SCIENTIFIC CONTRIBUTIONS
8.1. A BBREVIATIONS listed in alphabetical order
A
A adenine/adenosine purine base AKT1 protein kinase B/AKT1 AMPK AMP-activated protein kinase ASH1 achaete-scute homologue 1
ASSP1/2 argininosuccinate synthetase pseudogene 1/2 ATM ataxia telangiectasia mutated
ATR ataxia telangiectasia and Rad3-related protein ATRIP ATR interacting protein
A549 adenocarcinomic human alveolar basal epithelial cells B
BAX Bcl-2-associated X protein
Bmal-1 brain and muscle aryl hydrocarbon receptor nuclear translocator-
like 1
CARM1 coactivator-associated arginine methyltransferase 1
Cas9 Caspase-9
CBP CREB binding protein
CDC25 cell division cycle phosphatase 25
CDKN1A cyclin dependent kinase inhibitor 1A (p21) CDK cyclin-dependent kinase
CDK1 cyclin-dependent kinase 1 CDK2 cyclin-dependent kinase 2
CDS coding sequence
CREB cAMP response element binding protein
Ct cycle threshold value (Cq cycle quantification value) CtSD standard deviation of Ct values
CTD C-terminal domain, used for the C-term of p53 and RNAP2 C-term C-terminus/carboxyl-terminus, end of an amino acid chain CV coefficient of variation
D
dB decibel
DBD DNA binding domain
DDB1 damage specific DNA binding protein 1 DDB2 damage specific DNA binding protein 2 DMSO dimethyl sulfoxide
DNA deoxyribonucleic acid
DNA-PKcs DNA-dependent protein kinase
�Np63� an isoform of tumor protein p63 DRAM damage-regulated autophagy modulator
DSB double strand break
E
E Exon
EC ethylene carbonate
ECFP enhanced cyan fluorescent protein ECM extracellular matrix
EF elongation factor
EF1𝛼 elongation factor 1 subunit 𝛼
EGF epidermal growth factor ER endoplasmatic reticulum Erk extracellular-regulated kinase
EtOH Ethanol FI fluorescence intensity
Fig. figure
FIJI Fiji Is Just ImageJ
FISSEQ fluorescent in-situ sequencing FIT (probe) forced intercalation probe
FPKM fragments per kilobase of exon model per million reads mapped FUTP 5-fluoro-uridine-5‘-triphosphate
G
G guanine/ guanosine pyrimidine base
GADD45 growth arrest and DNA damage protein family GAPDH glyceraldehyde 3-phosphate dehydrogenase GFP green fluorescent protein
𝛄-IR 𝛄-irradiation
Golgi Golgi apparatus
GPCR G-protein coupled receptor GTF general transcription factor
Gy gray
G1-phase growth 1 (cell cycle) phase G2-phase growth 2 (cell cycle) phase G418 geniticindisulfate
H
HAT histone-acetyltransferase
HAL/R genomic homology arm left/right
HDR homology-directed repair
HER2/ERBB2 erb-B2 receptor tyrosine kinase 2
HMBS hydroxmethylbilanesynthase
HMT Histone Methyl Trasnferase
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HPRT hypoxanthine Phosphoribosyltransferase 1 IQR interquartile range
IR ionizing radiation
IRES internal ribosomal entry site J
l gene length (in the model to calculate transcription rate) L3MBTL1 lethal(3)malignant brain tumor-like protein
LPS lipopolysaccharide
LUT lookup table
M
M RNAP2 occupancy (in the model to calculate transcription rate) MAD mean absolute deviation
MAPK mitogen-activated protein kinase
MCF7 breast cancer cell line (Michigan Cancer Foundation-7) MCF10A immortalized breast epithelial cell line (Michigan Cancer Foundation-10A)
MCP MS2 coat protein
MDMX mouse double minute 2, also known as MDM4 MDM2 mouse double minute 2
MERFISH multiplexed error-robust fluorescence in-situ hybridization MES 2-(N-morpholino) ethanesulfonic acid
min minutes
miR-34a microRNA 34a
miRNA micro ribonucleic acid mInt average fluorescence intensity
M-phase mitotic phase
Mre11 double strand break repair protein MRE11A, part of the MRN complex
MRN protein complex consisting of Mre11, Rad50 and Nbs1 mRNA messenger ribonucleic acid
Msum RNAP2 coccupancy of all TSS per cell
MS2 stem-loop RNA structure from the MS2 bacteriophage genome mTOR mammalian target of rapamycin
MYC myelocytomatosis oncogene N
n sample size, or the number of genomic loci (in the model to calculate transcription rate) in this thesis
NA numerical aperture
Nbs1 nibrin, part of the MRN complex
NCS neocarcinostatin
NES nuclear export sequence
NF-�B nuclear factor kappa-light-chain-enhancer of activated B cells NGF nerve growth factor
NH2 primary amine (amino group) NHEJ non-homologous end joining
NHS N-Hydroxysuccinimide (1-Hydroxy-2,5-pyrrolidindione)
nm nanometer
NOXA also known as PMAIP1, phorbol-12-myristate-13-acetate-induced
