Nucleic Acids - MED 2024-25-L10 -BA PDF

 LECTURE 10 Regulation of gene expression 2nd Year Medicine 2024-2025 By the end of this lecture you will be able to: 1. Describe regulation of eukaryotic gene Expression 2. Differentiate between the different levels of regulation 3. Identify basal expression ele...

 LECTURE 10 Regulation of gene expression 2nd Year Medicine 2024-2025 By the end of this lecture you will be able to: 1. Describe regulation of eukaryotic gene Expression 2. Differentiate between the different levels of regulation 3. Identify basal expression elements ,regulatory elements and describe their role in gene expression 4. Recall concept and examples of specific transcription factors  What is meant by gene expression regulation Different levels of regulation Chromatin remodeling and role of acetylation Basal expression elements and regulatory elements Characteristic features of regulatory elements Transcription factors (general vs specific) and their structure Example of Post transcriptional regulation Gene Expression Post-translation modification & Regulation of gene expression All cells have the same DNA; why are they different ? Switch on and off controlling mechanism  Functional Gene product expression (RNA + Protein ) Regulation determines: When, how much, how long, where a product is formed in tissue.  Types of Definition Type of Genes Example Expression Genes for enzymes Constitutive Housekeeping genes Genes are always ON involved in glycolysis (unregulated) (regulatory genes) (e.g., GAPDH) HSP70 (Heat Shock Inducible Genes are only turned Structural genes Proteins induced by (regulated) ON as needed stress) Ferritin (repressed Repressible Genes are only turned Structural genes when iron levels are (regulated) Off as needed low)  Feature Constitutive Expression Inducible Expression Constitutive expression refers to Inducible expression refers Definition the gene expression of to the gene expression of constitutive genes inducible genes Genes Involved Constitutive genes Inducible genes Occurs under certain Expression Occurs at a constant rate conditions when there is a need Genes involved in metabolism, Genes involving the Processes glycolysis, transcription, catabolism of certain translation, etc. substrates Regulation of Constitutive gene expression is Inducible gene expression is Expression not regulated regulated Need for Products Required all the time for the cell Required at certain times Genes involved in glycolysis, citric Examples acid cycle, electron transport Ferritin chain, etc.  Amount of the DNA Gene Modification Access to the DNA Arrangement of the DNA Regulatory Element Transcription Cis-acting regions and trans acting elements Transcription factors Alternative splicing mRNA stability(e.g. miRNA) Post-transcription Alternative Polyadenylation Control of translation by initiation factors, Translation translational repressors, including microRNAs Chemical modification (glycosylation, phosphorylation) Post translation Ubiquination targets proteins for destruction by proteasome Which one is the most important?  Regulation of variations in DNA  Alteration of gene content Amount of DNA /Arrangement 1-Gene amplification: Increasing the number of genes encoding for this product (e.g, in Cancer) Repeated rounds of DNA replication yield multiple copies of a particular chromosomal region.  Alteration of gene content Amount of DNA /Arrangement 2-Gene diminution: Removal of gene( eg eg RBCs & Cancer).  Alteration of gene content Amount of DNA /Arrangement 3-Gene Recombination Immunoglobulin production  Access to DNA Chromatin remodelling  Acetylation of lysine residues on histones  Neutralizes the positive charge of lysine  Less binding between histones and DNA  More access to transcription factors >>>> more transcription Deacetylation reverses the process HAT =Histone acetyl transferase. HDAC=Histone deacetylase  Access to DNA Chromatin remodeling Basal regulatory elements can be methylated  Feature Acetylation Deacetylation Methylation Molecular Addition of an acetyl group Removal of an acetyl group Addition of a methyl group Process Histones (primarily lysine DNA (cytosine bases CpG) or Target Histones (lysine residues) residues) histones (lysine residues) DNA methyltransferases Histone acetyltransferases Histone deacetylases (DNMTs), Main Enzymes (HATs) (HDACs) histone methyltransferases (HMTs) Causes chromatin Mainly leads to chromatin Effect on Causes chromatin relaxation condensation condensation but can cause it Chromatin (euchromatin) (heterochromatin) to relax (site dependent) Generally activates gene Represses gene expression Effect on Gene expression by making DNA Represses gene expression ( Long term) Expression more accessible Gene silencing X-inactivation, genomic Regulation of gene Cellular differentiation, DNA imprinting, tumor Biological Role expression, cell cycle control, repair, apoptosis suppression, epigenetic and DNA repair inheritance Transcription Regulation The main method for regulation  Gene Coding regions Regulatory regions Proximal regulatory Core promoters Distal regulatory elements elements Upstream promoter TATA box Specific DNA sequence elements (UPE): CAAT and GC same