Getting into DNA Methylation

I have to share some information with several new folks, and there are likely old folks that should give this a refresh… thus I am posting it here.

What to read

A good place to start in term of biology are a few reviews including

  • Gavery, M., & Roberts, S. (2018). Genetics & Epigenetics in Life History and Reproduction: Oysters. In M. K. Skinner (Ed.), Encyclopedia of Reproduction. vol. 6, pp. 736–742. Academic Press: Elsevier. http://dx.doi.org/10.1016/B978-0-12-809633-8.20621-3 : pdf
  • Gavery MR, Roberts SB. (2017) Epigenetic considerations in aquaculture. PeerJ 5:e4147 https://doi.org/10.7717/peerj.4147
  • Mackenzie R. Gavery, Steven B. Roberts; A context dependent role for DNA methylation in bivalves, Briefings in Functional Genomics, Volume 13, Issue 3, 1 May 2014, Pages 217–222, https://doi.org/10.1093/bfgp/elt054

Some good primary papers include

  • Dimond JL, Gamblewood SK, Roberts SB. (2017) Genetic and epigenetic insight into morphospecies in a reef coral Molecular Ecology. 00:1–12. doi: 10.1111/mec.14252
  • Olson CE and Roberts SB. (2014). Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes Frontiers in Physiology. 5:224. doi: 10.3389/fphys.2014.0022
  • Gavery MR and Roberts SB. (2013) Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc PeerJ 1:e215. doi:10.7717/peerj.215

There are a few other relevant products

  • Gavery M, Delrow J, Basom R, Roberts S (2015) Influence of 17α-ethinylestradiol on DNA methylation in oysters. GitHub
  • Olson CE, Roberts SB (2015) Indication of family-specific DNA methylation patterns in developing oysters. bioRxiv (preprint). doi: https://doi.org/10.1101/012831

If you are looking for an older deep dive.

Computational Approaches

Jumping into our Onboarding repo: Computing · RobertsLab/onboarding Wiki · GitHub is a good place to start.

Some examples of how we work can be seen here 9 Ways to Make Papers a Little More Open and Reproducible – Roberts Lab

And a recent review Roberts and Gavery (2018) OPPORTUNITIES IN FUNCTIONAL GENOMICS: A PRIMER ON LAB AND COMPUTATIONAL ASPECTS . Journal of Shellfish Research, Vol. 37, No. 3, 1–8, 2018. DOI: 10.2983/035.037.0300

Good books

Gitting to Work

So now you have mastered Git, fluent in Bash, and are launching Jupyter notebooks on a regular basis. Here are some resources to get you going on analysis.

Just data

If you want to play around with some data…

Questions

Post any practical how-to questions here.

Written on August 23, 2018