Chromatin recruitment of OGG1 requires cohesin and mediator and is essential for efficient 8-oxoG removal

Abstract One of the most abundant DNA lesions induced by oxidative stress is the highly mutagenic 8-oxoguanine (8-oxoG), which is specifically recognized by 8-oxoguanine DNA glycosylase 1 (OGG1) to initiate its repair. How DNA glycosylases find small non-helix-distorting DNA lesions amongst millions of bases packaged in the chromatin-based architecture of the genome remains an open question. Here, we used a high-throughput siRNA screening to identify factors involved in the recognition of 8-oxoG by OGG1. We show that cohesin and mediator subunits are required for re-localization of OGG1 and other base excision repair factors to chromatin upon oxidative stress. The association of OGG1 with euchromatin is necessary for the removal of 8-oxoG. Mediator subunits CDK8 and MED12 bind to chromatin and interact with OGG1 in response to oxidative stress, suggesting they participate in the recruitment of the DNA glycosylase. The oxidative stress-induced association between the cohesin and mediator complexes and OGG1 reveals an unsuspected function of those complexes in the maintenance of genomic stability.

[1]  B. Epe,et al.  Determination of steady-state levels of oxidative DNA base modifications in mammalian cells by means of repair endonucleases. , 1997, Carcinogenesis.

[2]  Rainer Pepperkok,et al.  Simultaneous detection of multiple green fluorescent proteins in live cells by fluorescence lifetime imaging microscopy , 1999, Current Biology.

[3]  B. Epe,et al.  Overexpression of Ogg1 in mammalian cells: effects on induced and spontaneous oxidative DNA damage and mutagenesis. , 1999, Carcinogenesis.

[4]  G. Verdine,et al.  Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA , 2000, Nature.

[5]  J. Peters,et al.  Scc1/Rad21/Mcd1 is required for sister chromatid cohesion and kinetochore function in vertebrate cells. , 2001, Developmental cell.

[6]  A. Taylor,et al.  Specific Recruitment of Human Cohesin to Laser-induced DNA Damage* , 2002, The Journal of Biological Chemistry.

[7]  A. Favier,et al.  Cellular background level of 8-oxo-7,8-dihydro-2'-deoxyguanosine: an isotope based method to evaluate artefactual oxidation of DNA during its extraction and subsequent work-up. , 2002, Carcinogenesis.

[8]  J. Reese,et al.  SWI/SNF-dependent chromatin remodeling of RNR3 requires TAF(II)s and the general transcription machinery. , 2003, Genes & development.

[9]  K. Shirahige,et al.  Postreplicative recruitment of cohesin to double-strand breaks is required for DNA repair. , 2004, Molecular cell.

[10]  R. Conaway,et al.  RNA polymerase II bypass of oxidative DNA damage is regulated by transcription elongation factors , 2006, The EMBO journal.

[11]  Antoine M. van Oijen,et al.  A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[12]  A. Lamond,et al.  Detecting Protein‐Protein Interactions In Vivo with FRET using Multiphoton Fluorescence Lifetime Imaging Microscopy (FLIM) , 2007, Current protocols in cytometry.

[13]  J. Cadet,et al.  ATP-Dependent Chromatin Remodeling Is Required for Base Excision Repair in Conventional but Not in Variant H2A.Bbd Nucleosomes , 2007, Molecular and Cellular Biology.

[14]  D. Taatjes,et al.  The Human CDK8 Subcomplex Is a Histone Kinase That Requires Med12 for Activity and Can Function Independently of Mediator , 2008, Molecular and Cellular Biology.

[15]  D. Taatjes,et al.  The human CDK8 subcomplex is a molecular switch that controls Mediator coactivator function. , 2009, Genes & development.

[16]  J. Svejstrup The interface between transcription and mechanisms maintaining genome integrity. , 2010, Trends in biochemical sciences.

[17]  B. Epe,et al.  Oxidative stress triggers the preferential assembly of base excision repair complexes on open chromatin regions , 2010, Nucleic acids research.

[18]  David A. Orlando,et al.  Mediator and Cohesin Connect Gene Expression and Chromatin Architecture , 2010, Nature.

[19]  D. Taatjes,et al.  The human Mediator complex: a versatile, genome-wide regulator of transcription. , 2010, Trends in biochemical sciences.

[20]  T. Carell,et al.  8-Oxo-7,8-dihydroguanine in DNA does not constitute a barrier to transcription, but is converted into transcription-blocking damage by OGG1 , 2011, Nucleic acids research.

