Nucleotide excision repair (NER) is the most versatile DNA repair system that deals with the major UV photoproducts in DNA, as well as many other DNA adducts. The early steps of NER are well understood, whereas the later steps of repair synthesis and ligation are not. In particular, which polymerases are definitely involved in repair synthesis and how they are recruited to the damaged sites has not yet been established. We report that, in human fibroblasts, approximately half of the repair synthesis requires both pol kappa and pol delta, and both polymerases can be recovered in the same repair complexes. Pol kappa is recruited to repair sites by ubiquitinated PCNA and XRCC1 and pol delta by the classical replication factor complex RFC1-RFC, together with a polymerase accessory factor, p66, and unmodified PCNA. The remaining repair synthesis is dependent on pol epsilon, recruitment of which is dependent on the alternative clamp loader CTF18-RFC.

Cockayne syndrome (CS) is a genetic disorder characterized by developmental abnormalities and photodermatosis resulting from the lack of transcription-coupled nucleotide excision repair, which is responsible for the removal of photodamage from actively transcribed genes. To date, all identified causative mutations for CS have been in the two known CS-associated genes, ERCC8 (CSA) and ERCC6 (CSB). For the rare combined xeroderma pigmentosum (XP) and CS phenotype, all identified mutations are in three of the XP-associated genes, ERCC3 (XPB), ERCC2 (XPD), and ERCC5 (XPG). In a previous report, we identified several CS cases who did not have mutations in any of these genes. In this paper, we describe three CS individuals deficient in ERCC1 or ERCC4 (XPF). Remarkably, one of these individuals with XP complementation group F (XP-F) had clinical features of three different DNA-repair disorders--CS, XP, and Fanconi anemia (FA). Our results, together with those from Bogliolo et al., who describe XPF alterations resulting in FA alone, indicate a multifunctional role for XPF.

Highlights d RNAPII RPB1-K1268 ubiquitination is essential for transcription recovery and DNA repair d Sequential ubiquitination of RNAPII and UVSSA coordinates the recruitment of TFIIH d Strand-specific ChIPseq enables mapping of RNAPII and reveals genome-wide repair kinetics d RNAPII ubiquitination protects against neurodegeneration phenotype in Cockayne syndrome

(1) Mature miRNAs, ranging from 18 to 25 nucleotides in length, processed by two-step cleavage involving Drosha and Dicer are thought to negatively regulate messenger RNA (mRNA). The mature miRNA binds to target mRNA and induces its cleavage or translational repression depending on the degree of complementarity.(2) Although hundreds of miRNAs have been already cloned, only a small number of them have been characterized.Recently, several miRNAs have been reported to be involved in cell proliferation or apoptosis in various types of cancers. (3,4) MiR-15a and miR-16 induce apoptosis by targeting BCL2, and these miRNAs are frequently deleted or underexpressed in chronic lymphocytic leukemia.(5) Let-7 expression is reduced in lung cancer with poor prognosis, (6) and inversely correlates with expression of RAS protein, suggesting a possible mechanism for cancer cell proliferation.(7) Compared to these underexpressed miRNAs, miR-21 has an antiapoptotic function and is overexpressed in glioblastoma. Knockdown of miR-21 in glioblastoma cells induced caspase activation, resulting in apoptotic cell death.(8) Thus, miRNAs can act as both tumor suppressor and oncogene.The miR-17-92 cluster, composed of seven miRNAs (miR-17-5p, miR-17-3p, miR-18a, miR-19a, miR-20a, miR-19b, and miR-92-1) and located in intron 3 of the C13orf25 gene, is overexpressed in lung cancer and B-cell lymphoma.(9,10) Enforced expression of truncated clusters comprising miR-17-5p~19b (miR-17-19b), the vertebrate-specific portion of the miR-17-92 cluster, accelerated tumor development in a mouse B-cell lymphoma model, suggesting oncogenic function of miR-17-19b. On the other hand, O'Donnell et al. have reported that expression of oncogenic E2F1 is negatively regulated by miR-17-5p and miR-20a, members of the cluster, implying that they act as a tumor suppressors.(11) Thus, the function of the cluster is still controversial.In thyroid cancer, overexpression of several miRNAs has been reported. He et al. have reported that three miRNAs (miR-221, miR-222, and miR-146) are overexpressed in papillary thyroid carcinomas (PTC) and regulate KIT expression.(12) Another group has also shown that miR-221, miR-222 and miR-181b are overexpressed in PTC, and inhibition of miR-221 by antisense oligonucleotides led to attenuation of cell growth.(13) In follicular thyroid cancers (FTC), miR-197 and miR-346 are significantly overexpressed. (14) In vitro overexpression of either miRNA induced cell proliferation, whereas inhibition led to growth arrest. Very recently, Visone et al. have reported that significant decrease in miR-30d, miR-125b, miR-26a, and miR-30a-5p was detected in human anaplastic thyroid cancers (ACT). (15) ATC are highly aggressive and fatal tumors with less than 8 months of mean survival after diagnosis.(16) Various treatment patterns including radiation and chemotherapy have been tried in ATC, but they are mostly unsuccessful.(17) Therefore, the identification of miRNAs involved in proliferation or apoptosis in ATC cells has important therapeutic imp...

