32 Gene regulation in Eukaryotes

Lecture Outline 11/28/05 Gene regulation in eukaryotes –Chromatin remodeling –More kinds of control elements Promoters, Enhancers, and Silencers Combinatorial control Cell-specific transcription –Post transcription gene regulation mRNA processing Micro RNAs Protein degradation –Differentiation and Development A cascade of transcription regulators Examples from flowers and fruit flies

Gene Regulation in Prokaryotes and Eukarykotes Prokaryotes –Operons 27% 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 –RNA processing –Chromatin remodeling Histones must be modified to loosen DNA –Short- and long-term regulation

Figure 19.3 Signal NUCLEUS Chromatin modification: Gene DNA RNA Transcription RNA processing Transport to cytoplasm CYTOPLASM Degradation of mRNA Translation Polypetide Cleavage Chemical modification Transport to cellular destination Active protein Degradation of protein Degraded protein

Nucleosome 30 nm (b) 30-nm fiber DNA Packing Protein scaffold 300 nm (c) Looped domains (300-nm fiber) Loops Scaffold 700 nm 1,400 nm (d) Metaphase chromosome Figure 19.2

Histone Modification Figure 19.4a Chromatin changes Transcription RNA processing mRNA degradation Translation Protein processing and degradation DNA double helix Amino acids available for chemical modification Histone tails

Histone acetylation loosens DNA to allow transcription Figure 19.4 b Unacetylated histones Acetylated histones

Activator recruits chromatin remodeling and acetylation proteins Densely packed chromatin Transcription RNA Pol

Review transcription in Eukarkyotes Enhancer (distal control elements) Proximal control elements DNA Upstream Promoter Exon IntronExon Intron Poly-A signal sequence Exon Termination region Transcription Downstream Poly-A signal ExonIntron Exon IntronExon Primary RNA transcript (pre-mRNA) 5 Intron RNA RNA processing: Cap and tail added; introns excised and exons spliced together Coding segment P P P G mRNA 5 Cap 5 UTR (untranslated region) Start codon Stop codon 3 UTR (untranslated region) Poly-A tail Chromatin changes Transcription RNA processing mRNA degradation Translation Protein processing and degradation Cleared 3 end of primary transport

Many components must be assembled to initiate transcription Those common components are called “General Transcription Factors” 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

Distal control element Activators Enhancer Promoter Gene TATA box General transcription factors DNA-bending protein Group of Mediator proteins RNA Polymerase II RNA Polymerase II RNA synthesis Transcription Initiation complex Chromatin changes Transcription RNA processing mRNA degradation Translation Protein processing and degradation A DNA-bending protein brings the bound activators closer to the promoter. 2 Activator proteins bind to distal control elements. 1 The activators bind to certain general transcription factors and mediator proteins. 3 Enhancers and activators Fig 19.5

Transcriptional synergy Combinations of different enhancers affect the strength of transcription

How eukaryotic gene repressors can function:

Cell type–specific transcription EnhancerPromoter Control elements Albumin gene Crystallin gene Liver cell nucleus Lens cell nucleus Albumin gene expressed Albumin gene not expressed Crystallin gene not expressed Crystallin gene expressed Liver cellLens cell Fig 19.7 All cells have the same genes, but only certain genes are expressed in each tissue Different set of activator proteins in the two cell types

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.

