New info for exam 1 Flashcards
Describe Transient vs epigenetic processes
- mechanisms that alter chromatin structure may contribute to transient regulation of gene expression or epigenetic regulation
Examples of transient processes:
- Gal regulon
- regulation of PHO5
describe regulation of PHO5
- high phosphate = repression of transcription of pho5
- low phosphate = nucleosome ejection, swi/snf binding, transcription activation
PHO5
- used by the cell to metabolize and import phosphate under phosphate starvation conditions
What is a recurring signal?
- refers to the situation in which:
chromatin structure contributes to gene expression
What are epigenetic mechanisms examples?
- histone modification
- DNA methylation
- regulatory ncRNAs
- RNA modifications in mRNA and lncRNA
What are epigenetic marks?
- DNA methylation and histone modification
- regulate gene expression (genes on or off)
What is the epigenome?
- total of all epigenetic modifications
Epigenetic patterns?
- patterns of epigenetic modifications can be passed to daughter cells through cell division
Methylome
- sum of all DNA methylation changes in an individual’s genome
What are examples of stable epigenetic regulation?
- automatic, no specific stimulus
- X-inactivation, parental imprinting
What is epigenetic memory?
- heritable change in gene expression or behavior that is induced by a previous stimulus
- can either be developmental or environmental
Types of epigenetic memory:
- cellular memory
- transcriptional memory
- transgenerational memory
What is cellular memory?
- mitotically heritable transcriptional states established during development in response to developmental cues (through epigenetic marks)
What is transcriptional memory?
- mitotically heritable changes in the responsiveness of organisms to environmental stimuli due to previous experiences
What is transgenerational memory?
- meitotically heritable changes in the gene expression and physiology of organisms in response to experiences in the previous generations
Explain the role of epigenetics in development
- produce patterns of gene expression in different cells as needed for growth and development of the organism
- differences in gene expression are maintained by epigenetic mechanisms
- dividing and differentiating cells remember what they are supposed to do through preserving epigenetic marks (cellular memory)
Explain the analogy of the epigenome
- similar to a barcode. The barcode is the epigenome that scans for a specific organ… the bars on the barcode are histone mods and dna methylations
Describe propagation of epigenetic marks: DNA methylation
- unmethylated –> methylated –> silenced –> hemi methylated –> restored methylation –> unmethylated
(draw the circle)
Describe propagation of epigenetic marks: histone modification
- nucleosomes are separated from original parental DNA during synthesis of daughter
- partial disassembly + reassembly of nucleosomes during cell division = maintanance of chromatin states from one cell generation to the next
- nucleosomes partially break.. new components added… new strand == old and new histones
- original epigenetic state reestablished after replication based on epigenetic marks on the newly deposited nucleosomes
Can epigenetic marks be inherited?
- yes
How are epigenetic marks inherited?
- can be altered by environmental conditions (diet, stress)
- if they are acquired due to the environment, they may be passed on to the next generation if present in the germ line
- epigenetic modifications can be triggered by toxins, alcohol, addictive drugs, diet, exercise, trauma
describe the link between epigenetics and cancer
- alteration of genes regulating epigenetic processes can be cancer drivers, caused by chamhes in DNA/RNA modifications, histone modifications, nucleosome remodeling
Describe the DNA modifications that take place in cancer
- global DNA HYPOmethylation is common
- HYPERmethylation is frequently detected in specific CpG-rich regions leads to the silencing expression of tumor suppressors (turning off tumor suppressor genes)
Why is studying epigenetic changes difficult when it comes to cancer?
- high degree of genomic instability in cancer
- difficulty distinguishing driver from passenger mutations
What is parental imprinting?
- involves expression of only one of the inherited alleles of a gene, depending on the parent
- expressed gene copy is always maternal in some imprinted genes and always paternal in others
- recognized by different diseases caused by the same deleted region depending on whether the deletion was inherited form mother or father
Describe prader-willi syndrome
- IGF2 (insulin growth factor 2) is expressed only on the paternally derived chromosome
- deletion of part of the paternal copy of chromosome 15 that contains H19 and IGF2 results in prader-Willi syndrome
Describe Angelman syndrome
- H19 gene is only expressed on the maternally derived chromosome
- Same deletion results in Angelman syndrome
Describe X-inactivation
- during early development (cleavage) one of the x chromosomes is inactivated in cells of a female which one is random
Condensed and silenced X chromosome becomes a…
- barr body
Describe the role of Pol II pausing in transcribed genes
- transcribed genes echibit transient pausing of pol II at promotor-proximal regions
- release of Pol II into gene bodies is controlled by many regulatory factors
- pause can affect: RNA splicing, type of protein produced
Describe elongation rates
- vary between and within genes, play a part in co-transcriptional processes such as splicing and transcription termination and maintenance of genome stability
- many factors can modulate elongation rates, including histone marks and features of genes such as the number of axons
What factors are responsible for differential mRNA processing?
- 5’ capping and 3’ polyadenylation for mRNAs
- alternative RNA splicing
- RNA modification or RNA editing
Describe alternative RNA slicing
- results in generation of alternative mRNAs from a single gene
- essential mechanism to increase complexity of gene expression
- important role in cell differentiation
- MAY be cell specific
What is the term for the variants produced by alternative RNA splicing?
