Chapter 12 Control of Gene Expression A Transcription Factors and Transcriptional Activator Proteins 1 General transcription factors and RNA polymerase assemble into a basal transcription apparatus which binds to a core promoter located immediately upstream of a gene 2 Transcriptional activator proteins are required to bring about normal levels of transcription the core promoter i These proteins bind to a regulatory promoter which is located upstream of the core promoter and to enhancers which many be located some distance from the gene 3 Transcriptional activator proteins stimulate and stabilizer the basal transcription apparatus at i May interact directly or indirectly through coactivators 4 Some regulatory proteins act as repressors that bind to sequences in the regulatory promoter or to silencers which are position and orientation independent i They may compete with activators for DNA binding sites with activator transcription is activated with repressor there is no activation ii Repressors may bind near the activator and prevent the activator from contacting the basal transcription apparatus iii Or direct interference with the assembly of basal transcription apparatus thereby blocking initiation 5 Enhancers and Insulators i Enhancers are capable of affecting transcription at distant promoters a Most are capable of stimulating any promoter in their vicinities b Insulators or boundary elements which are DNA sequences that block or insulate the effect of enhancers in a position dependent manner 1 If an insulator lies between the enhancer and the promoter it blocks the action of the enhancer If the insulator lies outside the region between the two it has no effect 6 Coordinated Gene Regulation 2 i Several eukaryotic genes may be activated by the same stimulus a Heat shock proteins help prevent damage from stressing agents and are produced by a large number of different genes b Groups of bacterial genes are often coordinately expressed turned off and on together 1 Expressed genes in eukaryotic cells are not clustered ii Response elements Genes that are coordinately expressed in eukaryotic cells are able to respond to the same stimulus because they have regulatory sequences in common in their promoters or enhancers a They typically contain short consensus sequences at varying distances from the gene being regulated which provide binding sites for transcriptional activators b During times of stress a transcriptional activator protein binds to this regulatory element and elevates transcription B Gene Regulation by RNA Processing and Degradation 1 Gene regulation through RNA splicing i Alternative splicing allows a pre mRNA to be spliced in multiple ways generating different proteins in different tissues or at different times in development a The regulation of splicing is an important means of controlling gene expression in eukaryotic cells C RNA Interference and Gene Regulation also affect mRNA stability 2 The degradation of RNA b Example of alternative mRNA splicing that regulates gene expression is the control of whether a fruit fly develops as male or female 1 Tra Tra 2 and Sxl proteins regulate alternative splicing that produces male and female phenotypes i The amount of a protein that is synthesized depends on the amount of corresponding ii The amount of available mRNA depends on both the rate of mRNA synthesis and mRNA available for translation the rate of mRNA degradation a Some mRNAs persist for only a few minutes up to months b These variations can result in large differences in the amount of protein that is synthesized c 5 cap and the poly A tail affect the stability of eukaryotic mRNA 1 Poly A binding proteins PABPs normally bind to the poly A tail and contribute to its stability enhancing effect 2 3 end of the mRNA protects the 5 cap When the 5 cap is removed and the mRNA is degraded by removal of nucleotides from the 5 end iii The degradation takes place in the P bodies that help control the expression of genes by regulating which RNA molecules are degraded and which are sequester for later release iv Sequences in the 5 untranslated region 5 UTR the coding region and the 3 UTR 1 RNA interference controls the expression of a number of eukaryotic genes i It is triggered by small RNA molecules known as microRNAs miRNA and small interfering RNAs siRNA ii Dicer an enzyme cleaves and processes double stranded RNA to produce siRNAs and miRNAs that are 21 to 25 nucelotides in length and pair with proteins to form an RNA induced silencing complex RISC iii The RNA component of the RISC then pairs with complementary base sequences of specific mRNA molecules iv Small interfering RNAs and miRNAs regulate through at least three distict mechanisms 2 RNA cleavage 3 Inhibition of translation mRNAs 4 Transcriptional silencing i Slicer activity RISCs that contain an siRNA pair with mRNA molecules and cleave the mRNA near the middle of the bound siRNA a The presence of siRNAs and miRNAs increase the rate of mRNAs being broken down and decreases the amount of protein produced i Some miRNAs regulate genes by inhibiting the translation of their complementary i Other siRNAs silence transcription by altering chromatin structure ii These siRNAs combine with proteins to forms RITS which is analogus to RISC then binds to its complementary sequence in DNA or RNA in the process of being transcribed and repress transcription by attracting enzymes that methylate the tails of histone proteins iii The addition of methyl groups to the histone causes them to bind to DNA more tightly restricting the access of proteins and enzymes necessary to carry out transcription
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