Trans - Regulation of Gene Expression Flashcards
Importance of regulation of gene expression (3), give examples of each
- adaptation to environmental changes –> ex. memory B cell antibody production during immune response
- development –> ex. pluripotential stem cells
- differentiation of cells –> ex. specific proteins for specific cell function
Levels of eukaryotic gene regulation (6)
- epigenetic control
- transcriptional control
- post-transcriptional control
- RNA transport control
- Translational control
- Post-translational control
Heterochromatin vs Euchromatin
- heterochromatin –> dense, transcriptionally silent, tightly packed, inaccessible to polymerases and other enzymes
- euchromatin –> loosely packed and active in gene transcription
Define differential gene expression
Some genes are expressed while others are repressed
a) structure and b) significance of telomeres
a) complexes of DNA and proteins at the end of chromosomes
b) maintain structural integrity, prevent attack by nucleases, allow repair systems to differentiate between ends and breaks
Mechanisms to increase/decrease access to DNA sequence (2)
- gene regulatory proteins
2. RNA polymerases
Mechanisms to alter chromatin structure (2)
- cytidine methylation
2. histone methylation
Old and new concepts related to genetic switches
Old: “loss” of genesNew: genes can be turned “on” or “off”
Principle of DNA methylation
[1] Silencing genes to reduce unnecessary gene expression
[2] Methylation of CG dinucleotide (CpG) in promoter causes silencing of genes
Principle of DNA methylation
[1] Silencing genes to reduce unnecessary gene expression
[2] Methylation of CG dinucleotide (CpG) in promoter causes silencing of genes
CpG
Cytosine-phosphate-guanine
Characteristic of promoter region related to methylation
10-20x more CpG dinucleotides –> more affected by methylation
Effect of methylation on promoter
[1] High methylation / hypermethylation –> transcriptionally silent
[2] Low methylation / hypomethylation –> transcriptionally active
Other effects of methylation
Prevent binding of regulatory factors by stearic hindrance
Mediators of methylation
MeCP1 and MeCP2 (Methylated CpG binding proteins 1 & 2)
Fragile X syndrome
Mental retardation caused by expansion of CGG at 5’ UTR of FMR1 gene –> increased methylation causing silencing of FMR and brain-specific mRNA during development
Histones
Order DNA into nucleosomes, (+) charged due to high lysine and arginine content –> form ionic bonds with (-) charged DNA
Principle of histone acetylation
Acetyl groups attached to lysine in histone, forming tails that protrude from the nucleosome –> repulsion between tails causes more open DNA structure
Effect of histone acetylation
More acetylation –> more open DNA structure –> more accessible for transcription
Histone aminotransferases - function?
Eliminate positive charge on lysine, decreasing interaction of histone and negative DNA
Histone deacetylases - function?
Restore positive charge of lysine, increasing interaction of histone and negative DNA
Relationship between DNA methylation and histone acetylation
Reciprocal –> when DNA is methylated, histone is deacetylated, and vice versa
Sites of histone methylation to hinder transcription
Histone H3 lysine 9, 27
Histone H4 lysine 2
Sites of histone methylation to enhance transcription
Histone H3 lysine 4, 27, 36
Effect of histone methylation
Activate or deactivate DNA, depending on methylation site
Ubiquitin - function?
Marks defective protein for destruction
Effects of histone ubiquitination
[1] disruption and spreading of chromatin allowing binding of transcription proteins;
[2] binding of effector proteins for other regulatory processes;
[3] allows other histone modifications to occur
Principle of histone ubiquitination
Attachment of ubiquitin to histone in order to modulate gene expression
Histone ubiquitination is required for these specific regulatory processes
di- and tri- methylation of H3 lysine 4 and lysine 79
Effects of histone phosphorylation
[1] chromatin condensation during mitosis;
[2] unknown effect on gene regulation
Modulator of histone ubiquitination
Ubiquitine proteases (mediate reversible process of ubiquitination)
Site of histone phosphorylation for chromatin condensation
H3 serine 10 and serine 28
Gene regulation at level of DNA - other types (5)?
[1] gene deletion (ex. RBCs);
[2] gene duplication;
[3] gene amplification;
[4] DNA rearrangement (ex. antigen recognition);
[5] chemical modification of DNA (ex. methylated globin genes)
Tumor suppressor genes - significance?
important in cell cycle & control of cell division –> prevent changes in methylation (mutation can lead to cancer)
Trans acting factors - characteristics [4]?
[1] proteins with 2 binding domains –> DNA binding domain, transcription activation domain;
[2] coded by distant genes;
[3] migrate to site of action;
[4] bind to cis acting elements
Trans-acting factors - function?
Transcriptional activators / transcription factors
How can trans-acting factors control gene expression [4]?
[1] expression of factors in a specific type of tissue;
[2] expression of factors at a specific time of development;
[3] may be required for protein modification;
[4] may be activated by ligand binding
Trans-acting factors interact with cis-acting elements through:______ [4]
[1] Helix-turn-helix,
[2] Helix-loop-helix;
[3] zinc finger;
[4] leucine zipper
Trans acting factors - significance in transcription
RNA polymerase II cannot initiate transcription alone; it needs transcription factors!
