Regulation of Gene Expression (BMS 141) Lecture Notes Fall 2024 PDF

BMS: 141 Lecture No: 12 Title: Regulation of Gene Expression Instructor Name: Dr Lamees Dawood Medicine and Surgery Program Fall 2024 Regulation of Gene Expression: Different Control Sites 1. Control at the...

BMS: 141 Lecture No: 12 Title: Regulation of Gene Expression Instructor Name: Dr Lamees Dawood Medicine and Surgery Program Fall 2024 Regulation of Gene Expression: Different Control Sites 1. Control at the level of transcription 2. Control at the level of posttranscriptional processes of mRNA 3. Control at the level of posttranslational processes 4. Control by DNA-related mechanisms in eukaryotes  Introduction Constitutive Vs Regulated Genes Not all genes are regulated Constitutive or housekeeping genes: Genes that encode products required for basic cellular functions They are continually expressed (not regulated) Regulated genes: - They are expressed only under certain conditions - They maybe expressed in all cells or only in a subset of cells (differential or cell specific expression) - Their expression is regulated (Where?, When?, and How much?) - Their regulated expression is the basis for: cellular differentiation, morphogenesis and adaptability of organisms I- At the level of Transcription It is the synthesis of RNA under the direction of DNA (DNA-directed RNA synthesis), By a DNA-dependent RNA polymerase. Glossary: Cis-acting dna sequences Cis-acting elements: DNA sequences on the same chromosome as the gene whose transcription they regulate: 1. Promotor sequences: Upstream of the transcription start site (+1 position), serve as binding sites for basal transcription protein factors and RNA polymerase. 2. Enhancer sequences: Upstream or downstream of the transcription start site (+1 position), close or thousands base pairs away from the promoter, serve as binding sites for specific transcription factors (activators). 3. Silencer sequences: Similar to enhancer sequences but serve as binding sites for specific transcription factors (repressors).  Glossary: trans-acting transcription Factors (protein factors) Trans-acting elements: Protein factors that are encoded by different genes, synthesized in the cytosol and then translocated into the nucleus (hence the name as “trans”) to control transcription of genes. 1. General (basal) transcription factors: protein factors that recognize and bind to promotor sequences for the initiation of transcription through recruitment of RNA polymerase (i.e., both protein/DNA and protein/protein interactions). 2. Specific transcription factors: Protein factors (activators or repressors) that bind to DNA sequences. Activators bind to enhancer sequences & repressors bind to silencers DNA sequences. They regulate transcription in response to different signals, e.g., hormones. Through bending of DNA, specific TFs can also interact with the basal TFs and RNA polymerase to modulate the efficiency of initiation of transcription. Note: Co-activators: are proteins that bind to and interact with the specific TFs and control transcription. In contrast to activators, coactivators does not bind to DNA (have no DNA-binding domain), e.g., HAT. 1. General or basal TFs - Bind to consensus sequences of promoter; e.g., CTF, SP1 and TFIID - Facilitate assembly of the initiation complex and recruitment of RNA polymerase II, e.g., TFIIF - Catalyze basal or constitutive transcription 2- Specific or Regulatory TFs Function: Bind to regulatory sequences of DNA known as enhancers or silencers Modulate the efficiency of initiation of transcription Mediate the response to signals, e.g., hormones Regulate which genes are expressed at a given time 2- Specific or Regulatory TFs  Specific or Regulatory TFs Mechanism Specific TFs interact with: - DNA sequences (enhancer or silencer) by the DNA-binding domain - General TFs and RNA Polymerase at the initiation complex by protein-binding domain - Coactivator proteins (e.g., histone acetyltransferase) by transcription activation domain Specific or Regulatory TFs N.B: Bending of DNA molecule can allow the interaction between specific TFs (bound to enhancer/silencer DNA sequences at far distal region from the promoter) with basal TFs and RNAP at the promoter region  2- Regulation of transcription by epigenetic mechanisms DNA accessibility by transcription machinery A - Chromatin Remodeling by acetylation/deacetylation B - DNA methylation on cytosine of CpG dinucleotide at the promoter region Epigenetic changes: Control of gene expression by other mechanisms than regulatory DNA sequences.  A- Chromatin REMODELLING The association of DNA with histones to form nucleosomes affect the ability of the transcription machinery (RNA polymerase and transcriptional factors) to access the DNA to be transcribed as the promoter regions are wrapped up in the nucleosomes.  A- Chromatin Remodeling The interconversion between active and inactive forms of chromatin is called chromatin remodeling. Most actively transcribed genes are found in a relatively relaxed form of chromatin called euchromatin (without nucleosomes), whereas most inactive segments of DNA are found in highly condensed heterochromatin (with nucleosomes).  