Chapter 7 Flashcards
Control of gene expression (38 cards)
In your body osteoblasts cells (bone cells) produce bone tissue but cannot store fat, while adipocyte cells (fat cells) store fat but cannot produce bone tissue? Why?
Cell types are differentiated by the amount of RNA, proteins and their modifications.
Osteoblast and adipocytes in your body share the same DNA, but express different genes.
Approximately 30-60% of genes are expressed in any given cell type, which means that a lot of genes are expressed in widely different cell types.
Alternative splicing contributes as well.
What is a housekeeping gene and what can it be use for?
A gene expressed in most cell types and encodes genes necessary for basic functions such a transcription, translation, cytoskeleton and so forth.
Housekeeping genes are generally expressed at approximately the same levels across cell type.
Housekeeping genes can normalize expression of a target gene, for example DKK-1, to the expression of a housekeeping gene.
How to TFs bind to DNA?
TFs recognize the major groove surface using multiple interactions (hydrogen, ionic and hydrophobic) rather than the actual base pairs. However, sequence specificity is achieved as the surface features are sequence-dependent. TFs use different structural motifs, commonly involving either α-helices contacting DNA (HTH, Homeodom ain, bZip, HLH), zinc fingers or β-sheets.
A motif is recognized by a TF (recepter). The genomes has several motifs, but the receptor never bind more than 10% of the motifs.
What determines which motifs are bound by the receptor?
Transcription factor cooperativity - several factors working together. It can be achieved by dimerization or by other types of protein-protein interactions and it helps to increase specificity as a larger surface is required.
This decreases the randomness.
Another contributor is DNA accessibility. A binding site may be located in nucleosome dense regions.
Cooperativity between TFs can also help overcome these boundaries by chromatin remodeling or nucleosome displacement.
What is a transcriptional co-regulator and how is it recruited to DNA?
A transcriptional co-regulator is a protein which is recruited to regulatory elements and assists in regulating transcription (remodels chromatin, modifies histone) , but is does not contact the DNA directly. Co-regulators typically bind indirectly to DNA by tethering to other proteins such as transcription factors.
What sort of mechanisms can activators use to increase transcription?
Transcriptional activators …
… promote binding of additional transcriptional regulators.
… recruit and position the RNA polymerase
… release a positioned polymerase, initiating transcription.
…release stalled polymerases.
Describe different mechanisms by which transcriptional repressors can decrease transcription?
Signal is turned off
- TFs inactivated.
TFs or co-repressors can recruit chromatin remodelers or histone modifiers to create a more closed chromatin structure, which does not allow transcription.
Another mechanism for gene repression is squelching, in which competition for co-activators between transcription factors results in re-distribution of co-activators from existing enhancers to newly formed enhancers
8) How is developmental control of gene expression achieved?
The specific combination of transcription factors and their activities determine developmental control.
For example: In drosophila embryos (single giant cell, multiple nuclei) cis-regulatory elements of the Eve gene is recognized by both transcriptional activators and repressors. The transcriptional outcome is determined by the concentrations of these transcriptional regulators.
How does eukaryotes regulate their gene expression?
Chromatin is repressive in nature
Transcriptional regulation depends on activation by making the DNA accessible.
Histone modification and transcription factors with strong motifs can penetrate heterochromatin and facilitate binding of additional TFs.
This facilitates co-factor recruitement and transcriptional activation. Is dependent on several distal regulatory regions(enhancers) and Mediator complex bridging 3d structure between enhancer and promotor.
How does prokaryotes regulate their gene expression?
Repressive structure,
Transcriptional regulation of prokaryotes is highly dependent on repressive functions.
In contrast to eukaryotes, they rely on proximal promotor regions. An example would be the LacZ operon.
What is an operon?
A functioning unit of DNA containing a cluster of genes under the control of a single promoter.
What is a locus?
Fixed position on a chromosome, like the position of a gene or a marker (genetic marker)
What is an IPS cell?
iPS cells stand for Induced Pluripotent Cells, and are non-stem cells which have been dedifferentiated by expression of master transcriptional regulators of pluripotency
(the so-called Yamanaka factors)
What is cell memory?
Cell memory is the ability of daughter cells to know what genes the parent cells expressed and thereby maintain the same cell type
What mechanisms help maintain cell memory?
It can be maintained by logical loops, such as positive feedback where TF A activates its own expression. This means that when proteins are distributed between daughter cells, the expression of A will be maintained
Why are genes close to sites occupied by various TFs higher expressed than genes near single TF binding events?
The more TFs bind, the more co-regulators are recruited.
Each TF itself is capable of interacting with various co-regulators, therefore more TFs lead to more recruitment in quantity and diversity of the TFs.
The increase in cofactor load will increase in activity.
How is eukaryotic DNA methylated?
DNA can be methylated on cytosine in the sequence CpG.
DNA methylation is typically present on both strands due to an enzyme called maintenance methyl transferase, which recognizes a methylated cytosine on one strand and methylates the paired sequence on the other strand.
How is inheritance in a daughter cell ensured?
By DNA methylation
This ensures inheritance, such that after replication one strand in each daughter cell will be methylated in the same pattern as the parent cell.
Describe how DNA methylation can repress transcription and the role of reader and writer proteins in this
One way by which DNA methylation represses transcription is by directly interfering with DNA:protein interactions.
Methyl groups on methylated cytosine bases lie in the major groove where transcription factors often contact the DNA. By blocking binding of transcription factor needed for initiation of transcription, methylation can repress gene transcription.
Furthermore, methylated CpG recruits Methyl CpG binding proteins (readers) that act as scaffold proteins for co-repressor complexes containing histone modifying enzymes such histone deacetylases and DNA methylases (writers). This leads to spreading of the repressive marks because neighboring nucleosomes and CpGs are modified and this results in repression of gene loci.
How is the methylation status correlated to differentiation capacity? How can a nuclei with highly methylated DNA in nuclei transplantation assays give rise to a new organism?
Methylation status and different capacity are inversely correlated. The more specialized a cell is, the more DNA methylation are present. Methyl transferases methylate DNA, while other proteins are capable of demethylating DNA. Thus, under the right circumstances DNA methylation can be reversed to increase a cells differentiation capacity
What is genomic imprinting and what mechanisms contribute to genomic imprinting?
Genomic imprinting is the process whereby only either the maternal or the paternal allele is expressed and the other is silenced. DNA methylation helps to control this by a variety of mechanisms. E.g. methylation of a promoter can silence the gene or it can silence an insulator such that enhancers can work across insulators
What is X chromosome inactivation and what is the mechanism of inactivation?
One of the X chromosomes in fetal embryos (at 100 cell stage) is randomly selected and silenced, and maintained throughout life as silent.
A lncRNA called Xist is expressed from a locus on the X chrosome. Xist spreads to the majority (90%) of the X chromosome recruits co-repressors and induces a stable repressive chromatin structure
What is a riboswitch? In which cells are they common?
Riboswitches are short RNA sequences present in the growing mRNA which form secondary structures.
Riboswitches are most common in bacteria.
How do riboswitches help the cell to adjust gene expression to levels of specific metabolites?
Upon binding of a small molecule riboswitches can alter conformation to affect positively or negatively transcription or translation of the mRNA.
They thus represent a way for the cell to adapt gene expression to the presence of specific metabolites.