Cis-acting elements - characteristics [3]
[1] DNA sequences close to a gene that are required for gene expression;
[2] lie on the same strand as the gene being transcribed;
[3] bind to trans-acting factors
Cis-acting elements - features [6]
[1] promoters; [2] enhancers; [3] terminators; [4] silencers; [5] insulators; [6] response elements
Promoters
[1] located upstream of the start point;
[2] determine if transcription begins, and/or where transcription begins
Main mechanisms of transcriptional control
Through action of trans-acting factors (transcription factors) and cis-acting factors (promoters, terminators, enhancers, silencers, insulators, response elements, etc.)
Examples of promoters
TATA box, Initiator (Inr)
Promoter-proximal elements
Upstream to promoter; tightens control; helps promoter do its job
Examples of promoter-proximal elements
CAAT box, GC box
Terminators
Downstream of coding segment, recognized by RNA polymerase as a signal to stop transcription –> stop codon (UAA, UAG, UGA)
Enhancer
Greatly enhances transcription by increasing rate of initiation of transcription by RNA polymerase II; varied location
Silencer
DNA sequence that helps reduce or shut off the expression of a nearby gene; binding to trans-acting factors causes repression of gene expression
Location of insulators [2]
[1] between enhancer and promoter of adjacent genes;
[2] between silencer and promoter of adjacent genes
Insulator
DNA sequence that prevents a gene from being influenced by activation or repression of its neighbors
Factors conferring specificity of tissue gene regulation [2]
[1] presence or absence of transcription factors;
[2] use of alternative promoters for a single gene
Transcription factors may be activated by: ____ [2]
[1] environmental stimuli (ex. Heat shock TF);
[2] signals from other cells (ex. hormones, growth factors)
Response elements
DNA sequence that allows specific stimuli (e.g. hormones, cAMP, IGF-1) to control gene expression
Mechanisms in post-translational control [3]
[1] alternative splicing;
[2] alternative polyadenylation;
[3] RNA editing
Significance of alternative promoters
A single gene may have different promoters at different exons, in order to express different isoforms of the gene in different tissues (ex. Human Dystrophin Gene)
Alternative splicing
Production of multiple related proteins (isoforms) from a single gene; different exon and intron combinations from the same gene
Alternative polyadenylation vs alternative promoter
[1] alternative promoter –> different start, same stop;
[2] alternative polyadenylation –> same start, different stop
Alternative polyadenylation
Variation in the location of the poly-A-tail produce different proteins from the same gene
RNA editing
Insertion, deletion, substitution of nucleotides to create protein variations (similar to missense, nonsense, and framerate mutations) –> ex. ApoB100 & ApoB48
Gene - historical definition
Region of the genome that segregates as a single unit during meiosis and gives rise to a definable phenotypic trait (ex. red eyes vs white eyes)
Gene - molecular definition
Stretch of DNA transcribed into RNA, coding for a single polypeptide chain
Gene - modern definition
DNA sequence that is transcribed as a single unit and encodes one set of closely related polypeptide chains
RNA Transport Control
Nucleases may degrade mRNA as it travels from nucleus to cytoplasm
What determines half-life of mRNA
Sequences at the 3’-end (poly-A-tail)
Mechansims of translational control [2]
[1] bidning of protein factors to response elements in mRNA;
[2] phosphorylation of initiation factors
Fates of unfolded proteins after emerging from ribosome [3]
[1] correctly folded without help;
[2] correctly folded with help from molecular chaperone;
[3] cannot be correctly folded, digested by proteasome
Significance of short mRNA half-life
Constant transcription is needed to maintain protein levels
Why is it important to correctly fold proteins?
Incorrectly folded proteins may form clumps, precipitate, and damage cells
Molecular chaperones
HSP70 and HSP60-like proteins that aid in folding newly synthesized proteins
Alzheimer’s disease
Accumulation of misfolded protein amyloid beta in the brain parenchyma & blood vessels
Creutzfeldt-Jakob disease
Results from a change in configuration (alpha helix to beta sheet) in PrP^c due to infection by prions –> formation of insoluble aggregates of fibrils in the brain
Huntington’s disease
Amplification of CAG codon (glutamine) results in abnormal translation of mRNA protein to huntingtin with abnormal repeats –> aggregation of glutamine –> neurodegenerative disorder
Role of ubiquitin in post-translational control
Misfolded proteins are marked for degeneration by ubiquitin
Proto-oncogene
Normal gene that can become an oncogene due to mutations or increased expression
Oncogene
Protein-encoding gene which, when deregulated, participates in the onset and development of cancer
Causes of cancer [6]
[1] Viruses; [2] tobacco smoke; [3] food; [4] radiation; [5] chemicals; [6] pollution
Tumor supressor gene
Also called anti-oncogenes; protects a cell from mutating into a cancer cell
