32 Gene regulation in Eukaryotes

1. 32 Gene regulation in Eukaryotes

2. 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

3. 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 Gene Regulation in Prokaryotes and Eukarykotes

4. Signal NUCLEUS Chromatin modification: DNA Gene Transcription RNA 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 Figure 19.3

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

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

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

8. Densely packed chromatin Activator recruits chromatin remodeling and acetylation proteins RNA Pol Transcription http://cats.med.uvm.edu

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

10. 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

11. Control of Galactose metabolism in yeast Two Repressor proteins bind to control region

12. Control of Galactose metabolism in yeast Galactose can bind to repressor complex. Opens activation site to stimulate transcription

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

14. Transcriptional synergy • Combinations of different enhancers affect the strength of transcription

15. How eukaryotic gene repressors can function:

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

17. 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

18. Genomic imprinting: inactivation of maternal or paternal genes Some alleles are tagged by methyl C.

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

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

21. 5 Micro-RNAs One strand of miRNA associates with protein. The bound miRNA can base-pair with any complementary mRNA 3 1 2 4 Dicer cuts dsRNA into short segments Prevents gene expresion The micro- RNA (miRNA) precursor folds back on itself Chromatin changes Transcription RNA processing mRNA degradation Translation Protein complex Protein processing and degradation Dicer Degradation of mRNA OR miRNA Target mRNA Blockage of translation Hydrogen bond Fig 19.9

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

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

24.  Determination and differentiation of muscle cells Nucleus myoD Other muscle-specific genes DNA OFF OFF Embryonicprecursor cell 1 Determination. Signals from other cells activate a masterregulatory gene, myoD, myoD is a “master control” gene: it makes a transcription factor that can activate other muscle specific genes. OFF mRNA The cell is now ireversibly determined MyoD protein(transcription factor) Myoblast (determined) 2 Differentiation. MyoD protein activatesother muscle-specific transcription factors, which in turn activate genes for muscle proteins. The embryonic precursor cell is still undifferentiated mRNA mRNA mRNA mRNA Myosin, othermuscle proteins,and cell-cycleblocking proteins MyoD Anothertranscriptionfactor Muscle cell(fully differentiated) The cell is now fully differentiated Fig 21.10

25.  Determination and differentiation of muscle cells Nucleus Master control gene myoD Other muscle-specific genes DNA OFF OFF Embryonicprecursor cell Determination. Signals from other cells activate a master regulatory gene, myoD, 1 OFF mRNA The cell is now ireversibly determined to become a muscle cell. MyoD protein(transcription factor) Myoblast (determined) 2 Differentiation. MyoD protein activatesother muscle-specific transcription factors, which in turn activate genes for muscle proteins. mRNA mRNA mRNA mRNA Myosin, othermuscle proteins,and cell-cycleblocking proteins MyoD Anothertranscriptionfactor Muscle cell(fully differentiated) The cell is now fully differentiated Fig 21.10

26.  Determination and differentiation of muscle cells Nucleus Master control gene myoD Other muscle-specific genes DNA OFF OFF Embryonicprecursor cell 1 Determination. Signals from other cells activate a masterregulatory gene, myoD, OFF mRNA The cell is now ireversibly determined MyoD protein(transcription factor) Myoblast (determined) 2 Differentiation. MyoD protein activatesother muscle-specific transcription factors, which in turn activate genes for muscle proteins. mRNA mRNA mRNA mRNA Myosin, othermuscle proteins,and cell-cycleblocking proteins MyoD Anothertranscriptionfactor Muscle cell(fully differentiated) The cell is now fully differentiated Fig 21.10

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

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

29. 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

31. Egg cell Nurse cells Developing egg cell 1 bicoid mRNA Bicoid mRNA in mature unfertilized egg 2 Fertilization 100 µm Translation of bicoid mRNA Bicoid protein in early embryo 3 Anterior end (b) Gradients of bicoid mRNA and bicoid protein in normal egg and early embryo. Drosophila pattern formation

32. Homeotic genes

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