32 Gene regulation in Eukaryotes Lecture Outline 11/28/05. Gene Regulation in Prokaryotes and Eukarykotes

Transcription

1 3 Gene regulation in Eukaryotes Lecture Outline /8/05 Gene regulation in eukaryotes Chromatin remodeling More kinds of control elements Promoters, Enhancers, and Silencers Combinatorial control Cell-specific transcription Post transcription gene regulation processing Micro s Protein Differentiation and Development A cascade of transcription regulators Examples from flowers and fruit flies Gene Regulation in Prokaryotes and Eukarykotes Prokaryotes Operons 7% of E. coli genes (Housekeeping genes not in operons) simultaneous transcription and translation Eukaryotes No operons, but they still need to coordinate regulation More kinds of control elements Chromatin remodeling Histones must be modified to loosen Short- and long-term regulation Figure 9.3 Signal Degradation of Polypetide Chromatin modification: Gene Active protein NUCLEUS Transport to cytoplasm CYTOPLASM Cleavage Chemical modification Transport to cellular destination Degradation of protein Degraded protein

2 Packing Histone Modification 30 nm Nucleosome (b) 30-nm fiber Protein scaffold (c) Looped domains (300-nm fiber) 300 nm Loops Scaffold and Histone tails Figure nm,400 nm Figure 9.4a double helix Amino acids available for chemical modification Histone acetylation loosens to allow transcription Densely packed chromatin Activator recruits chromatin remodeling and acetylation proteins Unacetylated histones Acetylated histones Pol Figure 9.4 b

3 Enhancer (distal control elements) Review transcription in Eukarkyotes Proximal control elements Poly-A signal sequence Termination region Many components must be assembled to initiate transcription Exon Intron Exon Intron Exon Upstream Promoter Primary Exon transcript 5 (pre-) Intron Intron Poly-A signal Exon Intron Exon : Cap and tail added; introns excised and exons spliced together Downstream Cleared 3 end of primary transport Those common components are called General Factors and G P P P 5 Cap 5 UTR (untranslated region) Coding segment Start Stop codon codon 3 UTR Poly-A (untranslated tail region) There are also many other transcription factors that control transcription of particular genes in particular conditions Control of Galactose metabolism in yeast Two Repressor proteins bind to control region Control of Galactose metabolism in yeast Galactose can bind to repressor complex. Opens activation site to stimulate transcription 3

4 Enhancers and activators Distal control element Activators Promoter Gene al synergy Enhancer Activator proteins bind to distal control elements. A -bending protein brings the bound activators closer to the promoter. TATA box -bending protein General transcription factors Group of Mediator proteins Polymerase II Combinations of different enhancers affect the strength of transcription 3 The activators bind to certain general transcription factors and mediator proteins. Fig 9.5 and Initiation complex Polymerase II synthesis How eukaryotic gene repressors can function: Cell type specific transcription All cells have the same genes, but only certain genes are expressed in each tissue Control elements Enhancer Liver cell nucleus Promoter Albumin gene Crystallin gene Lens cell nucleus Different set of activator proteins in the two cell types Liver cell Albumin gene expressed Albumin gene not expressed Lens cell Fig 9.7 Crystallin gene not expressed Crystallin gene expressed 4

5 Long-term control of transcription: methylation Certain cytosine bases can be methylated, which blocks transcription Usually CG dinucleotides Recruits proteins which deacetylate histones, inactivating nearby genes Genomic imprinting: inactivation of maternal or paternal genes Some alleles are tagged by methyl C. Post-transcription control of gene expression Signal Chromatin modification: Gene Degradation of NUCLEUS Transport to cytoplasm CYTOPLASM Alternative splicing and Exons Polypetide Primary transcript Active protein Degradation of protein splicing or Degraded protein Fig 9.8 5

6 Degradation of a protein by a proteasome Micro-s 3 One strand Dicer cuts The micro- ds into of mi (mi) short segments associates with precursor folds protein. back on itself The bound mi can basepair with any complementary 4 5 Prevents gene expresion Protein complex mi Target Hydrogen bond 3 The proteasome cuts the protein into small peptides. Proteasome and ubiquitin to be recycled Ubiquitin Proteasome and Degradation of OR Blockage of translation Fig 9.9 The ubiquitin-tagged protein is recognized by a proteasome. and Dicer Ubiquitin molecules are attached to a protein Protein to be degraded Ubiquinated protein Protein fragments (peptides) Protein entering a proteasome Fig 9.0 Determination and differentiation of muscle cells Development Nucleus myod Other muscle-specific genes Embryonic precursor cell Determination. Signals from myod is a master control gene: it makes a transcription factor that can activate other The cell is now protein ireversibly muscle specific genes.myod (transcription factor) other cells activate a master regulatory gene, myod, Myoblast (determined) Mutant Drosophila with an extra small eye on its antenna determined Differentiation. MyoD protein activates The embryonic precursor other muscle-specific cell is stilltranscription undifferentiated factors, which in turn activate genes for muscle proteins. Muscle cell (fully differentiated) Figure. Fig.0 MyoD The cell is now fully differentiated Another transcription factor Myosin, other muscle proteins, and cell-cycle blocking proteins 6

7 Determination and differentiation of muscle cells Determination and differentiation of muscle cells Nucleus Master control gene myod Other muscle-specific genes Nucleus Master control gene myod Other muscle-specific genes Embryonic precursor cell Embryonic precursor cell Myoblast (determined) Determination. Signals from other cells activate a master regulatory gene, myod, Differentiation. MyoD protein activates other muscle-specific transcription factors, which in turn activate genes for muscle proteins. MyoD protein (transcription factor) The cell is now ireversibly determined to become a muscle cell. Myoblast (determined) Determination. Signals from other cells activate a master regulatory gene, myod, Differentiation. MyoD protein activates other muscle-specific transcription factors, which in turn activate genes for muscle proteins. MyoD protein (transcription factor) The cell is now ireversibly determined Fig.0 Muscle cell (fully differentiated) MyoD The cell is now fully differentiated Another transcription factor Myosin, other muscle proteins, and cell-cycle blocking proteins Fig.0 Muscle cell (fully differentiated) MyoD The cell is now fully differentiated Another transcription factor Myosin, other muscle proteins, and cell-cycle blocking proteins Genetic control of Flower Development The effect of the bicoid gene, an egg-polarity gene in Drosophila Normal Flower Head T T A8 T3 A A A3 A4 A5 A6 A7 Tail Normal larva ABC Model Figure.4 Tail Tail Apetala Class A Pistillata Class B Agamous Class C These genes all code for transcription factors A8 A7 A6 A7 Mutant larva (bicoid) A mutation in bicoid leads to tail structures at both ends (bottom larva). A8 7

8 Hierarchy of Gene Activity in Early Drosophila Development Maternal effect genes (egg-polarity genes) Gap genes Segmentation genes of the embryo Pair-rule genes Segment polarity genes Homeotic genes of the embryo Other genes of the embryo Drosophila pattern formation Nurse cells Homeotic genes Egg cell Developing egg cell bicoid Bicoid in mature unfertilized egg Fertilization of bicoid 00 µm 3 Bicoid protein in early embryo Anterior end (b) Gradients of bicoid and bicoid protein in normal egg and early embryo. 8

9 Homeotic genes Regulatory genes that control organ identity Conserved from flies to mammals 9