GEBELEIN 2 Flashcards
The Mediator complex recruits the ________ after PolII clearance from the PIC.
super-elongation complex (SEC)
CDK9 and ________ are the same and are part of the SEC.
P-TEFb
Much of the _______ can remain associated at the core promoter after PolII release – may contribute to transcriptional bursting!
PIC
The processes of RNA polII initiation (TFIIH) and elongation (SEC/Cdk9/P-TEFb) are differentially controlled by ________!
kinases
_________ contain information necessary to initiate transcription at the proper base-pair.
Core promoters
Other elements contain the information to control time, place, and amount of transcription - These are ________ and _________.
promoter-proximal elements, enhancers
These control elements function by recruiting ___________.
sequence-specific TFs
________% of the genome is regulatory sequence.
20
Regulatory sequences (CRMs) account for _______ more of the human genome than exons.
10x
Disease-associated SNPs are often located in ___________ (some estimates as high as 95%).
non-coding DNA
The phenotype of a Belgian family with autosomal dominant preaxial polydactyly was caused by a mutation within an _________.
enhancer
The mutation responsible for autosomal dominant preaxial polydactyly was mapped to a long-range enhancer element within the _________ gene.
Sonic-hedgehog (Shh)
Most genes have multiple enhancers. This is known as ________.
Modularity
Enhancers can be located _______ of the promoter.
up or downstream
Enhancers can be located in ________ regions.
intronic
Enhancers can be located varying distances up to _______ away.
1mb
Enhancers regulate the _________ of transcription.
rate
Enhancers regulate the _______ of transcription.
quantity
Enhancers regulate the _______ of transcription.
time
Enhancers regulate the _______ of transcription.
place
Enhancers typically have binding sites for several different _______ – each of which is required to mediate appropriate output.
TFs
Key binding sites in enhancers are more likely to be ________ = utility of phylogenetic footprinting.
conserved
Different enhancers for different tissues is an example of ________.
Modularity
Separate enhancers and ________ contribute to making stripes in flies.
combinatorial control
Different Enhancers of the ________ gene control distinct transcription bands in the embryo.
even-skipped (eve)
________ encode ‘instructions’ for gene expression.
Cis-regulatory modules (CRMs)
A ‘typical’ CRM is _______ bps.
~200
A ‘typical’ CRM has binding sites for ______ individual transcription factors.
~3-10
TFs often have multiple regulatory domains that can participate in ______, ______, or ________.
activation, repression, or both
The ________ binds DNA in a sequence-specific manner.
DNA binding domain
Examples of DNA binding domains include _________.
homeodomain, zinc finger
Regulatory domains activate or repress by recruiting _________.
co-regulatory proteins
Examples of co-regulatory proteins include ________ such as P300 or _________.
Histone acetyltransferases (HATs), histone deacetylases (HDACs)
TFs have _________ and can tolerate some non-optimal nucleotides.
binding site preferences
___________ are more likely to be conserved than non-critical sites.
Critical binding sequences
Once bound, the TF recruits regulatory proteins that can alter __________ activity in a number of ways.
RNA polII
_______ is targeted to the HRE DNA sequence
GR
Once bound, GR interacts with multiple co-___________ proteins.
regulatory
________ is an ATPase that can move nucleosomes to expose additional TF binding sites.
SWI/SNF
_______ is a histone acetyltransferase (HAT) that alters histones to promote chromatin opening.
p300/CBP
________ is the Mediator! It bridges the distant enhancer to the promoter and RNAPolII.
ARC/DRIP/TRAP
The Mediator interacts with ________ to promote looping.
Cohesion Complexes
The Mediator links distant _______ to _________.
enhancers, promoters
The Mediator is part of the ________ that can promote RNA polII initiation.
PIC
The Mediator can promote RNA polII elongation by activating the _______.
SEC
The Mediator is part of the ________ that promotes RNA polymerase initiation via TFIIH.
preinitiation complex (PIC)
Mediator stays at the core promoter after ________ –recruit additional RNA polII which may contribute to transcriptional bursting!
PolII release
The Mediator promotes RNA polII elongation by activating the ________ that phosphorylates Ser2 on the RNA polII CTD.
SEC/cdk9/P-TEFb kinase
_________ is a transcriptional repressor that recruits an HDAC complex that promotes nucleosome closing and blocks binding.
Hairy
Regulatory proteins can have a direct link to _______ to increase PIC loading.
GTFs/RNA polII
Regulatory proteins can be multi-functional – link to GTFs/PolII and provide __________.
enzyme activities
Regulatory proteins can be ________ (modify histones)
Chromatin modifying
Regulatory proteins can be ___________ (move nucleosomes)
ATP-dependent chromatin remodeling
_________ promoters tend to be accessible (no nucleosome)
TATA box
_________ promoters tend to be bound by nucleosomes and require remodeling factors to remove them
TATA minus
The rate-limiting step in transcription from paused promoters is __________
Elongation
_________ of metazoan genes pause after 20-60nts
~70%
_______ is a negative elongation factor
NELF
Pause release is mediated by ______ – Ser 2 Phosphorylation
P-TEFb (positive transcription elongation factor)
_______ is converted into a positive elongation factor via Phosphorylation
DSIF
_________ can be part of the super-elongation complex (SEC)
P-TEFb
Sequence-specific TFs can modulate RNA polII _______, _________, or ______!
initiation, elongation, or both
To identify the promoter of a specific gene, one could generate _______ data for RNA-polymerase and look for peaks at the 5’ end of the gene
ChIP
To identify the promoter of a specific gene, one could use _________ to identify the 5’ end of the gene using available RNA-seq analysis and then search for signature motifs found in promoters (TATA, lnr, DPE, etc).
bioinformatics
To test if a region has promoter activity, one could use ________ assays to assess for promoter activity in cells.
reporter
To determine if a specific DNA sequence is required for promoter activity, one could ________ the sites and test again in reporter assays to assess for promoter activity in cells.
mutate
