≠ Sigma-factors are part of the RNA pol in the elongation phase.

√ Different sigma factors conduct/dirigieren the RNA pol to specific gene groups
√ The electrophoretic mobility shift assay (EMSA) shows the binding of transcription factors from
nuclear extracts to regulatory dna sequences
√ operons lead to the generation of polycistronic RNA.
≠ Opening a promoter strukture leads to the shutdown of transcription
√ 2-component systems transfer phosphate groups
√ eukaryotic intiation complexes for all RNA polymerases contain tbp
√ the general transcription factor TBP changes the structure of DNA.
√ The general transcription factor TBP is involved in the initiation of all eukaryotic RNA polymerases
√ the general transcription factor TF-TFIIB interacts with both RNA polymerase and TF-TFIID
≠ The nuclear run on assay measures initiation by RNA polymerase
≠ All TF of the nuclear (hormone) receptor family (beta scaffold dbd) bind to direct repeat DNA
√ In the absence of a ligand, some nuclear hormone receptors act as gene compressors/ Some
nuclear hormone receptors act as transcription suppressors in the absence of hormone.
≠ Heterodimers of nuclear hromon receptors bind to inverted repetitions of a dna sequence
√ Some nuclear hormone receptors act as a repressor if they are not bound to hormones (ligand).
≠ Heterodimeric nuclear hormone receptors bind inverted repeats
√ some nuclear hormone receptors act as transcription suppressors in the absence of hormone
≠ all eukaryotic RNA polymerases are phosphorylated in the c-terminal domain
√ Elongation of transcription requires complete removal of nucleosomes
√ In elongation, nucleosomes are completely removed from the transcribed area
√ transcription starts of transcribed genes are free of nucleosomes
√ Nucleosomes consist of one H3/H4 tetramer and two H2a/H2b dimers
≠ Nucleosomes contain accumulations of negatively charged amino acids for interaction with DNA
≠ Histon chaperone keep nucleosomes stable so that they are not destroyed by the elongating RNA pol
√ Both prokaryotes and eukaryotes have TF that react to heavy metals
≠ Transcription factors in the liver respond to the presence of lactose
√ Dimerization of STAT is regulated by tyrosine phosphorylation
√ STAT TF are activated by tyrosine phosphorylation
≠ STAT TF form dimers when their helix-turn-helix structure binds to phosphotyrosine of the partner
protein.
≠ Transcription activation domains do not receive a distinct secondary structure
≠ TF bind to the RNA polymerases
≠ monomeric transcription factors bind palindromic DNA (dimeric tacno)
≠ All bacterial TF exert negative transcription control
≠ Lactose is a co-activator for the lac-repressor (treba allolactose)
≠ the zinc finger structure contacts the small groove of DNA
√ Zn fingers form contacts to the large furrow of DNA.
√ Leucine zippers are associated with an base region in eukaryons tf
√ leucine zippers are, for example, amphipathetic helix
√ leucine zipper binds to the large furrow of DNA
√ Eukaryotic TF can regulate the elongation of transcription
≠ all eukaryotic promoters have a TATA-box
≠ the general transcription factor TFIID contains a histone methyltransferase
√ the order in which the general Tfs bind to the promoter was determined by EMSA
√ Chromatin remodelling complex contain ATPases
≠ The mediator complex mediates the bond between chromatin remodeling complex and RNA pol
√ Transcription factors can associate hats and hdacs with the chromatin of promoters
√ Chip or chip seq. are used to create chromatin characterized by histone modifications
√ Chromatin immunprecipitation and next gen seq are used to establish chromatinlandscapes,
characterized by specific histone modifications
√ Chromatin remodelling complexes can exchange histones in a nucleosome
√ Chromatin hubs can separate transcribed and non-transcribed areas of the genome.
