Differences of gene expression between human populations

Razib found this really fascinating paper which compares differences in gene expression between populations. The results of the study has been published in an open access paper in the American Journal of Human Genetics. The paper is titled, “Evaluation of Genetic Variation Contributing to Differences in Gene Expression between Populations,” and comes from researchers in the University of Chicago and the gene expression company, Affymetrix.

The authors sampled blood from 180 individuals (actually samples were collected from closely related three individuals from 60 different families) and created cell lines from lymphoblastoid cells. The families were either white people from Utah or Yorubans from Nigeria. The cells were lysed and the transcripts were hybridized to microarray chips, which show the expression pattern for lots of genes at once.

How do microarrays work? MicroarrayWell, each chip has microscopic spots loaded with single stranded fragments of one gene. There’s so many spots on each chip that almost all the known genes from the organism of the interest are there. Transcripts, genes that are transcribed and expressed, are single stranded and when they are isolated from cells and washed over microarrays with the little fragments they hybridize or latch onto their complement. The fragments act like anchors since they are bound to the chip. Every time a hybridization event occurs, a florescence reaction also occurs and is picked up by a computerized eye. The amount of transcripts that hybridize can tell us the relative expression level of the gene. The image to your right is an actual scan of a microarray that I’ve put up just so you can see what it looks like. Microarrays aren’t always the best way to compare gene expression differences between populations because SNPs and other allelic differences between genes could affect the hybridization and ultimately the quantification — but there’s really no other high throughput method out there that’s better than this.

Since they were dealing with somewhat differentiated immune system stem cells, the authors limited their results of differences in gene expression they observed. So, it’s not too surprising that they saw big differences between the populations among genes involved in producing antibodies to potential microbial invaders. The unexpected differences were,

“significant differences in expression levels among genes involved in fundamental cellular processes such as ribosomal biogenesis, transfer RNA processing, and Notch-signaling–part of a complex system of communication that governs basic cellular activities and coordinates cell actions.”

Last year we saw the first population comparison of gene expression in the American Journal of Human Genetics paper, “Gene-Expression Variation Within and Among Human Populations,” which found a 17% difference in gene expression between European and African populations. I appreciate this sort of research because our phenotypic differences are not just due to the little differences we harbor in the actual sequence of our DNA but also into the patterns in which genes are expressed or regulated. I’ve said this time and time again, and am happy to see people are continuing to investigate the differences in gene expression between human populations.

    STOREY, J. (2007). Gene-Expression Variation Within and Among Human Populations. The American Journal of Human Genetics, 80(3), 502-509. DOI: 10.1086/512017

3 thoughts on “Differences of gene expression between human populations

  1. The Storey et al. paper was the second paper comparing gene expression in human populations – the first (that I’m aware of!) was in Nature Genetics at the beginning of last year:

    Spielman RS, Bastone LA, Burdick JT, Morley M, Ewens WJ, Cheung VG (2007). Common genetic variants account for differences in gene expression among ethnic groups. Nat Genet 39: 226–231.

    I had even had a commentary published on this (hey, why can’t I indulge in shameless self-promotion?). It looks like they might have used some of the same data (or at least the same individuals from Utah).

  2. Wow, thanks for the comment Dr. O’Hara. I gonna try and download the Spielman et al. paper as well as yours. All I knew of was the Storey et al., which didn’t refer to the Spielman et al. paper nor yours. I love this sorta research, I know people have compared expression patterns between humans and chimpanzees but I’m only beginning to get into some of the expression differences between human populations. Anyways, thanks for the comment, again!


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