List of Abbreviations Thesis Henry Jonker: PC4 and VP16 List of Abbreviations AF-1,2 Transcriptional Activation Function of RAR, RXR AH Amphipathic Helix activation domain AP-2 Activation domain in ras-transformed PA-1 cells ARIA Ambiguous Restraints for Iterative Assignment (software for automated NOE assignment and NMR structure calculation) ARC Activator-Recruited Cofactor (Mediator complex) ATF-2 Activating transcription factor-2 ATP Adenosine triphosphate BHV-1 Bovine Herpesvirus 1 BIGGER Protein docking software (Biomolecular complex Generation with Global Evaluation and Ranking) Bob-1 B cell-specific transcription co-activator (also known as OCA-B or OBF-1) BRCA1 Breast and ovarian specific tumor suppressor protein CAK CDK-activating kinase CBP CREB binding protein CTD Carboxy Terminal Domain of the largest subunit of RNAPII CDK Cyclin-dependent protein kinase CKII Casein Kinase II c-Myb Cellular DNA-binding proto-oncogene protein encoded by the myb gene c-Myc Cellular DNA-binding proto-oncogene protein encoded by the myc gene CREB Cyclic-AMP response element binding protein CstF-64 Cleavage Stimulation Factor (polyadenylation), Human (Rna15p in yeast) CSI Chemical Shift Index, for deriving secondary structure information CTF CCAAT-binding transcription factor CYANA Combined assignment and dynamics algorithm for NMR applications (software for automated NOE assignment and NMR structure calculation) DBP Adenovirus DNA-binding protein DNA Doexyribonucleic acid ssDNA single-stranded DNA dsDNA double-stranded DNA bubble DNA open DNA, melted dsDNA DTT 1,4-dithiothreitol E2 Activation domain of the papillomavirus E1a Adenovirus activation protein EDTA Ethylene Diamine Tetra-acetic Acid EHV-1 Equine Herpesvirus 1 EMSA Electrophoretic Mobility Shift Assay ERCC2, 3 TFIIH Helicases (Excision Repair Cross Complementing), also known as XPD and XPB (Xeroderma Pigmentosum), respectively ESI Electrospray Ionization FCP1 TFIIF-associated CTD phosphatase GRIP-1 Glucocorticoid Receptor Interacting Protein 1 GST Glutathion S-transferase GTF General Transcription Factors H1,2A, ..5 Histone (1, 2A, 2B, 3, 4, 5) HADDOCK Protein docking software (High Ambiguity Driven protein-protein Docking) HAT Histone acetyl transferase HCF-1 Host Cell Factor-1 HDAC Histone deacetylase HIF1a Hypoxia-inducible transcription factor HIV Human Immunodeficiency Virus HMT Histone methyltransferase HNF4a Hepatocyte Nuclear Factor 4a HP1 Heterochromatin Protein 1 HSQC Heteronuclear single-quantum coherence HSV Herpes Simplex Virus IE Immediate Early genes of HSV IPTG Isopropyl-b-D-thiogalactopyranoside ISWI Class of chromatin remodeling complexes, (named after a drosophila ATP hydrolysing protein called Imitation SWItch) IUP Intrinsically Unstructured Protein KID Kinase-inducible activation domain of CREB KIX Domain of the coactivator CREB binding protein (CBP) MALDI-TOF Matrix Assisted Laser Desorption Ionization Time-of-Flight MDV Marek's disease virus MED Mediator polypeptides MS Mass Spectrometry MW Molecular weight NCoR Nuclear receptor core-repressor NMR Nuclear Magnetic Resonance NMRPipe Multidimensional Spectral processing software based on UNIX pipes NOE Nuclear Overhauser Enhancement NOESY NOE spectroscopy NF-B Nuclear Factor B NF-Y Nuclear Factor Y, a trimeric CCAAT-binding factor Oct-1 Octamer-motif-binding factor (POU domain transcription factor) PC4 Human Positive Cofactor 4, yeast homologue Sub1/Tsp1 PC4ntd Amino terminal domain of PC4 PC4ctd Carboxy terminal domain of PC4 PCR Polymerase Chain Reaction PDB Protein Data Bank, protein structure coordinate file PIC Pre-initiation complex Pit-1 Pituitary-specific transcription factor PKC Protein Kinase C PMSF Phenylmethylsulfonylfluoride POU DNA binding domain (acronym derived from mammalian Pit-1, Oct-1, Oct-2 and C. elegans Unc-86 factors) PSSI Probability based Secondary Structure Identification using combined chemical shift data RAP30, RAP74 RNA Polymerase-associated proteins, also known as TFIIFb and TFIIFa RAR, RXR Retinoic Acid Receptor, Retinoid X Receptor RNA Ribonucleic acid mRNA messenger RNA tRNA transfer RNA RNAPII RNA Polymerase II RPA Replication Protein A RPB1,2, ..12 RNA Polymerase II subunit 1-12 SEAC Serine and Acidic rich region of PC4ntd SMCC SRB/MED-containing cofactor complex SMRT Silencing Mediator for Retinoid and Thyroid receptors SPARKY Graphical NMR assignment and analysis program SP1 Cellular transcription factor SRB Suppressor of RNA Polymerase B (Mediator proteins) SRC-1 Steroid receptor co-activating factor-1 SWI/SNF Class of chromatin remodeling complexes, (named after the mating type SWItching and Sucrose Non Fermenting yeast genes) TAD Transcription Activation Domain TALOS Torsion Angle Likelihood Obtained from Shift and sequence similarity TAR Transactivation response element of Tat Tat Transcription Activator of HIV TAFII TBP associated factor TATA-box Core promotor DNA sequence TBE Mix for 89 mM Tris-HCl (pH 8.3), 89 mM boric acid and 2 mM EDTA TBP TATA-box Binding Protein TFIIA, B, .. Transcription factor II (A, B, D, E, F, H) TOCSY Total correlation spectroscopy TRAP Thyroid-hormone Receptor Associated protein coactivator complex VP16 Herpes Simplex virion protein 16, also known as a-TIF, ICP25 and VMW65 VP16ad VP16 activation domain VP16ad/n amino terminal part of VP16ad VP16ad/c carboxy terminal part of VP16ad VZV Varicella-Zoster virus (chicken pox and shingles)