Mapping the genome landscape using tiling array technology

Abstract

With the availability of complete genome sequences for a growing number of organisms, high-throughput methods for gene annotation and analysis of genome dynamics are needed. The application of whole-genome tiling microarrays for studies of global gene expression is providing a more unbiased view of the transcriptional activity within genomes. For example, this approach has led to the identification and isolation of many novel non-protein-coding RNAs (ncRNAs), which have been suggested to comprise a major component of the transcriptome that have novel functions involved in epigenetic regulation of the genome. Additionally, tiling arrays have been recently applied to the study of histone modifications and methylation of cytosine bases (DNA methylation). Surprisingly, recent studies combining the analysis of gene expression (transcriptome) and DNA methylation (methylome) using whole-genome tiling arrays revealed that DNA methylation regulates the expression levels of many ncRNAs. Further capture and integration of additional types of genome-wide data sets will help to illuminate additional hidden features of the dynamic genomic landscape that are regulated by both genetic and epigenetic pathways in plants.

Figure 1. Mechanisms of genome regulation revealed by whole genome tiling array

(A) A schematic of DNA methylation and demethylation in Arabidopsis. (Top) Whole-genome tiling array revealed that the methyltransferases MET1, DRM1, DRM2, and CMT3 are responsible for the establishment and maintenance of most DNA methylation in Arabidopsis. (Bottom) DML DNA demethylases (ROS1, DML2, and DML3) primarily demethylate the very 5′ and 3′ ends of open reading frames including promoter and downstream regions. (B) Regulation of gene expression by a ncRNA located in the promoter region of an ORF. Transcription of the ncRNA. Which is located in the promoter region of an ORF blocks the binding of transcription factors and/or RNAPII necessary for proper gene expression from this locus. This has been aptly named the transcription interference model for regulation by ncRNAs. (C) Expression of intergenic noncoding RNAs regulated DNA methylation. Genome-wide gene expression studies in combination with genome-wide mapping of DNA methylation sites in Arabidopsis identified a number of ncRNAs with increased expression in the absence of DNA methylation. Thus, suggesting that the over-expression of these ncRNAs may indeed be a bi-product of the loss of DNA methylation, which when present would act to silence expression from these loci. (D) Over-lapping anti-sense gene products regulate P5CDH levels during response to salt stress in Arabidopsis. P5CDH is expressed under normal Arabidopsis growth conditions. However, salt stress conditions induce expression of SRO5, a gene of unknown function. The 3′ ends of the SRO5 and P5CDH transcripts overlap, thereby forming a region of dsRNA. This dsRNA region initiates a series of siRNA processing steps that ultimately result in the downregulation of P5CDH in response to salt stress. Thus, anti-sense transcripts can regulate neighboring genes through formation of regions of dsRNA that subsequently recruit various RNA silencing pathways. For simplicity only the dsRNA region (blue box) of the two overlapping transcripts is shown in this figure.