protein 1
N-term N-terminus/amino-terminus, start of an amino acid chain O
OD oligomerization domain
P
PAGE polyacrylamide gel electrophoresis PAI-1 plasminogen activator inhibitor-1
PAM protospacer adjacent motif PBS phosphate buffered saline PCNA proliferating cell nuclear antigen
PCR polymerase chain reaction
PC12 pheochromocytoma cell line (rat adrenal medulla)
PCP PP7 coat protein
PIKK phosphatidylinositide 3-kinase-related kinase
PIN1 peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 PI3K phosphatidylinositol 3-kinase
PKA protein kinase A
PRMT1 protein arginine N-methyltransferase 1
PRD proline-rich domain
PTM post-translational modification
PPM1D protein phosphatase Mg2+/Mn2+ dependent 1D (Wip1)
poly-A polyadenylation
PP7 stem-loop RNA structure from the PP7 bacteriophage genome PUMA p53 upregulated modulator of apoptosis
PUM-HD pumilio homology domain
PUM1 pumilio RNA binding family member 1 p14ARF an alternate reading frame product of p16
p16 cyclin-dependent kinase inhibitor 2A
p300/CBP E1A binding protein p300/CREB-binding protein p53 tumor suppressor p53
Q
QCD quartile coefficient of dispersion qRT-PCR quantitative real-time PCR R
R stands for a purine base in the p53 response element Rad50 DNA repair protein RAD50, part of the MRN complex RBP RNA binding protein
RE response element
RNA ribonucleic acid
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RNAP1 DNA-directed RNA polymerase 1 RNAP2 DNA-directed RNA polymerase 2 RNAP3 DNA-directed RNA polymerase 3
RNAScope Specific RNA in-situ hybridation technique RNA-Seq RNA sequencing
RPA replication protein A
RPKM reads per kilobase million rpm revolutions per minute
RRM2B ribonucleotide reductase regulatory TP53 inducible subunit M2B
RQ relative quantification
RSD root square difference
RT room temperature
RTK receptor tyrosine kinase S
S Serine
SDHA succinate dehydrogenase complex flavoprotein subunit1 SDS sodium dodecyl sulfate
SE standard error of the mean
SESN1 sestrin1
SetD8 Set8/KMT5a, SET-Domain containing Lysine Methyltransferase 5A shRNA small hairpin ribonucleic acid
SI supplementary information
SMAD SMA (‘small’, phenotype in C. elegans) and MAD (‘mothers against decapentaplegic’, phenotype in D. melanogaster)
SMC1 structural maintenance of chromosomes protein 1 smFISH single-molecule fluorescence in-situ hybridization
Smyd2 KMT3C, SET and MYND Domain Containing Protein 2 SNR S/N, signal to noise ratio
SP1 specificity protein 1 S-phase synthesis phase (cell cycle) SSB single strand breaks
STAT signal transducer and activator of transcription protein
STD standard deviation
S100B S100 calcium-binding protein B T
T thymine/ thymidine pyrimidine nucleobase T amino acid threonine
t time
TAD trans-activation domain (of the p53 protein) TBP TATA-box binding protein
TBS tris-buffered saline
TBS-T tris-buffered saline with Tween TF transcription factor
TFIIB,D,E,F,H general transcription factors B, D, E, F, H that build the pre-
initiation complex
TGFß transforming growth factor beta TIP60 histone acetyltransferase KAT5
TNF tumor necrosis factor Top II topoisomerase II TP53 tumor protein p53
Tris tris (hydroxymethyl) aminomethane TSS transcriptional start site
U
UbCP Ubiquitine C promoter
UTR untranslated region
UV ultraviolet (radiation) U-2 OS human osteosarcoma cell line V
v RNAP2 elongation speed (in the model to calculate transcription rates)
VDAC voltage-dependent anion channel W
W adenine or thymine base in the p53 response element X
XL413 CDC7 kinase inhibitor
XRNA RNA counts per cell (in the model to calculate transcription rates) Y
Y stands for a pyrimidine base in the p53 response element Y amino acid tyrosine
YFP yellow fluorescent protein Z
Zn2+ zinc ion
0-9
5-FU 5-fluorouracil
53BP1 p53 binding protein 1 𝛼-�
𝛽 RNA export rate (in the model to calculate transcription rates) 𝛿 degradation rate (in the model to calculate transcription rates) 𝜂 correction factor for probe position (in the model to calculate
transcription rates)
𝜘 correction factor for inferred RNAP2 occupancies (in the model to calculate transcription rates)
µ transcription rate (in the model to calculate transcription rates)
µm micrometre
µTSS transcription rate per TSS (in the model to calculate transcription rates)
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