Genome Structure Flashcards
How big (roughly) is the human genome?
3 gbps
Roughly how many genes does the human genome contain?
20000 genes
Which histones form the nucleosome?
2 each of H2A, H2B, H3 and H4
What does histone 1 do?
Binds linker DNA between nucleosomes
What is a metacentric chromosome?
Where short and long arms are of equal length
What is a submetacentric chromosome?
Long long arm and short short arm
What is an Acrocentric chromosome?
When a chromosome doesnt have a short arm
What is the arm length of a chromosome defined by?
The position of the centromere
What are the different definitions of an exome?
all of the coding sequence or the whole gene sequence
What is a gene?
All the DNA that is transcribed into RNA + all the local control regions that are required to ensure quantitatively appropriate tissue-specific expression of the final protein
How much of the genome is intergenic?
98%
What does the intergenic region contain?
Sequences of no known function
What do gene clusters allow for?
Coordinated gene regulation but may just reflect the evolutionary history
If you have ‘n’ exons, how many introns do you have?
N-1
Can you have a gene with no introns?
Yes
Where are TATA boxes found and what do they do?
Promoter region
Recruit general transcription factors and RNA polymerase
Where are regulatory elements found and what do they do?
Promoter regions
Regulate recruitment of RNA polymerase
What direction can RNA polymerase move in?
5’ to 3’
What are the three types of regulatory regions?
Enhancers, silencers and insulators
What do enhancers do in regulatory regions?
Upregulate gene expression
What does position independant mean?
They can take affect from anywhere (ie in the gene or many kilo bases away)
What type of transcription factors are the enhancers targets for?
Activators
What type of transcription factors are the silencers targets for?
Repressors
What do silencers do in regulatory regions?
Downregulate gene expression
What are insulators in regulatory regions?
Short sequences that act to prevent enhancers/ silencers influencing other genes
How has the organisation of somatic nuclear DNA been identified?
Hi-C and high throughput microscopy
What does Hi-C detect?
Genomic DNA sequences in close proximity
What does the organisation of somatic nuclear DNA involve?
CTCF protein and cohesin protein complex, as well as transcription machinery
What are the names of the two compartments that the genome is split into?
Compartment A and B
What do the genes in compartment A do?
Transcriptionally active with active histone modifications
What do the genes in compartment B do?
Transcriptionally repressed with repressive histone modifications
When are the compartments made apparent?
In the 3D genome structure
What are the compartments made up of?
Non-interacting topologically associated domains (TADs)
What are topologically associated domains (TADs) seperated by?
The transcriptional repressor CTCF protein
How do the CTCF proteins control transcription?
The cohesin complex starts loading and extruding a length of DNA until it hits the CTCF proteins, which block any further extrusion taking place and forming a loop
