Long-range control of gene expression via RNA-directed DNA methylation.
M Jordan RowleyM Hafiz RothiGudrun BöhmdorferJan KucińskiAndrzej T WierzbickiPublished in: PLoS genetics (2017)
RNA-mediated transcriptional silencing, in plants known as RNA-directed DNA methylation (RdDM), is a conserved process where small interfering RNA (siRNA) and long non-coding RNA (lncRNA) help establish repressive chromatin modifications. This process represses transposons and affects the expression of protein-coding genes. We found that in Arabidopsis thaliana AGO4 binding sites are often located distant from genes differentially expressed in ago4. Using Hi-C to compare interactions between genotypes, we show that RdDM-targeted loci have the potential to engage in chromosomal interactions, but these interactions are inhibited in wild-type conditions. In mutants defective in RdDM, the frequency of chromosomal interactions at RdDM targets is increased. This includes increased frequency of interactions between Pol V methylated sites and distal genes that are repressed by RdDM. We propose a model, where RdDM prevents the formation of chromosomal interactions between genes and their distant regulatory elements.
Keyphrases
- genome wide
- dna methylation
- gene expression
- long non coding rna
- copy number
- poor prognosis
- wild type
- transcription factor
- arabidopsis thaliana
- bioinformatics analysis
- genome wide identification
- lymph node
- nucleic acid
- genome wide analysis
- binding protein
- minimally invasive
- oxidative stress
- heat shock
- long noncoding rna