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This slide is
illustrates two major types of QTLs that modulate variability in
transcript-relative steady state abundance.
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1. cis QTLs are defined
as QTLs that are closely linked to the gene whose transcript is the measured
trait. For example, a polymorphism in the promoter that affects binding of a
transcription factor. However, cis QTLs can be far upstream or downstream polymorphisms
in enhancers or may be in 3Õ UTR binding sites that affect message stability.
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2. trans QTLs map far
enough away from the location of the gene that gives rise to the transcript
that is being measured so that we can be fairly certain that the QTL is not
in the gene itself. The most blatant type of trans QTL would be a
polymorphism in a transcription factor. But in the majority of cases, the
trans QTLs can be far removed in a mechanistic sense from the actual events
modulating transcript abundance. That is why there are three overlapping
arrows in the figure. The way in
which an upstream polymorphism influences a downstream difference in mRNA
abundance can be indirect. Effects can:
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a. cross tissue types (a polymorphic liver enzyme may affect
CNS gene expression)
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b. cross time (the modulator is only expressed for one day
during development but has permanent effects in adults)
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c. may be contingent on environmental factors (heat shock may
trigger the expression of a polymorphic factor that affects mRNA abundance).
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