Chapter Introduction

The Control of Gene Expression in Eukaryotes

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Complex biological processes often require coordinated control of the expression of many genes. The maturation of a tadpole into a frog is largely controlled by thyroid hormone. This hormone regulates gene expression by binding to a protein, the thyroid-hormone receptor, as shown at the right. In response to the hormone’s binding, this protein binds to specific DNA sites in the genome and modulates the expression of nearby genes.

OUTLINE

  1. Eukaryotic DNA Is Organized into Chromatin

  2. Transcription Factors Bind DNA and Regulate Transcription Initiation

  3. The Control of Gene Expression Can Require Chromatin Remodeling

  4. Eukaryotic Gene Expression Can Be Controlled at Posttranscriptional Levels

Many of the most important and intriguing features in modern biology and medicine, such as the pathways crucial for the development of multicellular organisms, the changes that distinguish normal cells and cancer cells, and the evolutionary changes leading to new species, entail networks of gene-regulatory pathways. Gene regulation in eukaryotes is significantly more complex than in prokaryotes in several ways. First, the genomes being regulated are significantly larger. The E. coli genome consists of a single, circular chromosome containing 4.6 megabases (Mb). This genome encodes approximately 2000 proteins. In comparison, one of the simplest eukaryotes, Saccharomyces cerevisiae (baker’s yeast), contains 16 chromosomes ranging in size from 0.2 to 2.2 Mb (Figure 32.1). The yeast genome totals 12 Mb and encodes approximately 6000 proteins. The genome within a human cell contains 23 pairs of chromosomes ranging in size from 50 to 250 Mb. Approximately 21,000 genes are present within the 3000 Mb of human DNA.

Megabase

A length of DNA consisting of 106 base pairs (if double stranded) or 106 bases (if single stranded).

1 Mb = 103 kb = 106 bases

Figure 32.1: Yeast chromosomes. Pulsed-field electrophoresis allows the separation of 16 yeast chromosomes.

Second, whereas prokaryotic genomic DNA is relatively accessible, eukaryotic DNA is packaged into chromatin, a complex between the DNA and a special set of proteins (Figure 32.2). Although the principles for the construction of chromatin are relatively simple, the chromatin structure for a complete genome is quite complex. Importantly, in a given eukaryotic cell, some genes and their associated regulatory regions are relatively accessible for transcription and regulation, whereas other genes are tightly packaged and are thus rendered inactive. Eukaryotic gene regulation frequently requires the manipulation of chromatin structure.

Figure 32.2: Chromatin structure. An electron micrograph of chromatin showing its “beads on a string” character. The beads correspond to DNA complexes with specific proteins.

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A manifestation of this complexity is the presence of many different cell types in most eukaryotes. A liver cell, a pancreatic cell, and an embryonic stem cell contain the same DNA sequences, yet the subset of genes highly expressed in cells from the pancreas, which secretes digestive enzymes, differs markedly from the subset highly expressed in the liver, the site of lipid transport and energy transduction. Embryonic stem cells do not express any subset of genes at high levels; the most highly expressed genes are “housekeeping” genes involved in the cytoskeleton and processes such as translation (Table 32.1). The existence of stable cell types is due to differences in the epigenome, differences in chromatin structure, and covalent modifications of the DNA, not in the DNA sequence itself. Thus, different cell types share the same genome (DNA sequence) but differ in their epigenomes, the packaging and modification of this genome.

Rank

Proteins expressed in pancreas

%

Proteins expressed in liver

%

Proteins expressed in stem cells

%

1

Procarboxypeptidase A1

7.6

Albumin

3.5

Glyceraldehyde-3-phosphate dehydrogenase

0.7

2

Pancreatic trypsinogen 2

5.5

Apolipoprotein A-I

2.8

Translation elongation factor 1 α1

0.6

3

Chymotrypsinogen

4.4

Apolipoprotein C-I

2.5

Tubulin α

0.5

4

Pancreatic trypsin 1

3.7

Apolipoprotein C-III

2.1

Translationally controlled tumor protein

0.5

5

Elastase IIIB

2.4

ATPase 6/8

1.5

Cyclophilin A

0.4

6

Protease E

1.9

Cytochrome oxidase 3

1.1

Cofilin

0.4

7

Pancreatic lipase

1.9

Cytochrome oxidase 2

1.1

Nucleophosmin

0.3

8

Procarboxypeptidase B

1.7

α1-Antitrypsin

1.0

Connexin 43

0.3

9

Pancreatic amylase

1.7

Cytochrome oxidase 1

0.9

Phosphoglycerate mutase

0.2

10  

Bile-salt-stimulated lipase

1.4

Apolipoprotein E

0.9

Translation elongation factor 1 β2

0.2

Sources: Data for pancreas from V. E. Velculescu, L. Zhang, B. Vogelstein, and K. W. Kinzler, Science 270:484–487, 1995. Data for liver from T. Yamashita, S. Hashimoto, S. Kaneko, S. Nagai, N. Toyoda, T. Suzuki, K. Kobayashi, and K. Matsushima, Biochem. Biophys. Res. Commun. 269:110–116, 2000. Data for stem cells from M. Richards, S. P. Tan, J. H. Tan, W. K. Chan, and A. Bongso, Stem Cells 22:51–64, 2004.
Table 32.1: Highly expressed protein-encoding genes of the pancreas, liver, and embryonic stem cells (as percentage of total mRNA pool)

In addition, eukaryotic genes are not generally organized into operons. Instead, genes that encode proteins for steps within a given pathway are often spread widely across the genome. This characteristic requires that other mechanisms function to regulate genes in a coordinated way.

Despite these differences, some aspects of gene regulation in eukaryotes are quite similar to those in prokaryotes. In particular, activator and repressor proteins that recognize specific DNA sequences are central to many gene-regulatory processes. In this chapter, we will focus first on chromatin structure. We will then turn to transcription factors—DNA-binding proteins similar in many ways to the prokaryotic proteins that we encountered in the preceding chapter. Eukaryotic transcription factors can act directly by interacting with the transcriptional machinery or indirectly by influencing chromatin structure. Finally, we examine selected posttranscriptional gene-regulatory mechanisms, including those based on microRNAs, an important class of gene-regulatory molecules discovered in recent years.

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