Signal NUCLEUS Chromatin modification: Gene DNA RNA Transcription RNA processing Transport to cytoplasm CYTOPLASM Degradation of mRNA Translation Polypetide Active protein Degradation of protein Degraded protein Post-transcription control of gene expression

Alternative RNA splicing Chromatin changes Transcription RNA processing mRNA degradation Translation Protein processing and degradation Exons DNA Primary RNA transcript mRNA RNA splicing or Fig 19.8

Micro-RNAs Chromatin changes Transcription RNA processing mRNA degradation Translation Protein processing and degradation Degradation of mRNA OR Blockage of translation Target mRNA miRNA Protein complex Dicer Hydrogen bond The micro- RNA (miRNA) precursor folds back on itself 1 Dicer cuts dsRNA into short segments 2 One strand of miRNA associates with protein. 3 The bound miRNA can base- pair with any complementary mRNA 4 Prevents gene expresion 5 Fig 19.9

Degradation of a protein by a proteasome Chromatin changes Transcription RNA processing mRNA degradation Translation Protein processing and degradation Ubiquitin Protein to be degraded Ubiquinated protein Proteasome and ubiquitin to be recycled Protein fragments (peptides) Ubiquitin molecules are attached to a protein 1 The ubiquitin-tagged protein is recognized by a proteasome. 2 The proteasome cuts the protein into small peptides. 3 Protein entering a proteasome Fig 19.10

Figure 21.1 Mutant Drosophila with an extra small eye on its antenna Development

DNA OFF mRNA Another transcription factor MyoD Muscle cell (fully differentiated) MyoD protein (transcription factor) Myoblast (determined) Embryonic precursor cell Myosin, other muscle proteins, and cell-cycle blocking proteins Other muscle-specific genesmyoD Nucleus Determination. Signals from other cells activate a master regulatory gene, myoD, 1 Differentiation. MyoD protein activates other muscle-specific transcription factors, which in turn activate genes for muscle proteins. 2 Determination and differentiation of muscle cells Fig The cell is now ireversibly determined The cell is now fully differentiated myoD is a “master control” gene: it makes a transcription factor that can activate other muscle specific genes. The embryonic precursor cell is still undifferentiated

DNA OFF mRNA Another transcription factor MyoD Muscle cell (fully differentiated) MyoD protein (transcription factor) Myoblast (determined) Embryonic precursor cell Myosin, other muscle proteins, and cell-cycle blocking proteins Other muscle-specific genesMaster control gene myoD Nucleus Determination. Signals from other cells activate a master regulatory gene, myoD, 1 Differentiation. MyoD protein activates other muscle-specific transcription factors, which in turn activate genes for muscle proteins. 2 Determination and differentiation of muscle cells Fig The cell is now fully differentiated The cell is now ireversibly determined to become a muscle cell.

DNA OFF mRNA Another transcription factor MyoD Muscle cell (fully differentiated) MyoD protein (transcription factor) Myoblast (determined) Embryonic precursor cell Myosin, other muscle proteins, and cell-cycle blocking proteins Other muscle-specific genesMaster control gene myoD Nucleus Determination. Signals from other cells activate a master regulatory gene, myoD, 1 Differentiation. MyoD protein activates other muscle-specific transcription factors, which in turn activate genes for muscle proteins. 2 Determination and differentiation of muscle cells Fig The cell is now ireversibly determined The cell is now fully differentiated

Genetic control of Flower Development Apetala Class A Agamous Class C Pistillata Class B “ABC Model” These genes all code for transcription factors Normal Flower

The effect of the bicoid gene, an egg-polarity gene in Drosophila Tail Head Normal larva Tail Mutant larva (bicoid) A mutation in bicoid leads to tail structures at both ends (bottom larva). T1 T2 T3 A1 A2 A3 A4 A5 A6 A7 A8 A7A6A7 A8 Figure 21.14

Hierarchy of Gene Activity in Early Drosophila Development Maternal effect genes (egg-polarity genes) Gap genes Pair-rule genes Segment polarity genes Homeotic genes of the embryo Other genes of the embryo Segmentation genes of the embryo

Drosophila pattern formation Translation of bicoid mRNA Fertilization Nurse cells Egg cell bicoid mRNA Developing egg cell Bicoid mRNA in mature unfertilized egg 100 µm Bicoid protein in early embryo Anterior end (b) Gradients of bicoid mRNA and bicoid protein in normal egg and early embryo

Homeotic genes

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