Control of Gene Expression Part I 2023 PDF

Control of gene expression in eukaryotes Different cell types of a multicellular organism Cells in different tissues are different in their morphology and function because they produce different types proteins. Do they have different genes? Figure 7-1 Molecular Biology of the Cell (© Garland Sci...

Control of gene expression in eukaryotes Different cell types of a multicellular organism Cells in different tissues are different in their morphology and function because they produce different types proteins. Do they have different genes? Figure 7-1 Molecular Biology of the Cell (© Garland Science 2008) Different cell types of a multicellular organism contain the same DNA v The cell types in a multicellular organism become different from one another because they synthesize and accumulate different sets of RNA and proteins. v Many processes are common to all cells, therefore cells have many common gene products v Some RNAs and proteins are abundant in the specialized cells in which they function and cannot be detected elsewhere Evidence that a differentiated cell contains all the genetic information necessary to direct the formation of a complete organism The nucleus of a skin cell from an adult frog transplanted into an enucleated egg can give rise to an entire tadpole. Therefore, Skin cell nucleus contains all the genetic information that is needed to make different cell types. Figure 7-2a Molecular Biology of the Cell (© Garland Science 2008) Steps at which eukaryotic gene expression can be controlled Post-transcriptional control Figure 7-5 Molecular Biology of the Cell Transcriptional control of gene expression Glossary for transcriptional control Promoter: Nucleotide sequence in DNA to which RNA polymerase binds to begin transcription. Positive control: Type of control of gene expression in which the active DNAbinding form of the regulatory protein turns the gene on. Negative control: type of control of gene expression in which the active DNAbinding form of the regulatory protein turns the gene off. Repressor: protein that binds to a specific region of DNA to prevent transcription of an adjacent gene. Activator: protein that binds to a specific region of DNA to increase transcription of an adjacent gene. Enhancer element: Regulatory DNA sequence to which gene regulatory proteins bind, influencing the rate of transcription of a structural gene that can be many thousands of base pairs away. TATA box: Consensus sequence in the promoter region of many eukaryotic genes that binds a general transcription factor and hence specifies the position at which transcription is initiated. Initiation of transcription of a eukaryotic gene by RNA polymerase II General transcription factors: TFIID, TFIIA, TFIIB, TFIIE, TFIIF, TFIIH Figure 6-15 Molecular Biology of the Cell The gene control region of a typical eukaryotic gene • • • • There are thousands of gene regulatory proteins in eukaryotes Each gene is regulated individually The regulation of each gene is different in detail from that of every other genes Gene regulatory protein can act even when they are bound to DNA thousands of nucleotide pairs away from the promoter region Figure 7-17 Molecular Biology of the Cell DNA-looping allows gene regulatory proteins to work from a distance • DNA looping allows gene regulatory proteins that bound at a distance from the promoter to interact with the proteins that assembled at the promoter • Many transcription regulators act through mediators Figure 7-17 Molecular Biology of the Cell Regulation of the 𝞬-globin gene GATA-2, YA, NF-E4 are activator GATA-1, BCL, TR2/TR4, CoupTF II are repressor YA, YB, and YC are DNA bending protein TBP: TATA binding protein (general transcription factor) Pol II: RNA polymerase II Regulation of transcription in eukaryotic cell ØEukaryotic RNA polymerase II, which transcribes all protein-coding genes, cannot initiate transcription on its own. It requires a set of proteins called general transcription factors, which must be assembled at the promoter before transcription can begin. ØEukaryotic gene regulatory protein can act even when they are bound to DNA thousands of nucleotide pairs away from the promoter region. ØA single promoter can be controlled by a number of regulatory sequences scattered along the DNA. ØThe rate of transcription initiation can be speeded up or slowed down in response to regulatory signals. ØThe packaging of eukaryotic DNA into chromatin provides opportunities for regulation, which is not available to bacteria. Gene regulatory proteins work in combination Ø An individual transcription factor can participate in more than one type of gene regulatory complexes Ø Function of the regulatory complexes depends on the final assembly of the individual components Ø Each eukaryotic gene is therefore regulated by a committee of proteins Figure 7-51 Molecular Biology of the Cell Combinatorial gene control creates many different cell types As a result of the combinatorial gene control, Ø A limited number of transcription factors