Limits...
Genome-wide association between DNA methylation and alternative splicing in an invertebrate.

Flores K, Wolschin F, Corneveaux JJ, Allen AN, Huentelman MJ, Amdam GV - BMC Genomics (2012)

Bottom Line: We found that exons that are included in transcription are higher methylated than exons that are skipped during transcription.We performed a statistical analysis to reveal that the presence of DNA methylation or alternative splicing are both factors associated with a longer gene length and a greater number of exons in genes.The results from our cross-species homology analysis suggest that DNA methylation and alternative splicing are genetic mechanisms whose utilization could contribute to a longer gene length and a slower rate of gene evolution.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Life Sciences, Arizona State University, PO Box 874501, 85287, Tempe, AZ, USA. kevinflores83@gmail.com

ABSTRACT

Background: Gene bodies are the most evolutionarily conserved targets of DNA methylation in eukaryotes. However, the regulatory functions of gene body DNA methylation remain largely unknown. DNA methylation in insects appears to be primarily confined to exons. Two recent studies in Apis mellifera (honeybee) and Nasonia vitripennis (jewel wasp) analyzed transcription and DNA methylation data for one gene in each species to demonstrate that exon-specific DNA methylation may be associated with alternative splicing events. In this study we investigated the relationship between DNA methylation, alternative splicing, and cross-species gene conservation on a genome-wide scale using genome-wide transcription and DNA methylation data.

Results: We generated RNA deep sequencing data (RNA-seq) to measure genome-wide mRNA expression at the exon- and gene-level. We produced a de novo transcriptome from this RNA-seq data and computationally predicted splice variants for the honeybee genome. We found that exons that are included in transcription are higher methylated than exons that are skipped during transcription. We detected enrichment for alternative splicing among methylated genes compared to unmethylated genes using fisher's exact test. We performed a statistical analysis to reveal that the presence of DNA methylation or alternative splicing are both factors associated with a longer gene length and a greater number of exons in genes. In concordance with this observation, a conservation analysis using BLAST revealed that each of these factors is also associated with higher cross-species gene conservation.

Conclusions: This study constitutes the first genome-wide analysis exhibiting a positive relationship between exon-level DNA methylation and mRNA expression in the honeybee. Our finding that methylated genes are enriched for alternative splicing suggests that, in invertebrates, exon-level DNA methylation may play a role in the construction of splice variants by positively influencing exon inclusion during transcription. The results from our cross-species homology analysis suggest that DNA methylation and alternative splicing are genetic mechanisms whose utilization could contribute to a longer gene length and a slower rate of gene evolution.

Show MeSH

Related in: MedlinePlus

Methylated genes are enriched for alternative splicing. Genome-wide DNA methylation data was overlaid with genes and the occurrence of alternative transcripts predicted from a de novo transcriptome assembly. The proportion of methylated genes that were alternatively spliced (triangles) was significantly greater than for unmethylated genes (circles) for several minimum expression thresholds (Fisher’s exact test, P < 1e-10 for each minimum FPKM); expression is measured as the expected number of fragments per kilobase of transcript per million reads (FPKM). We tested several minimum FPKM values to show that enrichment is robust despite the possibility that transcript abundance estimation may be inaccurate at low expression (FPKM). Raw data were the same as for Figure1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3526459&req=5

Figure 2: Methylated genes are enriched for alternative splicing. Genome-wide DNA methylation data was overlaid with genes and the occurrence of alternative transcripts predicted from a de novo transcriptome assembly. The proportion of methylated genes that were alternatively spliced (triangles) was significantly greater than for unmethylated genes (circles) for several minimum expression thresholds (Fisher’s exact test, P < 1e-10 for each minimum FPKM); expression is measured as the expected number of fragments per kilobase of transcript per million reads (FPKM). We tested several minimum FPKM values to show that enrichment is robust despite the possibility that transcript abundance estimation may be inaccurate at low expression (FPKM). Raw data were the same as for Figure1.

Mentions: To test whether methylated genes are enriched for splice variants when compared to unmethylated genes we assembled a honeybee transcriptome that included alternatively spliced transcripts using a de novo gene prediction from genome-wide RNA-seq data. We found that alternative transcripts occurred significantly more often in methylated genes as compared to unmethylated genes (Fisher’s exact test, P < 1e-10, Figure2), over several different expression thresholds to ensure RNA-seq data quality. In contrast to our above results that suggest a general association between methylation and expression at the exon level, these data indicate that intragenic DNA methylation is positively related with alternative splicing at the gene level. This result corroborates on a genome-wide scale what has previously been predicted on the basis of individual genes: that honeybees display a close relationship between DNA methylation and alternative splicing. Given prior observations that DNA methylation and gene length appear to be associated in the honeybee, we decided to test whether DNA methylation, splicing, and gene length are linked.


