The "human" genome?

The topic this week in my Intro to Bioanthro course is genetics, with the subtheme being the mechanisms getting us from a genotype to “the” human phenotype (next week is variation and population genetics). Of course we talked about things like DNA, simple Mendelian inheritance (even though many traits/diseases probably aren’t really Mendelian), and even epigenetics and genomic imprinting. But I also wanted to point out the many ways that our very existence relies on life extrinsic to that encoded by our personal genomes (this was inspired by the intriguingly titled, “A symbiotic view of life: We have never been individuals,” [Gilbert et al., 2012; free pdf]).

Mitochondria are classic examples. These “powerhouses of the cell” or “cellular powerplants” (thanks, Wikipedia!) seem to have once been, at least a billion years ago, their own unicellular organisms that somehow came under the employ of early enterprising eukaryotes. These little organelles are indispensable players in cell metabolism, implicated also in ageing and certain diseases.

In addition, there’s been a lot of research lately on the human ‘microbiome‘ – the specific set of bacteria living in and on our bodies, which aren’t incorporated into our individual cells like mitochondria, but are nevertheless requisite for us to thrive. Analyses of poop, of all things (a scatological lecture is always a good one), have revealed that the bacterial composition of human digestive tracts varies between geographical regions, but also that age-related changes in the microbiome are similar between regions (Yatsunenko et al., 2012; see the review by Ed Yong). These bacteria are crucial to our ability to digest certain foods, and some variation in gut flora probably underlies some diseases (Smith et al., 2013); this is why you may have read about a rise in poop transplants lately (van Nood et al., 2013).

Finally, and I think perhaps most intriguingly, there is evidence that our own genes may be commandeered by the the RNA produced by the things we eat. Now, the regulation of gene expression is bewilderingly complex, and one important player in this are various types of non-coding RNA, including micro RNA (miRNA), piwi-interacting RNA, etc. (I grew up under the paradigm ‘a gene codes for a protein and our genomes contain all this “junk” DNA,’ so RNA-interference and the like blow my mind). Recently, Lin Zhang and colleagues (2012) have found that some miRNA produced by plants can not only survive cooking and digestion, but that these miRNAs can actually interact with, and alter the expression of, at least one human gene (involved in removing bad cholesterol in this case). WHAT?!

ResearchBlogging.orgOne of the most exciting areas of modern biology is the discovery of the various genetic and developmental mechanisms and processes that literally make us human. Of course the genetics of human uniqueness and variation are, to use a phrase I hate, ‘much more complex than previously thought’ (such a pervasive mantra in any field of research…). Not only that, but being human, arguably the most successful complex organism in recent history, is something we cannot even do on our own.

Gilbert, S., Sapp, J., & Tauber, A. (2012). A Symbiotic View of Life: We Have Never Been Individuals The Quarterly Review of Biology, 87 (4), 325-341 DOI: 10.1086/668166

Smith MI, Yatsunenko T, Manary MJ, Trehan I, Mkakosya R, Cheng J, Kau AL, Rich SS, Concannon P, Mychaleckyj JC, Liu J, Houpt E, Li JV, Holmes E, Nicholson J, Knights D, Ursell LK, Knight R, & Gordon JI (2013). Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor. Science PMID: 23363771

van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG, Speelman P, Dijkgraaf MG, & Keller JJ (2013). Duodenal infusion of donor feces for recurrent Clostridium difficile. The New England Journal of Medicine, 368 (5), 407-15 PMID: 23323867

Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, & Gordon JI (2012). Human gut microbiome viewed across age and geography. Nature, 486 (7402), 222-7 PMID: 22699611

Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X, Yin Y, Wang C, Zhang T, Zhu D, Zhang D, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen J, Wang J, Wang M, Zhang Q, Zhang J, Zen K, & Zhang CY (2012). Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Research, 22 (1), 107-26 PMID: 21931358

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