Lecture 9: Regulation of Gene Expression in Eukaryotes - New Mansoura University PDF

Molecular Biology I BIO316 Lecture 9 Regulation of Gene Expression in Eukaryotes Prepared by Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics ...

Molecular Biology I BIO316 Lecture 9 Regulation of Gene Expression in Eukaryotes Prepared by Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli Gene Regulation in Eukaryotes Associate Professor of Biochemistry and Molecular Genetics  Gene regulation refers to the phenomenon whereby the level of genes can be expressed at high or low rates.  The eukaryotic organisms include protists, fungi, plants, and animals.  Gene regulation is necessary to ensure the differences in structure and function among distinct cell types. Regulatory transcription factors  The term transcription factor is used to describe a category of proteins that influence the ability of RNA polymerase to transcribe a given gene.  These transcription factors regulate the binding of RNA polymerase to the core promoter.  They control the switch from the initiation to the elongation stage of transcription.  Dr. Rami Elshazli Regulatory transcription factors Associate Professor of Biochemistry and Molecular Genetics  Two types of transcription factors play a key role in this process.  The general transcription factors (GTFs) are required for the binding of RNA polymerase to the core promoter and its progression to the elongation stage.  Eukaryotic cells possess a diverse array of regulatory transcription factors that serve to regulate the rate of  Activators: transcription of target genes.  Activator proteins are regulatory transcription factors  When a regulatory transcription  Some regulatory transcription factors exert their that bind to specific sequences factor binds to a regulatory effects by influencing the ability of RNA polymerase to called enhancers to accelerate element, it affects the begin transcription of a particular gene. transcription. transcription of specific gene.  They recognize cis-acting elements that are often  Repressors:  The binding of regulatory located in the vicinity of the core promoter.  Repressor proteins are transcription factors may enhance  In eukaryotes, these DNA sequences are generally regulatory transcription factors the rate of transcription. known as regulatory elements. that bind to specific sequences called silencers and preventing transcription.   Eukaryotic Protein-Encoding Genes  For eukaryotic protein-encoding genes, three features are common among most promoters:  Regulatory elements.  TATA box.  Transcriptional start site.  The TATA box and transcriptional start site form the core promoter.  The transcriptional start site is the place in the DNA where transcription begins.  The TATA box which is a 5′–TATAAA–3′ sequence, is usually about 25 bp upstream from a transcriptional start site.  The TATA box determines the precise starting point for transcription. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Combinatorial control Factors contributed to combinatorial control  In eukaryotic species, genes are always organized  Activators may stimulate the ability of RNA polymerase to individually, not in operons. initiate transcription.  Many eukaryotes are multicellular and contain  Repressors may inhibit the ability of RNA polymerase to initiate transcription. different cell types.  The function of activators and repressors modulated by  Most eukaryotic genes are regulated by many factors. binding of small effector molecules, protein-protein  This phenomenon is called combinatorial control interactions, and covalent modifications. because the combination of many factors determines  Activators are necessary to alter chromatin structure in the the expression of any given gene. region where a gene is located.  DNA methylation usually inhibits transcription, either by  Regulation of transcription in eukaryotes has some of preventing the binding of an activator or by recruiting the characteristics seen in bacteria. proteins that inhibit transcription.  Activator and repressor proteins are involved in regulating genes by influencing the ability of RNA polymerase to initiate transcription. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics   Eukaryotic Protein-Encoding Genes  Regulatory elements are DNA segments that regulate eukaryotic genes.  Regulatory elements are recognized by regulatory transcription factors that control the ability of RNA polymerase to initiate transcription at the core promoter.  Some regulatory elements known as enhancers, play a role in the ability of RNA polymerase to begin transcription and  A common location for regulatory elements is the region that is enhancing the rate of transcription. 50–100 bp upstream from the transcriptional start site.  When enhancers are not functioning, most eukaryotic genes  However, the locations of regulatory elements vary greatly among have very low levels of transcription. different eukaryotic genes.  Other regulatory elements known as silencers, prevent  Regulatory elements exert strong effects on the ability of RNA transcription of a given gene when its expression is not needed. polymerase to initiate transcription at the core promoter.  When these sequences function, the rate of transcription is decreased. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Regulatory Transcription Factors  When the binding of a regulatory transcription factor to a regulatory element increases transcription, the regulatory element is known as an enhancer.  