Set 8 Flashcards
. Describe the role of histone acetylation/deacetylation in regulation of transcription.
The N terminals of histones contain a lysine residue. This is generally deacetylated, and thus carries a positive charge. This allows it to bind tightly to negatively charged DNA and cause it to condense. When acetylated, the positive charge on the lysine is neutralized, so it interacts less strongly with DNA. The DNA is now less condensed and promoter regions are more available.
Describe the role of chromatin remodelling complexes in regulation of transcription.
Even when histones are acetylated, nucleosomes are still intact and in the way. Acetylation is necessary but not sufficient. Chromatin remodelling complexes Swi/Snf and RSC will allow nucleosome mobilization by translocating DNA through ATP hydrolysis. This positions enhancers and promoters in the nucleosome free gap.
Ways to remodel nucleosome organization:
- Sliding histone octamers along DNA to change sequence position
- Changing the spacing between the octamers
- Displacing octamers to form a nucleosome-free gap
Describe an influence of activators and repressors on assembly of initiation complexes.
TF can either promote or prevent GTF from binding, allowing DNA to switch transcription on/off depending on conditions within the cell.
Activators interact with GTF to promote RNAP binding to DNA.
Repressors can compete for activator binding sites, inhibit activators by interfering with their binding domains, directly repress transcription by preventing RNAP from re-entering, or indirectly repress by preventing histone acetylation.
Role of mediator?
Explain the role of enhanceosomes and architectural proteins in regulation of
transcription initiation?
An enhanceosome is the combination of TF present that promote or prevent transcription depending on the conditions of the cell. Architectural proteins will bend, loop, and change the shape of DNA within a control region so that other TF can interact with each other and GTF to promote RNAP binding and stimulate transcription.
Explain the role of mediators and insulators in regulation of transcription initiation.
Insulators set up boundaries between DNA domains which prevent activation/repression of genes; also prevent gene silencing.
Mediator controls transcription by mediating signals between DNA-binding TFs and core transcriptional machinery; forms scaffold around which the PIC forms; molecular bridge - enables communication between activators and RNAP II.
What is the role of DNA methylation in regulation of transcription initiation?
Methylated DNA = inactive chromatin (heterochromatin) - chromatin is condensed
Methylated DNA has different properties that influence the binding of regulatory proteins. The absence of methylation is necessary but not sufficient for transcription. Methylation is used to turn genes on/off during development. Housekeeping genes that are always expressed are protected from methylation: the mechanism for this is unclear, probably contain specific sequences that prevent the binding of DNA methyl transferase.
Describe how steroid hormones regulate transcription (one example is enough; remember: nuclear receptor could be in cytoplasm or in nucleus, already bound to DNA).
Ex: Nuclear steroid receptor family, class I (heat shock proteins found in the cytoplasm). When the hormone binds, steroid receptors dissociate, allowing specific response elements to enter the nucleus and influence target genes. Essentially, the receptor, when bound to its ligand, will act as a TF. May need to enter nucleus from cytoplasm, then influences gene expression.
. What is (are) the role(s) of transcription factors during development?
Distribution by diffusion of TFs during development leads to differential transcription and as a result cell differentiation. TF will regulate changes in chromatin structure and control histone acetylation. They are involved in assembling the initiation complex depending on conditions within a cell. Will also impact development, they may influence the expression of genes that code for more TF.
- Different concentrations of TFs in a developing cell can affect gene expression.
Describe the role of TBP during transcription (think about promoters for all three eukaryotic RNAPs and TATA-less RNAPII promoters – how do RNAPs bind to them; also, think about coordination of activities of all three polymerases).
TBP acts as a positioning factor for all RNAP, allowing each type to bind to its promoter: it is a commitment factor.
In RNAPI it interacts with SL1 to position it.
In RNAPII it is part of TFIID
In RNAPIII it is found in TFIIIB.
TBP also coordinates the activity of all three RNAP types by binding to other polymerase specific factors. This allows it to direct the transcription of the type of RNAP that is needed.
What is the role of Sp1 protein? What is the role of SL1 protein? What do they have in common?
- Both increase the rate of transcription and bind directly to DNA
- both associate with TBP
- Sp1: transcription factor that binds directly to DNA via a C2H2 zinc finger, enhancing transcription
Sp1 protein has a role in TATA-less promoters involving GC boxes; it binds GC boxes and interacts with TAFs which anchor TBP and allow TFIID binding to the promoter. - SL1: core-binding factor assembled by UBF- TBP + 4 TBP-associated factors specifically for RNAPI
o (sigma) responsible for ensuring RNAP is properly positioned at start point
o required for high-frequency initiation
What is unusual about type 1 and 2 promoters for RNAPIII polymerase??
Promoters are downstream and recruit TFIIIB at start and then fall off once it has bound.
-Even though both are internal, the efficiency of transcription is altered by changes in region upstream from the startpoint.
Type 1: found in genes for 5S rRNA; TFIIIA binds to box A and TFIIIC binds to boxC, enabling TFIIIB to bind upstream from start point, recruiting RNAPIII
Type 2: found in genes for tRNA; TFIIIC binds to both box A and box B downstream of start point; enables TFIIIB to bind near start point, recruiting RNAPIII (TFIIIC have to come off then)
Describe the mechanism of attenuation of the Trp operon. Explain the importance of this mechanism for a bacterium?
Attenuation depends on self binding of mRNA from the trp operon, as it is transcribed region 1 can bind with region 2 because there is lots of trp, and then the following sequence codes for a stop and only a short aa will be transcribed,
but if there is low trp in cell, the ribosome will pause waiting for that trp, and in that time sequence 2 will base pair with sequence 3, because sequence 1 is hidden within the ribosome. Then the operon is fully transcribed then translated as the two are coupled in prokaryotes. This gives basically instant response to environmental changes
Could you imagine a mechanism similar to the mechanism of attenuation of the Trp operon in Eukaryotes? Explain your reasoning.
Transcribing of rRNA in the nucleolus because there is translational activity happening there possibly coupled with transcription also if an RNA is palindromic and transcribed in the nucleus it could bind with itself if there were too many copies and the transport out of the nucleus could be paused preventing too many of something that is not needed as much to be utilized.
riboswitch.
This method of attenuation requires that transcription and translation are coupled, so it could not happen in eukaryotes. Maybe through another method.
Describe two distinctly different ways in which the trp operon is controlled by the overall availability of tryptophan.
See question 12 (if there is low tryptophan in the cell, the ribosome will pause waiting for that trp) + negative transcription regulation
Describe the mechanism responsible for shutdown of the trp operon when a plentiful supply of free tryptophan is available.
Region 1&2 of mRNA may form loop transiently - RNAP continues transcribing region 3 and 4. Ribosomes readily synthesizes Trp-enriched leader peptide coded by region 1 as plenty of Trp-charged tRNAs are available for ribosomes to rapidly incorporate Trp.
This results to termination of transcription by RNAP before reaching trp structural genes
