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Biophysics and molecular biology have revealed that chromatin consists of a repetitive nucleoprotein complex, the nucleosome. This particle consists of a histone octamer, with two copies of each of the histones (H2A, H2B, H3, and H4), wrapped by 147 base pairs of DNA. In the octamer, histones H3 and H4 are assembled in a tetramer, which is flanked by two H2A–H2B dimers. A variable length of DNA completes the second turn around the histone octamer and interacts with a fifth histone, H1. H2A, H2B, H3, and H4 are variously modified at their amino- and carboxyl-terminal tails to influence the dynamics of chromatin structure and function (Ballestar and Esteller 2002; Keshet et al. 1986; Kornberg and Lorch 1999; Strahl and Allis 2000). Although chromatin provides structure to chromosomes, it also plays a critical role in transcriptional regulation in eukaryotes because it can repress gene expression by inhibiting the ability of transcription factors to access DNA. In fact, chromatin ensures that genes are inactive until their expression is commanded. In the activation process, cells must attenuate nucleosome-mediated repression of an appropriate subset of genes by means of activator proteins that modify chromatin structure. An activator protein displaces nucleosomes, which permits a complex of proteins (general transcription factors) to bind DNA at a promoter and to recruit RNA polymerase.

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FIGURE 2–2. Transcription factors and RNA polymerase II complex.Typical transcription factors contain DNA-binding domains, protein dimerization domains, and transcription activation domains. Some transcription factors (e.g., cAMP response element–binding protein [CREB]) may be modified by phosphorylation. The transcription activation domain interacts with an RNA polymerase II (Pol II) complex to induce transcription. TATA binding protein (TBP) binds to the TATA box element and associates with general transcription factors (TFII). This gene transcription apparatus recruits Pol II to the appropriate gene.

FIGURE 2–3. Activation of cAMP response element–binding protein (CREB) via different signal transduction pathways.Signal cascades are activated by external stimuli, such as hormones or neurotransmitters and growth factors. Arrows indicate the interaction between pathways. AC = adenylyl cyclase; C = catalytic subunits of PKA; Ca++ = calcium; CaMK IV = calmodulin-dependent kinase IV; cAMP = cyclic 3'-5'-adenosine monophosphate; CBP = CREB-binding protein; Epac = exchange protein activated by cAMP; ERK = extracellular-regulated kinase; Gs = subunit of the stimulatory G protein; P = phosphorylation; PKA = cAMP–dependent protein kinase; R = regulatory subunits of PKA; Rap and Ras = small GTPases (small proteins that bind to guanosine triphosphate [GTP]); RSK2 = ribosomal S6 kinase 2.

FIGURE 2–4. Transcription and RNA splicing.The horizontal black line between exons indicates an intron. The region before the first exon is the 5' regulatory region of the gene, such as a TATA box. There also are cis-regulatory elements in introns and downstream of the last exon. The heterogeneous nuclear RNA (hnRNA), containing both exons and introns, is spliced to form mRNA. mRNAs are then exported from the nucleus to the cytoplasm, where they will direct the synthesis of distinct proteins.

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