Inherited Diseases - Transcriptional Regulation - Dalibor Blažek
Inherited Diseases - Transcriptional Regulation - Dalibor Blažek

PhD Topics

1.  Characterization of cyclin-dependent kinase 12 (CDK12) substrates and their roles in regulation of transcription and tumorigenesis

Supervisor: Dalibor Blažek, Ph.D.

Annotation: Cdk12 is transcriptional cyclin-dependent kinase (Cdk) found mutated in various cancers. In previous studies we found that Cdk12 maintains genome stability via optimal transcription of key homologous recombination repair pathway genes including BRCA1. Apart from the C-terminal domain of RNA Polymerase II other cellular substrates for both kinases are not known. In this research we propose using a screen in cells carrying an analog sensitive mutant of CDK12 to discover its novel cellular substrates. The substrates and their roles in normal and cancerous cells will be characterized by various techniques of molecular biology and biochemistry.

Recommended literature:

  1. Pilarova K, Herudek J, Blazek D.*: CDK12: Cellular functions and therapeutic potential of versatile player in cancer: Nucleic Acids Research Cancer (Oxford University Press) k2 (1): zcaa003 (2020)
  2. Chirackal Manavalan A.P., Pilarova K., Kluge M., Bartholomeeusen K., Oppelt J., Khirsariya P., Paruch K., Krejci L., Friedel C.C., Blazek D* : CDK12 controls G1/S progression via regulating RNAPII processivity at core DNA replication genes. EMBO reports 20(9):47592 (2019)
  3. Ekumi KM, Paculova H, Lenasi T, Pospichalova V, Bösken CA, 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 Research  43(5):2575-89 (2015)
  4. Bösken CA, Farnung L, Hintermair C, Merzel Schachter M, Vogel-Bachmayr K, Blazek D, Anand K, Fisher RP, Eick D, Geyer M. The structure and substrate specificity of human Cdk12/Cyclin K. Nature Communications 5 (2014).
  5. Blazek D*., Kohoutek J., Bartholomeeusen K., Johansen E., Hulinkova P., Luo Z., Cimermancic P.,Ule J., Peterlin B.M.: The CycK/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes. Genes and Development  25 (20): 2158-2172 (2011).

Funding: NPU

Keywords: transcription, DNA damage, cancer, genomics, proteomics

Number of positions: 1

Information on the supervisor: current PhD students: 1, alumni: 1, terminated studies: 1

Keywords: cyclin-dependent kinases, Cdk12, transcription, recombination repair pathway genes, genome stability, DNA damage, BRCA1, cancer

2. Functions of cyclin-dependent kinase 11 (CDK11) in regulation of gene expression

Supervisor: Dalibor Blažek

Annotation: CDK11 is ubiquitously expressed in all tissues and the CDK11 null mouse is lethal at an early stage of development indicating an important role for Cdk11 in the adult as well as during development. CDK11 is believed to play a role in RNAPII-directed transcription and co-transcriptional mRNA-processing, particularly alternative splicing and 3´end processing. However, its genome-wide function in regulating the human transcriptome is unknown. Notably, several recent studies identified CDK11 as a candidate essential gene for growth of several cancers therefore, understanding the molecular mechanism(s) of CDK11-dependent gene expression would be also of significant clinical interest. In this research we will use various techniques of molecular biology and biochemistry to characterize genome-wide role of CDK11 in regulation of gene expression.

Recommended literature:

  1. Gajduskova, P., Ruiz de Los Mozos I, Rajecky M., Hluchy M., Ule J., Blazek D*: CDK11 is required for transcription of replication dependent histone genes. Nature Structural & Molecular Biology  27 (5):500-510 (2020)

Funding: NPU

Keywords: CDK11, histone genes, cancer, proteomics, genomics

Number of positions: 1Information on the supervisor: current PhD students: 1, alumni: 1, terminated studies: 1