26 Questions
What is the term for the physical compaction of genomes where each chromosome has its own 'space or neighbourhood' within the nucleus?
Spatial chromatin organization
Which area of a chromosome is generally genetically active?
Euchromatin
What do interphase chromosomes occupy within the nucleus?
Discrete territories
What is the term for the evolutionarily controlled process of packaging DNA into a particular space within the nucleus?
Nuclear compaction
Which protein associates with the Stag protein of cohesin?
Rad21
What is the chromatin residence time of cohesin?
20 minutes
What results from the loss of insulation between TADs after cohesin and CTCF knock-down?
Decrease in intra-TAD contact frequency
What model supports the theory of 'stable' TAD structures?
Cohesin loading and dissociation model
What forms between convergent CTCF sites, thus regulating structure specificity?
DNA loops
Which factor does NOT localise at CTCF sites, suggesting cohesin must travel on chromatin to reach CTCF?
Nipbl
What is associated with transient loops within TADs (intra-TAD DNA loops) and influences specific gene expression?
Cohesin-Mediator complex association
Which technique highlights the co-localisation of cohesin and CTCF at TAD boundaries?
Chromatin Conformation Capture techniques
What can Cohesin associate with to influence specific gene expression?
Transcription Factors localising Cohesin
What do Population-based Chromatin Conformation Capture techniques create?
An average of most ‘stable’ domain structure.
What is the function of cohesin during the G1 phase?
Associates with single-stranded chromatin to form loop structures that are essential for genome organization and cell-specific gene expression
What can methylation of a CTCF site dictate?
Ability of cohesin to interact with DNA in trans and cis
What is the role of topologically associated domains (TADs)?
Creating domains of topological association of high interaction frequency
What do enhancers do in the context of long-range gene regulation?
Can be involved with multiple promoters both simultaneously and sequentially
What is the biological importance of TADs/structure?
DNA replication, recombination, gene regulation
What is the function of CTCF during the G1 phase?
Recognises 11 nucleotides only when facing a particular way and sitting on the right place, where the cohesin ring can hold
What does cohesin do during DNA replication?
Associates with single-stranded chromatin to form loop structures that are essential for genome organization and cell-specific gene expression
'CTCF Code': x11 Zinc Finger protein gives multivalence to CTCF's recognition sequence, which fine-tunes its insulator 'strength'. What does this statement imply?
'CTCF Code' recognizes 11 nucleotides only when facing a particular way and sitting on the right place, where the cohesin ring can hold
What are the functions of TADs?
Act as a chromatin barrier between TADs, creating insulation to TAD contacts
What is the role of enhancers in long-range gene regulation?
Can be brought into close proximity physically so that expression can be driven which wasn’t close to the gene before
What dictates the ability of cohesin to interact with DNA in trans and cis?
'CTCF Code': x11 Zinc Finger protein gives multivalence to CTCF's recognition sequence
What does methylation of a CTCF site protect from?
Binding of Zinc Fingers 4-7 cluster together to conserved insulator (CRE) consensus sequence CCGCGNGGNGGCAG
Test your knowledge of genome organization, including physical compaction of chromosomes, nucleolus function, and evolutionary control processes. Explore how DNA is packaged into specific spaces and how chromosomes interact with each other.
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