Plicates and time points, as measured via internal quality controls of the Affymetrix chips. We also measured the correlation of signal intensity involving two replicas of every single time point. All samples shared a higher degree of similarity (P = 0.005 ). Extraction and Alignment of ATF3 ChIP-Seq Data. The worldwide ATF3 occupancy was extracted from ATF3 ChIP-Seq data readily available at the ENCODE database (http://genome.ucsc.edu/cgi-bin/hgFileUidb=hg19 g=wgEncodeHaibTfbs) (24, 37). Particularly, the Bed files had been extracted and proceed via GPAT software program (http://bips.u-strasbg.fr/GPAT/) to retrieve genomic annotations of ATF3 peak positions by means of the promoter window. The extracted ATF3 peak data were aligned for the microarray dataset from the CS1AN+CSBwt and CS1AN UV-treated cells, working with Galaxy software program (https://main.g2.bx.psu.edu) (Fig. S1H and Table S2). ACKNOWLEDGMENTS. We thank R. Velez Cruz, A. Zadorin, and E. Compe for fruitful discussions; Charlotte Saint-Andrfor assisting with antibody production and protein expression; plus the Institute of Genetics and Molecular and Cellular Biology Cell Culture Facility. This study was supported by grants from the European Investigation Council Advanced Scientists (to J.-M.E.), the Institut National du Cancer Grant INCA-2008-041 (to F.C.), and l’Association de la Recherche contre le Cancer (ARC) Grant 3153. U.K, was supported by a JME (Jean-Marc Egly) Sophisticated European Study Council grant and by an ARC fellowship for young scientists.Cefotaxime sodium salt M.Sigma-2 receptor antagonist 1 -A.PMID:25027343 R. was supported by the French Minist e des Affaires Etrang es (S our Scientifique de Haut Niveau).six. Eisen JA, Sweder KS, Hanawalt Pc (1995) Evolution from the SNF2 family members of proteins: Subfamilies with distinct sequences and functions. Nucleic Acids Res 23(14):2715723. 7. Troelstra C, et al. (1992) ERCC6, a member of a subfamily of putative helicases, is involved in Cockayne’s syndrome and preferential repair of active genes. Cell 71(6):93953. 8. Selby CP, Sancar A (1997) Human transcription-repair coupling factor CSB/ERCC6 is really a DNA-stimulated ATPase but is just not a helicase and will not disrupt the ternary transcription complicated of stalled RNA polymerase II. J Biol Chem 272(3):1885890. 9. Le May possibly N, et al. (2010) NER elements are recruited to active promoters and facilitate chromatin modification for transcription in the absence of exogenous genotoxic attack. Mol Cell 38(1):546. ten. Proietti-De-Santis L, DranP, Egly J-M (2006) Cockayne syndrome B protein regulates the transcriptional program just after UV irradiation. EMBO J 25(9):1915923.Kristensen et al.PNAS | Published on the internet June three, 2013 | EBIOCHEMISTRYPNAS PLUS11. van den Boom V, et al. (2004) DNA harm stabilizes interaction of CSB with the transcription elongation machinery. J Cell Biol 166(1):276. 12. Bradsher J, et al. (2002) CSB is actually a element of RNA pol I transcription. Mol Cell 10(4): 81929. 13. Balajee AS, Might A, Dianov GL, Friedberg EC, Bohr VA (1997) Lowered RNA polymerase II transcription in intact and permeabilized Cockayne syndrome group B cells. Proc Natl Acad Sci USA 94(9):4306311. 14. Selby CP, Sancar A (1997) Cockayne syndrome group B protein enhances elongation by RNA polymerase II. Proc Natl Acad Sci USA 94(21):112051209. 15. Dianov GL, Houle JF, Iyer N, Bohr VA, Friedberg EC (1997) Decreased RNA polymerase II transcription in extracts of cockayne syndrome and xeroderma pigmentosum/ Cockayne syndrome cells. Nucleic Acids Res 25(18):3636642. 16. Tantin D, Kansal A, Carey M (1997) Recruitment on the putative transc.
