Flatworm CpG methylation exploration

Aim:

There is no real consensus of CpG methylation presence in flatworm genomes ^1,2,3,4.

Using PacBio HiFi read kinetics I attempt to find evidence for CpG methylation in flatworms.

Repo structure:

I divided the project into two subparts.

1. Indirect evidence for mCpG presence could be the presence of CpG islands. Hence a CpG island analysis of flatworm and other genomes is found in the cpg_island/ directory.
2. Using kinetic information extracted during the sequencing and deep learning models I called CpG modifications in the S.mediterranea genome. The analyses for this sub-project can be found in the cytosine_methylation/ directory.

Some VERY SUPERFICIAL conclusions:

• CpG methylation might be present at very low levels (see: cytosine_methylation/outputs/cpg_methlyation-perc_genome-wide_histogram.pdf).

• The methylation percentage around gene bodies is low, especially in the promoter regions (see: cytosine_methylation/outputs/ssmed_5mC_profile-mean.pdf).

• As the PacBio reads originate from whole adults information is lost from different cell lineages. Might be some more interesting things present in specific cell lines. Or not.

Bibliography:

1: Geyer, Kathrin K., Iain W. Chalmers, Neil MacKintosh, Julie E. Hirst, Rory Geoghegan, Mathieu Badets, Peter M. Brophy, Klaus Brehm, and Karl F. Hoffmann. 2013. “Cytosine Methylation Is a Conserved Epigenetic Feature Found throughout the Phylum Platyhelminthes.” BMC Genomics 14(1):462. doi: 10.1186/1471-2164-14-462.

2: Geyer, Kathrin K., Carlos M. Rodríguez López, Iain W. Chalmers, Sabrina E. Munshi, Martha Truscott, James Heald, Mike J. Wilkinson, and Karl F. Hoffmann. 2011. “Cytosine Methylation Regulates Oviposition in the Pathogenic Blood Fluke Schistosoma Mansoni.” Nature Communications 2(1):424. doi: 10.1038/ncomms1433.

3: Jaber-Hijazi, Farah, Priscilla J. K. P. Lo, Yuliana Mihaylova, Jeremy M. Foster, Jack S. Benner, Belen Tejada Romero, Chen Chen, Sunir Malla, Jordi Solana, Alexey Ruzov, and A. Aziz Aboobaker. 2013. “Planarian MBD2/3 Is Required for Adult Stem Cell Pluripotency Independently of DNA Methylation.” Developmental Biology 384(1):141–53. doi: http:///10.1016/j.ydbio.2013.09.020.

4: Raddatz, Günter, Paloma M. Guzzardo, Nelly Olova, Marcelo Rosado Fantappié, Markus Rampp, Matthias Schaefer, Wolf Reik, Gregory J. Hannon, and Frank Lyko. 2013. “Dnmt2-Dependent Methylomes Lack Defined DNA Methylation Patterns.” Proceedings of the National Academy of Sciences 110(21):8627–31. doi: 10.1073/pnas.1306723110.