Engineering an analog-sensitive CDK12 cell line using CRISPR/Cas

Biochimica et Biophysica Acta - Gene Regulatory Mechanisms

Volumn 1849, Issue 9, 2015, Pages 1179-1187

  Bartkowiak, Bartlomiej ^a   Yan, Christopher ^a   Greenleaf, Arno L ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Analog sensitive; CDK12; Cell line; CRISPR Cas; CTD phosphorylation; Unintended splice site

Indexed keywords

CYCLIN DEPENDENT KINASE; CDK12 PROTEIN, HUMAN; DNA;

ARTICLE; CELL CLONING; CELL GROWTH; CELL LINE; CELL PROLIFERATION; CONTROLLED STUDY; CRISPR CAS SYSTEM; GENETIC ENGINEERING; GROWTH RATE; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; GENE SILENCING; GENETICS; HELA CELL LINE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY;

MAMMALIA;

BASE SEQUENCE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CYCLIN-DEPENDENT KINASES; DNA; GENE KNOCKDOWN TECHNIQUES; HELA CELLS; HUMANS; MOLECULAR SEQUENCE DATA; SEQUENCE HOMOLOGY, NUCLEIC ACID;

EID: 84938149922     PISSN: 18749399     EISSN: 18764320     Source Type: Journal    
DOI: 10.1016/j.bbagrm.2015.07.010     Document Type: Article

References (29)