We initially performed exome-sequencing 11 of the two UV S S-A patients, Kps3 and XP24KO (details described in Methods, Supplementary Note, Table 2c). The patients were homozygous for c.367A>T mutation in UVSSA, which led to a premature termination, p.Lys123* (Fig. 1a, b). We identified the same homozygous mutation in Kps2 (sib. of Kps3), and a homozygous c.87delG, causing a frameshift p.Ile31Phefs*9, in an Israeli patient UV S S24TA (Fig. 1b, c, Supplementary Note, Supplementary Fig. 1). The identified mutations are summarized in Fig. 1d. We did not detect the 80kDa UVSSA protein in any of the UV S S-A patients (Fig. 1e). We additionally examined several mild xeroderma pigmentosum (XP) cases; in one such case, XP70TO 12 (Supplementary Table 1), we identified a homozygous p.Cys32Arg, in the UVSSA (Fig. 1c, d), implying that XP70TO is also in the UV S S-A group. The mutant protein was stably expressed in XP70TO cells (Fig. 1f, Supplementary Fig. 2a-d). 4Allele frequencies of the identified mutations in a control population were examined (Supplementary Note, Supplementary Fig. 3a). Haploinsufficiency for UVSSA is negligible as the parents of Kps2/Kps3 showed no symptoms 4 . In parallel with exome-sequencing, we performed whole-genome SNP-genotyping to identify runs-of-homozygosity (ROH) shared among the patients. We identified three overlapping-ROHs (> 1Mbps) on autosomes, one of which encompasses the UVSSA locus (Fig. 1g, Supplementary Table 3a, b, Supplementary Fig. 3b, c). No chromosome copy number variation was detected (Supplementary Fig. 3d).The above findings strongly suggest that the mutations in UVSSA in the UV S S-A patients are causal for the disease; we therefore, next examined the NER-activities in the UV S S-A cells (Fig. 2). Unscheduled-DNA-synthesis (UDS 13 , defective in XP) was nearly normal; however, RNA-synthesis-recovery (RRS 14 , defective in UV S S and in CS) was reduced in all cell-strains mutated in UVSSA ( Fig. 2a, b; UDS and RRS were measured using a recently-developed rapid non-radioactive system 15,16 ). Similarly, siRNA-based depletion of the UVSSA gene (Fig. 2c) caused a drastic reduction of RRS (Fig. 2d, Supplementary Fig. 4), whereas UDS was unaffected (Fig. 2e). Ectopic-expression of the wild-type UVSSA cDNA in UV S S-A cells restored normal RRS ( Fig. 2f; V5-tagged-UVSSA immunofluorescent-staining shown in Fig. 2g), while it did not affect RRS-level in normal, CS-A, or CS-B cells; neither ERCC8 nor ERCC6 cDNA expression in UV S S-A cells restored the RRS-level.We conclude that KIAA1530/UVSSA is the causal gene for UV S S-A.ERCC8 and ERCC6 genes are responsible for both CS and UV S S 7,8 . To evaluate whether UVSSA mutations may also result in CS-phenotypes, we sequenced 5 the UVSSA gene of 61 CS-patients whose genetic defects had not yet been determined (Supplementary Table 4). We found no obvious mutations except for four novel heterozygous changes. These changes as well as the SNPs, also found in control and UV S S-A individuals, do not affect the RRS-activity (Suppleme...