Genome Structure Flashcards
What are histones? What does each type of histone do?
Basic (+vely charged) proteins that bind DNA
Eight histones 2x(H2A+H2B+H3+H4) form the nucleosome
Histone 1 binds the linker DNA
What are the different levels of DNA packing?
- DNA double helix
- Nucleosomes
- Chromatin fiber
- Extended section of chromosome
- Loops of chromatin fiber
- Metaphase chromosome
What are the three types of chromosome structure
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What is the exome?
The exome is made up of gene sequences
Some definitions use all of the coding sequences (~37 Mbp – 1.2% of genome)
Some definitions use all of the gene sequences (~60Mbp – 2% of genome)
What are intergenic regions for?
Intergenic regions contain sequences of no known function, such as repetitive DNA, endogenous retroviruses, pseudogenes.
They may contain many regulatory elements.
Genes often cluster in families – e.g. globin clusters
- allows for co-ordinated gene regulation
- may just reflect evolutionary history
What does the typical structure of a gene look like?
The promoters- the CAAT and TATA boxes being the basal promoter regions
Transcription initiation is at the beginning of exon 1
The translation initiation is where translation starts usually with an ATG sequence
At the 3’ end are the translation and transcription termination sequences
What do promoters do?
Promoters recruit RNA polymerase to a DNA template
TATA box needed to recruit general transcription factors and RNA polymerase
The regulatory element affects (regulates) the recruitment of RNA polymerase.
So if something is bound to the regulatory element then recruitment of RNA polymerase will be harder.
RNA polymerase binds asymmetrically and can only move 5’ to 3’
What are some other regulatory regions? And what do they do?
Enhancers upregulate gene expression – they are short sequences that can be in the gene or many kilobases distant. They are targets for transcription factors (activators).
Silencers downregulate gene expression. They are also position-independent and are also targets for transcription factors (repressors).
Insulators are short sequences that act to prevent enhancers/silencers influencing other genes
How does transcription work?
Messenger RNA synthesis (transcription) is catalysed by RNA Polymerase II
Transcribes in 5’ to 3’ direction
Transcribes everything after the transcription start site (exons and introns)
mRNA is post-transcriptionally modified
RNA polymerase II recognises promoters efficiently with the assistance of many other transcription factors
How does the capping process of the DNA occur?
After 25-30nts are synthesised, a methylated cap is added to the 5’ end by three enzyme activities to protect it from nuclease activities:
RNA 5’-triphosphatase
Guanylyltransferase
N7G-methyltransferase
The first two activities are carried out by a bifunctional capping enzyme (CE)
RNA Pol II is also required for it to happen- involved in positioning these enzymes and the message in the right place
What happens during the splicing of introns?
The spliceosome catalyses the connection of that A in the intron to the phosphate at the end of the blue exon
The frees up the hydroxyl at the end of the blue exon
That can then be linked to the phosphate at the yellow exon
The spliceosome creates a 2’ to 5’ linkage of the intron forming a lariat structure and is spliced out
How is the 3’ poly-A tail attached?
CPSF (Cleavage and Polyadenylation Stimulating Factor) recognises the PAS (Polyadenylation signal) and acts on cleavage site
CSTF (Cleavage Stimulating Factor) recognises GU-rich Downstream Elements (DSE) so it recruits
PAP (Poly-A polymerase) is recruited and adds multiple A bases after cleavage site
PAB is Poly-A Binding Protein.
Other proteins appear to be required for this process – CFIm (Cleavage Factor Im), CFIIm and Simplekin
How can the genome be separated into compartments?
The genome can be separated into compartments:
- Compartment A – transcriptionally active with active histone modifications
- Compartment B – transcriptionally repressed with repressive histone modifications
These are interspersed throughout the 2D sequence but the same compartment types are brought close together in the 3D genome
What are TADs?
Individual compartments are made up of several non-interacting sub-compartments
These are Topologically-Associated Domains (TADs)
They are usually separated by the Transcriptional Repressor CTCF protein
How is DNA transcriptionally controlled in its 3D form?
The DNA is fed in through the Cohesin complex which stops once the complex comes into contact with the CTCF proteins
This forms a separated loop of DNA where the opportunity for enhancers and silencers to influence transcription comes in, which is why their distance from the exon doesn’t matter
