RNA Polymerase and Transcription: E. coli RNA polymerase consists of α, β, β′, ω, and σ subunits. Transcription is initiated by the binding of σ to promoter sequences. After synthesis of about the first ten nucleotides of RNA, the core polymerase dissociates from σ and travels along the template DNA as it elongates the RNA chain. Transcription then continues until the polymerase encounters a termination signal.
Repressors and Negative Control of Transcription: The prototype model for gene regulation in bacteria is the lac operon, which is regulated by the binding of a repressor to specific DNA sequences overlapping the promoter.
Positive Control of Transcription: Some bacterial genes are regulated by transcriptional activators rather than repressors.
Eukaryotic RNA Polymerases: Eukaryotic cells contain three distinct nuclear RNA polymerases that transcribe genes encoding mRNAs and miRNAs (polymerase II), rRNAs (polymerases I and III), and tRNAs (polymerase III).
General Transcription Factors and Initiation of Transcription by RNA Polymerase II: Eukaryotic RNA polymerases do not bind directly to promoter sequences; they require additional proteins (general transcription factors) to initiate transcription. The promoter sequences of genes transcribed by RNA polymerase II are recognized by the general transcription factor TFIID, which recruits additional transcription factors and RNA polymerase to the promoter.
Transcription by RNA Polymerases I and III: RNA polymerases I and III also require additional transcription factors to bind to the promoters of rRNA, tRNA, and some snRNA genes.
cis-Acting Regulatory Sequences: Promoters and Enhancers: Transcription of eukaryotic genes is controlled by proteins that bind to regulatory sequences, which can be located more than 50 kilobases away from the transcription start site. Enhancers typically contain binding sites for multiple proteins that work together to regulate gene expression.
Transcription Factor Binding Sites: Eukaryotic transcription factors bind to short DNA sequences, usually 6–10 base pairs, in promoters or enhancers.
Transcriptional Regulatory Proteins: Many eukaryotic transcription factors have been isolated on the basis of their binding to specific DNA sequences.
Structure and Function of Transcriptional Activators: Transcriptional activators are modular proteins, consisting of distinct DNA-binding and activation domains. DNA-binding domains mediate association with specific regulatory sequences; activation domains stimulate transcription by interacting with Mediator proteins and general transcription factors, as well as with coactivators that modify chromatin structure.
Eukaryotic Repressors: Gene expression in eukaryotic cells is regulated by repressors as well as by activators. Some repressors interfere with the binding of activators or general transcription factors to DNA. Other repressors contain discrete repression domains that inhibit transcription by interacting with Mediator proteins, general transcription factors, transcriptional activators, or corepressors that affect chromatin structure.
Regulation of Elongation: Transcription is regulated at the level of elongation as well as initiation. Many genes have molecules of polymerase II that have initiated transcription but then paused immediately downstream of the promoter. These paused polymerases are poised to resume transcription in response to appropriate extracellular signals.
Relationship of Chromatin Structure to Transcription: The packaging of DNA in nucleosomes presents an impediment to transcription in eukaryotic cells. Modification of histones by acetylation is tightly linked to transcriptional regulation and enzymes that catalyze histone acetylation are associated with transcriptional activators, whereas histone deacetylases are associated with repressors. Histones are also modified by phosphorylation and methylation, and specific modifications of histones affect gene expression by serving as binding sites for other regulatory proteins. In addition, chromatin remodeling factors facilitate the binding of transcription factors to DNA by altering the arrangement or structures of nucleosomes.
Regulation of Transcription by Noncoding RNAs: Transcription can be regulated by noncoding RNAs, as well as by regulatory proteins. siRNAs repress transcription of homologous genes by associating with a protein complex (RITS) that induces histone modifications resulting in formation of heterochromatin. X chromosome inactivation in mammals is also mediated by a noncoding RNA.
DNA Methylation: Methylation of cytosine residues can inhibit the transcription of eukaryotic genes and is important in silencing transposable elements. Regulation of gene expression by methylation also plays an important role in genomic imprinting, which controls the transcription of some genes involved in mammalian development.
Processing of Ribosomal and Transfer RNAs: Ribosomal and transfer RNAs are derived by cleavage of long primary transcripts in both prokaryotic and eukaryotic cells. Methyl groups are added to rRNAs, and various bases are modified in tRNAs.
Processing of mRNA in Eukaryotes: Eukaryotic pre-mRNAs are modified by the addition of 7-methylguanosine caps and 3′ poly-A tails, in addition to the removal of introns by splicing.
Splicing Mechanisms: Splicing of nuclear pre-mRNAs takes place in large complexes, called spliceosomes, composed of proteins and small nuclear RNAs (snRNAs). The snRNAs recognize sequences at the splice sites of pre-mRNAs and catalyze the splicing reaction. Some mitochondrial, chloroplast, and bacterial RNAs undergo self-splicing in which the splicing reaction is catalyzed by intron sequences.
Alternative Splicing: Exons can be joined in various combinations as a result of alternative splicing, which provides an important mechanism for tissue-specific control of gene expression in complex eukaryotes.
RNA Editing: Some mRNAs are modified by processing events that alter their protein-coding sequences. Editing of mitochondrial mRNAs in some protozoans involves the addition and deletion of U residues at multiple sites in the molecule. Other forms of RNA editing in plant and mammalian cells involve the modification of specific bases.
RNA Degradation: Introns are degraded within the nucleus, and abnormal mRNAs lacking complete open-reading frames are eliminated by nonsense-mediated mRNA decay. Functional mRNAs in eukaryotic cells are degraded at different rates, providing an additional mechanism for control of gene expression. In some cases, rates of mRNA degradation are regulated by extracellular signals.
