A role for cdk9-cyclin k in maintaining genome integrity

Cyclin-dependent kinase 9 (CDK9), with its cyclin T regulatory subunit, is a component of the positive transcription elongation factor b (P-TEFb) complex, which stimulates transcription elongation and also functions in co-transcriptional histone modification, mRNA processing, and mRNA export. CDK9 also binds to cyclin K but the function of this CDK9-cyclin K complex is less clear. We and others have recently shown that CDK9 functions directly in maintaining genome integrity. This activity is restricted to CDK9-cyclin K. Depletion of CDK9 or its cyclin K but not cyclin T regulatory subunit impairs cell cycle recovery in response to replication stress and induces spontanous DNA damage in replicating cells. CDK9-cyclin K also interacts with ATR and other DNA damage response and DNA repair proteins. CDK9 accumulates on chromatin and limits the amount of single-stranded DNA in response to replication stress. Collectively, these data are consistent with a model in which CDK9 responds to replication stress by localizing to chromatin to reduce the breakdown of stalled replication forks and promote recovery from replication arrest. The direct role of CDK9-cyclin K in pathways that maintain genome integrity in response to replication stress appear to be evolutionarily conserved.

[1]  P. Cramer,et al.  The Transcription Elongation Factor Bur1-Bur2 Interacts with Replication Protein A and Maintains Genome Stability during Replication Stress* , 2010, The Journal of Biological Chemistry.

[2]  Y. Shyr,et al.  Cyclin‐dependent kinase 9–cyclin K functions in the replication stress response , 2010, EMBO reports.

[3]  J. Lis,et al.  CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. , 2010, Genes & development.

[4]  L. Donehower,et al.  55K isoform of CDK9 associates with Ku70 and is involved in DNA repair. , 2010, Biochemical and biophysical research communications.

[5]  R. Rothstein,et al.  The ribonucleotide reductase inhibitor, Sml1, is sequentially phosphorylated, ubiquitylated and degraded in response to DNA damage , 2010, Nucleic acids research.

[6]  S. Jentsch,et al.  The RAD6 DNA Damage Tolerance Pathway Operates Uncoupled from the Replication Fork and Is Functional Beyond S Phase , 2010, Cell.

[7]  Z. Obradovic,et al.  Selective control of gene expression by CDK9 in human cells , 2010, Journal of cellular physiology.

[8]  K. Shirahige,et al.  SCFDia2 regulates DNA replication forks during S‐phase in budding yeast , 2009, The EMBO journal.

[9]  M. Oren,et al.  CDK9 directs H2B monoubiquitination and controls replication‐dependent histone mRNA 3′‐end processing , 2009, EMBO reports.

[10]  P. Pasero,et al.  The MRX complex stabilizes the replisome independently of the S phase checkpoint during replication stress , 2009, The EMBO journal.

[11]  A. Giordano,et al.  Role of the cyclin-dependent kinase 9-related pathway in mammalian gene expression and human diseases , 2008, Cell cycle.

[12]  W. Chazin,et al.  The Basic Cleft of RPA70N Binds Multiple Checkpoint Proteins, Including RAD9, To Regulate ATR Signaling , 2008, Molecular and Cellular Biology.

[13]  K. Cimprich,et al.  ATR: an essential regulator of genome integrity , 2008, Nature Reviews Molecular Cell Biology.

[14]  L. Johnson,et al.  The structure of P‐TEFb (CDK9/cyclin T1), its complex with flavopiridol and regulation by phosphorylation , 2008, The EMBO journal.

[15]  K. Jones,et al.  The multi-tasking P-TEFb complex. , 2008, Current opinion in cell biology.

[16]  R. Zhao,et al.  TopBP1 activates ATR through ATRIP and a PIKK regulatory domain. , 2008, Genes & development.

[17]  R. Fisher,et al.  The CDK-Activating Kinase (CAK) Csk1 Is Required for Normal Levels of Homologous Recombination and Resistance to DNA Damage in Fission Yeast , 2008, PloS one.

[18]  J. Bartek,et al.  DNA Damage Response as an Anti-Cancer Barrier: Damage Threshold and the Concept of 'Conditional Haploinsufficiency' , 2007, Cell cycle.

[19]  A. Kumagai,et al.  The Rad9-Hus1-Rad1 Checkpoint Clamp Regulates Interaction of TopBP1 with ATR* , 2007, Journal of Biological Chemistry.

[20]  L. Karnitz,et al.  The Rad9-Hus1-Rad1 (9-1-1) clamp activates checkpoint signaling via TopBP1. , 2007, Genes & development.