1. Corden J.L. RNA polymerase II C-terminal domain: tethering transcription to transcript and template. Chem. Rev. 2013, 113:8423-8455.
2. Bartkowiak B., Mackellar A.L., Greenleaf A.L. Updating the CTD Story: from tail to epic. Genet. Res. Int. 2011, 2011:623718.
3. Eick D., Geyer M. The RNA polymerase II carboxy-terminal domain (CTD) code. Chem. Rev. 2013, 113:8456-8490.
4. Hsin J.P., Manley J.L. The RNA polymerase II CTD coordinates transcription and RNA processing. Genes Dev. 2012, 26:2119-2137.
5. Phatnani H.P., Greenleaf A.L. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 2006, 20:2922-2936.
6. Bartkowiak B., Liu P., Phatnani H.P., Fuda N.J., Cooper J.J., Price D.H., Adelman K., Lis J.T., Greenleaf A.L. CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1. Genes Dev. 2010, 24:2303-2316.
7. Blazek D., Kohoutek J., Bartholomeeusen K., Johansen E., Hulinkova P., Luo Z., Cimermancic P., Ule J., Peterlin B.M. The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes. Genes Dev. 2011, 25:2158-2172.
8. Bowman E.A., Bowman C.R., Ahn J.H., Kelly W.G. Phosphorylation of RNA polymerase II is independent of P-TEFb in the C. elegans germline. Development 2013, 140:3703-3713.
9. Marshall N.F., Peng J., Xie Z., Price D.H. Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J. Biol. Chem. 1996, 271:27176-27183.
10. Marshall N.F., Price D.H. Purification of P-TEFb, a transcription factor required for the transition into productive elongation. J. Biol. Chem. 1995, 270:12335-12338.
11. Chao S.H., Price D.H. Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription in vivo. J. Biol. Chem. 2001, 276:31793-31799.
12. Davidson L., Muniz L., West S. 3' end formation of pre-mRNA and phosphorylation of Ser2 on the RNA polymerase II CTD are reciprocally coupled in human cells. Genes Dev. 2014, 28:342-356.
13. Eifler T.T., Shao W., Bartholomeeusen K., Fujinaga K., Jager S., Johnson J., Luo Z., Krogan N., Peterlin B.M. CDK12 increases 3' end processing of growth factor-induced c-FOS transcripts. Mol. Cell. Biol. 2004, 35:468-478.
14. Bartkowiak B., Greenleaf A.L. Expression, purification, and identification of associated proteins of the full-length hCDK12/CyclinK complex. J. Biol. Chem. 2015, 290:1786-1795.
15. Bosken C.A., Farnung L., Hintermair C., Merzel Schachter M., Vogel-Bachmayr K., Blazek D., Anand K., Fisher R.P., Eick D., Geyer M. The structure and substrate specificity of human Cdk12/Cyclin K. Nat. Commun. 2014, 5:3505.
16. Joshi P.M., Sutor S.L., Huntoon C.J., Karnitz L.M. Ovarian cancer-associated mutations disable catalytic activity of CDK12, a kinase that promotes homologous recombination repair and resistance to cisplatin and poly(ADP-ribose) polymerase inhibitors. J. Biol. Chem. 2014, 289:9247-9253.
17. Ekumi K.M., Paculova H., Lenasi T., Pospichalova V., Bosken C.A., Rybarikova J., Bryja V., Geyer M., Blazek D., Barboric M. Ovarian carcinoma CDK12 mutations misregulate expression of DNA repair genes via deficient formation and function of the Cdk12/CycK complex. Nucleic Acids Res. 2015, 43:2575-2589.
18. Bajrami I., Frankum J.R., Konde A., Miller R.E., Rehman F.L., Brough R., Campbell J., Sims D., Rafiq R., Hooper S., Chen L., Kozarewa I., Assiotis I., Fenwick K., Natrajan R., Lord C.J., Ashworth A. Genome-wide profiling of genetic synthetic lethality identifies CDK12 as a novel determinant of PARP1/2 inhibitor sensitivity. Cancer Res. 2014, 74:287-297.
19. Blazek D. The cyclin K/Cdk12 complex: an emerging new player in the maintenance of genome stability. Cell Cycle 2012, 11:1049-1050.
20. Liang K., Gao X., Gilmore J.M., Florens L., Washburn M.P., Smith E., Shilatifard A. Characterization of human cyclin-dependent kinase 12 (CDK12) and CDK13 complexes in C-terminal domain phosphorylation, gene transcription, and RNA processing. Mol. Cell. Biol. 2015, 35:928-938.
21. Blethrow J., Zhang C., Shokat K.M., Weiss E.L. Design and use of analog-sensitive protein kinases. Curr. Protoc. Mol. Biol. 2004, Suppl. 66:18.11.1-18.11.19.
22. Shah K., Liu Y., Deirmengian C., Shokat K.M. Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:3565-3570.
23. Mali P., Yang L., Esvelt K.M., Aach J., Guell M., DiCarlo J.E., Norville J.E., Church G.M. RNA-guided human genome engineering via Cas9. Science 2013, 339:823-826.
24. Ran F.A., Hsu P.D., Wright J., Agarwala V., Scott D.A., Zhang F. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 2013, 8:2281-2308.
25. Rodrigues F., Thuma L., Klambt C. The regulation of glial-specific splicing of Neurexin IV requires HOW and Cdk12 activity. Development 2012, 139:1765-1776.
26. Jones J.C., Phatnani H.P., Haystead T.A., MacDonald J.A., Alam S.M., Greenleaf A.L. C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA polymerase II C-terminal domain repeats. J. Biol. Chem. 2004, 279:24957-24964.
27. Chapman R.D., Heidemann M., Albert T.K., Mailhammer R., Flatley A., Meisterernst M., Kremmer E., Eick D. Transcribing RNA polymerase II is phosphorylated at CTD residue serine-7. Science 2007, 318:1780-1782.
28. Heidemann M., Hintermair C., Voss K., Eick D. Dynamic phosphorylation patterns of RNA polymerase II CTD during transcription. Biochim. Biophys. Acta 2013, 1829:55-62.
29. Vaughn J.P., Davis P.L., Jarboe M.D., Huper G., Evans A.C., Wiseman R.W., Berchuck A., Iglehart J.D., Futreal P.A., Marks J.R. BRCA1 expression is induced before DNA synthesis in both normal and tumor-derived breast cells. Cell Growth Differ. 1996, 7:711-715.