Note: Differential usage of non-homologous end-joining and homologous recombination in double strand break repair

Note: Differential usage of non-homologous end-joining and homologous recombination in double strand break repair

(doi: 10.1016/j.dnarep.2006.05.022)

they mentioned that HR play dominant role in yeast, however, NHEJ contributes to DSB repair in vertebrates (my guess is that higher vertebrate genome is more complex, NHEJ is much easier to solve DSB very quick).

There is the tight regulation on the switching HR and NHEJ -- events that determine the cell to go for either HR or NHEJ is cell cycle phase and DSB nature.

DSB is lethal damage, if there is one unrepaired DSB, it can induce apoptosis.

For the cycling cell, DSB occurs mainly during the replication.

For the ionizing radiation -- i can generate break at any stages, or even the "packed chromatin" -- therefore, during the G2 and G1 which the chromosomes are packed -- it will be hard to find the homology in G2 (from sister-chromatid which is "packed") and the homology in G1 (from homology sequence in the other chromosome that is "packed". Therefore, vertebrate tends to use NHEJ more frequently than yeast.

DNA lesions associated with DNA replication --> fixed by Hr since there will be available template.

Once, there is the dsb, Ku70/80 will bind first, then, dna-pk and end up with ligase 4. HR, it requires trimming at the end of break, leaving 3’ overhang - then Rad52 and then Rad51, exit search for sequence homology, this step requires Rad54 to help searching.

This paper focuses on dt40 and yeast since those two models have been done a lot. They will focus on mammalian as well but very little, since not much studies are available.

The authors mention that S-G2 phase — there is the competition between hr and nhej for the dsb induced by gamma-irradiation, by which they observe from the KO from DT40. Rad54+Ku70 - showed more severe sensitivity toward gamma-irradiation challenge. The authors also mentioned that HR can switch back to NHEJ, if the effector molec. like Rad54 is malfunction — 3’overhang is trimmed and blunt end is generated or the specific pol (pol mu) comes to join and fill in the gap, thus, generate the blunt end again.

Focusing on S-G2 phase, it has been proposed that the choice between hr and nhej are determined by which sensor of each pathway firstly bind to the dsb. Because of the amount of Ku is much higher than the hr sensor, therefore, it it very likely nhej is much favor.

It sounds to me that Ku is the major determinant for switching to the hr. If there is any defect protein in nhej downstream of Ku, it still interferes with the rate to entering the hr. Therefore, it sound to me, in each step of nhej, there might be some feedbacks to tell the system that it should change to another available pathway to fix the remaining break.

There is the evident showed that Parp could control the hr through the interaction with Ku.  By interacting with Ku, it inhibits the function of Ku, thereby, the hr factor could access the dsb.

There are two types of induced dsb that we have to take consideration, 1.gamma irradiation and 2.replication blocked. For the yeast, any type of dsb is majorly fixed by hr. Whereas, in the higher eukaryote, the organism appeared to fix by nhej. However, it depends on the cell cycle. For the replication blockage, during the S phase, it has been reported that parp and rad18 play role in controlling nhej, thereby, hr is used during the S-phase. 

The authors mentioned that, even the same species but different cell line, the distribution between nhej and hr is also different. They also mentioned that DT40 has higher hr bc of G1 has only 20%. The authors mentioned that, even the same species but different cell line, the distribution between nhej and hr is also different. They also mentioned that DT40 has higher hr bc of G1 has only 20%.

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