- protein isoforms
Describe RNA modification
- cells make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase
describe RNA nucleotide modifications
- chemical modifications of the nucleotides in RNA molecules that occur post-transcriptionally (ex: addition of a methyl to adenosine)
examples of post-transcriptional chemical modification of RNA?
- deaminations
- isomerizations
- glycosylatins
- thiolation
- transglycosylations
- methylation
How does RNA nucleotide modification affect RNA?
- affects folding, processing, localization, function, stability…
- distinct local effects at the site of modification
- globally to affect the structure of the particular RNA
What type of RNA undergoes the most post-transcriptional modification?
- tRNAs (transfer RNAs)
What is the relationship between mRNA stability and RNA modification?
- stability may be controlled by RNA modifications
What determines the fate of a modified transcript?
- writer proteins, RNA-binding proteins (recognize readers), and eraser proteins
Describe the two major groups of tRNA modifications?
those that:
- affect overall structure of tRNA
- target function centers of tRNA (anticodon seq…), direct effect on decoding and protein synthesis
describe RNA editing
- alters RNA sequence
- two distinct mechanisms
- chemical/enzymatic modification
- insertion/deletion editing
describe chemical /enzymatic modification
- targets and individual nucleotide
- C-to-U:
cytidine deaminases convert a C in RNA to a U - A-to-I:
adenosine deaminases convert A to I (inosine), which ribosome translates as a G
Describe insertion/deletion editing
- insert or delete nucleotides in RNA
How are the mechanisms of RNA editing mediated?
- mediated by guide RNA molecules in editosomes
- these RNA molecules base pair with RNA to be edited and serve as a template for the addition of nucleotides in the target
What are the functions/consequences of RNA editing
- alter amino acid seq (substitutions)
- modulate RNA stability (down-regulation/degredation)
- alter splice sites (alt splicing)
- alter secondary structure generating a different protein-binding site
- modification of regulatory RNAs
How does RNA editing affect pre-mRNA splicing
- RNA editing can create or eliminate splice sites and branch points
- intron removal can determine availability of editing complementary sequences that are required to form dsRNA substrates for editing
Describe selective mRNA translation?
- mRNAs may be sequestered so that translation is delayed or inhibited
- accomplished by
small regulatory RNAs
Inhibitory protein binding
Describe control of mRNA degredation
- mRNAs can be targeted for degredation by miRNAs
- process is known as RNA interference (RNAi)
Describe control of translation initiation
- masking mRNA to delay/prevent translation
Describe phosphorylation of eIF2 by stress-activated kinases?
- when eIF2 is phosphorylated, translation is blocked
- when eIF2 is not phosphorylated, translation occurs
Describe codon usage bias
- synonymous codons for the same amino acid are NOT used with equal frequencies in genome
More tRNA = more likely for A site location
Silent mutations
- synonymous codon mutations that do not change protein sequences
describe protein post-translational modification
(PTMs)
- increase the functional diversity of the proteome
1. covalent additional of functional groups or proteins
2. Proteolytic cleavage of regulatory subunits
3. degredation of entire proteins
gene expression can be regulated post-translationally by:
- proteolytic processing
- chemical modification’
- localization
- degradation
describe proteolytic processing
- occurs when a protease cleaves one or more bonds in a target protein to modify activity
- may lead to activation, inhibition or destruction of the proteins activity
(cleavage is a molecular switch, a pivotal regulator)
Phosphorylation main cellular function
- intracellular signaling
- cellcycle, growth, apoptosis
Ubiquitination main cellular function
- protein degradation
acetylation and methylation main cellular function
- chromatin regulation
- transcriptional regulation
glycosylation main cellular function
- extracellular signaling
- significant effects on protein folding, conformation, distribution, stability and activity
SUMOylation main cellular function
- intracellular transport
- transcription regulation
- apoptosis
- protein stability
-stress response - cell cycle regulation
What causes an increase in proteome complexity
- increase of complexity is caused by protein post-translational modification
What is proteolysis?
- degradation or breakdown of proteins into smaller polypeptides or amino acids
- catalyzed by enzymes called proteases
Purpose of intracellular degradation of entire protein:
- removal of misfolded and damaged proteins
- regulation of cellular processes, removal of enzymes and regulatory proteins
two major proteolysis pathways:
- ubiquitin-proteasome pathway
- lysosomal proteolysis
What is the ubiquitin-proteasome system
- selective protein degradation
- proteins tagged by covalent linkage to ubiquitin
ubiquitylation
- attachment of ubiquitin to a substrace protein
1. ubiquitin activating enzyme (E1) activates ubiquitin (Ub)
2. activated Ub is transferred to a ubiquitin- conjugating enzyme (E2)
3. target protein recognized by ubiquitin ligase enzyme (E3), facilitates transfer of Ub from E2 to lysine residue in target protein
Deubiquitinase (DUB)
- cleaves ubiquitin from proteins including:
ubiquitin tagged proteins
ubiquitin units in a free polyubiquitin chain
Draw the ubiquitin-proteasome system (simple)
-
What is another role of ubiquitin other than degradation?
- can serve as a tag for many processes depending on the lys residue
