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.
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.
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
- Bioinformatics Data Skills: Reproducible and Robust Research with Open Source Tools: Vince Buffalo: 9781449367374: Amazon.com: Books
- R for Data Science
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.
- From when Jupyter was still IPython GitHub - che625/olson-ms-nb
- A set of notebooks from on coral epigenetics. GitHub - jldimond/Coral-CpG: Repository associated with article “Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change”
- Some recent work in R : gavery-testdrive-Rproject/DMR-2-GeneIDs.Rmd at master · sr320/gavery-testdrive-Rproject · GitHub
- and my notebooks GitHub - sr320/nb-2018
If you want to play around with some data…
- Geoduck Genome : Genomic Resources · RobertsLab/resources Wiki · GitHub
- Lots of RRBS data (prefix
EPI: Index of /nightingales/P_generosa ;sample description · hputnam/project_juvenile_geoduck_OA · GitHub - manuscript draft .
- Eastern Oyster Genome: Genomic Resources · RobertsLab/resources Wiki · GitHub
- Simple Oyster BS Comparison Data
http://owl.fish.washington.edu/halfshell/bu-serine-wd/18-04-10/oil/20150414_trimmed_2112_lane1_HB2_Oil_25000ppm_ATCACG.fastq.gzhttp://owl.fish.washington.edu/halfshell/bu-serine-wd/18-04-10/oil/20150414_trimmed_2112_lane1_HB16_Oil_25000ppm_TTAGGC.fastq.gzhttp://owl.fish.washington.edu/halfshell/bu-serine-wd/18-04-10/oil/20150414_trimmed_2112_lane1_HB30_Oil_25000ppm_TGACCA.fastq.gzhttp://owl.fish.washington.edu/halfshell/bu-serine-wd/18-04-10/oil/20150414_trimmed_2112_lane1_NB3_NoOil_ACAGTG.fastq.gzhttp://owl.fish.washington.edu/halfshell/bu-serine-wd/18-04-10/oil/20150414_trimmed_2112_lane1_NB6_NoOil_GCCAAT.fastq.gzhttp://owl.fish.washington.edu/halfshell/bu-serine-wd/18-04-10/oil/20150414_trimmed_2112_lane1_NB11_NoOil_CAGATC.fastq.gz
Post any practical how-to questions here.