BIO SCI 98 Lecture Notes - Lecture 4: Histone Deacetylase, Chromatin Remodeling, Anaerobic Digestion

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CHAPTER 21
Transcriptional Regulation of Gene Expression in Eukaryotes
pp. 728-752
Eukaryotic genomes
- More complex, more genes
- Complex response to environment
- Gene expression control different cell types
Eukaryotic vs prokaryotic gene transcription
Prokaryotes Eukaryotes
Transcriptional ground
state: promoter activity
and transcription
machinery without
activators or repressors
- promoters have low transcription rate
that increase/decrease with activators
+ repressors
- promoters are OFF without regulatory
factors
Chromosomal
packaging
- chromosomes associated with DNA
binding proteins → polyamines
- DNA is wound onto histone containing
nucleosomes
- DNA + protein packaging termed
chromatin
- access to eukaryotic promoters
regulated by chromatin structure
Chromatin and Transcription
- Average human chromosome ~ 2 in of DNA
- DNA interacts w histones to form chromatin
- DNA in chromatin not accessible to transcription machinery
- Chromatin remodeling allows transcription
- Histones: basic proteins that package + order eukaryotic DNA into nucleosomes
-Heterochromatin: DNA tightly packed on nucleosomes → cannot be transcripted
-Euchromatin: DNA more loosely packed → can be transcripted
- Heterochromatin + euchromatin states regulated by different post-translational
modifications to histones
- (acetylation, phosphorylation, methylation)
Turning on and off genes:
1) Histones are acetylated by histone acetyl transferases (HATs) to reduce affinity for DNA
→ transcribed gene turned on
a) Activators, coactivators, RNA polymerase bind at promoter
2) Repressor + corepressor binds → turns gene off
3) Histone deacetylase (HDAC) removes acetylation to increase affinity of histones for DNA
and cause chromosome condensation to prevent more transcription
4) Steps 2 + 3 induce RNA polymerase to dissociate from DNA and chromatin
condensation further represses transcription
Eukaryotic promoters must be activated → without additional factors RNA polymerases have
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little affinity for promoters
Combinatorial control: specific combination of TFs bound at promoter to express a specific
gene
- Eukaryotic promoters are bigger than prokaryotic promoters
General transcription factors binds at core promoter
Transcriptional activators (bind DNA) and coactivators (bind activators) bind at up and
downstream regulatory sequences
Yeast is a unicellular eukaryote
- Use sugar as carbon and energy source to grow
- Fermentation: anaerobic conversion of sugar → CO2 and EtOH
- Asexual growth
- Stress induces sexual recombination + spore formation
- Used to understand eukaryotic transcription
Yeast Gene Nomenclature
-GAL4 wild type gene
- gal4: mutant gene
- Gal4p of Gal4 = wild type protein
- gal4p or gal4 = mutant protein
Yeast promoters vs. mammalian promoters
- Yeast promoters used to study eukaryotic promoters
- Yeast promoters simpler than vertebrate promoters
- Shorter region for regulation
- Activators only act upstream of gene
- Vertebrate organisms need better control over transcription
- During development
- In specific cell types
- In response to specific environmental conditions
- Vertebrate enhancers can be upstream or downstream
Properties of enhancers
- Regulatory DNA sequence
- Act at a distance
- Upstream or downstream of transcription initiation site
- Orientation-independent
- Yeast upstream activating sequences (UAS) similar to enhancers but do not function
when placed downstream of transcription initiation site
Mechanisms for transcriptional activation by activator proteins
- By recruitment
- Activation domain interacts with transcriptional machinery + stabilizes binding to
DNA template
- By conformational change
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Document Summary

Transcriptional regulation of gene expression in eukaryotes pp. Transcriptional ground state: promoter activity and transcription machinery without activators or repressors. Promoters have low transcription rate that increase/decrease with activators. Chromosomes associated with dna binding proteins polyamines. Dna is wound onto histone containing nucleosomes. Access to eukaryotic promoters regulated by chromatin structure. Average human chromosome ~ 2 in of dna. Dna interacts w histones to form chromatin. Dna in chromatin not accessible to transcription machinery. Histones: basic proteins that package + order eukaryotic dna into nucleosomes. Heterochromatin: dna tightly packed on nucleosomes cannot be transcripted. Euchromatin: dna more loosely packed can be transcripted. Heterochromatin + euchromatin states regulated by different post-translational modifications to histones (acetylation, phosphorylation, methylation) Turning on and off genes: histones are acetylated by histone acetyl transferases (hats) to reduce affinity for dna. Eukaryotic promoters must be activated without additional factors rna polymerases have little affinity for promoters.