List of abbreviations and acronyms
Å Ångstrom
ac acetylation
ACF ATP-utilising chromatin remodelling and assembly Factor
ADP adenosine diphosphate
APS ammonium persulfate
Arg arginine
ARP actin related protein
Asf1 histone chaperone asf1
ATP adenosine triphosphate
ATR ataxia telangiectasia and Rad3 related
attB bacterial attachment site
attP phage attachment site
BAF BRG1-associated factors
BMP bone morphogenetic protein
bp base pair
BRCA1 breast cancer type 1 susceptibility protein
BRG1 Brahma-associated gene 1
BRK Brahma and Kismet domain
BRM brahma
Bromo Bromodomains
BSA bovine serum albumine
c-MyB transcriptional activator MyB C-terminal carboxy terminal
CATD domain CENP-A Targeting Domain
CenH3.3 centromere-specific histone 3 variant
CENP-A Centromere protein A
CHD chromo-helicase-DNA- binding
CHRAC chromatin remodeling and assembly complex
Chromo Chromodomain
Ci Curie
CoREST corepressor for REST
cryo-EM cryo-electron microscopy
Cys cysteine
DBD DNA binding domain
dCTP Deoxycytidine triphosphate
DDR DNA damage response
dMec Drosophila MEP-1-containing complex dMEP-1 mog interacting ectopic P granulocytes 1
DMSO Dimethyl sulfoxide
DNA deoxyribonucleic acid
dNTP desoxyribonucleotidetriphosphate
DOC1 deleted in oral cancer 1
Dpp Decapentaplegic
dsDNA double stranded
DTT Dithiothreitol
E. coli Escherichia coli
EcR ecdysone receptor
EDTA ethylenedioxy-diethylene-dinitrilo-tetraacetic acid EGTA ethylene glycol-bis-(2-aminoethyl)-N,N,N',
N'-tetraacetic acid
EMT epithelial-mesenchymal transition
en engrailed
EtBR ethidium bromide
F phenylalanine
FBS fetal bovine serum
fwd forward
Gln glutamine
H histone
HAT’s histone acetyltransferases
HDAC histone deacetylases
HDAC histone deacetylase
His histidine
HMT’s histone methyltransferases
HP1 heterochromatin protein 1
HRP horseradish peroxidase
HSA helicase sant domain
HSP90 heat shock protein 90
HSS Hand sant domain
IgG immunoglobuline G
INO80 inositol requiring 80
ISWI imitation switch
K lysine
KDM lysine demethylases
L leucine
LB Luria Bertani
Leu leucine
LSD1 Lysine-specific histone demethylase 1A
M molar
MBD2 methylated DNA binding domains 2
MBT malignant brain tumour
MDC1 Mediator of DNA damage Checkpoint 1
me methylation
ml mililiter
MTA metastasis-associated protein N-terminal amino terminal
Nap1 Nucleosome assembly protein
NASP Nuclear autoantigenic sperm protein
NuRD nucleosome remodelling and deacetylation
NURF nucleosome remodeling factor
P proline
p53 Cellular tumor antigen p53
PAA polyacrylamide
PAGE polyacrylamide gel electrophoresis
PAR poly(ADP-ribose)
PARP Poly (ADP-ribose) polymerase
PBAF polybromo-associated BAF
PBS Phosphate Buffered Saline
Pc Polycomb
PCR polymerase chain reaction
PCV posterior cross vein
PHD plant homeodomain
Phe phenylalanine
postHSA post helicase sant domain
PP1 protein phosphatase 1
PRC2 Polycomb repressive complex 2
PRMT’s protein arginine methyltransferases PVDF polyvinylidene difluoride membrane
Q glutamine
R arginine
REA restriction enzyme accessibility
rev reverse
RNA ribonucleic acid
RNA Pol II RNA polymerase II
RNAi RNA interference
RSC Remodelling the structure of chromatin
RT room temperature
S serine
SDS sodium dodecyl sulphate
SEM standard error of mean
SET-domain Su(var)3-9, Enhancer-of-zeste and Trithorax
SF2 helicase superfamily 2
SHL superhelical location
SMAD4 Mothers against decapentaplegic homolog 4 SMAD4 Mothers against decapentaplegic homolog 4
SnAC Snf2 ATP coupling
SNF sucrose non-fermentation
ssDNA single stranded DNA
Sth1 SNF2 (Two) homolog 1
SWI mating type switch
SWI/SNF switch/sucrose non-fermenting
Swr1 Swi2/Snf2-related 1
T threonine
TE Tris-EDTA
TEMED tetramethyl-ethylene diamine
TGF-β transforming growth factor β
TGFβRII transforming growth factor beta receptor II
TSG tumour suppressor genes
Tyr tyrosine
UAS Upstream activation sequence
ub ubiquitination
UV Ultra violet
V valine
Val valine
WT wild type
Y tyrosine
Zeb2 zinc-finger E-box-binding homeobox 2 ZNF521 Zinc finger protein 521
Curriculum Vitae
Publications
1) Kreher J*, Kovač K*, Bouazoune K, Mačinković I, Ernst AL, Engelen E, Pahl R, Finkernagel F, Murawska M, Ullah I, Brehm A, EcR recruits dMi-2 and increases efficiency od dMi-2-mediated remodelling to constrain transcription of hormone-regulated genes, Nature Communications (2017), Apr 5; 8:14806 (*equal contribution)
2) Kovač K et al. - Tumour-associated missense mutations in CHD4 ATPases alter their nucleosome remodelling properties (Nature Communications, in press)
List of academic teachers
My academic teachers at the University of Zagreb were: Bajraktarević, Bakran-Petricioli, Balabanić, Dolenec, Erben, Franjević, Goldstein, Habdija, Hršak, Jalšovec, Jelenić, Kalafatić, Krajačić, Krsnik-Rasol, Kučinić, Lacković-Venturin, Liber, Marinković, Marušić, Miljković, Mišetić, Mitić, Mrakovčić, Mrvoš-Sermek, Oršolić, Pavlina, Pavlica, Pevalek-Kozlina, Plenkovic-Moraj, Rudan, Sremac, Stilinović, Tadić, Ternjej, Tomić
At AgroParisTech: Mijaković
Acknowledgements
Here, I would like to thank everyone that supported me during my PhD thesis.
First and foremost, to my supervisor Alexander for giving me the opportunity to do my PhD work in his lab. Alex, thank you for your guidance and endless amounts of patience. May the Force be with you!
I would like to thank my lab colleagues - Igor, Jonathan, Stephan and Ulla for all the help and support, as well as the other members of the Brehm lab. I would like to thank former lab member - Judith Kreher, for much needed help and advice at the beginning of my work. Special thanks goes to my lab and flatmate Igor for all the conversations and, of course, endless supply of 8% SDS gels. :) Thanks to other colleagues and friends - Sara, Satis, Peeyush and Joanna, for making me laugh so many times.
Additionally, I would like to express my gratitude to prof. dr. Uta-Maria Bauer and prof. dr. Rainer Renkawitz for being part of my thesis committee throughout the years. Thank you for your suggestions and helpful comments.
Last, but definitely, not least, I want to thank my family for understanding my love for science and supporting my curiosity since childhood.
Hvala mami i tati, evo i ovo ste preživjeli. :)