1. Control of gene expression
Transcriptional
Post-transcriptional
Epigenetics and long range control

2. Control of gene expression
Transcriptional
Initiation of transcription
Transcription factors
Tissue specific transcription factors
Binding of hormones, growth factors etc. to response elements
Use of alternative promoters in a single gene

3. Control of gene expression
Initiation of transcription (RNA pol I)
Confined to the nucleolus
Transcribes rRNAs
Two transcription factors required to bind to a core promoter and the upstream control element
UBF(x2) binds first, recruiting SL1 to create the complete RNA pol I complex

5. Control of gene expression
Initiation of transcription (RNA pol III)
tRNA and 5s RNA promoter elements
A, B, and C boxes located within the coding sequence
A, B form a bipartite promoter, C is a single independent promoter for 5s RNAs
Several transcription factors bind, recruiting RNA pol III

7. Control of gene expression
RNA pol II
Trancription of polypeptide and snRNA genes
Conserved locations of promoter elements in eukaryotes

9. Control of gene expression
Tissue-specific transcription factors
The DNA complement in all cells of an organism is essentially identical.
cis-acting factors aid in regulating tissue-specific gene expression.
Enhancers and silencers

10. Control of gene expression
Insulin gene promoter organization
NRE negative regulatory element
CRE cAMP response element

12. Control of gene expression
HS-40 alpha-globin regulatory site
Tissue specific regulation (many sites)

14. Control of gene expression
Structural domains in transcription factors
Alpha-helices – amino-acid cylinders constructed via hydrogen bonding
HTH
HLH
Leucine zipper - amphipathic alpha-helices
Zn Finger

17. Control of gene expression
Steroid receptors and response elements
Gene expression can be altered by external factors
Response elements – DNA elements that are not constitutive but are bound in response to an activator transcription factor
Steroid receptors (GR, ER,PR, RAR,TR,VDR) bind to specific response elements

19. Control of gene expression
Transcription regulation by glucocorticoids
Glucocorticoid receptor is normally inactive due to binding by Hsp90
When glucocorticoids are present, Hsp90 is released and the receptors bind to any of several glucocorticoid response elements, activating gene expression

21. Control of gene expression
Target gene expression via signal transduction
Hydrophilic molecules cannot diffuse through the plasma membrane
The “water-line” approach
Kinases and phosphatases induce conformational changes via phosphorylation/dephosphorylation
Protein kinase: hormonal signaling through cAMP-protein kinase A pathway
Cytoplasmic transcription factor NF kappa B and translocation to the nucleus

22. Regulatory
subunits
Catalytic
subunits

24. Control of gene expression
Major Classes of Cell Surface Receptor
G protein
Inactive – trimer bound to GDP
Activation - GDP replaced by GTP
Active – monomer + GTP, dimer
Serine-Threonine kinase - phosphorylate serine or threonine in the affected polypeptide
Tyrosine kinase
Tyrosine kinase associated JAK (janus protein kinase) activity in JAK-STAT signaling
Ion channel-linked – channels can be opened to allow signal transduction

25. Control of gene expression
Secondary Messengers in Cell Signaling
Cyclic AMP (cAMP)
Cyclic GMP (cGMP)
Phospholipids/Ca

26. Control of gene expression
Alternative transcription
Genes with multiple promoters
Dystrophin has at least 7 promoters

28. Control of gene expression
rRNA synthesis
The major human rRNAs are transcribed from a common 13 kb transcription unit.
Arrows indicate cleavage sites

30. Control of gene expression
Post-transcriptional control
Alternative splicing

32. Control of gene expression
Differential RNA splicing
Wt1 Wilm’s tumor (four splice forms)
Calcitonin gene (tissue specific products)

35. Control of gene expression
Post-transcriptional control
Alternative splicing
Alternative polyadenylation
Tissue specific RNA editing - rare
Translational control mechanisms

36. Control of gene expression
Tissue specific RNA editing
Apolipoprotein B gene (rare)

38. Control of gene expression
Translational control
Changing the fate of already existing transcripts
The IRE binding protein and iron-response elements (IREs)

40. Control of gene expression
Epigenetics
Epigenetics – inheritable but not caused by a change in DNA sequence
Methylation and cell memory

41. Control of gene expression
Methylation and gene expression
Largely confined to CpG dinucleotides
CpG islands
Methylation patterns change during development
Sex-specific regulation

43. Control of gene expression
Methylation
CpG islands – associated with human genes
Regions of ‘normal’ GC content

45. Control of gene expression
Methylation
Changes in methylation throughout development

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48. Control of gene expression
Methylation
Sex-specific regulation of the Dnmt1 methyl transferase gene through specific promoters
1so somatic
1sp spermatocytes
1oo oocytes

50. Control of gene expression
Transcriptional repression by histone deacetylation
The presence of acetyl groups at the N-terminus of histones promotes an open conformation, transcriptional activity.
Mediated by methylation
Methylated CpG’s bound by MeCP2 repressor which, in turn, recruites HDAC.

52. Control of gene expression
Gene clusters
Coordinated switching within a locus control region (LCR)
LCR = a cluster of hypersensitive sites
- Globin genes

55. Control of gene expression
Chromatin structure
Allelic exclusion (rearrangements, imprinting, X inactivation)
Long range control by chromatin structure (position effects Pax6 in aniridia)
Cell position-dependent, short range signaling

56. Control of gene expression
Imprinting
DNA methylation key component
Selective expression of genes
Nonequivalence of maternal and paternal genomes

58. Control of gene expression
Monoallelic expression from biallelic genes
Allelic exclusion according to parent of origin
Genomic imprinting
Allelic exclusion independent of parent of origin
X-chromosome inactivation and dosage compensation – female mosaics
Programmed DNA rearrangement
Unknown mechanism

60. Control of gene expression
Programmed rearrangement
Ig and TCR loci in B and T lymphocytes
The adaptive immune system is required to recognize and respond to millions of different antigens

61. Control of gene expression
Programmed rearrangement
Ig heavy chain locus on 14q32
86 variable (V) sequences
30 diversity (D) sequences
9 joining (J) segments
11 constant (C) sequences

63. Control of gene expression
Programmed rearrangement
Light chain synthesis
Somatic recombination V to J
RNA splicing VJ to C
Heavy chain synthesis
Two sequential somatic recombination events yield DJ and VDJ
RNA splicing VDJ to C
Somatic recombination VDJ to different C (switching)

65. Control of gene expression
Inversion or deletion based splicing
Ig kappa light chain
V-J splicing