Review: A Draft Sequence of the Neanderthal Genome

In this article, i’m just taking forward some of the analysis from this previous post reviewing the Science paper on a draft sequence of the Neanderthal genome (Pääbo et al, 2010). Specifically i’m interested in the alleles which have the researchers suggest have been positively selected for in humans since the divergence from Neanderthal some 400,000 years ago. These alleles may perhaps tell us something about what makes humans unique. This preliminary analysis is rather superficial and simply consists of a more detailed description of the specified alleles together with speculation as appropriate. Excerpts are from Entrez Gene. This is an analysis of the alleles identified on Chromosome although I couldn’t think of an immediate direct association with psychiatric illness.

Chromosome 1

SELENBP1: ‘This gene product belongs to the selenium-binding protein family….It has been proposed that the effects of selenium in preventing …… neurologic diseases may be mediated by selenium-binding proteins’. Speculation: If these assumptions hold, then the alleles may have been selected for reducing neurological disease. From other suggested functions this allele may also have been associated with longevity.

POGZ: ‘The protein encoded by this gene appears to be a zinc finger protein’. Speculation: As this is coding for a zinc finger protein it may be influencing the expression of other genes and characterisation of these relationships is necessary before speculation.

MIR554: ‘microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs’. Speculation: More information needed – as it may be influencing the expression of one or more other genes.

RFX5: ‘A lack of MHC-II expression results in a severe immunodeficiency syndrome called MHC-II deficiency, or the Bare Lymphocyte Syndrome‘. Speculation: Does this mean that BLS would be a recent illness? (<400,000 years).

SNX27:  ‘A highly similar protein in mouse is responsible for the specific recruitment of an isoform of serotonin 5-hydroxytryptamine 4 receptor into early endosomes, suggesting the analogous role for the human protein’. This receptor is found in cells in the gut and heart. Speculation: Could a role in gut motility be a reason for positive selection?

CGN: From Entrez Gene it appears to have the following functions – Actin binding, protein binding, motor activity (‘Catalysis of movement along a polymeric molecule such as a microfilament or microtubule, coupled to the hydrolysis of a nucleoside triphosphate’). Speculation: Maybe like the genes that influence other genes, the possible functions here are so diverse it is not easy to offer a simple suggestion for the possible selective advantage. As it may bind Actin perhaps there is some modification of muscle activity in humans that may confer adaptive advantage.

TUFT1: Possible function in multiple tissues including tooth enamel. Speculation: More information required.

PI4KB: Inositol phosphate metabolism, metabolic pathways and Phosphatidylinositol signaling system. There is also some research on the modification of the PI4KB gene produce in relation to Hepatitis C infection. Speculation: Could positive selection for this allele be related to Hepatitis C in recent human evolution?

PSMB4:  ‘An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit’. Speculation: Could this allele hve been positively selected to protect against certain viral infections.

Conclusions

This is admittedly a rather superficial look at several apparently positively selected alleles from Chromosome 1. While all of the above is speculation on reading through the possible functions of the above genes I thought perhaps that mutations in immune-related genes,  transcription factors and genes coding for cellular components had potentially far-reaching effects. Maybe recent human adaptation involved producing adequate defences against viral infections and making potentially multiple and simultaneous changes to genes through transcription factors or microRNA’s.

If you have any suggestions, please leave them below.

References

A Draft Sequence of the Neandertal Genome.Richard E. Green, Johannes Krause, Adrian W. Briggs, Tomislav Maricic,  Udo Stenzel, Martin Kircher, Nick Patterson,  Heng Li, Weiwei Zhai,  Markus Hsi-Yang Fritz, Nancy F. Hansen, Eric Y. Durand, Anna-Sapfo Malaspinas, Jeffrey D. Jensen, Tomas Marques-Bonet, Can Alkan, Kay Prüfer, Matthias Meyer, Hernán A. Burbano, Jeffrey M. Good, Rigo Schultz, Ayinuer Aximu-Petri,  Anne Butthof, Barbara Höber, Barbara Höffner,  Madlen Siegemund, Antje Weihmann, Chad Nusbaum,  Eric S. Lander, Carsten Russ, Nathaniel Novod,  Jason Affourtit, Michael Egholm, Christine Verna, Pavao Rudan, Dejana Brajkovic,  Zeljko Kucan, Ivan Gusic,  Vladimir B. Doronichev, Liubov V. Golovanova,  Carles Lalueza-Fox, Marco de la Rasilla, Javier Fortea,  Antonio Rosas, Ralf W. Schmitz,  Philip L. F. Johnson, Evan E. Eichler, Daniel Falush, Ewan Birney, James C. Mullikin, Montgomery Slatkin, Rasmus Nielsen, Janet Kelso, Michael Lachmann, David Reich,Svante Pääbo. Science 7 May 2010:Vol. 328. no. 5979, pp. 710 – 722.

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2 thoughts on “Review: A Draft Sequence of the Neanderthal Genome

  1. Pingback: Did the Neanderthals Teach Our Human Ancestors the Art of Cave Painting? « The Amazing World of Psychiatry: A Psychiatry Blog

  2. Pingback: New Video on Neanderthal-Human Comparison Including Neanderthal Documentary « The Amazing World of Psychiatry: A Psychiatry Blog

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