Lecture 5: Regulation of Gene Expression Flashcards
Constitutive Genes
Aka “housekeeping genes.”
Genes expressed in all cells because they provide basic functions needed for sustenance of all cells.
Global Regulatory Mechanism
Not specific for a given gene, but affect the expression of many genes.
Nucleosome
A complex of an octomer of histones with wound DNA.
Heterochromatin
Transcriptionally inactive and not accessible to limiting amounts of DNase I.
Euchromatin
Transcriptionally active and accessible to limiting amounts of DNase I.
Hypersensitive Sites
Sections of chromatin (usually in control regions) that are very sensitive to DNase I.
Locus Control Region
Appears to regulate chromatin organization over chromosomal domains.
Is where sensitivity to DNase I begins along the gene.
SWI-SNF
Protein complexes that can alter chromatin structure.
“Pushin’ nucleosomes around.”
Where can SWI-SNF complexes be found?
Globally.
However, it is thought that some complexes may target specific genes.
Histone Acetylation
Occurs on LYSINE residues, which leads to unfolding of chromatin.
What enzyme is responsible for acetylation of lysine residues on chromatin?
Histone Acetyltransferase (HAT)
HAT
Histone Acetyltransferase; a transcriptional “activator.”
HDAC
Histone Deacetylase; a transcriptional “repressor.”
What is the role of methylation on promoter regions?
More methylation is associated with diminished gene expression.
Hypermethylation
Diminished gene expression.
Hypomethylation
Increased gene activity.
CpG Methylation
A key mediator of X-inactivation and other epigenetic effects.
What is the significance of understanding CpG?
It provides a mechanism for producing heritable changes in gene expression that does not depend on DNA sequence changes.
DNA Methyltransferase
Adds a methyl group to the fifth carbon of atom of some, but not all cytosine residues in CpG dinucleotides.
Why are CpG sequences hotspots for mutations?
Deamination of 5-methyl cytosine produces thymine, which is not “noted” by repair machinery.
CpG Island
They are long stretches of CpG-rich DNA in the promoter regions of genes that are actively transcribed in all cell types.
What % of human genes have a CpG island near their promoter?
50%
True or False?
CpG islands are almost always methylated, regardless of gene activity.
False.
They almost always LACK methylation, regardless of gene activity.
Inducible Gene Expression
Gene expression that is influenced by various signals (developmental, nutritional, hormonal) or short transcription factors that interact with promoter or enhancer elements.
Steroid Hormone
Derived from cholesterol; includes estrogen, testosterone, and progesterone.
Soluble in lipid membranes.
How do steroid hormones exert their effects?
Bind to intracellular steroid receptor, which is usually a site-specific DNA binding molecule which binds to response (or enhancer) elements.
Intracellular Steroid Receptor
Binds steroids in the cytoplasm and goes to the nucleus.
Response (enhancer) Elemetns
Binding sites on DNA for the hormone-steroid receptor.
What is a way to detect those mRNAs that have aberrant expression?
DNA Microarrays.
DNA Microarray: Preparation
- Glass slides prepared with DNA of interest after it has been denatured to ssDNA ready for hybridization.
DNA Microarray: RNA Isolation
- Must have two cell types to compare. Therefore, mRNA is converted into cDNA. The cDNA from that given cell type is colored with a fluorescent probe.
DNA Microarray: Hybridization
- The cDNAs are pooled and hybridized to the DNA on the microarrays. Microscopes are used to measure amount of hybridization based on colors.
After a microarray has been run, how can one tell if there are abnormal levels of mRNA?
The spot will not be a blend of two colors, but will be one of the primary colors.
What is RNA-Seq?
Relatively new method used to determine the composition and quantity of RNA present in a cell; relies on NGS and is replacing DNA microarray.
RNA interference (RNAi) via small interfering RNA (siRNA)
Targeted destruction of a particular mRNA via complementarity to double stranded RNA activators.
RISC
RNA-induced silencing complex.
What is the normal function of the siRNA pathway?
Antiviral?
