Gene Regulation In Eukaryotes - Biol 3250 Chapter 15 PDF

Chapter 15 Gene Regulation In Eukaryotes I: Transcriptional And Translation Regulation © McGraw Hill Courtesy of Song Tan, Penn State University. 1  Introduction Gene regulation is necessary to ensure: 1. Expression of genes in an accurate pattern dur...

Chapter 15 Gene Regulation In Eukaryotes I: Transcriptional And Translation Regulation © McGraw Hill Courtesy of Song Tan, Penn State University. 1  Introduction Gene regulation is necessary to ensure: 1. Expression of genes in an accurate pattern during the various developmental stages of the life cycle Some genes are only expressed during embryonic stages, whereas others are only expressed in the adult 2. Differences among distinct cell types Nerve and muscle cells look so different because of gene regulation rather than differences in DNA content © McGraw Hill 2  Figure 15.1 Regulation Of Gene Expression © McGraw Hill 3  15.1 Regulatory Transcription Factors Transcription factors proteins that influence the ability of RNA polymerase to transcribe a given gene There are two main types: 1.) General transcription factors Required for the binding of the RNA pol to the core promoter and its progression to the elongation stage Necessary for basal transcription 2.) Regulatory transcription factors Serve to regulate the rate of transcription of target genes They influence the ability of RNA pol to begin transcription of a particular gene © McGraw Hill 4  Enhancers and Silencers The binding of a transcription factor to an enhancer increases the rate of transcription This up-regulation can be 10- to 1,000-fold The binding of a transcription factor to a silencer decreases the rate of transcription This is called down-regulation © McGraw Hill 5 Figure 15.2 © McGraw Hill 6  Combinatorial Control Most eukaryotic genes are regulated by many factors Common factors contributing to combinatorial control are: One or more activator proteins may stimulate transcription One or more repressor proteins may inhibit transcription Activators and repressors may also be modulated © McGraw Hill 7  Modulation of Regulatory Transcription Factor Functions Three common ways the function of regulatory transcription factors can be modulated: 1. Binding of a small effector molecule 2. Protein-protein interactions 3. Covalent modification © McGraw Hill 8  Figure 15.6 a (a) Binding of a small effector molecule such as hormone © McGraw Hill 9  Figure 15.6 b © McGraw Hill 10  Figure 15.6c (c) Covalent modification such as phosphorylation © McGraw Hill 11  Steroid Hormones and Regulatory Transcription Factors Cells respond to steroid hormones in different ways Glucocorticoids These influence nutrient metabolism in most cells Gonadocorticoids These include estrogen and testosterone They influence the growth and function of the gonads GRE (Glucocorticoid Response Elements) function as enhancers located near dozens of different genes, so the hormone can activate many genes © McGraw Hill 12  Figure 15.7 © McGraw Hill 13  15.2 Chromatin Remodeling and Histones ATP-dependent chromatin remodeling refers to dynamic changes in chromatin structure These changes range from a few nucleosomes to large scale changes Carried out by diverse multi-protein machines that reposition and restructure nucleosomes © McGraw Hill 14  Chromatin Structure - The three-dimensional packing of chromatin is an important parameter affecting gene expression - Chromatin is a very dynamic structure that can alternate between two conformations Closed conformation Chromatin is very tightly packed Transcription may be difficult or impossible Open conformation Chromatin is accessible to transcription factors Transcription can take place © McGraw Hill 15  ATP-dependent Chromatin Remodeling All remodeling complexes have a catalytic ATPase subunit called DNA translocase Eukaryotes have multiple families of chromatin remodelers: SWI/SNF, ISWI, INO80, Mi-2 Chromatin remodeling complexes change chromatin structure in one of 3 ways: Change in the position of nucleosomes Eviction of histone octamers Change in the composition of nucleosomes © McGraw Hill 16  Figure 15.9a (a) Change in nucleosome position © McGraw Hill 17  Figure 15.9b (b) Histone eviction © McGraw Hill 18  Figure 15.9c (c) Replacement with histone variants © McGraw Hill 19  Histone Variants Play Specialized Roles in Chromatin Structure and Function The five histone genes are moderately repetitive H1, H2A, H2B, H3 and H4 Human genome contains over 70 histone genes Most encode standard histones A few of these genes have accumulated mutations that alters the amino acid sequence These are termed histone variants Some histone variants are incorporated into a subset of nucleosomes to create specialized chromatin See Table 15.1 © McGraw Hill 20  Histone Code Over 50 enzymes have been identified in mammals that selectively modify the amino terminal tails of histones Acetylation, methylation and phosphorylation are common (see Figure 15.10) These modifications affect the level of transcription May influence interactions between nucleosomes Occur in patterns that are recognized by proteins Called the histone code The pattern of modifications provide binding sites for proteins that specify alterations to be made to chromatin structure These proteins bind based on the code and affect transcription © McGraw Hill 21  Figure 15.10a p = phosphate ac = acetyl group m = methyl group Why these amino acids? (a) Examples of possible histone modifications © McGraw Hill 22  Figure 15.10a p = phosphate ac = acetyl group m = methyl group (a) Examples of possible histone modifications © McGraw Hill 23  Figure 15.10b (b) Effect of acetylation © McGraw Hill 24  Nucleosome Arrangements in the Vicinity of a Protein- encoding Gene A nucleosome-free region (NFR) is found at the beginning and end of many genes. Nucleosomes tend to be precisely positioned near the beginning and end of a gene, but are less regularly distributed elsewhere Can you think of an explanation for this? © McGraw Hill 25  15.3 DNA Methylation DNA methylation is the covalent attachment of methyl groups Carried out by DNA methyltransferase It is common in some eukaryotic species, but not all Yeast and Drosophila have little DNA methylation Vertebrates and plants have abundant DNA methylation In mammals, ~ 2 to 7% of the DNA is methylated DNA methylation usually inhibits eukaryotic gene transcription © McGraw Hill 26  Figure 15.14 (a) The methylation of cytosine © McGraw Hill 27  Figure 15.14 (b) Unmethylated (c) Hemimethylated (d) Fully methylated © McGraw Hill 28  CpG Islands In vertebrates and plants, many genes contain CpG islands near their promoters These CpG islands are 1,000 to 2,000 nucleotides long Contain high number of CpG sites In housekeeping genes The CpG islands are unmethylated Genes tend to be expressed in most cell types © McGraw Hill 29  CpG Islands In tissue-specific genes The expression of these genes may be silenced by the methylation of CpG islands Methylation may influence the binding of transcription factors Methyl-CpG-binding proteins may recruit factors that lead to compaction of the chromatin © McGraw Hill 30  Figure 15.15a (a) Methylation inhibits the binding of an activator protein. © McGraw Hill 31  DNA Methylation is Heritable! Methylated DNA sequences are inherited during cell division May explain genomic imprinting! (Chapter 5) Specific genes are methylated in gametes from mother or father Pattern of one copy of the gene being methylated and the other not is maintained in the resulting offspring © McGraw Hill 32  Molecular Model for Inheritance of DNA Methylation De novo methylation is an infrequent and highly regulated event Figure 15.16 © McGraw Hill 33