Chromatin remodling by Histone Acetylation/deacetylation http://thepointeedition.lww.com/FullTextService/CT%7b06b9ee1beed59419cc706ceee9ddda6cc77b987fd7479682287ccc275ac7ca3bb38b2b3d0236d7708568555d93246333%7d/DA6C30FF11.gif?geom=200x200 Acetylation of lysine residues at the amino terminus of histone proteins by acetyl transferase. Acetylation eliminates the positive charge on the lysine and thereby decreases the interaction of the histone with the negatively charged DNA, forming the relaxed euchromatin. Removal of the acetyl group by histone deacetylase reverses the process and produces the condensed heterochromatin. Euchromatin and its effect on transcription Following acetylation and nucleosomal removal: The promoter is opened (accessible by transcription machinery) and the transcription is active Chromatin remodeling  B- DNA Methylation Cytosine residues in vertebrate DNA can be modified by the addition of methyl groups at the C5 position. DNA is methylated specifically at the C's that precede G's in the DNA chain (CpG dinucleotides) in the gene promoter. Methylation at CpG dinucleotides is carried out by DNA methyltransferase and reversed by DNA demethylase. DNA Methylation  B- Regulation of transcription by DNA Methylation: Mechanisms 1- The most direct mechanism by which DNA methylation can interfere with transcription is to prevent the binding of basal transcriptional factors with promoter cytosines. 2- Recruiting histone deacetylase and formation of heterochromatin (inactive)  Transcriptionally Active chromatin Acetylated and hypomethylated Transcriptionally active chromatin is predominantly unmethylated and has high levels of acetylated histone tails.  II- Regulation of Gene Expression at mRNA Posttranscriptional Level 1. Splice-site choice and differential tissue expression 2. mRNA editing: modifications for mRNA after it is fully processed 3. Coordinate expression in euokaryotes 4. mRNA stability 1- Splice-site choice: Alternative splicing of mRNA molecules Discussed before (Revise post transcription modification) 2- The Editing of mRNA: Modifications for mRNA after it is Fully Processed, e.g., Apo B mRNA Apo B mRNA (4563 codons) is expressed in both hepatocytes and small intestinal cells. Two different-size protein are produced that are important components of chylomicrons and very low density lipoproteins (VLDLs): Apo B-100 protein of VLDLs in the liver (full length protein of 512 kDa). Apo B-48 protein of chylomicrons in the small intestine (shorter protein of 250 kDa, only 48% of apo B-100 protein). The Editing of mRNA: Modifications for mRNA after it is Fully Processed, e.g., Apo B mRNA Apo B gene, its primary mRNA transcript and the posttranscriptionally-modified apo-B mRNA are the same in both hepatocytes and intestinal cells. The editing of fully processed mRNA occurs only in the intestinal cells by the deamination of cytosine (C) into uracil (U) in the codon number 2153 so that CAA (glutamine) UAA (stop codon). A shorter apo B-48 protein product is produced Apo B-48 mRNA editing in which represents only 48% of the full length Small intestine apo B-100 protein.  3- Co-ordinated Expression in Eukaryotes: Hormonal Effects and Transcription Factors Cell-surface hormones e.g., glucagon cAMP Activation Protein kinase A Phosphorylation Activation of CREB DNA/protein Binding CREB to CRE Activation Expression of genes with CRE in their promoters Co-ordinated Expression in Eukaryotes: Hormonal Effects and Transcription Factors Intracellular hormones e.g., steroid hormones Hormone/receptor complex Activation and binding GRE Binding and activation Coactivators Activation Basal TFs & RNA polymerase Activation Expression of genes with GRE in their promoters  4- Regulation of Gene Expression at mRNA Stability Level: Example - Transferrin (iron transport protein). Carries iron and bind to cell surface receptors and internalized to transport iron to the cell. - Transferrin receptor mRNA possess multiple cis-acting iron response elements (IRES). IRES has a short stem-loop structure that can be bound by trans-acting iron regulatory protein (IRPs). - When iron conc. Is low IRP bind to IRES and stabilize transferrin receptor mRNA, leading to increase synthesis of transferrin receptors  III- Regulation of Gene Expression by DNA-related mechanisms in eukaryotes 1. DNA accessibility by transcription machinery e.g., chromatin remodeling and DNA methylation 2. DNA copy number (amount of DNA) e.g., drug resistance to methotrexate due to gene amplification 3. DNA rearrangements e.g., production of immunoglobulins by B-lymphocytes 4. DNA mobile elements (transposons) e.g., in patients with hemophilia A and Duchenne muscular dystrophy Regulation of Gene Expression by DNA Rearrangements Permanent rearrangement of DNA in B-lymphocytes during production of immunoglobulins through somatic recombination of segments within both light- and heavy-chain genes DNA arrangements allow generation of 109 -1011 different Igs from a single gene providing the diversity of antibodies 🞂 Lippincott Illustrated Review Integrated system 🞂 Lippincott Illustrated Review 6th edition 🞂 Oxford Hand book of Medical Science 2nd edition 🞂 Clinical Key Student