DNA in human cells is constantly assaulted by endogenous and exogenous DNA damaging agents. It is vital for the cell to respond rapidly and precisely to DNA damage to maintain genome integrity and reduce the risk of mutagenesis. Sophisticated reactions occur in chromatin surrounding the damaged site leading to the activation of DNA damage response (DDR), including transcription reprogramming, cell cycle checkpoint, and DNA repair. Histone proteins around the DNA damage play essential roles in DDR, through extensive post-translational modifications (PTMs) by a variety of modifying enzymes. One PTM on histones, monoubiquitylation, has emerged as a key player in cellular response to DNA damage. In this review, we will (1) briefly summarize the history of histone H2A and H2B ubiquitylation (H2Aub and H2Bub, respectively), (2) discuss their roles in transcription, and (3) their functions in DDR. KeywordsUV damage; RNA Pol II stalling; Deubiquitylation; Chromatin remodeling PrologueAs a part of Mick Smerdon's "DNA Repair Shop" group, Peng (a former postdoctoral fellow) and I (Rithy, his last graduate student) would like to thank Mick for his guidance and for allowing us to work for him. It has been easy to discuss our projects with Mick, and his breadth of knowledge on DNA repair has allowed us to gain new perspectives on our projects. Our conversations with Mick will not just give us insight on DNA repair but also life. Sometimes a "quick" 5-min conversation in his office may turn into one hour plus tangent on the ETH Zürich University or his makeshift fluorometer, but it will eventually relate back to the original topic of nucleosomes and excision repair. Mick has been a supportive mentor and an invaluable teacher; therefore, we would like to dedicate this review to Mick Smerdon.

Histone H2B monoubiquitylation plays an important role in RNA polymerase II (RNAPII) elongation. Whether this modification responds to RNAPII stalling is not yet known. We report that both yeast and human cells undergo a rapid and significant H2B deubiquitylation after exposure to UV irradiation. This deubiquitylation occurs concurrently with UV-induced transcription arrest and is significantly reduced in a DNA damage-bypassing RNAPII yeast mutant. Consistent with these results, yeast deubiquitylases Ubp8 and Ubp10 are associated with the RNAPII complex. Moreover, simultaneous deletion of Ubp8 and Ubp10 leads to a lack of H2B deubiquitylation after UV exposure. Consequently, nucleotide excision repair at an actively transcribed gene locus is decreased, whereas UV-induced RNAPII degradation is increased in ubp8Δubp10Δ mutant cells. These results indicate that eukaryotic cells respond to RNAPII arrest by deubiquitylating H2B to coordinate DNA repair and RNAPII degradation.chromatin | nucleosome | epigenetics | transcription-coupled repair

A critical feature of the intermolecular contacts that bind DNA to the histone octamer is the series of histone arginine residues that insert into the DNA minor groove at each superhelical location where the minor groove faces the histone octamer. One of these "sprocket" arginine residues, histone H4 R45, significantly affects chromatin structure in vivo and is lethal when mutated to alanine or cysteine in Saccharomyces cerevisiae (budding yeast). However, the roles of the remaining sprocket arginine residues (H3 R63, H3 R83, H2A R43, H2B R36, H2A R78, H3 R49) in chromatin structure and other cellular processes have not been well characterized. We have genetically characterized mutations in each of these histone residues when introduced either singly or in combination to yeast cells. We find that pairs of arginine residues that bind DNA adjacent to the DNA exit/entry sites in the nucleosome are lethal in yeast when mutated in combination and cause a defect in histone occupancy. Furthermore, mutations in individual residues compromise repair of UV-induced DNA lesions and affect gene expression and cryptic transcription. This study reveals simple rules for how the location and structural mode of DNA binding influence the biological function of each histone sprocket arginine residue.KEYWORDS nucleotide excision repair; cryptic transcription; nucleosome; histone assembly T HE histone octamer, which is composed of two copies each of histones H2A, H2B, H3, and H4, binds with high affinity to $147 bp of DNA to form the nucleosome core particle. Histone-DNA binding is mediated by .100 histone main-chain and side-chain interactions with the DNA sugarphosphate backbone and a similar number of indirect water-mediated interactions (Davey et al. 2002;Muthurajan et al. 2003). These interactions occur primarily at 14 locations in the nucleosome structure where the DNA minor groove faces the histone octamer [superhelical locations (SHL) 26.5 to 6.5] (Luger et al. 1997). At each of these locations, an arginine side chain extends into the DNA minor groove and makes extensive contacts with the DNA backbone ( Figure 1A).We will refer to the arginine residues that insert into the DNA minor groove as "sprocket" arginines, since they engage the DNA "chain" like the teeth of a bicycle sprocket wheel. Sprocket arginine residues are highly conserved (Muthurajan et al. 2003;Sullivan and Landsman 2003), and the insertion of sprocket arginine side chains into the DNA minor groove comprises a significant fraction of the solvent accessible surface area that is buried upon histone-DNA binding (Davey et al. 2002). Studies have suggested that sprocket arginine-DNA contacts may play an important role in the rotational positioning of nucleosomes (Luger et al. 1997;Harp et al. 2000;Rohs et al. 2009;Wang et al. 2010;West et al. 2010). For example, short poly(A) stretches narrow the DNA minor groove, potentially enhancing electrostatic interactions between the DNA phosphate backbone and the sprocket arginine (Rohs et al. 2009;West et al. 201...

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with no known cure that affects at least five million people worldwide. Monozygotic twin concordance and familial aggregation studies strongly suggest that lupus results from genetic predisposition along with environmental exposures including UV light. The majority of the common risk alleles associated with genetic predisposition to SLE map to genes associated with the immune system. However, evidence is emerging that implicates a role for aberrant DNA repair in the development of lupus. Here we summarize our current knowledge of the potential association of lupus with mutations in DNA repair genes. We also discuss how defective or aberrant DNA repair could lead to the development of lupus.

Histone amino-terminal tails (N-tails) are required for cellular resistance to DNA damaging agents; therefore, we examined the role of histone N-tails in regulating DNA damage response pathways in Saccharomyces cerevisiae. Combinatorial deletions reveal that the H2A and H3 N-tails are important for the removal of MMS-induced DNA lesions due to their role in regulating the basal and MMS-induced expression of DNA glycosylase Mag1. Furthermore, overexpression of Mag1 in a mutant lacking the H2A and H3 N-tails rescues base excision repair (BER) activity but not MMS sensitivity. We further show that the H3 N-tail functions in the Rad9/Rad53 DNA damage signaling pathway, but this function does not appear to be the primary cause of MMS sensitivity of the double tailless mutants. Instead, epistasis analyses demonstrate that the tailless H2A/H3 phenotypes are in the RAD18 epistasis group, which regulates postreplication repair. We observed increased levels of ubiquitylated PCNA and significantly lower mutation frequency in the tailless H2A/H3 mutant, indicating a defect in postreplication repair. In summary, our data identify novel roles of the histone H2A and H3 N-tails in (i) regulating the expression of a critical BER enzyme (Mag1), (ii) supporting efficient DNA damage signaling and (iii) facilitating postreplication repair.