can regulate thousands of different genes. Ø Also creates different cell types Figure 7-33 Molecular Biology of the Cell De-differentiation of the differentiated cells by gene regulatory protein Figure 7-36 Molecular Biology of the Cell Different ways by which gene regulatory proteins are activated Figure 7-32 Molecular Biology of the Cell 1) Gene regulatory proteins can be synthesized only when it is needed 2) It can be activated by ligand binding 3) It can be activated by phosphorylation 4) It can be activated by binding or removal of a second subunit 5) It can only enter into nucleus when needed Structures of different DNA binding motifs The outside of the DNA helix can be read by proteins Ø Each gene regulatory protein binds DNA with specific sequence Ø Gene regulatory proteins binds outside of the double helix Ø The edge of each base pair presents a distinctive pattern of hydrogen bond donor, hydrogen bond acceptor, and hydrophobic patches in both major and minor grooves Ø Most of the gene regulatory proteins bind at the major grooves of DNA double helix Ø Amino acid side chains in gene regulatory proteins make hydrogen bonds with bases from outside Figure 7-6, 9, 25 Molecular Biology of the Cell Helix-turn-helix motif Panel 7-1 Molecular Biology of the Cell Examples Oct 1: octamer binding protein Homeodomain protein POU domain DNA binding Zinc-finger motifs Cys-cys-his-his family of Zincfinger protein Examples SP1: specific protein 1, Arylhydrocarbon receptor Estrogen receptor DNA binding by a Zinc-finger protein Figure 7-14 and 15 Molecular Biology of the Cell (© Garland Science 2008) Homo and heterodimerization of Leucine Zipper motifs Heterodimers typically form from two proteins with distinct DNA-binding specificities. Thus heterodimerization greatly expands the repertoire of DNA-binding specificities that these proteins can display. Examples AP1: activator protein 1, c-fos, c-jun C/EBP: CAAT enhancer binding protein HSF: heat shock factor Panel 7-1 Molecular Biology of the Cell Helix-loop-helix motif Inhibitory regulation by truncated HLH protein The two monomers are held together in a four-helix bundle: each monomer contributes two alpha-helices connected by a flexible loop of protein Panel 7-1 Molecular Biology of the Cell Examples C Myc MyoD A homeodomain protein bound to its specific DNA sequence Homeodomain proteins are the special class of gene regulatory proteins that play critical part in orchestrating fly development. Each contain almost identical stretch of 60 amino acid, that defines this class of protein and is termed the homeodomain. The homeodomain is folded into three a-helices, which are packed tightly together by hydrophobic interactions. The part containing helix 2 and 3 closely resembles the helix-turn-helix motif. Panel 7-1 Molecular Biology of the Cell Examples of gene regulatory proteins containing different DNA-binding motifs DNA-binding motif Example Recognition sequence Functions ___________________________________________________________________________________________________ Helix-turn-helix Lambda cro HSF-1 AACACCGT CNNGAANNTTGNNG regulates lysogenic state of Lambda phage Activate heat-shock Protein’s gene expression Zn-finger steroid hormone receptor SNAIL and SLUG-family repressor proteins TGTTCT E2-box CCATGTG cell-specific and hormone-specific functions control metastasis by regulating tight-junction proteins Leucine Zipper AP1 transcription factor c-jun, c-fos TGAG/CTCA induced by tetradecanoate phorbol ester (TPA), interleukin-1, UV-radiation growth control, inflammation , apoptosis Helix-loop-helix Myogenic transcription factor MyoD, MRFs Myc CANNTG Muscle development CA(C/T)GTG growth control Regulation of Gene expression by HSF1 DBD: DNA binding domain, NTA: N-terminal transactivation domain, CTA: C-terminal transactivation domain Regulation of gene expression by nuclear hormone receptors DBD: DNA-binding domain LBD: ligand-binding domain Regulation of gene expression by AP1 transcription factor NF𝛋B-mediated regulation of gene expression Control of gene expression by alteration of chromatin structure Local alteration in chromatin structure directed by eukaryotic gene activator protein Ø Chromatin remodeling complex can alter chromatin structure by 1) 2) 3) Remodeling of nucleosomes Histone Removal Histone replacement Ø Histone tail modification by histone modifier enzymes also alter chromatin structure Figure 7-19 Molecular Biology of the Cell How Histone codes affect transcription initiation Successive histone modification 1) Histone acetyl transferase put acetyl group on K9 of H3 and K8 of H4 2) Histone kinase phosphorylates S10 of H3 3) Histone acetyl transferase then acetylate K14 of H3 Then TFIID and the chromatin remodeling complex binds to the specific marked area to initiate transcription Figure 7-20 Molecular Biology of the Cell Five ways in which eukaryotic gene repressor proteins can operate 1) 2) 3) 4) 5) Activator and repressor protein can compete for the same binding site on the DNA. Activator and repressor proteins binds on