Chapter 17 and 18 notes - regulation of gene expression in eukaryotes

Regulation of gene expression in eukaryotes I (KCSPK 17) • Genetic information carried on many chromosomes
• RNA transcripts are processed before transport to
Some principles are the same as for prokaryotes, but more
cytoplasm
complex
• Eukaryotic mRNA has longer half-life
• Cell di9erentiation • Eukaryotes also have a translational level of gene
- Only those genes needed for cellular functioning are regulation
expressed (di9erential– e.g. IgG)
- Not due to elimination of genetic information
• Positive (activation of transcription) and negative
(suppression) mechanisms
• Incorrect expression could be fatal – cancer
• Predominantly post-transcriptional regulation



• Prokaryote gene expression often regulated by an operon What does this figure show? What is this process?
• Eukaryote gene expression regulated in discrete units of
protein-coding sequences and adjacent controlling sites Interphase chromatin – relaxed compared to mitosis but some areas
(no operons) are more relaxed than others: euchromatin and heterochromatin
• Because of the nucleus, transcription and translation are
not coupled making Eukaryotic gene regulation more
complex Levels of eukaryotic gene regulation
• Two “categories” for eukaryotic gene regulation:
Prokaryotes: transcriptional regulation
- Short-term - genes quickly turned on or o9 in response
to stimuli (environmental, metabolic demands) • Eukaryotes: 7 levels
- Long-term - genes coordinately expressed at
- RNA polymerase II
programmed stages (development and di9erentiation)
o Di9erent for RNAPs I and III
Why is regulation of gene expression so much more complex in - 4 in nucleus
eukaryotes o Chromatin remodeling
o Transcriptional regulation
• Considerably more, and more complex DNA
o Splicing and processing
- Chromatin
o Transport

, - 3 in cytoplasm Chromatin modifications
o mRNA stability
• Role of the interphase (when cell is not dividing)
o Translational regulation
chromosome structure
o Post-translational regulation
- Chromosome territories (non-random areas in the
nucleus)
- Interchromosome compartments
Euchromatin/active
- Transcription factories (shared hubs)
• Chromatin modifications are required
- “Open” vs “Closed” formation
- Modification of nucleosomes
- Modification of DNA


Heterochromatin/silent




Transcription “factories)
Multiple active genes are transcribed simultaneously

FISH

Chromatin remodeling (1)
RNA polymerase (mostly II) and Modification to nucleosomes
transcription factors concentrate
1. Modifications to nucleosomes
• Nucleosome composition
- Normal: H2A & H3
- Variant: H2A.Z & H3.3 – not as stable, more access to
DNA
- Nucleosome repellant
- Facilitates transcription
• Histone modification

, - Acetylation by HAT (histone acetyltransferase) Chromatin remodeling (2)
- De-acetylation by HDAC (histone deacetylase) Modification of DNA – methylation chemically modifies DNA bases
- Access to promoter regions by DNA methyl transferase
• Repositioning/removal of nucleosomes
2. Modification of DNA - methylation
- Remodeling complexes e.g. SWI/SNF
• Regulation at the genomic DNA level
- Enhanced access for RNAP and TFs
• Chemical modification of DNA bases
• Enzyme-mediated addition of methyl groups
- DNA methyl transferases (DNAMTs)
• 5’-position of cytosine in CG doublets
- Concentrated in CpG islands
- Promoter regions of genes (5’-UTR)
• Inverse relationship between methylation and expression
Histone acetylation relaxes chromatin structure – promotes gene expression • Di9ering levels of methylation in di9erent eukaryotes
- 14% in Arabidopsis, 1% in humans, absent in
Caenorhabditis
SWI/SNF: three ways of altering the association of nucleosomes and DNA CpG islands are often located in / near promoters


5’ – NNNNNNCGCGCGCGNNNNNN – 3’
3’ – NNNNNNGCGCGCGCNNNNNN – 5’




Methyl group added