Harpers

REGULATION OF GENE EXPRESSION / 383To date, this system provides the best understanding ofthe molecular events involved in gene regulation.Detailed analysis of the lambda repressor led to theimportant concept that transcription regulatory proteinshave several functional domains. For example, lambdarepressor binds to DNA with high affinity. Repressormonomers form dimers, dimers interact with eachother, and repressor interacts with RNA polymerase.The protein-DNA interface and the three proteinproteininterfaces all involve separate and distinct domainsof the repressor molecule. As will be noted below(see Figure 39–17), this is a characteristic shared bymost (perhaps all) molecules that regulate transcription.SPECIAL FEATURES ARE INVOLVEDIN REGULATION OF EUKARYOTICGENE TRANSCRIPTIONMost of the DNA in prokaryotic cells is organized intogenes, and the templates can always be transcribed. Avery different situation exists in mammalian cells, inwhich relatively little of the total DNA is organizedinto genes and their associated regulatory regions. Thefunction of the extra DNA is unknown. In addition, asdescribed in Chapter 36, the DNA in eukaryotic cells isextensively folded and packed into the protein-DNAcomplex called chromatin. Histones are an importantpart of this complex since they both form the structuresknown as nucleosomes (see Chapter 36) and also factorsignificantly into gene regulatory mechanisms as outlinedbelow.Chromatin Remodeling Is an ImportantAspect of Eukaryotic Gene ExpressionChromatin structure provides an additional level ofcontrol of gene transcription. As discussed in Chapter36, large regions of chromatin are transcriptionally inactivewhile others are either active or potentially active.With few exceptions, each cell contains the same complementof genes (antibody-producing cells are a notableexception). The development of specialized organs, tissues,and cells and their function in the intact organismdepend upon the differential expression of genes.Some of this differential expression is achieved byhaving different regions of chromatin available for transcriptionin cells from various tissues. For example, theDNA containing the β-globin gene cluster is in “active”chromatin in the reticulocyte but in “inactive” chromatinin muscle cells. All the factors involved in the determinationof active chromatin have not been elucidated.The presence of nucleosomes and of complexes ofhistones and DNA (see Chapter 36) certainly provides abarrier against the ready association of transcription factorswith specific DNA regions. The dynamics of the formationand disruption of nucleosome structure are thereforean important part of eukaryotic gene regulation.Histone acetylation and deacetylation is an importantdeterminant of gene activity. The surprisingdiscovery that histone acetylase activity is associatedwith TAFs and the coactivators involved in hormonalregulation of gene transcription (see Chapter 43) hasprovided a new concept of gene regulation. Acetylationis known to occur on lysine residues in the amino terminaltails of histone molecules. This modification reducesthe positive charge of these tails and decreases thebinding affinity of histone for the negatively chargedDNA. Accordingly, the acetylation of histone could resultin disruption of nucleosomal structure and allowreadier access of transcription factors to cognate regulatoryDNA elements. As discussed previously, thiswould enhance binding of the basal transcription machineryto the promoter. Histone deacetylation wouldhave the opposite effect. Different proteins with specificacetylase and deacetylase activities are associated withvarious components of the transcription apparatus. Thespecificity of these processes is under investigation, asare a variety of mechanisms of action. Some specific examplesare illustrated in Chapter 43.There is evidence that the methylation of deoxycytidineresidues (in the sequence 5′- m CpG-3′) in DNAmay effect gross changes in chromatin so as to precludeits active transcription, as described in Chapter 36. Forexample, in mouse liver, only the unmethylated ribosomalgenes can be expressed, and there is evidence thatmany animal viruses are not transcribed when theirDNA is methylated. Acute demethylation of deoxycytidineresidues in a specific region of the tyrosine aminotransferasegene—in response to glucocorticoid hormones—hasbeen associated with an increased rate oftranscription of the gene. However, it is not possible togeneralize that methylated DNA is transcriptionally inactive,that all inactive chromatin is methylated, or thatactive DNA is not methylated.Finally, the binding of specific transcription factorsto cognate DNA elements may result in disruption ofnucleosomal structure. Many eukaryotic genes havemultiple protein-binding DNA elements. The serialbinding of transcription factors to these elements—in acombinatorial fashion—may either directly disrupt thestructure of the nucleosome or prevent its re-formationor recruit, via protein-protein interactions, multiproteincoactivator complexes that have the ability to covalentlymodify or remodel nucleosomes. These reactionsresult in chromatin-level structural changes that in theend increase DNA accessibility to other factors and thetranscription machinery.Eukaryotic DNA that is in an “active” region ofchromatin can be transcribed. As in prokaryotic cells, a