Related Experiment Video
Updated: May 16, 2026
11:19
Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets
Published on: July 7, 2010
Co-expression analysis identifies putative targets for CBP60g and SARD1 regulation
William Truman1, Jane Glazebrook
1Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, 1500 Gortner Avenue, Saint Paul, MN 55108, USA. wtruman@umn.edu
BMC Plant Biology
|November 17, 2012
Summary
Calmodulin binding protein CBP60g and SARD1 regulate plant defense by controlling salicylic acid (SA) biosynthesis. Co-expression analysis identified new genes in this signaling network, revealing insights into plant immunity.
Area of Science:
- Plant Molecular Biology
- Plant Immunity
- Gene Regulation
Background:
- Salicylic acid (SA) is crucial for plant defense signaling.
- Isochorismate synthase (SID2) is essential for SA biosynthesis in Arabidopsis.
- CBP60g and SARD1 bind the SID2 promoter, and their loss impairs SA production and increases susceptibility to pathogens.
Purpose of the Study:
- To identify novel components of the CBP60g and SARD1 signaling pathway.
- To understand the gene regulatory network controlling salicylic acid biosynthesis.
Main Methods:
- Gene expression profiling using custom microarrays.
- Co-expression analysis across ATH1 full genome microarray experiments.
- Clustering analysis to group co-expressed genes.
- Electrophoretic mobility shift assay (EMSA) to confirm DNA binding.
Main Results:
- Identified genes, including calmodulin-like genes, co-expressed with SID2 and regulated by CBP60g and SARD1.
- SID2 and co-expressed genes show promoter enrichment for GAAATT motifs.
- Genes regulated by CBP60g and SARD1 exhibit varied expression patterns in the double mutant.
Conclusions:
- Co-expression analysis successfully uncovered putative components of the CBP60g/SARD1 signaling network.
- Some identified genes are repressed by CBP60g and SARD1, highlighting their regulatory role.
Related Concept Videos
01:23Regulation of Expression at Multiple Steps
The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
02:24Regulation of Expression Occurs at Multiple Steps
Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
02:24Regulation of Expression Occurs at Multiple Steps
Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
02:33Combinatorial Gene Control
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
02:02Cis-regulatory Sequences
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...