The Genom of Homo sapiens.pdf

Genetic Variation and the Control of TranscriptionC. COTSAPAS, E. CHAN, M. KIRK, M. TANAKA, AND P. LITTLESchool of Biotechnology and Biomolecular Sciences, University of New South Wales,Sydney, New South Wales 2052, AustraliaIdentifying and understanding genetic variation is akey driver of agricultural, biotechnological, and biomedicalresearch and commercialization; the major focus ofgenetic variation research has until now been on changesto protein-coding sequences because these are computationallyand experimentally accessible. In contrast, thecontribution of genetic variation to the temporal or spatialcontrol of transcription is not well understood, in part becausewe have no simple technologies to identify functionalvariants in control regions, nor do we, for the majorityof genes, have a comprehensive understanding ofthe proteins that control gene expression.Only relatively recently (Jin et al. 2001; Schadt et al.2003) has it become apparent that levels of mRNA in acell are influenced by genetic variation (for review, seeCheung and Spielman 2002). Such quantitative variationin mRNA levels has two distinct origins, which we defineas cis- or trans-acting (Fig. 1).•Cis-acting variants: The underlying sequencechange(s) is in DNA that controls expression of anearby gene, including promoter/enhancers, splicedeterminants, poly(A) addition sequences, mRNAstability, and transport signals.•Trans-acting variants: These are located in geneswhose products, protein or RNA, in the broadestsense, control mRNA levels of genes. Thus, variationin a distant gene is responsible for alteration inthe transcript levels of a target gene—hence the descriptionof “trans” variation. The most obvious candidatesfor trans-acting effectors are transcriptionfactors.Figure 1. Two types of genetic variation influencing amounts ofmRNA in a cell or tissue (shown by large filled arrows). Sites ofvariations are marked by a star: those within the gene are actingin cis, those within effector proteins of any type are in trans.Cis-acting variation: Variation in mRNA levels hasbeen studied in a genetic context by Yan et al. (2002), whodemonstrated that allelic variation in expression of 6 humangenes was cis-acting and this was “relatively commonamong normal individuals.” Sandberg et al. (2000) usedcDNA microarrays to show that 24 genes were expressedat differing levels in the brains of 129SVEv and C57BL/6mice, and there have been reports of interstrain differencesin mRNA levels of individual genes, including Gas5(Muller et al. 1998). In humans, variations near the INSand IGF2 genes contribute to alteration in mRNA levels,and these are associated with susceptibility to type 1 diabetes(Bennett et al. 1995), and variations in the promoterregion of the presenilin 1 gene are associated with an increasedrisk of early-onset Alzheimer’s disease (Theuns etal. 2000). More generally, Cargill et al. (1999) andHalushka et al. (1999) estimated the frequency of singlenucleotidepolymorphisms (SNPs) near, but not within,coding sequences—and consequently candidates for promoterpolymorphisms—as 1/354 bp, and Yamada et al.(2000) found a value of 1/562 bases. These data show thatquantitative variation is relatively common and contributesto significant differences in phenotype.Trans-acting effects on transcript levels: This class ofquantitative variation is not well studied. Hustert et al.(2001) showed that variations in the pregnane X receptor,a transcription factor (TF) for the CYP3A4 gene, influencedexpression of the target gene. Schadt et al. (2003)used a mouse backcross approach to study the extent towhich variation occurred with two inbred strains ofmouse, and showed that 33% of all genes exhibited alterationsin the level of mRNA in at least 10% of the backcrossmice analyzed; they treated mRNA levels as classicquantitative trait loci and showed that 34–71% of thoseinfluences were in cis. These limited data suggest that intrans genetic variation occurs and is of significant physiologicalconsequence.For the sake of inclusiveness, we will refer to TFs,splice components, and stability determinant proteins assimply mRNA level “effectors,” since all might contributeto quantitative variation. We suggest that geneticvariation of trans-acting control of gene expression potentiallymay have more profound effects on cells thanvariations in other proteins, simply because such effectorsinfluence multiple genes and whole pathways, suggestinga potentially important role in evolution and in thegeneration of species diversity. For example, Enard et al.(2002) have suggested that amounts of mRNA expressedwithin the cells of the human and chimpanzee are alteredmore significantly in the brain than in the liver and arguedCold Spring Harbor Symposia on Quantitative Biology, Volume LXVIII. © 2003 Cold Spring Harbor Laboratory Press 0-87969-709-1/04. 109