Transcriptional Control of Gene Expression F2024

Transcriptional Control of Gene Expression  Overview: Eukaryotic Transcription Control Inactive genes are assembled into condensed chromatin which inhibits binding of RNA polymerase and general Transcription factors required for transcription initiation  Transc...

Transcriptional Control of Gene Expression  Overview: Eukaryotic Transcription Control Inactive genes are assembled into condensed chromatin which inhibits binding of RNA polymerase and general Transcription factors required for transcription initiation  Transcriptional Control Control of transcription initiation and of elongation – the first two steps are the most important mechanism for determining whether most genes are expressed and how much of the mRNA and proteins are produced. Overview: Eukaryotic Transcription Control Protein-binding to regulatory DNA sequences are associated with genes to turn up and down transcription Activator proteins bind control elements (near initiation site and far away) to promote chromatin decondensation Repressor proteins bind different control elements, lead to chromatin condensation  Control of Transcription All cells in an organism have the same genome, but all genes are not expressed in all cells. The rate of gene expression of identical genes also differs among cells, and in the same cell at different times. Measurement of RNA produced in various tissues shows that TS of a given gene occurs only in the cell types in which it is expressed.  Control of Transcription Prokaryotes and eukaryotes differ in the levels of the control of transcription. Prokaryotes control gene expression bycontrolling transcription, because there is no mRNA processing. Eukaryotes control gene expressions at many levels, including: Control of transcription (most common) Control at the level of RNA processing Control at the level of translation Post-translational modification General structure of an OPERON  Eukaryotic RNA Polymerases RNA polymerase: responsible for RNA synthesis in transcription – initiates TS at DNA sequences corresponding to the 5’ cap of mRNA 3 types of eukaryotic RNA polymerase exist that catalyze TS of genes encoding different classes of RNAs – RNA pol I: located in nucleolus, TS genes encoding pre-rRNA (processed to 28S, 5.8S, and 18S rRNAs) – RNA pol II: transcribes all protein-coding genes (mRNA) – Also produces four of the five small nuclear RNAs (snRNA) molecules involved in RNA splicing (U1, U2, U4, U5) and micro RNAs (miRNAs) – RNA pol III: transcribes genes encoding tRNA, 5S rRNA, and an array of small stable RNAs including U6 ( involved in RNA splicing), and the RNA component of the signal recognition particle –SRP – SRP is involved in directing nascent proteins to the endoplasmic reticulum. Table 9-2 in 8th edition of text book  Comparing Subunits of E.coli and Yeast RNA Polymerase Prokaryotes only have one type of RNA polymerase Extensive similarity in RNA polymerase core subunit structures from various sources – indicates that this enzyme arose early in evolution & was largely conserved – logical for an enzyme that carries out such a basic process as making RNA from DNA  Transcriptional Control Regions Expression of protein-coding genes is regulated by multiple protein-binding DNA sequences – generically referred to as transcriptional control regions These include: 1. Promoters 2. Promotor-proximal elements control elements located near promotor & TS start sites 3. Distal enhancers sequences located far away from genes they regulate Transcription from promoter is controlled by transcription factors (DNA-binding proteins) that bind DNA control regulatory sites basal (general) transcription factors  Promoters DNA sequence specifying RNA pol binding site, initiates TS of a gene, and influences rate of TS. Consensus sequences of promoters are important In eukaryotes, three types: 1. TATA box: usually -25 to -35bp from start site, most common 2. Initiator: alternative promoter element, not well defined 3. CpG island: many constitutive genes, TS at low rates  TS Control Regions Promoter-Proximal Elements: help regulate eukaryotic genes – control regions lying b/w 100-200bp upstream of start site – sometimes cell-type specific Distant Enhancers: stimulate TS by RNA pol II in eukaryotes – regulatory control regions far from start site (> all of these influence chromatin structure – Acetylation and deacetylation of lysine residues in histone tails determine how tightly DNA is bound by the histone and affects how condensed the chromosome will be. Human histones are modified Heterochromatin vs. euchromatin  Comparison of 2 types of chromatin The DNA/protein complex of the nucleus is called chromatin Chromatin in transcriptionally inactive regions of DNA within cells exists in a condensed fiber form Chromatin in transcriptionally active regions of DNA exists in an open, extended form Extended Condensed Low [salt] Isotonic/physiological Euchromatin, active Heterochromatin, inactive interphase metaphase Loose chromatin Tight chromosomes Actively transcribed TS inactive DNase I sensitive DNase I resistant hyperacetylated hypoacetylated  Mechanisms of TS Activation & Repression TS activators and repressors exert their effects largely by binding to multisubunit co-activators or co-repressors that influence assembly of pre-initiation complexes either by: – modulating chromatin structure (indirect effect) – interacting w/ Pol II & general TS factors (direct effect) Several DNA-bound activators interacting with a single mediator complex Different mediator subunits interact w/ specific activation domains this contributes to integration of signals from several activators at a single promoter Regulation of Transcription-Factor Activity Signals & Receptors – Chemical signals often alter the rate of TS These signals bind to cellular receptors: – Receptors may be 1. cell surface receptors – hydrophilic signal molecules 2. nuclear receptors, within the cell – hydrophobic signals  Examples of hormones that bind to nuclear receptors Small lipid-soluble hormones that can diffuse thru plasma and nuclear membranes and interact directly with TS factors they control – bind to receptors located in the cytosol or nucleus – Ligand-receptor complex functions as a transcription activator  Nuclear-Receptor Superfamily TS Factors General design includes common domain structure: Unique N-term region of variable length with activation domain DNA-binding domain with repeated Zn2+ finger motifs C-term hormone binding domain contains ligand-dependent activation subdomain  Homodimeric Nuclear Receptors Located in the cytosol when ligand is absent When bound to ligand, the complex translocates to the nucleus & activates TS of target genes Example: – glucorticoid receptor Figure 7-50: Model of hormone- dependent gene activation by a homodimeric nuclear receptor  Heterodimeric Nuclear Receptors Located in the nucleus Examples: – Estrogen receptor; Vit D receptor; Retinoic acid receptor In the absence of ligand, heterodimeric receptors are bound to their cognate DNA, direct histone deacetylation & suppress TS When bound to their ligands, complex directs histone hyperacetylation with HAT (unwinds DNA), ligand- binding domains stimulate pre-initiation complex & allows TS