What are trans-acting regulator sequences?
Proteins that act in trans by binding to cis-acting regulator sequences and consequently regulating nearby genes, either by activating or repressing transcription
aka transcription factors. An activator protein is one.
What are cis-acting regulator sequences? Where are they on the chromosome?
Sequences to which proteins bind to regulate transcription of genes located on the same chromosome as the sequence. In single-celled eukaryotes, they are upstream and near the gene they affect, in multicellular eukaryotes they can be anywhere on the chromosome
Enhancers and silencers are both cis-acting
Does distance to transcriptions start site play a major role in regulator proteins?
Distance does not play a role in influence of regulator proteins because of 3D looping
How is expression of the sonic hedgehog gene (SHH) differentially expressed in limb tissue and brain tissue?
It is modular, and there are two different enhancers for limb and brain cells. The one for brain cells is much closer to the start of transcroption, meaning the SHH gene is more often expressed in brain tissue.
What is an enhancer sequence?
A eukaryotic cis-acting DNA regulator sequence to which trans-acting factors
bind and stimulate transcription
What is an insulator sequence? Is an insulator cis-acting or trans-acting?
A cis-acting sequence that influences the ability of enhancers to initiate transcription and block enhancer actions and redirect the activity to another gene.
Why are enhancer sequences highly conserved among diverged organisms? What type of natural selection corresponds to this observation of highly conserved regions?
Natural selection makes sure that they are conserved because they are so valuable to life. Purifying selection in particular.
What is a nucleosome?
A segment of DNA
wound ~2X around eight histone
proteins.
They are not static.
Euchromatin vs heterochromatin
Euchromatin: the DNA is packaged in a way that makes it more accessible to transcription
Heterochromatin: the DNA is packaged in a way that makes it less accessible to transcription
What is facultative heterochromatin?
Accessible to transcription when there are reversible changes in nucleosomes
Open vs covered promoter
Genes that are constitutively expressed have “open” promoters that are not bound to histones.
Covered promoters have blocked transcription until nucleosomes are removed, and generally contain TATA boxes and other TF-binding sequences.
What is position effect variegation (PEV)?
A form of epigenetic modification, where a variegated eye (a mix of white and red eye colour) is due to a changed location to a heterochromatic region that partially prevents expression
What does the variegated eye phenotype look like in fruit flies? How does fruit fly eye phenotype if you SUPRESS variegation? If you ENHANCE variegation?
It looks like a mix between red and white eye colours (stripes). If you supress variegation, you partially restore the wildtype phenotype, but if you enhance variegation, you make the mutant phenotype (white) more extreme
Does histone acetylation increase or decrease gene expression? Histone deacetylation? DNA methylation?
Histone acetylation causes DNA to open up and be expressed (histone is less positively charged, making it bond less).
Histone deacetylation causes DNA to close and be less expressed.
DNA methylation generally causes less expression
What is the consequence on coat colour and body weight of hypomethylation vs methylation in the Agouti epigenetic model (i.e. in mice with the IAP promoter insertion)?
High methylation causes a darker coat colour and low Agouti expression. Low methylation caused a lighter coat colour, high Agouti expression, and overweight mice.
When a pregnant heterozygote mother mouse (with the IAP promoter insertion) is fed a normal mouse diet, what do her offspring predominantly look like? How does this compare to offspring of mothers who receive diets rich in methyl groups?
Agouti is highly expressed, and offspring appear yellow and overweight.
A diet rich in methyl groups silence the Agouti gene, and appear brown and a healthy weight.
What effect does BPA have on methylation state of the genome? Does this cause coat colour to shift towards brown or yellow?
BPA reduces methylation in the genome, causing the colour to shift towards yellow.
What is imprinting?
Most genes are expressed from both parental alleles, but imprinted genes are expressed from only one parental copy because the other is epigenetically silenced, typically via DNA methylation established in sperm or egg.
What genetic marker was used to measure methylation?
Insulin-like Growth Factor 2 (IGF2)
What made IGF2 an effective biomarker of genome methylation?
Its imprint marks are established around conception and are stable for life
How was methylation status impacted by the low caloric intake for individuals conceived during the famine? How did this differ for individuals who experienced late gestation during the famine?
Conception left adults with ~5% lower IGF2 methylation. This was not seen with late gestation exposure
What is the thrifty phenotype hypothesis?
Nutrient scarcity in utero can program energy-sparing metabolism that is great in scarcity but bad in postnatal abundance. It predisposes people to type 2 diabetes and obesity
What is epigenetic modification?
They influence transcription, and some important features are:
- chromatin structure change
- transmissible during mitosis
- reversible
- affects transcription
- does not alter nucleotide sequence of DNA
