Gene Expression Flashcards
What is differential gene expression?
Multicellular organisms have the same genes in all cells, but cells at different areas of the body express genes differently (specialised genes are expressed at their specific tissues). This happens due to a series of signalling events and regulation of gene regulatory proteins (transcriptional control).
Sites on DNA for protein binding:
- enhancer seq
- silencer seq
- promoter seq
Promoter seq on DNA includes binding sites such as:
- regulatory protein binding site
- transcriptional factor binding site
- RNA polymerase II binding site
How do transcriptional factors interact with DNA?
Transcriptional factors bind to TATA-binding protein that in turns bind to TATA box on DNA.
Examples of DNA-binding proteins and site of binding:
- activator (binds to enhancer seq)
- repressor (binds to silencer seq)
- TATA-binding protein (binds to TATA box)
- RNA polymerase II (binds to rna poly binding site)
What is modular domain?
Modular domain is the subunit on the transcriptional protein that regulates the interaction of that protein with other proteins (determines the binding partner for that protein)
What are motifs?
Motifs are the structure of the DNA-binding domain within a DNA-binding protein
Which are the 4 of the motifs?
- Leucine zipper (common)
- Helix-turn-helix (embryonic development)
- Helix-loop-helix (on activators, for binding to enhancer seq)
- Zinc finger
Function of non-DNA binding proteins:
They recognise the distinct surface created by DNA-binding protein and recruit other gene expression regulatory proteins such as activators/repressors.
7 types of gene regulatory protein regulation:
- Protein syn.
- Ligand binding
- Protein phosphorylation
- Addition of 2nd subunit
- Unmasking
- Stimulation of nuclear entry
- Release from membrane
RNAs involved in gene expression regulation:
- miRNA
- siRNA
- piRNA
How do the regulatory proteins gain access to the tightly coiled DNA?
There are mechanisms that alter the structure of the chromatin.
What is the function of barrier sequence?
To stop the spread of gene activation
How does a barrier protein work? (3 ways)
- tethering regions of chromosomes to fixed sites
- binding of proteins to groups of nucleosomes
- recruiting histone modifying enzymes (erase marks required for gene activation)
Why are DNA and histones tightly coiled together?
DNA is neg charged whereas histones are positively charged.
Function of acetylation:
A step in chromatin remodelling that disaggregates the tightly coiled nucleosomes/DNA.
When there’s acetylation (hyperacetylation), histones loosen up and chromatin is ACTIVATED.
When there’s de-acetylation (hypoacetylation), histones aggregates and chromatin is INACTIVATED.
Enzymes involved in acetylation/deactylation:
Acetylation: histone acetyltransferase
De-acetylation: histone de-acetylase
Function of DNA methylation:
- control of gene expression
- programs of gene expression (differentiation and development)
- preservation of chromosomal integrity
- X-chromosome inactivation
- alteration in genomic patterns
Difference between acetylation and methylation in terms of activation of genes?
Acetylation ACTIVATES the genes (chromatin deaggregates)
Whereas
Methylation DEACTIVATES the genes (chromatin aggregates)
Briefly define the characteristics of DNA methylation:
- occurs at 5’ position of CYTOSINE
- regulated by methyltransferase
- imprinted/inherited during DNA replication
- DOES NOT CHANGE base sequence of DNA (‘EPIGENETIC’)
Mechanism of DNA methylation in histone aggregation:
- methyl cytosine binding protein binds to methylated cytosine
- histone de-acetylase binds to MCPs
- de-acetylation of histones occurs
- histones aggregate
Genomic imprinting characteristics:
- as in the inheritance of methylated sequence
- happens in random
- methylated maternal allele can be inherited (vice versa)
- the methylated allele is silenced (could be either mat or pat)
- the difference of inheritance of methylated mat/pat alleles can cause two totally different diseases
- however some inheritance of methylated alleles is fixed
Detrimental effects of hypomethylation:
- hypomethylation causes overactivity of genes
- can cause activation and expression of unnecessary gene sequence (parasitic seq)
Detrimental effects of hypermethylation:
- hypermethylation causes inactivity of genes
- cause inactivation of genes necessary for DNA repairing and cell cycle control
Relation between importance of imprinting and failure of cloning:
The fact that donor nucleus does not go through the germ line state results in NO IMPRINTING, hence why cloning is inefficient
2 kinds of selective expression (mechanism of monoallelic expression of biallelic genes):
- Allelic exclusion according to parent of origin (imprinting) - for some genes, the repressed allele is always paternally inherited allele (vice versa)
- Allelic exclusion independent of parent of origin - choice of either expressing the maternally/paternally inherited allele is at random
X chromosome inactivation:
- one of the X chrom in EACH CELL of the female is inactivated early in development
- by using methylation of DNA
- HOWEVER, there is a gene in the (supposedly) inactivated X chrom (Xist) that will still be transcribed into a NON-TRANSLATING mRNA
- this mRNA will bind to the (going to be) inactivated X chrom itself and hence triggers inactivation
