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talk-ASLO-2019

COMPARATIVE ANALYSES OF DNA METHYLATION PATTERNS IN BIVALVES

Room 103 A => Fri, Mar 01, 2019 (09:45 AM - 10:00 AM)

ABSTRACT: The function of DNA methylation in species such as bivalves where the limited amount of DNA methylation is predominantly found in gene bodies is not completely understood. One emerging possible explanation is that the role of gene body DNA methylation is dependent on gene function, a potential phenomenon that has arisen from selective pressure on lineage-specific life history traits. We know that in other taxa epigenetic marks are associated with phenotypes independent of genetic variation, the environment can influence DNA methylation, and epigenetic marks can be inherited. Focusing on CpG methylation in several bivalve species the influence of environmental conditions on DNA methylation was examined. This included using a variety of approaches that examine DNA methylation in the context of different controlled and natural conditions in oysters and clams. These combined results suggest a predictable global response to stress in DNA methylation patterns that is impacted by environment, population, and ploidy-level. Together these data suggest DNA methylation is a mechanism regulating the physiological response of marine invertebrates to global ocean change.


Resources


Excerpt from Notebook Post for New Lab Members

What to read

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

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.

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