Regulation of Gene Expression in Eukaryotes:Transcriptional regulation I Flashcards
Eukaryotes are more complex and contain multiple organelles
- allows compartmentalisation
= optimisation of different reactions - different levels of organisation:
Cells - tissue - organ -system - organism
Cell differentiation
- Only those genes needed for cellular functioning are expressed
(differential – e.g. IgG only expressed in white blood cells) - Not due to elimination of genetic information - rather careful
regulation of gene expression - Positive (activation of transcription) and negative (suppression)
mechanisms - Incorrect expression could be fatal – cancer
- Predominantly post-transcriptional regulation
(prok are transcriptional regulation)
Prokaryote vs Eukaryotes
Prokaryote gene expression often regulated by an operon
Eukaryote gene expression regulated in discrete units of protein-coding sequences and adjacent controlling sites (no operons).
Because of the nucleus, transcription and translation are not coupled making Eukaryotic gene regulation more complex.
Two “categories” for eukaryotic gene regulation:
Short-term - genes quickly turned on or off in response to stimuli
(environmental, metabolic demands).
Long-term - genes co-ordinately expressed at programmed
stages (development and differentiation).
Why is regulation so much more complex?
- Considerably more, and more complex DNA
> Chromatin - Genetic information carried on many chromosomes
- RNA transcripts are processed before transport to cytoplasm
- Eukaryotic mRNA has longer half-life
- Eukaryotes also have a translational level of gene regulation
Chromatin
- complex of DNA, RNA, histones and non histone proteins
> makes up the uncoiled chromosome - Eukaryotic cells can modify the structural organisation of
chromatin to regulate gene expression - Eukaryotic genes are also spread across many linear
chromosomes, instead of singular circular chromosome in prok.
mRNA processing
- mRNA needs to be spliced, capped and polyA’ed after
transcription - before they get transported out of the nucleus and into the
cytoplasm (for translation) - Each of these processes can be regulated to influence the
number, and type of mRNA available for translation
7 Levels of eukaryotic gene regulation
4 in nucleus
- Chromatin remodelling
- Transcriptional regulation
- Splicing and processing
- Transport
3 in cytoplasm
- mRNA stability
- Translational regulation
- Post-translational regulation
- only looking RNA polymerase II transcribed genes
> translates mRNA and some small nuclear RNA’s
Two distinct features of Eukaryotic DNA:
- Genes located on chromosomes in the nucleus.
- DNA combined with histones and non-histone proteins to form
chromatin.
The presence of chromatin in Eukaryotic cells
inhibits many processes linked to DNA replication, repair and transcription
- as it is so tightly condensed
- Thus, chromatic modification plays an important role in transcriptional
regulation
Chromatin
= highly organised structure
chromosome territory
- each chromosome occupies a discrete region in the nucleus
- keeps it distinct from other chromosomes
Interchromosome compartments
- forms channels with little/ no DNA between the different
chromosomes
Transcriptionally active genes appear to be located on the edges of chromosome territories
- next to the interchromosomal compartmental channels
- this can help to bring them into contact with transcription factors or
other actively expressed genes to facilitate co-ordinated expression - transcripts produced at the end of chromosome territories move into
channels that house the RNA processing machinery - which are
contiguous with the nuclear pores
= Allows for capping, splicing and polyA of mRNA, during and after
transcription and eventual transport into the cytoplasm
transcription factories
are nucleosites containing most of the active RNA polym. and the transcription regulatory molecules
- Extremely dynamic structures
- can form and disassemble very quickly - as transcription is activated
and repressed
some evidence that suggests transciption factories transcribe genes
which are regulated by the same transcriptional activators
- By concentrating actively transcribed genes and transcription proteins in specific areas, the cell can enhance the expression of these genes
Structure of chromatin prevents transcription
- Chromatin modification is NB in order to allow the transcriptional
proteins to access the DNA - For some genes, chromatin modification is a prerequisite for
transcription - whilst in other genes, the two processes may occur
at the same time
2 ways that chromatin can be modified:
“Open” vs “Closed” formation
1. Modification of nucleosomes
2. Modification of DNA
Chromatin remodelling - Modifications to nucleosomes
- Nucleosome composition
- Histone modification
- Repositioning/removal of nucleosomes
- Nucleosome composition
- Modifications to nucleosomes
- Most nucleosomes contain 2 molecules each of histones:
H2A, H2B, H3 and H4
HOWEVER: some gene promotor regions are flanked by nucleosomes that bare a varient histone = H2A.Z and H3.3
H3.3:
- Causes higher order chromatin folding and promotes gene activation
- tends to mark enhancer regions associated with promoters
H2A.Z:
- promotes compaction of chromatin - prevents transcription
So:
Active recruitment of H3.3 and active removal of H2A.Z from promotor regions allows the loosening of the chromatin structure - makes transcription possible
- Histone modification
- Modifications to nucleosomes
Via:
1. Acetylation of histones - by HAT (histone acytyl transferase enzymes)
- Addition of an acetate group to specific basic amino acids on the
histone protein - there’s an interaction between the basic peptide tail and the acidic
DNA.
= This gives transcription factors greater access to the promotor
regions for transcription - The HATs may be recruited by transcription activator proteins - which bind to transcription regulatory regions
- De-acetylation
- by HDAC ( Histone deacetylases)
- tightens the interaction between DNA and histones = transcriptional repression
- HDAC can be recruited o the genes by repressor proteins on other
regulatory regions
other forms of histone modifications:
- Phosphorylation
- Methylation
- Repositioning/removal of nucleosomes
- Modifications to nucleosomes
- making regions of the chromosome accessible to the transcription
factors and RNA polymerase - May act by loosening the attachment between DNA and histones
= Nucleosome slides along the DNA to expose the regulatory regions - or they may release the DNA from the nucleosome core/ rearrange
the nucleosome components
Modification of DNA - Methylation
- Regulation at the genomic DNA level
- Chemical modification of DNA bases
- Enzyme-mediated addition of methyl groups
> via DNA methyl transferases (DNAMTs)
> uses SAM as the methyl donor (S-adenosyl methionine) - Only effects A and C bases
> Mostly in the 5’-position of cytosine
= 5-methyl-cytosine - the methyl groups extend out of the major grooves of the DNA
- Concentrated in CpG islands
> GC rich regions in promotor regions - When promotor unmethylated - gene is transcribed
- BUT, when promotor is heavily methylated - transcription is silenced
slide 17 - 20
Epigenetics
- Genome modified without affecting DNA sequence
DNA methylation
histone modification
non-coding RNAs
Epigenome-specific pattern of epigenetic changes
Can differ between different cell types as well as over time within
a specific cell - Will only ever have a single genome, but may
pass through many epigenetic states.
Combinations of histone modifications can activate or silence genes
= Histone code
Abnormal methylation patterns often associated with cancer
Hyper vs. hypomethylation
Epigenetic changes are reversible, but are also heritable
Epigenetic state can be influenced by environmental factors (both physical and behavioral)
