Philanthropology: Two years and a new 365 project. Day 1: Epigenetics.

So it has been two years to the day since I defended my dissertation (see pics below, appreciatively provided by Share and Enjoy). I have somehow managed to survive and the shell shocked look of a recent post Ph.D. has somewhat dimminishe since then, although my nutritional intake hasn't changed much - still consists of coffee and hefty dosages of water and my profile still isn't that great.

So in celebration (and procrastination), I thought it would be an interesting idea to start a new 365 project (one that I may actually be able to finish). Also, it will result in blog post 1000 for me. This project will look at a science article or science news item every day for a year. We are inundated with science news (some good, most bad), so I will seek to sift through it and find something of interest, at least to me but feel free to send suggestions. To start things off, I'm going to start with a post on epigenetics. This is somewhat appropos as a post on epigenetics was one of my first, and is still relevant if not even more important today.

My main argument is that from an anthropological/evolutionary perspective we need to get away from the idea of a direct impact between genotype = phenotype for complex traits. This does occur such as with sickle cell but these are rare. My interest primarily lies with complex traits. These compex traits are a mixture of the biology and the environment and there is a whole lot of biology that occurs after transcription (you know the part where DNA is made to messenger RNA). Geneticists tend to ignore the environment for the most part, but like politicians and social security, one day we will have to deal with it (more on another post in the future (how is that for foreshadowing and an inner join)). However ignoring the environment, once the mRNA passes through the nucleus boundary a whole bunch of stuff can happen and does to it. This is largely where epigenetics comes into play. Epigenetic changes can occur from DNA Methylation, microRNAs, histone modification, etc. This may result in a modified protein, which is part of a biological pathway that then turn impacts an endophenoytpe that effects the trait of interest. Anywhere along this path from gene to phenotype something can intersect and influence a complex trait making discovery of genes something of well a complexity - but that is what makes them interesting.

So it is therefore nice that PLoS in celebration of Ph.Diversary has listed a number of article over the last year that deal with epigentics in 2010. Here is a list of these articles, including two excellent primers.

Epigenetic Epidemiology of Common Complex Disease: Prospects for Prediction, Prevention, and Treatment. CL Relton, G Davey Smith (Research in Translation)

Centromeres Convert but Don’t Cross PB Talbert, S Henikoff (Primer)

Genomic Responses to Abnormal Gene Dosage: The X Chromosome Improved on a Common Strategy X Deng, CM Disteche (Primer)

Spatial Epigenetic Control of Mono- and Bistable Gene Expression JZ Kelemen, P Ratna, S Scherrer, A Becskei

Widespread Gene Conversion in Centromere Cores J Shi, SE Wolf, JM Burke, GG Presting, J Ross-Ibarra, RK Dawe

Expression in Aneuploid Drosophila S2 Cells Y Zhang, JH Malone, SK Powell, V Periwal, E Spana, DM MacAlpine, B Oliver

2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association S Maenner, M Blaud, L Fouillen, A Savoye, V Marchand, A Dubois, S Sanglier-Cianférani, A Van Dorsselaer, P Clerc, P Avner, A Visvikis, C Branlant

Poised Transcription Factories Prime Silent uPA Gene Prior to Activation C Ferrai, SQ Xie, P Luraghi, D Munari, F Ramirez, MR Branco, A Pombo, MP Crippa

Computational Analysis of Whole-Genome Differential Allelic Expression Data in Human JR Wagner, B Ge, D Pokholok, KL Gunderson, T Pastinen, M Blanchette

Altering a Histone H3K4 Methylation Pathway in Glomerular Podocytes Promotes a Chronic Disease Phenotype GR Dressler, G Lefevre , S Patel , D Kim , L Tessarollo

The IG-DMR and the MEG3-DMR at Human Chromosome 14q32.2: Hierarchical Interaction and Distinct Functional Properties as Imprinting Control Centers M Kagami, MJ O’Sullivan, AJ Green, Y Watabe, O Arisaka, N Masawa, K Matsuoka, M Fukami, K Matsubara, F Kato, AC Ferguson-Smith, T Ogata

siRNA-Mediated Methylation of Arabidopsis Telomeres J Vrbsky, S Akimcheva, JM Watson, TL Turner, L Daxinger, B Vyskot, W Aufsatz, K Riha

Initial Genomics of the Human Nucleolus A Németh, A Conesa, J Santoyo-Lopez, I Medina, D Montaner, B Péterfia, I Solovei, T Cremer, J Dopazo, G Längst

Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome JM Vaquerizas, R Suyama, J Kind, K Miura, NM Luscombe, A Akhtar

Maternal Ethanol Consumption Alters the Epigenotype and the Phenotype of Offspring in a Mouse Model N Kaminen-Ahola, A Ahola, M Maga, K-A Mallitt, P Fahey, TC Cox, E Whitelaw, S Chong

Epigenetic Analysis of KSHV Latent and Lytic Genome Z Toth, DT Maglinte, SH Lee, H-R Lee, L-Y Wong, KF Brulois, S Lee, JD Buckley, PW Laird, VE Marquez, JU Jung