√ Locus control regions may be involved in the formation of chromatin hubs
√ Chromatin remodeling can change the DnaSe I hypersensitivity of DNA areas
√ Transcription factors can cause the binding of chromatin remodelling complexes to chromatin
√ Active genes are recognizable by the exchange of histones for histone variants
≠ Active promoters are identified by their histone methylation pattern
√ Transcription start is generally free of histones
≠ Histone deacetylation causes methylation of DNA
≠ Elongation of transcription begins after histones have been phosphorylated
√ Bisulfide sequencing determines the methylation of histones
√ Transcription suppressors can cause the deacetylation of histones
√ With the help of reporter gene assays one can determine the binding of TFs to a promoter
≠ Chromatin immunoprecipitation/sequencing determines the position of nucleosomes within a gene
≠ Transactivating domains bind to RNA pol II
≠ Proteins of the TrithorAX group induce heterochromatin
√ DNA loops can contribute to gene expression in bacteria
≠ Activating TFs are always phosphorylated
√ The activity of TF can be determined in cotransfection assays
≠. mediatior increases the binding of TF to the general TFIID TF
√ Some tf cause the elongation factor ptefb to be caused
√ part of the general TF forms a framework structure for the rapid reinitiation of transcription
√ some transcription factors form homodimerics by interaction of zn fingers
≠. the ctd of RNA pol II binds transcription factors
√ At low oxygen partial pressure, TF yap1 is reduced and inactive
√ Tf hif is activated by low oxygen partial pressure
≠. All steroid hormone receptors bind/recognize the same DNA sequence
≠. Phosphorylation of Nfkb regulates interaction with the inhibitory subunit ikb
≠. all steroid hormone receptors are permanently bound to DNA
√ the ctcf protein is involved in the formation of DNA loops
√ Glucocorticoids increase the amount of ikb
≠. glucocorticoids release molecular chaperones from their cytoplasmic receptors
√ the activity of the co-activator beta-catenin occurs by inhibiting its degradation.
≠. Dna-binding regions of some transcription factors are formed by amphipathic helixes.
√ Phosphorylation of the coactivator Pcg1alpha (PGC1) inhibits the activation of TF Foxo1.
≠. High intracellular cholesterol levels lead to activation of TF SREB
√ Low Cholesterol concentrations cause intracellular cleavage and activation of TF SREBP
√ Tryptophan acts as corepressor of the trp operon
√ Transcription factors are able to cause binding of chromatin remodelers to chromatin
√ A transcription bubble contains mRNA DNA hybrids
≠. mRNA is complementary to the coding strand of DNA
√ DNA loop formation is important for the interaction between RNA pol and the intitation complex
√ Many transcription factors are activated by the formation of DNA loop
√ The CTCF protein is involved in the isolation of chromatin regions. The CTCF protein is at the isolation
of DNA areas involved
√ Bending of DNA by the cap protein allows the interaction of operators of the lac operon
≠. In bacterial two-component systems, a sensor protein acts as a transcription factor
√ The rudder of the Rna polymerase is needed to separate the DNA strands
≠. Backtracking of RNA polymerase is important for reverse transcription
√ The transcription factor TFIIH is an RNA polymerase kinase
≠. The mediator complex consists of basal (general) transcription factors.
≠. Insulator elements separate exon and intron sequences
≠. Catabolite repression causes inhibition of catabolic operons in E.coli
√ camp is a co-activator of catabolic genes in e.coli
≠. camp binds to plasma membrane receptors to activate TF CREB
√ The formation of DNA loops in E.coli can lead to both gene activation and gene pressure
√ Mediator makes both transcription factors and Pol II contacts
√ Polycomb complexes are epigenetic modifiers of chromatin
√ Pioneer transcription factors are due to the differentiation-related establishment of enhancer
elements involved.
√ The binding of the transcription factor CTCF is inhibited by histone methylation to imprinted loci
√ Signal transduction by MAP kinase (MAPK) activates transcription factors that contribute to serum
response bind element (SRE)
≠. CRP acts as a repressor in some prokaryotic promoters
√ CAP is a co-activator in the transcription of some bacterial genes
√ DNA secondary structure can have both activating and inhibiting effects in bacterial transcription
have.
√ polycomb complex is an epigenetic chromatin remodeller
≠. steroid hormones bind directly to DNA
√ Some nuclear hormone receptors form dimers with protein RXR
≠. Inverted sequence repetitions show that a TF binds to dNa as a dimer
√ Some Tf change their activity by changing the dimerisation partner
√ Proteolysis is necessary to activate nfkb
√ Nfkb is activated by proteolysis of an inhbitorial protein
√ Proteolysis sets the active form of TF SREBP
≠. Low oxygen concentrations lead to degradation of TF HIF-1Alpha
√ Signal transduction by the WNT receptor leads to stabilization and transcriptional activity of
betacatenin
√ Backtracking of rna polymerase is important for proofreading
√ the lac operon is under both positive and negative control
≠. in the 2-component system, the response regulator activates a histidine kinase
√ Different sigma factors bind to different RNA polymerase
≠. eukaryotic transcription starts contain binding sites for the TFIIS protein
≠. the pause of RNA polymerase is regulated by histone methylation transferase
√ Some transcription factors dimerize using amphipatic helices
≠. Nfkb is inhibited by a complex containing glycogen kinase 3a
√ Stat TF contain sh2 domains
≠. Activation of Tf srebp is on extracellular serumonz. Coupled
√ a transcription bubble contains unpaired dna strands
√ . in rna polymerase, a rudder structure helps to separate hybrid dna-rna strands
≠. backtracking of rna polymerase is important in promoter clearance
√ the mrna synthesis in e-coli ends where gene hairpin contain structures that act as transcription
terminators
≠. the termination eukaryotic transcription requires the rho factor
√ the initiation of transcription in e.coli requires the sigma factor
√ . the initiation of transcription in eukaryotes requires an initiation complex that is binds to the CTD of
RNA pol II
√ . For the elongation of eukaryotic genes, the DSIF and NELF proteins must be phosphorylated by the
ptefb complex
≠ The mediator, tFIIH and ptefb contain cyclin-dependent kinases
√. Chromatin is organized in topologically associated domains (TADS).
