Non-homologous end joining

Non-homologous end joining (NHEJ) is a pathway that can be used to repair double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homologous recombination, which requires a homologous sequence to guide repair. The term "non-homologous end joining" was coined in 1996 by Moore and Haber.

NHEJ is evolutionarily conserved throughout all kingdoms of life and is the predominant double-strand break repair pathway in many organisms, including higher eukaryotes such as human and mouse. In budding yeast (Saccharomyces cerevisiae), however, homologous recombination dominates when the organism is grown under common laboratory conditions. Some species of bacteria, such as Mycobacterium tuberculosis, have an end joining pathway, while it is absent in others, like Escherichia coli.

NHEJ typically utilizes short homologous DNA sequences, termed microhomologies, to guide repair. Microhomologies in the single-stranded overhangs that are often present on the ends of double-strand breaks are used to promote restorative repair. When these overhangs are compatible, NHEJ almost always repairs the break accurately, with no sequence loss. Imprecise repair leading to loss of nucleotides can also occur, but is much less common. Nevertheless, NHEJ is often somewhat misleadingly referred to as an "error-prone" repair mechanism. This is likely because NHEJ can lead to translocations when organisms are subjected to large doses of radiation that cause many breaks per cell. Additionally, the NHEJ pathway is responsible for fusing the ends of chromosomes that have undergone telomere failure. These translocations may result in incorrect gene regulation, and (ultimately) cancer.

Proteins involved in NHEJ
A number of proteins are involved in NHEJ. The Ku heterodimer, consisting of Ku70 and Ku80, forms a complex with the DNA dependent protein kinase catalytic subunit (DNA-PKcs), which is present in mammals but absent in yeast. Ku is also involved in telomere function. The DNA Ligase IV complex, consisting of the catalytic subunit DNA Ligase IV and its cofactor XRCC4, performs the ligation step of repair. The recently discovered protein XLF, also known as Cernunnos, is homologous to yeast Nej1 and is also required for NHEJ. In yeast, the Mre11-Rad50-Xrs2 (MRX) complex is required for NHEJ and is thought to promote bridging of the DNA ends, but the corresponding mammalian complex of Mre11-Rad50-Nbs1 does not seem to be necessary. Instead, DNA-PKcs is thought to mediate end bridging. The Pol X family DNA polymerases Pol λ and Pol μ (Pol4 in yeast) fill gaps during NHEJ, and the nuclease Artemis is required for hairpin opening and may also be involved in trimming damaged or non-homologous nucleotides. In yeast, Sir2 was originally identified as an NHEJ protein, but is now known to be required for NHEJ only because it is required for the transcription of Nej1.

V(D)J Recombination
NHEJ plays a critical role in V(D)J recombination, the process by which B-cell and T-cell receptor diversity is generated in the vertebrate immune system. In V(D)J recombination, hairpin-capped double-strand breaks are created by the enzymes RAG-1 and RAG-2, which cleave the DNA at recombination signal sequences. These hairpins are then opened by the Artemis nuclease and joined by NHEJ. A specialized DNA polymerase called terminal deoxynucleotidyl transferase (TdT), which is only expressed in lymph tissue, adds nontemplated nucleotides to the ends before the break is joined. This process couples "variable" (V), "diversity" (D), and "joining" (J) regions, which when assembled together create the variable region of a B-cell or T-cell receptor gene. Unlike typical cellular NHEJ, in which accurate repair is the most favorable outcome, error-prone repair in V(D)J recombination is beneficial in that it maximizes diversity in the coding sequence of these genes. This role of NHEJ has also contributed to its reputation as an error-prone DNA repair pathway. Patients with mutations in RAG-1, RAG-2, and Artemis are unable to produce functional B cells and T cells and suffer from severe combined immunodeficiency (SCID).