7: Gene Regulation

Question 1

Regulation of Transcription Initiation (general)

Answer 1

Pre initiation complex (TFIID and B) for RNA polymerase II.

Promoters and enhancers

DNA binding and activator binding domain
Dimerization domain

Question 2

Transcription Factor Types

Answer 2

General, Mediator, Gene Specific, Chromatin Remodeling Complexes (histone acetylases)

(Activators and repressors)

And long non-coding RNAs involved

Question 3

Transcription Factor Dimerization

Answer 3

Control gene activation
Can dimerize with protein and become activator or repressor

Example:
Myc dimerizes with Max, bind to E-box in the enhancers, activation

Mad and Max dimerize, inhibition of growth

Question 4

Histone Modification

Answer 4

Regulates gene transcription

H2A, H2B, H3, H4 core histones
H1, H5 link histones (packing chromatin)

Mediated by tails out of histone
HAT ON and HDAC OFF
Acetylation (lysines-more positive) and methylation

Question 5

Chromatin Remodeling Complexes

Answer 5

Moving histones out of the way while HAT opens it up.

Question 6

Splicing (regulation)

Answer 6

2 nucleophilic attacks (A branch point to 5’, then lariat closed off)
Snurps put them back together

Question 7

Alternative Splicing

Answer 7

Splice Variants (exon and introns can become each other)

Exon skipping, intron retention, alternative 5’ splice site, alternative 3’ splice site, mutually exclusive exons.

70% of all coding genes alternatively spliced

Question 8

Alternative Splicing (tissue)

Answer 8

Tissues can splice differently

Alpha-tropomyosin gene into striated, smooth, fibroblast or brain depending on splicing.

Question 9

Splicing Activators and Repressors

Answer 9

Positive control:
First case- no splicing
Second case- activator binds and spliced
(Shorter)

Negative control:
First case: splicing
Second case- repressor binds and no splice
(Longer)

Question 10

Beta-thalassemias

Answer 10

Anemia caused by lack of beta-globin subunits in hemoglobin.

Splice-site mutations:
End of creating beta-globin chains with exons as introns and vice versa.

MRNA degraded by nonsense mediated decay

Question 11

5’ and 3’ UTRs (regulation)

Answer 11

Contain signals that bind RNA Binding Proteins

Question 12

Translation Initiation (ferritin example)

Answer 12

Ferritin protein: sequence that sits right in front of AUG start codon, iron response element (IRE)

Adequate iron: translate ferritin (so it can transport iron)

Iron Scarce: translation blocked by binding protein (hide AUG start codon)

Question 13

Translation Initiation (3’ UTR and Poly(A) Tail with 5’ End)

Answer 13

Proteins bound to 3’UTR and Poly(A) Tail can block translation initiation at 5’ end

Question 14

RNA Degradation (regulation)

Answer 14

AU-Rich regions in mRNA 3’ UTR regulate mRNA decay:

1. Take off cap
2. Take off tail (happens normally at 200-300 nucleotides and fall off after 10)

Both nuclear and cytoplasmic poly(A) binding proteins

Question 15

MicroRNAs (molecular)

Answer 15

Discovered in C. Elegans
Made by genes that encode miRNA or by lariat structure of introns.
Cleaved into Pre-miRNA
Exported and made into ds-miRNA
Incorporated into RNA silencing complex (RISC) and becomes single stranded.

Match sequence of mRNAs:
Either block translation (block assembly of proteins for translation initiation) or catalyze mRNA degradation

Question 16

MicroRNAs (purpose)

Answer 16

Fine tune expression of mRNAs

Critical in regulation of stem cells (whether they divide asymmetrically or symmetrically)

MiRNA-encoding genes can function as tumor suppressor genes and oncogenes