My note on paper: The ubiquitous role of ubiquitin in the DNA damage response

Paper: The ubiquitous role of ubiquitin in the DNA damage response
(doi:10.1016/j.dnarep.2010.09.011)

Ubiquitination can lead to:
1. conformational changes
2. cellular localization
3. enzymatic activity
4. protein-protein interaction
5. life time of protein

Purpose of this review:
To inform the relationship between ubiquitination and DNA repair and checkpoint control

Now it changes to 3 types (E3 ubiquitin ligase):
1. HECT
2. RBR
3. RING type

Monoubiquitylation
1. endocytosis
2. DNA repair and replication
3. Transcriptional regulation and modulation of histone code

Ubiquitin has 7 lysine

Small Ubiquitin-like Modifier (or SUMO) 

proteins are a family of small proteins that are covalently attached to and detached from other proteins in cells to modify their function

DSB occur -- 

1. the franking chromatin on the DSB -- sites for recruiting the DNA repair factors -- cause the foci phenotype

2. Foci formation is the results of ubiquitylation

DSB recognized by --

1. MRN cpx (MRE11,RAD50,NBS1)

2. Ku70/80

---

Later recruit;

1. ATM (kinase) -- major player

2. DNA-PK (kinase) -- minor player 

These two work toward DNA damage response network;

1. activation of cell cycle checkpoint

2. initiate DNA repair

These two -- phosphorylated H2Ax variant and marking the damage site

- H2Ax is recognize by MDC1 (mediator of DNA damage checkpoint)

- MDC1 is important for 53BP1 foci and BRCA1 foci

Molecular mechanism of MDC1 to recruit the mediators; 53BP1 and BRCA1 - is related to ubiquitylation

RNF8 -- 

1. is E3 ubiquitin ligase and is recruited to MDC1-P

2. RNF8 interact with UBC13 (E2) and H2A/H2Ax (transferring Ub to both H2A/H2Ax) - not for proteasomal degradation but for DSB marking

3. is important for re-localization of 53BP1 and BRCA1 to DSB

4. ubiquitination process of RNF8 promotes downstream signalling and repair factors to damage site

5. RNF8 alone is not enough to recruit checkpoint and repair factors to DSB sites -- it requires RNF168 to amplify the signal by add more ubiquitin to histone and other substrate

6. RNF8-RNF168 ubiquitinylation is the  critical point to sustain downstream checkpoint recruitment and DNA repair factors; like BRCA1, RAD18 and 53BP1

RNF8 pathway:
Question remain for the cascade of RNF8-RNF168 and ubiquitinylation activity

More evident supports RAD18 (RING E3) accumulate at the DSB sites and downstream of RNF8-RNF168; by this time, 2010, the role of RAD18 is not clear yet but it appears to contribute on homologous recombination

The gap:
1. the mechanism of how SUMOylation play role in downstream process of RNF8 is still unclear
2. the crosstalk between ubiquitinylation+SUMOylation is still unclear

HERC2 (HECT-type E3) --
1. bind to FHA domain of RNF8
2. stabilize the interaction of RNF8-RNF168

The Gap;
Exact function is needed to be confirmed

BRCA1 --
accumulate the DSB site through the adaptor (RAP80; contain ubiquitin interacting motif -- can bind ubiquitin)

RAP80 --
selectively bind UbK63 but not bind monoubiquitylated protein or UbK48 chains

53BP1 --
relied on the RNF8-RNF168 ubiquitinylation complex to form foci formation

Research gap;
Exact function is still unclear how 53BP1 being recruited to DSB

It has been postulated that ubiquitinylation process remodels nucleosomes surrounding DSB sites (methylated H4K20 -- methylated histone 4 at Lys-20) and making 53BP1 can be accessed to the DSB

FANCL --
1. E3 Ubiquitin ligase
2. activation of FA -- monoubiquitinylation of FANCD2 and FANCI (very conserve)

Polycomb group proteins maintain the gene-expression pattern of different cells that is set during early development by regulating chromatin structure. In mammals, two main Polycomb group complexes exist — Polycomb repressive complex 1 (PRC1) and 2 (PRC2). PRC1 compacts chromatin and catalyses the monoubiquitylation of histone H2A

ICP0 protein --
virally encoded ligase can regulate the expression of RNF8 and RNF168 - therefore, limiting the foci of 53BP1 once treated with the IR

PCNA in TLS --
1. being control by ubiquitinylation
2. switching from replicative polymerases to translesion polymerases

DNA damage checkpoint control by ubiquitination:
1. cause the cell to divide slow or stop dividing
2. mammalian; ATM-CHK2 and ATR-CHK1

Conclusion:

Gap for RNF8/RNF168/BRCA1 pathway on the physiological function

Gap for ubiquitination type of histone (poly or mono), also which type of histone (H2Ax or H4) - that corresponding to the DNA damage,  repair and checkpoint