Gene Regulation Exam 4 Material

proto-oncogene

normal gene, frequently linked to the regulation of cell proliferation

oncogene

gene whose protein product can make cells cancerous when it is overexpressed or mutated

oncoprotein

protein encoded by an oncogene that can cause transformation of a cell into a tumor cell

retrovirus

has RNA genome; replicates by making an RNA-DNA hybrid and then double-stranded DNA which gets integrated into host chromosomes

transformation

how a cell becomes cancerous

double minute chromosomes

cytogenetic hallmarks of genomic amplification in cancer

ErbA

nuclear receptor family of TFs

trans-splicing

enables ligation of exons from different pre-mRNAs into a single transcript

tumor suppressor genes

prevents cancer

retinoblastoma protein

• tumor suppressor

• inhibits activation by TF E2F

• recruits HDACs and histone methylases

wild-type

gene that occurs most frequently in the population

quenching

any process that decreases Fluorescence intensity of Fluorophores

DNA tumor viruses

agents that cause malignancies in a large variety of cell types and tissues by interfering with cell cycle control and immortalization

haploid insufficiency

disease in which one copy of a gene is mutated and the remaining wild type copy cannot produce sufficient functional protein to prevent disease

triplet repeat diseases

diseases involving the abnormal amplification of a three base pair sequence

RNA translation

process through which info encoded in mRNA directs the addition of amino acids during protein synthesis

interferon

• class of cytokines secreted by virus-infected cells and certain T cells

• induce antiviral responses by activating JAK/STAT pathway to turn in antiviral genes

BRD4

the most important functional protein in the bromodomain and super terminal family protein

designer zinc finger

switch expression on or off

RNA interference

cellular mechanism that uses the gene’s own DNA sequence to turn it off

how do viruses manipulate gene expression?

they have possession of regulatory signals within viral mRNAs that are recognizable by the host cell. Enables virus to shut off host gene expression to ensure preferential viral gene expression

what are some triplet repeat diseases?

• Rubinstein-Taybi syndrome

• SCA7

• fragile X syndrome

• Huntingtin’s disease

• Type 1 Myotonic dystrophy

details of Rubinstein-Taybi syndrome

• condition characterized by short stature, moderate to severe learning difficulties, distinctive facial features, and broad thumbs and first toes

• single gene inactivation

• mutated Huntingtin binds normal CBP, TBP and SP1

• CAG expanded in Huntingtin coding sequence resulting in a run of glutamines

details of SCA 7 disease

• mutant ataxin has a CAG repeat

• this results in a stretch of polyglutamine

• the mutant form is a dominant negative inhibitor of the wild-type ataxin

• the mutant blocks wild-type ataxin from opening chromatin via acetylation

details of fragile X syndrome

• FMR-1 wild-type has 10-50 tandem copies of CGG

• get transcription with wild-type

• FMR-1 mutant is methylated

• get >230 tandem copies of extended CGG repeat in first exon

• get no transcription with mutant

details of type 1 myotonic dystrophy

• CUG repeats sequesters alternative splicing factor so it can’t bind its normal RNA targets

• sequestration of alternative splicing factor, and loss of its normal function

details of Huntingtin’s disease

RAN translation

• repeats hinder initiation at AUG

• abnormal proteins are produced

• translation proceeds normally→ poly Q

what genes are regulated by p53?

• genes whose proteins inhibit growth

• genes whose proteins stimulate growth

what is p53?

• a transcription factor

• induced by DNA damage

• mutated in many cancers

• can induce growth arrest

how does p53 repress GSGs?

direct mechanisms

• compete for activator binding sites

• close chromatin

• bind up activators

indirect mechanisms

• p21

• turn on miRNAs

• turn on IncRNAs

what is p21?

• inhibits cyclin-dependent kinases needed for growth

• growth arrest gene

how is p53 activity thwarted?

• gene gets deleted

• mutant p53 gene

• intact p53 gene with amplified MDM2 oncogene

what can mutant p53 bind?

• alternative sequences in promoters that wild-type p53 won’t

• other TFs

what happens when MDM2 binds to p53?

• partial ubquitination

• export from nucleus

what happens when MDM2 binds to partially ubquitinated p53?

degradation of p53

what does MDM4 do?

inhibits p53 by binding its activation domain

how can p53 evade MDM2?

via acetylation which

• inhibits MDM2 interaction

• recruits TAF1

what does p53 promote?

• p21

• Bax

• MDM2

what does p53 repress?

Nanog

what does increased p21 lead to?

increased growth arrest

what does increased Bax lead to?

increased cell death

what does decreased Nanog lead to?

increased differentiation

what does increased MDM2 lead to?

increased suppression of p53

What is RAN translation?

• repeat associated non-AUG

• repeats hinder initiation at AUG

• Abnormal proteins are produced

what mechanisms does V-ErbA use to regulate gene expression?

• dominant repressor

• blocks hormone-dependent gene expression

• inhibitory domain that recruits a co-repressor

• inhibitory domain is essential for transformation

• must repress transcription to transform

• repression required to turn off this terminal developmental process

what mechanisms does Myc use to regulate gene expression?

• bind to max to get DNA binding and enhanced transcriptional initiation

• bind to PTEF-b to get enhanced transcriptional elongation

• bind TFIIH to get GMT and enhanced translation

what mechanisms does MDM2 and MDM4 use to regulate gene expression?

• inactivates p53 expression

• bind L26 to get reduced translation

• MDM4 inhibits p53 by binding its activation domain

How would you cure a transcriptional disease?

• alter TF activity by promoting or inhibiting post-translation modifications

• alter TF activity by promoting or inhibiting protein:protein interactions

• target chromatin modifying proteins

• target epigenetic modifications

• nucleic acid-based therapies

• designer zinc fingers to switch expression off or on

what type of factors that regulate gene expression can be mutated in human diseases?

• transcription

• chromatin structure

• post-transcriptional

• regulatory RNAs

• infectious disease