Finding Epigenomic Sequencing Strategies

Question

[Lhl]

Hi,

I'm trying to figure out the way(s) to study epigenomic patterns of gene-rich regions of a plant species. The fact (problem) is that this plant species has no reference genome, but it does have published transcriptomes. I am wondering if anyone knows how to capture the gene-rich regions with differential methylation patterns. It would also be nice to know any companies or institutes offer this kind of service.

Regards,

Elzed

[Davy]

If you want to target gene rich regions you need to know what genes go where. I don't think transcriptomes can help you here because they won't necessarily tell you which genes are lying close together in the genome, which you need to know for designing your capture sets. If however you were to do whole genome sequencing, (a daunting task, I know) then you could build a reference using one of the de novo assembler programs that are out there. Since BS-seq requires you to compare bisulfite treated samples and untreated samples, you could conceivably do this one go. Someone else may know more or correct me on this.

[Lhl]

hmm, make sense. Thanks for your comments. I will try to survey more methodologies.

[Leonor Palmeira]

You could add this as an answer, so that Lhl could tick it to validate it :-)

[brentp]

where are you at in this process? Do you already have BS-Seq data? Are you trying to decide on the measurement technique to use, or on the analysis.

[Lhl]

Hi Brentp, Many thanks for your response. I haven't really started. I am still not sure which technology should i choose. My first concern is on how to target gene rich regions. This seems needs sort of probe designing and hybridising technology or subsampling the genome with specific enzyme. Then, after subsampling the genome, i need to decide technology to tell differential DNA-methylation patterns among populations ( I think this is the measurement technique you mentioned, i haven't reached that stage).

Regards,

Answer 1

[Davy]

If you want to target gene rich regions you need to know what genes go where. I don't think transcriptomes can help you here because they won't necessarily tell you which genes are lying close together in the genome, which you need to know for designing your capture sets. If however you were to do whole genome sequencing, (a daunting task, I know) then you could build a reference using one of the de novo assembler programs that are out there. Since BS-seq requires you to compare bisulfite treated samples and untreated samples, you could conceivably do this one go. Someone else may know more or correct me on this.

[Davy]

above comment added as answer as suggested by Leonor Palmeira