Eukaryotic Transcriptome (L18) Flashcards
Histones are rich with what 2 AA’s and why?
Lysine and Arginine b/c they have positive charges that facilitate binding to DNA.
In eukaryotic transription initiation, after TFIIF and RNAPII bind to the DNA, What 2 proteins join and what do they do?
TFIIE joins and recruits TFIIH to the complex. TFIIH has HELICASE, ATPase, and KINASE activity.
TFIIH unwinds DNA for RNAPII, and also PHOSPHORYLATES the Carboxy Terminal Domain (CTD), which is required for RNAPII to leave the initiation complex.
What are the 3 main domains of the Glucocorticoid Receptor?
Transactivation Domain (TAD): binds coactivators, (ie helps recruit TFs)
DNA-binding Domain (DBD): bind to hormone response element in DNA
Ligand-binding Domain (LBD): Binds the hormone (eg cortisol, estrogen, etc)
What is the inhibitor binding site in steroid hormone receptors (which are classic coactivators)
It is a site on the steroid hormone receptor that binds and inhibtor protein, and masks the nuclear localization signal (NLS).
Describe the process of transcriptional regulation by glucocorticoid receptors.
The Glucocorticoid receptor(GR) is bound by Heat Shock Protein (which obscures its NLS) in the cytosol. The addition of cortisol unbinds HSP and the GR-C complex binds to Glucocorticoid Response Element (GRE) in the nucleus to activate transcription of anti-inflammatory genes.
In the Thyroid Hormone Receptor Complex, how does presence of thyroid hormone regulate gene expression?
In the absence of Thyroid hormone, the receptors form a complex with corepressor-complex that has a Histone DeAcetylase Domain (HDAD).
In the presence of Thyroid hormone, the co-repressor-complex is displaced with coactivator-complex that has a Histone Acetylase Domain (HAD) which activates transcription.
NOTE: This is b/c when you acetylate histones you make them neutral, which opens up DNA to be actively transcribed.
What is special about plasma membrane receptors?
They activate signal transduction pathways.
Describe the SREBP protein and its correlation to LDL.
The Sterol Response Element Binding Protein (SREBP) is precursor protein that must be cleaved before it can act as a transcription factor.
It remains unprocessed in the Rough ER next to SCAP protein when cholesterol lvls are normal.
Low cholesterol, SCAP senses this and moves SREBP to cis-Golgi, where 2 diff proteases cleave SREBP. The cytoplasmic (N-terminal) domain is moved to the nucleus and activates the LDL receptor gene.
What do Histone Acetylase (HAC) and Histone Deacetylase (HDAC) do?
HAC (AKA HATransferase (HAT)) will acetylate the lysine residues, making the histone neutral and open for active transcription;
HDAC will deacetylate the lysine residues which condenses DNA and makes it transcriptionally inactive
What are the 3 major types of histone modifications to the N-terminus “tail” of H3?
Acetylation, Phosphorylation, and methylation
Typically methylation of DNA forms:
5-methyl cytosine, which provides steric hinderance, preventing transcription.
Describe the role of methylation in genomic imprinting.
Males methylate a diff set of genes in females. Disease occurs when a gene that is in the deleted region of one chromosome is methylated in the other chromosome (this is b/c that means the gene will not be express period).
Example: So in chromosome 15 in the same region, if genes 1,2,3 are deleted in paternal chromosome, and gene 2 is methylated in maternal, then gene 2 is not expressed but genes 1,3 are. This leads to prader willi syndrome. If maternal chromosome genes 1,2,3 are deleted and gene 1 is methylated in paternal, then this results in angelman syndrome.
What are 3 ways of DNA rearrangement that give diversity to human antibodies?
- VDJ recombination: diversity in antigen binding site
- Alternate exon usage: diversity in whether antibody is secreted or not
- Deletion of constant regions: diversity of permanent class (eg IgM or IgG)
The 2nd most common muscular dystrophy disorder is “myotonic dystrophy” (1st is duchane’s).
What is going on at a DNA level?
There is an addition of a DNA insertion thousands of bps long full of CTG-repeats. This transcribes to CUG in mRNA, which form long pin structures that causes myotonic dystrophy through sequestration of the splicing factor muscleblind (MBNL) and CUG-Binding Protein (CUG-BP).
What are the 5 steps of chromatin remodeling before initiation of transcription can occur?
- Transcription factor on packed DNA recruits a coactivator
- Acetylation of lysine residues in histone tails
- Binding of remodeling engine to acetylated lysine residues
- ATP-dependent remodeling of chromatin to expose binding site for RNAP
- Recruitment of RNAP and associated proteins