[21]  J. Sweasy,et al.  Base excision repair and cancer. , 2012, Cancer letters.

[22]  D. Dorsett,et al.  The Ancient and Evolving Roles of Cohesin in Gene Expression and DNA Repair , 2012, Current Biology.

[23]  Michael D. Wilson,et al.  Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules , 2012, Genome research.

[24]  Thomas Whitington,et al.  Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites , 2013, Cell.

[25]  P. Cook,et al.  Transcription factories: genome organization and gene regulation. , 2013, Chemical reviews.

[26]  M. Werner,et al.  Mediator links transcription and DNA repair by facilitating Rad2/XPG recruitment , 2013, Genes & development.

[27]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[28]  W. Vermeulen,et al.  Distinct spatiotemporal patterns and PARP dependence of XRCC1 recruitment to single-strand break and base excision repair , 2013, Nucleic acids research.

[29]  W. Vermeulen,et al.  Mammalian transcription-coupled excision repair. , 2013, Cold Spring Harbor perspectives in biology.

[30]  N. Curtin Inhibiting the DNA damage response as a therapeutic manoeuvre in cancer , 2013, British journal of pharmacology.

[31]  A. Losada,et al.  Cohesin in cancer: chromosome segregation and beyond , 2014, Nature Reviews Cancer.

[32]  M. Suyama,et al.  Genome-wide Profiling of 8-Oxoguanine Reveals Its Association with Spatial Positioning in Nucleus , 2014, DNA research : an international journal for rapid publication of reports on genes and genomes.

[33]  B. Chait,et al.  Reconstitution of active human core Mediator complex reveals a pivotal role of the MED14 subunit , 2014, Nature Structural &Molecular Biology.

[34]  S. Armstrong,et al.  Mediator Kinase Inhibition Further Activates Super-Enhancer Associated Genes in AML , 2015, Nature.

[35]  Ching-Wei Chang,et al.  Molecular Reproduction & Development 82 : 587 – 604 ( 2015 ) FRAP , FLIM , and FRET : Detection and Analysis of Cellular Dynamics on a Molecular Scale Using Fluorescence Microscopy , 2015 .

[36]  B. Epe,et al.  Interaction with OGG1 Is Required for Efficient Recruitment of XRCC1 to Base Excision Repair and Maintenance of Genetic Stability after Exposure to Oxidative Stress , 2015, Molecular and Cellular Biology.

[37]  Laurent Guyon,et al.  Φ-score: A cell-to-cell phenotypic scoring method for sensitive and selective hit discovery in cell-based assays , 2015, Scientific Reports.

[38]  Dylan J. Taatjes,et al.  The Mediator complex: a central integrator of transcription , 2015, Nature Reviews Molecular Cell Biology.

[39]  K. Sugasawa,et al.  Human mediator MED17 subunit plays essential roles in gene regulation by associating with the transcription and DNA repair machineries , 2015, Genes to cells : devoted to molecular & cellular mechanisms.

[40]  Christopher C. Ebmeier,et al.  Identification of Mediator Kinase Substrates in Human Cells using Cortistatin A and Quantitative Phosphoproteomics. , 2016, Cell reports.

[41]  J. Guirouilh-Barbat,et al.  The Cohesin Complex Prevents the End Joining of Distant DNA Double-Strand Ends. , 2016, Molecular cell.

[42]  J. Guirouilh-Barbat,et al.  The cohesin complex prevents the end-joining of distant DNA double-strand ends in S phase: Consequences on genome stability maintenance , 2016, Nucleus.

[43]  Kian Behbakht,et al.  PARP inhibitors: Clinical utility and possibilities of overcoming resistance. , 2017, Gynecologic oncology.

[44]  Erez Lieberman Aiden,et al.  Cohesin Loss Eliminates All Loop Domains , 2017, Cell.

[45]  C. Burrows,et al.  Oxidative DNA damage is epigenetic by regulating gene transcription via base excision repair , 2016, Proceedings of the National Academy of Sciences.

[46]  J. Ellenberg,et al.  Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins , 2017, The EMBO journal.

[47]  Jaakko Nevalainen,et al.  Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields , 2017, Bioinform..

[48]  J. Soutourina Transcription regulation by the Mediator complex , 2017, Nature Reviews Molecular Cell Biology.

[49]  D. Taatjes,et al.  Regulatory functions of the Mediator kinases CDK8 and CDK19 , 2018, Transcription.