Concepts Summary

• Eukaryotic cells differ from bacteria in several ways that affect gene regulation, including, in eukaryotes, the absence of operons, the presence of chromatin, and the presence of a nuclear membrane.
• In eukaryotic cells, chromatin structure represses gene expression. In transcription, chromatin structure may be altered by repositioning of nucleosomes and the modification of histone proteins, including acetylation, phosphorylation, and methylation. The methylation of DNA also affects transcription.
• The initiation of eukaryotic transcription is controlled by general transcription factors that assemble into the basal transcription apparatus and by transcriptional regulator proteins that stimulate or repress normal levels of transcription by binding to regulatory promoters and enhancers.
• Enhancers affect the transcription of distant genes. Regulatory proteins bind to enhancers and interact with the basal transcription apparatus by causing the intervening DNA to loop out.
• DNA sequences called insulators limit the action of enhancers by blocking their action in a position-dependent manner.
• Some regulatory factors cause RNA polymerase to stall downstream of the promoter.
• Coordinately controlled genes in eukaryotic cells respond to the same factors because they have common response elements that are stimulated by the same transcriptional activator.
• Gene expression in eukaryotic cells can be influenced by RNA processing.
• Gene expression can be regulated by changes in RNA stability. The 5′ cap, the coding sequence, the 3′ UTR, and the poly(A) tail are important in controlling the stability of eukaryotic mRNAs. Proteins binding to the 5′ and 3′ ends of eukaryotic mRNA can affect its translation.
• RNA silencing plays an important role in eukaryotic gene regulation. Small RNA molecules (siRNAs and miRNAs) cleaved from double-stranded DNA combine with proteins and bind to sequences on mRNA or DNA. These complexes cleave RNA, inhibit translation, affect RNA degradation, and silence transcription.
• Control of the posttranslational modification of proteins may play a role in gene expression.