CMB2001/L04 Chromatin & Transcription Flashcards
Give the 4 main mechanisms that control chromatin structure.
Acetylation
Methylation
Ubiquitylation
Phosphorylation
Which remodelling complex is held by all cells?
Snf2-related ATPase
What is SF2?
Helicase and NTP-driven nucleic acid translocase superfamily 2
Give the 5 stages of ATP-dependent chromatin remodelling.
Sliding
Unwrapping
Eviction
Spacing
Histone variant exchange
What is Snf2?
Catalytic subunit of SWI/SNF
What does Snf2 do?
Hydrolyses 1000 ATP molecules per minute in presence of DNA or nucleosomes
Describe how SWI/SNF acts as a molecular motor.
Uses energy from ATP hydrolysis to track along DNA and induce torsion
What is the homologue of SWI/SNF in yeast?
GCN5 HAT
What is the function of bromodomains in Snf2?
Tethering to acetylated nucleosomes
Where are HATs and ATP-dependent remodellers commonly recruited?
To the same promoters
Name 3 SWI/SNF complexes in humans.
PBAF
cBAF
ncBAF
Give 2 roles of SWI/SNF complexes in humans.
General transcription
Cell cycle control via interaction with Rb & cyclin E
Development, deletion in mice results in embryonic lethality
Tumour suppression pathways
Explain how SWI/SNF is related to cancer.
Different mutations confer distinct vulnerabilities in mouse models
Tumour suppressor activity most likely due roles in facilitating transcription factor function
How do cells repress transcription?
Exploiting chromatin structure
What is chromatin structure mediated by to repress transcription?
Histone deacetylases (HDACs)
ATP-dependent remodellers
Histone methylases (heterochromatin)
What are the 4 major groups of histone deacetylases?
Class I-IV
Class III Sir2 family (SIRTUINS) require NAD as a cofactor
What are active and repressed regions of the genome described as?
Hyper/hypoacetylated
What is deacetylated of the genome mediated by?
Histone deacetylases
Act as corepressors
How do HDACs usually function?
In the context of large multi-subunit complexes
How are HDAC co-repressor complexes recruited to promoters?
By interaction with site-specific DNA binding proteins
What is the function of the NuRD complex?
Roles in normal differentiation and tumourogenesis
Which family does the NuRD complex belong to?
Mi2/CHD family
What is euchromatin? (2)
Gene-rich
Potential to be transcribed
What is heterochromatin? (3)
Gene-poor
Repetitive regions
Transcriptional silencing
E.g., centromeres and telomeres
Give 3 biochemical features of heterochromatin.
Hypoacetylation
Specific histone H3 methylation
Association of specific silencing factors
Describe the assembly of heterochromatin. (5)
Histone modifications
Binding of HP1
Nucleosome compaction
Nucleosome compaction
Recruitment of additional factors
What kind of protein is heterochromatin protein 1?
A chromodomain protein
What do chromodomains often recognise and bind?
Methylated lysine residues
What is the chromodomain of HP1 specific for?
H3 Lys9me2/3
What does the binding of HP1 trigger? (2)
Compacting of nucleosomal arrays
Recruitment of further activities that prevent recruitment/activity of RNA pol II
Describe the analysis of heterochromatin using reporter silencing analysis using ade6.
Normal wild-type - ade6 gene expressed white colonies
Silencing reported strain - ade6 silenced red colonies (red pigment from build up of adenine biosynthetic intermediate)
Mutation in gene encoding a component of heterochromatin - ade6 silencing alleviated white/pink colonies
How is the number of X-linked genes equalised in males and females?
X chromosome inactivation
By which proteins are Barr body formation controlled? (3)
Non-coding RNAs, Xist and Tsix
Describe the process of X chromosome inactivation. (5)
Later development - Xist upregulated
Xist coats chromosome
Xist recruits H3K27 methylase
Recruitment of further silencing factors
Inactive X (Xi)
