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*The abbreviations for eukaryotic genes and proteins are often more confusing or obscure than those used for bacteria. The complex of GCN5 (general control nonderepressible) and ADA (alteration/deficiency activation) proteins was discovered during investigation of the regulation of nitrogen metabolism genes in yeast. These proteins can be part of the larger SAGA complex (SPF, ADA2,3, GCN5, acetyltransferase) in yeasts. The equivalent of SAGA in humans is PCAF (p300/CBP-associated factor). SWI (switching) was discovered as a protein required for expression of certain genes involved in mating-type switching in yeast, and SNF (sucrose nonfermenting) as a factor for expression of the yeast gene for sucrase. Subsequent studies revealed multiple SWI and SNF proteins that acted in a complex. The SWI/SNF complex has a role in the expression of a wide range of genes and has been found in many eukaryotes, including humans. NURF is nuclear remodeling factor; CAF1, chromatin assembly factor; and NAP1, nucleosome assembly protein.

*The abbreviations for eukaryotic genes and proteins are often more confusing or obscure than those used for bacteria. The complex of GCN5 (general control nonderepressible) and ADA (alteration/deficiency activation) proteins was discovered during investigation of the regulation of nitrogen metabolism genes in yeast. These proteins can be part of the larger SAGA complex (SPF, ADA2,3, GCN5, acetyltransferase) in yeasts. The equivalent of SAGA in humans is PCAF (p300/CBP-associated factor). SWI (switching) was discovered as a protein required for expression of certain genes involved in mating-type switching in yeast, and SNF (sucrose nonfermenting) as a factor for expression of the yeast gene for sucrase. Subsequent studies revealed multiple SWI and SNF proteins that acted in a complex. The SWI/SNF complex has a role in the expression of a wide range of genes and has been found in many eukaryotes, including humans. NURF is nuclear remodeling factor; CAF1, chromatin assembly factor; and NAP1, nucleosome assembly protein.

1104 Chapter 28 Regulation of Gene Expression bind to DNA so as to preclude access of RNA polymerase (negative regulation) would often be simply redundant. Other factors are at play in the use of positive regulation, and speculation generally centers around two: the large size of eukaryotic genomes and the greater efficiency of positive regulation.

First, nonspecific DNA binding of regulatory proteins becomes a more important problem in the much larger genomes of higher eukaryotes. And the chance that a single specific binding sequence will occur randomly at an inappropriate site also increases with genome size. Specificity for transcriptional activation can be improved if each of several positive-regulatory proteins must bind specific DNA sequences and then form a complex in order to become active. The average number of regulatory sites for a gene in a multicellular organism is probably at least five. The requirement for binding of several positive-regulatory proteins to specific DNA sequences vastly reduces the probability of the random occurrence of a functional juxtaposition of all the necessary binding sites. In principle, a similar strategy could be used by multiple negative-regulatory elements, but this brings us to the second reason for the use of positive regulation: it is simply more efficient. If the 30,000 to 35,000 genes in the human genome were negatively regulated, each cell would have to synthesize, at all times, this same number of different repres-sors (or many times this number if multiple regulatory elements were used at each promoter) in concentrations sufficient to permit specific binding to each "unwanted" gene. In positive regulation, most of the genes are normally inactive (that is, RNA polymerases do not bind to the promoters) and the cell synthesizes only the activator proteins needed to promote transcription of the subset of genes required in the cell at that time. These arguments notwithstanding, there are examples of negative regulation in eukaryotes, from yeast to humans, as we shall see.

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