ATR, I-kB, Cyclin D, Chk2, GADD45 beta, Ubiquitin, Nibrin, USP1, MDM2, GADD45 alpha, BLM, NFBD1, p53, p21, SMC1, Brca1, Claspin, CDC25A, FANCD2, FANCL, Chk1, PCNA, ATRIP, Cyclin E, Cyclin A, ATM, NF-kB, Bard1, CDK4, c-Myc, CDK2, RAD9
ATM/ATR regulation of G1/S and S/G2 checkpoints
DNA damage checkpoints are biochemical pathways that delay or arrest the cell cycle progression in response to the DNA damage. All eukaryotic cells have four phases within the cell cycle, G1, S, G2, and M, and one outside, G0 .
The G1/S checkpoint prevents cells from entering the S phase in the presence of the DNA damage by inhibiting the initiation of replication. There are two signal transduction pathways, one to initiate and one to maintain the G1/S arrest .
If the DNA damages are double-strand breaks (DSB) caused by ionizing radiation or radiomimetic agents, ataxia telangiectasia mutated serine-protein kinase ( ATM ) is activated .
The reaction that initiates the G1/S arrest is phosphorylation of cell cycle checkpoint kinase 2 ( Chk2 )  or cell cycle checkpoint kinase 1 ( Chk1 )  by ATM. Nuclear factor with BRCT domians protein 1 ( NFBD1 ) may participates in transfer signal from ATM to Chk2  and other regulators (e.g. tumor suppressor p53 ,  and breast and ovarian cancer susceptibility protein 1 ( Brca1 ) .
Phosphorylated Chk2 in turn inactivates by phosphorylation cell division cycle 25A phosphatase ( Cdc25A ). Lack of active Cdc25A results in the accumulation of the phosphorylated (inactive) form of Cdk2, which is incapable to participate in initiation of replication .
In addition, ATM may regulate oxidative stress-induced signaling cascades involving nuclear factor-kappaB ( NF-KB ), a transcription factor that is upstream of a wide variety of stress-responsive genes. For example, NF-KB activates the transcription of c-Myc  (which in turn activates transcription of Cdc25A  and tumor suppressor p53 .
If the DNA damage is caused by UV light or UV-mimetic agents, the signal leads to phosphorylation of serine/threonine-protein kinase Chk1 by ataxia telangiectasia and Rad3 related protein kinase ( ATR ) with a participation cell cycle checkpoint control rell cycle regulator RAD9 and claspin. The activated Chk1 then phosphorylates Cdc25A, leading to G1 arrest. It is shown, that ATR phosphorylates ATR interacting protein ( ATRIP ), which in turn regulates ATR expression, and is an essential component of the DNA damage checkpoint pathway .
Then this rapid response via Chk - Cdc25A pathways is followed by the p53 -mediated maintenance of G1/S arrest. In the maintenance stage, ATM or ATR phosphorylates Ser15 of p53 directly and Ser20 through activation of Chk2 or Chk1 . In addition, the essential elements of p53 regulation are ubiquitination  and sumoylation .
Phosphorylated p53 activates its target genes, including cyclin-dependent kinase inhibitor 1A ( p21 ), which binds to cyclin-dependent kinase 2 ( Cdk2 ) and cyclin-dependent kinase 4 ( Cdk4 ). It inhibits binding between Cdk and cyclins . Moreover, the DNA damage activates p53 via inhibition its repressor - the ubiquitin-protein ligase E3 MDM2 .
The intra-S-phase checkpoint is activated by damage encountered during the S phase or by unrepaired damage that escapes the S/G2 checkpoint and leads to a block in replication. In this pathway ATM phosphorylation of structural maintenance of chromosomes 1-like 1 protein ( SMC1 ) and Fanconi anemia complementation group D2 protein, isoform 1 ( FANCD2 ), with the help of Nibrin, leads to inhibition of replication. It supposed, that phosphorylation of SMC1 results to the repression sister chromatid cohesion . FANCD2 may participate in inhibition of replication via activation Brca1. Brca1 is phosphorylated by ATR (perhaps, with the aid of BML ) or ATM, and activates transcription of growth arrest and DNA-damage-inducible transcripts alpha and beta ( GADD45 alpha/beta ). In addition, the transcription of GADD45 alpha/beta may be regulated by p53. GADD45 alpha/beta was found to bind to proliferating cell nuclear antigen ( PCNA ), a protein involved in DNA replication and repair. p21 blocks the ability of PCNA to bind with Gadd45 .
In addition, Chk2/ Cdc25A pathway participates in the S/G2 checkpoint arrest too .