of B73 zmet2-m1 mutant plants; 3 biological replicates of Mo17 wild-type plants and 3 biological replicates of Mo17 zmet2-m1 mutant plants.
Publication: 'Natural variation for alleles under epigenetic control by the maize chromomethylase zmet2.', Makarevitch I, Stupar RM, Iniguez AL, Haun WJ et al.
Genetics 2007 Oct;177(2):749-60.
pubmed: 17660570
Created: 2009-04-30 15:07:50
Last Update: 2009-04-30 15:37:20
GEO Accession GSE8188
Submitter: PLEXdb Curator
Name: Nathan,M,Springer
Institution: University of Minnesota, Saint Paul, Minnesota
Head of Laboratory: --
email(s):
Homepage:

 
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