Nucleotide excision repair: new tricks with old bricks Irene Kamileri 1, 2 , Ismene Karakasilioti 1, 2 and George A. Garinis 1, 2 1 Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece 2 Department of Biology, University of Crete, Vassilika Vouton, GR71409, Heraklion, Crete, Greece Nucleotide excision repair (NER) is a major DNA repair pathway that ensures that the genome remains func- tionally intact and is faithfully transmitted to progeny. However, defects in NER lead, in addition to cancer and aging, to developmental abnormalities whose clinical heterogeneity and varying severity cannot be fully explained by the DNA repair deficiencies. Recent work has revealed that proteins in NER play distinct roles, including some that go well beyond DNA repair. NER factors are components of protein complexes known to be involved in nucleosome remodeling, histone ubiqui- tination, and transcriptional activation of genes involved in nuclear receptor signaling, stem cell reprogramming, and postnatal mammalian growth. Together, these find- ings add new pieces to the puzzle for understanding NER and the relevance of NER defects in development and disease. NER: safeguarding genome integrity Despite its inherent physicochemical stability, the somatic genome is subject to damage that must be repaired and preserved throughout the lifetime of a cell. To meet this challenge, cells have evolved machineries to maintain telomeres intact, as well as overlapping repair pathways to counteract structural DNA modifications [e.g., nicks, gaps, DNA double-strand breaks (DSBs), and the myriad alterations that may block DNA transcription or replica- tion] [1,2]. For bulky helix-distorting damage, such as lesions induced by UV light, the principal repair mecha- nism is the evolutionarily conserved NER pathway (Figure 1). NER recognizes and removes helical distortions in two modes: throughout the genome (i.e., global genome repair, GGR), or selectively from the transcribed strand of active genes (i.e., transcription-coupled repair, TCR) [3]. In GGR, the DNA is surveyed by the xeroderma pigmento- sum, complementation group C (XPC)-RAD23-centrin, EF- hand protein, 2 (CETN2) complex [4,5], and the UV- damaged DNA-binding protein (UV-DDB) complex (DDB1-DDB2-containing E3-ubiquitin ligase complex) [6] (Figure 1a). Once the complex binds damaged DNA, RAD23 dissociates from XPC and does not participate in the remaining NER process [7]. Unwinding the DNA around a lesion and stabilizing the single-stranded DNA requires transcription factor II H (TFIIH), a 10/11-subunit complex containing XPB, p62, p52, p44, p34, p8, and XPD in addition to the Cdk-activating-kinase (CAK) complex and XPG [8] (Figure 1c). CAK is released from the core during the NER reaction. Unwinding of the DNA relies on the ATPase activity of XPB to form a 27-nucleotide bubble asymmetrically flanking the damage [9]. Together with XPA and replication protein A (RPA), XPB and XPD stabi- lize the damaged DNA for incision [10]. RPA activates XPG and excision repair cross-complementing rodent repair deficiency, complementation group 1 (ERCC1)-XPF, struc- ture-specific endonucleases that cleave the 3 0 and 5 0 side of the 24–32-nucleotide fragment containing the damaged DNA (Figure 1d). RPA is then released from DNA to initiate new incision events [10]. The single-strand gap is then filled by the replicative DNA polymerases d and e or the translesion DNA polymerase k (Figure 1e); their poly- merase activity is stimulated and coordinated by prolifer- ating cell nuclear antigen (PCNA) loaded onto the DNA by replication factors C (RFC) and A [11]. The nascent DNA fragment is finally sealed by DNA ligase III-XRCC1 [12] and DNA ligase I [13,14]. In the other mode of NER, TCR, damage recognition requires RNA polymerase II (RNAPII) (Figure 1b). Stalled RNAPII does not dissociate from its damaged template during assembly of the TCR complex [15,16]. Instead, it colocalizes with Cockayne syndrome B (CSB), a DNA- dependent ATPase [17–19] and CSA, a protein that is part of an E3-ubiquitin ligase complex [containing DDB1, Cul- lin 4A, and ring-box 1 (ROC1/Rbx1)] [20]. The E3 ligase activity is inactivated when CSA associates with the COP9 signalosome in response to UV-induced DNA damage. UV- sensitive syndrome protein A (UVSSA), a newly discovered TCR, is part of a UV-induced ubiquitinated protein com- plex that interacts with the elongating form of RNAPII and stabilizes CSB [21,22]. CSB binds stalled RNAPII and triggers the assembly of the remaining NER factors and histone acetyltransferase p300 [23]. In turn, CSA recruits (together with CSB) the nucleosomal binding protein high mobility group nucleosome binding domain 1 (HMGN1) [15,24], XPA binding protein 2 (XAB2) [25], and TFIIS [15,26]. Once chromatin is accessible for TCR, the lesion is removed by the core NER reaction [27]. NER defects: the puzzle of clinical heterogeneity and pleiotropy In humans, inborn defects in 11 out of the approximately 30 proteins involved in NER lead to the skin cancer-prone Review Corresponding author: Garinis, G.A. (garinis@imbb.forth.gr). Keywords: nucleotide excision repair; chromatin; transcription; development; aging; cancer. TIGS-970; No. of Pages 8 0168-9525/$ – see front matter ß 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.tig.2012.06.004 Trends in Genetics xx (2012) 1–8 1