strand near (proximal to core distal to the core promoter promoter Distal Proximal  Upstream elements UPE: Activator NF-1 TFIID Enhancers CAAT TATAA Gene Distal Proximal Core Core promoters bind with Transcription factors, e.g., TFIID, to regulate expression. Proximal and Distal elements can bind to other proteins, they are also called transcription factors but have various names Upstream elements UPE: CCAAT box (around –75) that binds a transcription factor Nuclear factor I (NF-1) GC-rich sequence that binds a general transcription factor specificity protein 1 (SP-1)  Regulatory elements - They act as specific CIS element sequences… Remember they are DNA sequence - Some are known as enhancers some are known as silencers, while others have other regulatory functions - Specific proteins can bind to these regulatory sequence and regulate gene expression - These proteins can be inducers (or activators) or repressors and are usually made by other genes that might be even found on the different strand , thus these proteins are named Trans- elements or Trans-factors  DNA 2 Protein or mRNA DNA 1  DNA regulatory elements CIS element a-Enhancers: DNA Sequences that interact with gene regulatory proteins or trans-factors and increase the expression rate. b-Silencers: DNA Sequence that interact with gene regulatory proteins or trans-factors and decrease the rate of expression. c-Other regulatory elements: They mediate response to various signals, including hormones (termed hormone response elements or HRE), chemicals, and metals.  Feature Cis-acting Elements Trans-acting Elements Proteins or RNAs that regulate genes DNA sequences that regulate nearby Definition from a different location in the genes (same chromosome) genome Encoded by genes elsewhere in the Located on the same DNA molecule Location genome (can be on different as the gene they regulate chromosomes) Serve as binding sites for regulatory Bind to cis-acting elements to Function proteins (trans-acting factors) regulate transcription Promoters, enhancers, silencers, Transcription factors, activators, Examples HRE repressors, non-coding RNAs Act at a distance by diffusing through Act locally, affecting the Mode of Action the nucleus to interact with target transcription of adjacent genes genes  Enhancer and silencer characteristics They may be upstream, downstream, or within an intron of the gene they control They can act in a tissue-specific manner (if the protein they interact with is in a specific tissue). It can come close to the basal promoter region by DNA bending.  Regulatory Promoter gene DNA lacI Repressor No RNA made 3′ mRNA RNA 5′ polymerase Active Protein repressor DNA lacI repressor RNA polymerase 3′ mRNA mRNA 5′ 5′ Protein Protein Inactive repressor (inducer)  DNA regulatory factors Several proteins have been identified as DNA regulatory factors (Transcription factors like hormones e.g estrogen receptors ) Match the binding with the effect Match the binding with the effect  Transcription factors (TF) Activator proteins that bind to response elements Contain at-least two domains (DNA binding domain, activating domain) DNA binding domain Activating domain Binds to the promoter or response Elements contain specific motifs -Zinc fingers - Allows the TF to bind to: -Leucine zippers - Other TF or regulators -Helix-loop-Helix - RNA polymerase -Helix-turn-Helix - Chromatin remodeling proteins  Zinc finger motif Helix-turn-Helix Leucine zipper motif Helix-Loop-helix motif  Transcription factors 1-General : In Eukaryotes, General TF Must bind to the promoter to allow the binding of RNAP II to start transcription (TFDIID) Other examples include SP-1 and NF-1, which modulate basal transcription of many genes. 2-Specific: Specific transcription factors bind to enhancer regions or, in a few cases, to silencers, regulating the rate of transcription initiation. They can be cell-specific Hormones can also regulate the activity of some specific TF, e.g steroid receptors. Transcription Factor Response Element (DNA-Binding Function Protein Class (Binding Site) Protein) Steroid receptors HRE Steroid response Zinc finger cAMP response element binding CRE Response to cAMP Leucine zipper (CREB) protein Regulate multiple Peroxisome aspects of lipid proliferator- metabolism; activated receptors PPREs Zinc finger Activated by (PPARs) fibrates and thiazolidinediones  Post-transcriptional regulation I. Splicing II. mRNA half-life: it is determined by poly-A tail length III. miRNA can target mRNA and prevent translation  Post-transcriptional regulation Splicing For example, In the thyroid gland, the calcitonin gene produces a transcript that codes for the hormone calcitonin, The same gene is expressed in neurons and produces a transcript that codes for calcitonin-related peptides involved in taste.  Calcitonin gene-related peptide 37 amino acids 32 amino acids vasodilator Reduces bone resorption  What do you think would increase/decrease the transcription of the telomerase gene in cancer cells CH3 CH3 case 1 TATAAGCGCGC GENE Histone deactylase of the the gene case 2 case 3 Lippincott’s Illustrated Reviews biochemistry, Seventh Edition, 2017. UNIT VI: Storage and Expression of Genetic Information.