Genome-wide association between DNA methylation and alternative splicing in an invertebrate.

Flores K, Wolschin F, Corneveaux JJ, Allen AN, Huentelman MJ, Amdam GV - BMC Genomics (2012)

Methylated genes are enriched for alternative splicing. Genome-wide DNA methylation data was overlaid with genes and the occurrence of alternative transcripts predicted from a de novo transcriptome assembly. The proportion of methylated genes that were alternatively spliced (triangles) was significantly greater than for unmethylated genes (circles) for several minimum expression thresholds (Fisher’s exact test, P < 1e-10 for each minimum FPKM); expression is measured as the expected number of fragments per kilobase of transcript per million reads (FPKM). We tested several minimum FPKM values to show that enrichment is robust despite the possibility that transcript abundance estimation may be inaccurate at low expression (FPKM). Raw data were the same as for Figure1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3526459&req=5

Figure 2: Methylated genes are enriched for alternative splicing. Genome-wide DNA methylation data was overlaid with genes and the occurrence of alternative transcripts predicted from a de novo transcriptome assembly. The proportion of methylated genes that were alternatively spliced (triangles) was significantly greater than for unmethylated genes (circles) for several minimum expression thresholds (Fisher’s exact test, P < 1e-10 for each minimum FPKM); expression is measured as the expected number of fragments per kilobase of transcript per million reads (FPKM). We tested several minimum FPKM values to show that enrichment is robust despite the possibility that transcript abundance estimation may be inaccurate at low expression (FPKM). Raw data were the same as for Figure1.
Mentions: To test whether methylated genes are enriched for splice variants when compared to unmethylated genes we assembled a honeybee transcriptome that included alternatively spliced transcripts using a de novo gene prediction from genome-wide RNA-seq data. We found that alternative transcripts occurred significantly more often in methylated genes as compared to unmethylated genes (Fisher’s exact test, P < 1e-10, Figure2), over several different expression thresholds to ensure RNA-seq data quality. In contrast to our above results that suggest a general association between methylation and expression at the exon level, these data indicate that intragenic DNA methylation is positively related with alternative splicing at the gene level. This result corroborates on a genome-wide scale what has previously been predicted on the basis of individual genes: that honeybees display a close relationship between DNA methylation and alternative splicing. Given prior observations that DNA methylation and gene length appear to be associated in the honeybee, we decided to test whether DNA methylation, splicing, and gene length are linked.

Bottom Line: We found that exons that are included in transcription are higher methylated than exons that are skipped during transcription.We performed a statistical analysis to reveal that the presence of DNA methylation or alternative splicing are both factors associated with a longer gene length and a greater number of exons in genes.The results from our cross-species homology analysis suggest that DNA methylation and alternative splicing are genetic mechanisms whose utilization could contribute to a longer gene length and a slower rate of gene evolution.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Life Sciences, Arizona State University, PO Box 874501, 85287, Tempe, AZ, USA. kevinflores83@gmail.com

ABSTRACT

Background: Gene bodies are the most evolutionarily conserved targets of DNA methylation in eukaryotes. However, the regulatory functions of gene body DNA methylation remain largely unknown. DNA methylation in insects appears to be primarily confined to exons. Two recent studies in Apis mellifera (honeybee) and Nasonia vitripennis (jewel wasp) analyzed transcription and DNA methylation data for one gene in each species to demonstrate that exon-specific DNA methylation may be associated with alternative splicing events. In this study we investigated the relationship between DNA methylation, alternative splicing, and cross-species gene conservation on a genome-wide scale using genome-wide transcription and DNA methylation data.

Results: We generated RNA deep sequencing data (RNA-seq) to measure genome-wide mRNA expression at the exon- and gene-level. We produced a de novo transcriptome from this RNA-seq data and computationally predicted splice variants for the honeybee genome. We found that exons that are included in transcription are higher methylated than exons that are skipped during transcription. We detected enrichment for alternative splicing among methylated genes compared to unmethylated genes using fisher's exact test. We performed a statistical analysis to reveal that the presence of DNA methylation or alternative splicing are both factors associated with a longer gene length and a greater number of exons in genes. In concordance with this observation, a conservation analysis using BLAST revealed that each of these factors is also associated with higher cross-species gene conservation.

Conclusions: This study constitutes the first genome-wide analysis exhibiting a positive relationship between exon-level DNA methylation and mRNA expression in the honeybee. Our finding that methylated genes are enriched for alternative splicing suggests that, in invertebrates, exon-level DNA methylation may play a role in the construction of splice variants by positively influencing exon inclusion during transcription. The results from our cross-species homology analysis suggest that DNA methylation and alternative splicing are genetic mechanisms whose utilization could contribute to a longer gene length and a slower rate of gene evolution.

Show MeSH
Related in: MedlinePlus