Up-regulation: regulatory elements that stimulate transcription 10- to 1000-fold are called activators, and their actions is called up-regulation.  Down-regulation: regulatory elements that inhibit transcription are called silencers, and their action is called down-regulation.  Regulatory elements are often located in a region within 50-100 base pairs upstream from the transcriptional start site.  They exert strong effects on the ability of RNA polymerase to initiate transcription at the core  Different mechanisms have been explained how a promoter. regulatory transcription factor can bind to a regulatory element and thereby affecting gene transcription. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli Regulatory Transcription Factors Associate Professor of Biochemistry and Molecular Genetics  Activator proteins can  Most regulatory transcription factors do not enhance the ability of TFIID bind directly to RNA polymerase. to initiate transcription.  Regulatory transcription factors commonly  Activator proteins might influence the function of RNA polymerase II by recruit TFIID to the TATA interacting with other proteins that directly box in a way that facilitates control RNA polymerase II. its ability to recruit RNA  Two protein complexes communicate with the polymerase II. effects of regulatory transcription factors are:  Transcription factor IID (TFIID).  Mediator.  TFIID is a general transcription factor that binds to the TATA box and is needed to recruit RNA polymerase II to the core promoter.  Some regulatory transcription factors bind to a regulatory element and then influence the function of TFIID.  Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics Regulatory Transcription Factors  Activator proteins exert their effects by interacting with coactivators.  Coactivators are proteins that increase the rate of transcription but do not directly bind to the DNA itself.  Repressor proteins inhibit the function of TFIID.  They exert their effects by preventing the binding of TFIID to the TATA box or  They exert their effects by inhibiting the ability of TFIID to recruit RNA polymerase II to the core promoter.  Regulatory Transcription Factors  Mediator: A second way that regulatory transcription factors control RNA polymerase II is via mediator.  The name mediator refers to that this complex mediates the interaction between RNA polymerase II and regulatory transcription factors.  Mediator controls the ability of RNA polymerase II to progress to the elongation stage of transcription.  Transcriptional activators stimulate the ability of mediator to facilitate the switch between the initiation and elongation stages, whereas repressors have the opposite effect.  A third way that regulatory transcription factors can influence transcription is by recruiting proteins that affect nucleosome positions and compositions to the promoter region.  Certain transcriptional activators recruit proteins that facilitate the conversion of chromatin to a conformation that is more accessible to RNA polymerase. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Regulatory Transcription Factors  The functions of regulatory transcription factor proteins are controlled in three common ways:  The binding of small effector molecules.  Protein-protein interactions.  Covalent modifications.  A small effector molecule may bind to a regulatory transcription factor and promote its binding to DNA.  Steroid hormones function in this manner.  Another important mechanism of modulation is via protein-protein interactions.  The formation of dimers is a common means of controlling transcription.  The function of regulatory transcription factors can be affected by covalent modifications such as the attachment of a phosphate group. Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics  Dr. Rami Elshazli Steroid Hormones Associate Professor of Biochemistry and Molecular Genetics  An example of regulatory transcription factor that responds to steroid hormones.  The ultimate action of a steroid hormone is to affect gene transcription.  Steroid hormones act as signaling molecules that are synthesized by endocrine glands and secreted into the bloodstream.  The hormones are then taken up by cells that respond to these substances.  Glucocorticoid hormones influence nutrient metabolism in most body cells.  The hormone enters the cytosol of a cell by diffusing through the plasma membrane.  Once inside, the hormone specifically binds to a glucocorticoid receptor.  After the hormone binds to the glucocorticoid receptor, HSP90  Prior to hormone binding, the glucocorticoid receptor is is released, thereby exposing a nuclear localization signal (NLS) complexed with proteins known as heat shock proteins (HSP), that directs the receptor protein into the nucleus. one example being HSP90.  Dr. Rami Elshazli Steroid Hormones Associate Professor of Biochemistry and Molecular Genetics  Two glucocorticoid receptors form a homodimer and then travel through a nuclear pore into the nucleus.  In the nucleus, the glucocorticoid receptor homodimer binds to a glucocorticoid response element (GRE) with two copies of the following consensus sequence:  where R is a purine and Y is pyrimidine.  The binding of the glucocorticoid receptor homodimer to a GRE activates the transcription of the nearby gene, eventually leading to the synthesis of the encoded protein.  Dr. Rami Elshazli Associate Professor of Biochemistry and Molecular Genetics