≠ In eubacteria, S5 of CTD is phosphorylated.
≠ DNAse I foot-printing is used to elucidated the mobility of promoters
√. Transcription launches of transcribed genes are free of nucleosomes. -false
≠ ptefb contains a histone acetyl transferase
√. CTCF binding to DNA is prevented by methylation of the binding site
≠ Active Tfs are always phosphorylated
≠ nucleosomes are formed by sequential binding of H3-H4 tetramers
√ The mediator complex mediates the contact between transcription factors and the initiation complex
of the Transcription.
≠ The general TF TFIID contains a cyclin dependent kinase
√. TBP TF leads to bending of DNA
√ The tryptophan operon in E.coli is negatively controlled and requires a co-repressor
√. Transcription factors can cause pausing RNA polymerase to elongation
≠ TEFIIb causes the phosphorylation of CTD. (Attention, this was a trap TEFIIb was misspelled)
√ DNA microarray enables expression control of multiple genes simultaneously
v Phylogenetic genome screening for transcription factor binding sequences in unknown promoter
√ Realtime PCR is a semi-quantitative method for RNA determination
≠ Y2H as evidence of binding the transcription factor to its DNA sequence
≠ Polycomb complexes have kinase function (No -> ubiquitinate)
≠ CTCF detects histone methylation
√. H3K27 Trimethylation is important for epigenetic gene regulation
≠ H3.3 found in transcriptively active regions
√ Activated promoters contain nucleosomes with K4-trimethylated H3
√ Coding DNA is always nucleosome-free
√ Chromatin Remodelling Proteins Need ATP
√ Lac-Repressor forms repression loop ?? CAP forms the loop structure: in absence of glucose and
lactose, CAP binds to CAP-binding site and allows formation of an loop, which brings the operators in
close contact? stable conformation ? respression = max!)
≠ Chromatin immunoprecipitation is a way to demonstrate transcription efficiency
√ Topoisomerases determine the twist number
≠ The initiation complex of transcription consists of polymerase-associated factors (PAFs) (Transcription
factors, form the initiation complex of transcription)
√ Histone acetylation inhibits the binding of transcriptional repressors
√ TAFs are part of the TFIID
≠ TFIIH contains histone acetyltransferase
√ TBP regulates promoters for all 3 eukaryotes RNA polymerases
√ TFIIB combines TFIID and RNA polymerase
≠ TFIIB facilitates strand separation in the formation of an open promoter complex
√ Phosphorylation of polymerase II CTD is important for mRNA capping reaction
√ Transactivating domains often do not have a clear secondary structure
√ Beta-scaffold domains contact the small furrow of DNA
≠ Bacterial transcription factors contact the -10 and -35 areas of the promoter
≠ Transcription factors bind to DNA, but always leave the DNA structure unchanged
≠ The general transcription factor TFIIH phosphorylates the alpha subunit of RNA polymerase II
≠ Some transactivating domains bind to the CTD of RNA pol II
√ In the elongation of transcription by RNA pol II, the nucleosome structure of the coding area fully
resolved
≠ Immediately after the opening of a promoter (i.e. "open conformation"), RNA pol II goes to elongation
above
≠ Phosphorylation of ctD of RNA pol II is requred DNA binding of the general TF TFIID
≠ The general transcription factor TFIIO recognizes DNA with its coiled-coil domain
≠ Transcription suppressors can cause acetylation of histones
√ TFs can recruit HATs to DNA
√ TFs can recruit HDACs to DNA
v TFs can recruit chromatin remodeling complexes to DNA