Genome Structure Flashcards
What are the bases like in 3D DNA?
→ Stacked
How much DNA is in a nucleated cell?
→ 2m
How wide is the average cell?
→ 50 micrometers
What are the 6 levels of DNA packing?
→ DNA helix
→ Nucleosomes
→ Chromatin Fibres
→ Chromatin loops
→ Loops of condensed chromatin
→ Chromosome
What are histones?
→ basic +ve proteins that bind DNA
How many histones form the nucleosome?
→ 8
→ 2A, 2B, 3, 4
What histone binds Linker DNA?
→ Histone 1
What is linker DNA?
→ piece of DNA that is between nucleosomes
What is an acrocentric chromosome?
→ They don’t have the short arms
What does the primary DNA sequence encode?
→ All the gene products necessary for an organism
→ Regulatory signals
What is the exome?
→ Sum of all the gene sequences
→includes a large number of regulatory signals- non coding
What do the two definitions of the exome include?
→ Coding sequences
→ whole gene sequences
What is a gene?
→ All of the DNA that is transcribed into RNA
→ all of the cis-linked (local) control regions that are required to ensure quantitatively appropriate tissue-specific expression of the final protein
What is the size of the human genome?
→ Upto 2 Giga base pairs
What % of the DNA is genes?
→ Less than 2%
What is the general trend linking genes and organism complexity?
→ The more genes the more complex
Why does the number of genes not necessarily correlate to complexity?
→ A marbled lungfish has 130Gbp
→ Paris Japonica (flower) has 149Gbp ( biggest genome)
What is an example of gene size variation?
→ globin gene 1.8kb
→ dystrophin gene 2.4mb
What do intergenic regions or pseudogenes contain?
→ Remnants of retroviruses
→contain sequences of no known function
→may contain many regulatory elements
How do genes often cluster and give an example?
→ In families
→ Globin clusters
What does gene clustering allow for?
→ Co-ordinate gene regulation
→ Reflect evolutionary history
What is the transcription unit divided into?
→ Exons
→ Introns
Where are introns found?
→ Between exons
→30bp to 1Mbp
What does the promoter do?
→ Recruits RNA polymerase to a DNA template
→ RNA polymerase binds asymmetrically and can only move 5’ to 3’
How does RNA polymerase bind and in what direction does it go?
→ Asymmetrically
→ 5’ to 3’
What are 2 regulatory signals?
→ CAAT
→ TATA
What are the 5 components of a gene?
→ exons and introns
→ regulatory signals CAAT and TATA
→ Signals that allow to start transcription and translation
→ Signals to stop transcription and translation
→ 3’ and 5’ UTR
What is the TATA box for?
→ recruit general transcription factors and RNA polymerase
How many polymerases are there in eukaryotes and what are they?
→RNA pol I
→ RNA pol II
→ RNA pol III
What are the RNA polymerases for in eukaryotes?
→ RNA pol I → transcribe rRNA genes
→ RNA pol II → transcribe mRNA
→ RNA pol III → Transcribe tRNA and other small RNAs
What do co-factors do?
→ Regulate how much and when transcription is occurring
What are the steps for transcription?
1) RNA polymerase is recruited (closed)
2) DNA helix is locally unwound (open)
3) RNA synthesis begins
4) Elongation
5) Termination
6) RNA polymerase dissociates
What do some introns contain?
→ Other genes
What are enhancers?
→ Short sequences that can be in the gene
→ or many Kb distant
→ Targets for transcription factors that activate expression
What do enhancers do?
→ upregulate gene expression
What are silencers?
→ Targets for transcription factors (repressors)
→ position independent
What do silencers do?
→ Downregulate gene expression
→position-independent and are also targets for transcription factors (repressors)
What are insulators?
→ Short sequences that act to prevent enhancers/silencers influencing other genes
How is eukaryotic mRNA modified after transcription?
→ Capped at 5’ end
→ Polyadenylated at 3’ end
→ Introns are removed
When and why is the 5’ cap added?
→ After RNA polymerase begins transcription
→ so the mRNA looks like the 5’ end of the message
→ also to protect it from nuclease activities
What are the two termination signals?
→ AAUAAA
→ G/U rich region
What happens when the termination signal is reached?
→ G/U rich region and everything after it is removed
→polyadenylate polymerase adds lots of As to the end of the sequence
Why is polyadenylation required?
→ Protects the end from degradation and targets it to leave the nucleus
How does splicing work?
→ Protein complex called a spliceosome
→ brings the ends of the exons together and removes the intron inbetween
→ joins exons together
→ Lariat is degraded
What is alternative splicing?
→ Exons can be skipped or added so variations of proteins (isoforms) can be made from the same gene
What targets mRNA for nuclear export?
→ TREX is bound to the cap
→ It is enhanced by the exon junction complex
What are pseudogenes?
Genes that have been at least partially inactivated by loss or gain of sequence that disrupt their transcription or translation
What is an example of a pseudogene?
→ glucocerebrosidase has an adjacent pseudogene
→ it differs in the coding region by one 55bp deletion
How are pseudogenes copied from mRNA?
→ retrotransposition
What proteins do not have introns in their mRNA?
histones
What enzymes are involved in 5’ Cap?
→RNA 5’-triphosphatase
→Guanylyltransferase
→N7G-methyltransferase
What are the 1st two activities carried out by in Capping?
a bifunctional capping enzyme (CE)
What is the role of CPSF?
Cleavage and Polyadenylation Stimulating Factor) recognises the PAS (Polyadenylation signal) and acts on cleavage site at about 20bps
What is the CSTF?
Cleavage Stimulating Factor) recognises GU-rich Downstream Elements (DSE) and helps recruit PAP
PAP (Poly-A polymerase) is recruited and adds multiple A bases after cleavage site
What are other proteins required for Poly A?
CFIm (Cleavage Factor Im), CFIIm and Simplekin.
They stabilise the process
What can compartments be separated into?
→Compartment A – transcriptionally active with active histone modifications
→Compartment B – transcriptionally repressed with repressive histone modifications
What are TADs?
→Individual compartments are made up of several non-interacting sub-compartments
→usually separated by the Transcriptional Repressor CTCF protein
What is 3D transcriptional control involving CTCF?
bidirectionally along DNA extrudes the chromatin fiber and generates chromatin loops when it pauses at CTCF binding sites.