different regions of DNA but repressor protein inhibits the activation domain of the activator protein. Repressor protein binds to the general transcription factor and create a hindrance for activator protein to bind on the same general transcription factor. Repressor protein recruits the repressive form of the chromatin remodeling complex Repressor protein recruits histone deacetylase or histone methylase Figure 7-23 Molecular Biology of the Cell Epithelial to mesenchymal transition by SLUG repressor Regulation of BRCA2 gene expression by SLUG Globin gene expression pattern α2β2 Adult hemoglobin: α2β2 Fetal hemoglobin: α2𝛄2 Locus control region: The region that regulates expression of multiple distant genes on a certain locus Insulator: The region that acts as barrier to spread the heterochromatin to the neighboring region Figure 7-60 and 61 Molecular Biology of the Cell (© Garland Science 2008) Sickle cell disease/β-thalassemia caused by β-globin gene mutation Sickle cell anemia: Hereditary genetic disorder caused by a mutation that replaces glutamic acid at residue 6 in β-globin with valine (β6 Glu to Val). This mutation leads to the formation of the linear polymer of the deoxygenated HbS. β-thalassemia: Hereditary genetic disorder in which the body does no make as much βglobin as needed Hydroxyurea treatment increases fetal globin gene expression and reduces symptoms in sickle cell patients Problem An African American patient has displayed vasoocclusive episodes for most of his life. The incidence are more prevalent under conditions in which blood oxygen levels are low, such as during exercise or taking trips to locations at high altitude. The patient has been placed on hydroxyurea. The rationale behind this treatmentis which of the following? A) To prevent vaso-occlusive episodes through hydroxyurea induced protein degradation B) To reduce synthesis of mutated globin gene C) To induce synthesis of another type of globin gene D) To enhance the oxygen levels in the blood Chromosome-wide alterations in chromatin structure can be inherited X-chromosome inactivation Figure 7-50 Molecular Biology of the Cell Fur color variegation in cat Molecular mechanism of X-inactivation § X chromosome contains Xinactivation center (XIC) § XIC contains an unusual gene called inactive X (Xi)-specific transcripts gene (XIST) § XIST expresses a noncoding functional RNA called XIST RNA § XIST RNA expressed only when more than one X chromosome found in one cell § XIST RNA coats the chromosome that produces it § DNA methylation locks the chromosome in inactive state Changes in chromatin structure by DNA-methylation DNA methylation DNA methylase (DNMT) demethylation DNA demethylase In vertebrates this event is confined to selected cytosine nucleotides located in the sequence CG Figure 7-43 anMolecular Biology of the Cell DNA methylation pattern is inherited in progeny cells Maintenance Methylase CpG islands Ø CpG islands are genomic regions that contain a high frequency of CG dinucleotides Ø Distribution of CpG dinucleotides are uneven in the genome Ø CpG islands particularly occur at or near the transcription start site of the house-keeping genes. Cytosine in this region are rarely methylated Methylation and transcription DNA hyper methylation causes gene silencing in cancer cells CpG islands at the promoter region of the housekeeping genes are not methylated CG-rich islands are associated with about 20,000 genes in mammal. The promoter of this genes that remains active are kept unmethylated Figure 7-46 Molecular Biology of the Cell Loss of CpG islands The accidental deamination of C produce U, which can be recognized by the DNA repair enzyme. But accidental deamination of a 5-methyl C produce T, which can not be recognized by the DNA repair enzyme. During course of evolution, most of the CGs are lost this way. Unmethylated C methylated C Deamination Deamination Figure 7-47 Molecular Biology of the Cell T U Repaired Not Repaired C T (loss of CG) Loss of CpG islands during evolution Class Objectives 1) What is differential gene expression. 2) At which steps gene expression can be regulated? 3) What are transcriptional and post-transcriptional control 4) How DNA looping facilitates gene regulatory protein to act? 5) Distinguish between general and specific transcription factors. 6) What are the structural motifs found in gene regulatory protein? 7) Explain the role of promoters, enhancers, activators, and repressors 8) How gene regulatory proteins bind DNA? 9) Explain how gene regulatory proteins bind cooperatively to DNA 10) How gene repressor protein works? 11) Explain how chromatin structure affects gene expression 11) Describe the function of the locus control region 12) How gene expression regulation creates specialized cells? 13) Explain the processes called X-chromosome inactivation and gene dosage compensation 14) Describe the role of DNA-methylation on gene expression 15) How DNA-methylation pattern inherited during cell division? 16) What is called CpG island? 17) How CpG island is maintained or lost?