[21]  Grant W. Brown,et al.  Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map , 2007, Nature.

[22]  W. Chazin,et al.  Function of a Conserved Checkpoint Recruitment Domain in ATRIP Proteins , 2007, Molecular and Cellular Biology.

[23]  J. Ladias,et al.  Crystal structure of human cyclin K, a positive regulator of cyclin-dependent kinase 9. , 2007, Journal of molecular biology.

[24]  M. Arno,et al.  Genomic Screening in Vivo Reveals the Role Played by Vacuolar H+ ATPase and Cytosolic Acidification in Sensitivity to DNA-Damaging Agents Such as Cisplatin , 2007, Molecular Pharmacology.

[25]  M. Tyers,et al.  The F-Box Protein Dia2 Overcomes Replication Impedance to Promote Genome Stability in Saccharomyces cerevisiae , 2006, Genetics.

[26]  A. Shilatifard,et al.  Bur1/Bur2 and the Ctk Complex in Yeast: The Split Personality of Mammalian P-TEFb , 2006, Cell cycle.

[27]  D. Koepp,et al.  The F-box protein Dia2 regulates DNA replication. , 2006, Molecular biology of the cell.

[28]  A. Kumagai,et al.  TopBP1 Activates the ATR-ATRIP Complex , 2006, Cell.

[29]  M. Pacek,et al.  Functional uncoupling of MCM helicase and DNA polymerase activities activates the ATR-dependent checkpoint. , 2005, Genes & development.

[30]  P. Dent,et al.  Characterization of Cdk9(55) and differential regulation of two Cdk9 isoforms. , 2005, Gene.

[31]  Dimitris Kletsas,et al.  Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions , 2005, Nature.

[32]  S. Gasser,et al.  Mechanistically distinct roles for Sgs1p in checkpoint activation and replication fork maintenance , 2005, The EMBO journal.

[33]  J. Bader,et al.  A robust toolkit for functional profiling of the yeast genome. , 2004, Molecular cell.

[34]  S. Elledge,et al.  Replication protein A-mediated recruitment and activation of Rad17 complexes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[35]  S. Elledge,et al.  Mrc1 is a replication fork component whose phosphorylation in response to DNA replication stress activates Rad53. , 2003, Genes & development.

[36]  Stephen J. Elledge,et al.  Sensing DNA Damage Through ATRIP Recognition of RPA-ssDNA Complexes , 2003, Science.

[37]  J. Hurwitz,et al.  Loading of the human 9-1-1 checkpoint complex onto DNA by the checkpoint clamp loader hRad17-replication factor C complex in vitro , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[38]  A. Baldi,et al.  Cyclin T: Three forms for different roles in physiological and pathological functions , 2003, Journal of cellular physiology.

[39]  Charles Boone,et al.  A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[40]  T. Glover,et al.  ATR Regulates Fragile Site Stability , 2002, Cell.

[41]  Boris Pfander,et al.  RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO , 2002, Nature.

[42]  P. Stiegler,et al.  Activation of MyoD-dependent transcription by cdk9/cyclin T2 , 2002, Oncogene.

[43]  B. Peterlin,et al.  P-TEFb Containing Cyclin K and Cdk9 Can Activate Transcription via RNA* , 2002, The Journal of Biological Chemistry.

[44]  Rodney Rothstein,et al.  The Dun1 checkpoint kinase phosphorylates and regulates the ribonucleotide reductase inhibitor Sml1 , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[45]  Yusuke Nakamura,et al.  Cyclin K as a direct transcriptional target of the p53 tumor suppressor. , 2002, Neoplasia.

[46]  Jun Qin,et al.  ATR and ATRIP: Partners in Checkpoint Signaling , 2001, Science.

[47]  D. Baltimore,et al.  ATR disruption leads to chromosomal fragmentation and early embryonic lethality. , 2000, Genes & development.

[48]  Junmin Peng,et al.  Cyclin K Functions as a CDK9 Regulatory Subunit and Participates in RNA Polymerase II Transcription* , 1999, The Journal of Biological Chemistry.

[49]  S. Elledge,et al.  Human Cyclin K, a Novel RNA Polymerase II-Associated Cyclin Possessing Both Carboxy-Terminal Domain Kinase and Cdk-Activating Kinase Activity , 1998, Molecular and Cellular Biology.

[50]  Ping Wei,et al.  A Novel CDK9-Associated C-Type Cyclin Interacts Directly with HIV-1 Tat and Mediates Its High-Affinity, Loop-Specific Binding to TAR RNA , 1998, Cell.