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Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression.

Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss SH - BMC Genomics (2012)

Bottom Line: We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data.We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined.In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Forest Ecosystems and Society, Oregon State University, Corvallis, 97331, USA.

ABSTRACT

Background: DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood.

Results: We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem) in the reference tree species black cottonwood (Populus trichocarpa). Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq), we mapped a total of 129,360,151 36- or 32-mer reads to the P. trichocarpa reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation") had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation.

Conclusions: We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.

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DNA methylation within and proximal to gene models. RPKM values of all genes with annotated UTRs were averaged over 100 bp tiled windows. Dashed lines delimit the transcribed region. The 5' and 3' UTRs shown represent the average size of these features in the P. trichocarpa genome. Windows were taken 2 kb upstream and downstream of the ends of 5' and 3' UTRs. Windows that overlapped adjacent gene models were excluded. If multiple splice variants of a gene model were annotated, only the first was used.
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Figure 3: DNA methylation within and proximal to gene models. RPKM values of all genes with annotated UTRs were averaged over 100 bp tiled windows. Dashed lines delimit the transcribed region. The 5' and 3' UTRs shown represent the average size of these features in the P. trichocarpa genome. Windows were taken 2 kb upstream and downstream of the ends of 5' and 3' UTRs. Windows that overlapped adjacent gene models were excluded. If multiple splice variants of a gene model were annotated, only the first was used.

Mentions: The P. trichocarpa v. 2.2 genome contains 39,756 annotated genes on chromosomal scaffolds. Of these, over all tissues, we identified 6,768 promoter-methylated genes (17.0% of all genes) and 6,207 body-methylated genes (15.6% of all genes), including genes that were methylated at both features. In order to determine patterns of 5meC relative to protein-coding genes, we used RPKM calculations to describe MeDIP-seq data distribution across promoters, 5' and 3' UTRs and coding regions (as well as introns and exons separately), and intergenic space. Gene promoters, gene bodies and intergenic regions had relatively high coverage in all tissue types from both unique reads and distributed repeats (Additional file 10). Across an idealized gene model, average RPKM values showed relatively high coverage in promoters, steadily decreasing 5' to 3', with a small peak 5' of the minimum at the transcription start site. There was higher coverage in the central portion of the transcribed region than at the 5' and 3' ends, and an increase of coverage 3' of the transcribed region (Figure 3).


Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression.

Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, Pellegrini M, Mockler TC, Freitag M, Strauss SH - BMC Genomics (2012)

DNA methylation within and proximal to gene models. RPKM values of all genes with annotated UTRs were averaged over 100 bp tiled windows. Dashed lines delimit the transcribed region. The 5' and 3' UTRs shown represent the average size of these features in the P. trichocarpa genome. Windows were taken 2 kb upstream and downstream of the ends of 5' and 3' UTRs. Windows that overlapped adjacent gene models were excluded. If multiple splice variants of a gene model were annotated, only the first was used.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3298464&req=5

Figure 3: DNA methylation within and proximal to gene models. RPKM values of all genes with annotated UTRs were averaged over 100 bp tiled windows. Dashed lines delimit the transcribed region. The 5' and 3' UTRs shown represent the average size of these features in the P. trichocarpa genome. Windows were taken 2 kb upstream and downstream of the ends of 5' and 3' UTRs. Windows that overlapped adjacent gene models were excluded. If multiple splice variants of a gene model were annotated, only the first was used.
Mentions: The P. trichocarpa v. 2.2 genome contains 39,756 annotated genes on chromosomal scaffolds. Of these, over all tissues, we identified 6,768 promoter-methylated genes (17.0% of all genes) and 6,207 body-methylated genes (15.6% of all genes), including genes that were methylated at both features. In order to determine patterns of 5meC relative to protein-coding genes, we used RPKM calculations to describe MeDIP-seq data distribution across promoters, 5' and 3' UTRs and coding regions (as well as introns and exons separately), and intergenic space. Gene promoters, gene bodies and intergenic regions had relatively high coverage in all tissue types from both unique reads and distributed repeats (Additional file 10). Across an idealized gene model, average RPKM values showed relatively high coverage in promoters, steadily decreasing 5' to 3', with a small peak 5' of the minimum at the transcription start site. There was higher coverage in the central portion of the transcribed region than at the 5' and 3' ends, and an increase of coverage 3' of the transcribed region (Figure 3).

Bottom Line: We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data.We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined.In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Forest Ecosystems and Society, Oregon State University, Corvallis, 97331, USA.

ABSTRACT

Background: DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood.

Results: We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem) in the reference tree species black cottonwood (Populus trichocarpa). Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq), we mapped a total of 129,360,151 36- or 32-mer reads to the P. trichocarpa reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation") had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation.

Conclusions: We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.

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