Gene Expression Control II Flashcards
How can packaging of DNA be loosened?
Aceylation, methylation, and phosphorylation.
Acetylation of the tails weakens their interaction with DNA and may permit some transcripion factors to bind to DNA.
If DNA is packaged around nucleosomes, how does the transcription machinery as well as transcription factors attach to the DNA?
Transcription activators trigger changes in chromatin structure making DNA accessible.
Histones are modified and nucleosomes are remodelled.
Histone modification enzymes are important for this.
What does acetylation do?
Acetylation neutralizes histones making them less attracted to the negative charge of DNA allowing to unwind to permit transcription.
What is the histone code?
Set of modifications to histone proteins which governs how tightly they bind to DNA
How is histone code maintain in the cell?
Parental patterns of modification are inherited in daughter chromosomes.
How do we know that histones are a mix of old and new proteins?
Using isotopically-labelled histones.
What is DNA’s charge?
Negative
What is a histone protein’s charge?
Positive
What proteins add or remove acetyl groups from histones?
Using histone acetylase and histone deacetylase
How can histones be modified to allow for DNA transcription to take place?
Nucleosome sliding
Nucleosome removal creating nucleosome free DNA
Histone variants allow greater access to nucleosomal DNA
Specific patterns of histone modification destabilize compact forms of chromatin and attract components of transcription machinery
How can histones be modified to allow for DNA transcription to take place?
Nucleosome sliding
Nucleosome removal creating nucleosome free DNA
Histone variants allow greater access to nucleosomal DNA
Specific patterns of histone modification destabilize compact forms of chromatin and attract components of transcription machinery
*all these modifications of histones can be done via chromatin remodeling complex
For some genes, nucleosomes may need to be moved. How does this take place?
SWI-SNF is an ATP dependent chromatin remodelling protein that activates transcription by moving nucleosome away from the TATA box allowing initiation complex to form.
What is SWI-SNF named after?
Switch & sugar non-fermenting mutants in yeast
What does SWI-SNF do?
Has helicase activity which pushes DNA around nucleosomes
Binds to histones with acetylated tails
Remains bound and maintains region in decondensed conformation
Allows access of TFs and RNApol to TATA box.
How is chromatin structure modified to alter gene transcription?
Modification of histone proteins (as mentioned before)
Chromatin remodeling
DNA methylation
What are epigenetics?
Some chromatin structure changes are retained when cells divide and can even be inherited
What are the mechanisms of epigenetics?
Histone modification
DNA methylation
What is DNA methylation?
Common modification to the primary structure of DNA. Cytosine is commonly methylated to 5-methyl C and hypermethylation suppresses transcription.
What does methylation do?
Condenses chromatin and represses transcription.
This process is reversed by demthylation
What does the ‘p’ refer to in CpG?
The phosphodiester bond between cytosine and guanine
What are CpG islands?
Many CpG arrangements in a row that are often methylated to suppress gene expression.
How is RNA exported?
Export of RNA is delayed until processed completely and damaged RNA is degraded by exosomes/exonucleases
How is RNA transported?
mRNAs are localised to specific regions in the cytosol. mRNA is met by ribosomes and translated.
What information does mRNA carry about its own expression?
Half-life
Efficiency of translation
3’ untranslated region contains specific signals to direct transport
How is mRNA translocation controlled?
mRNA travels along cytoskeleton and stopped by anchor proteins
Why must mRNA be transported near where the protein it produces is required?
To ensure that the protein is produced at the right location.
How is mRNA degradation controlled?
mRNA stability can modify half life between 30 minutes and 10 hours.
Shortening poly A tail by exonuclease when mRNA reaches cytosol. Poly A tail acts as a timer for mRNA.
How is mRNA destroyed?
2 general mechanisms after poly A tail reaches 25 nucleotides:
5’ cap is removed degrading mRNA from 5’ end.
mRNA continues to be degraded from 3’ end
What end of the mRNA is the poly A tail located?
3’
What end is the cap located on mRNA?
5’
How is mRNA translation controlled?
Control often exerted at initiation stage.
5’ cap important in binding small ribosomal subunit then finds AUG start site for translation.
3’-UTR is also important for translation initiation. Only when both ends of the mRNA are checked can translation take place
3’ and 5’ end must both bind simultaneously.
How is translation not overdone? (how is mRNA not constantly translated without stopping?)
There is competition between mRNA translation and decay.
5’ cap and 3’ polyA tail are used in both translation initiation and deadenylation-dependent mRNA decay.
