Regulation of Gene Expression II: Eukaryotic Principles and Mechanisms and Paradigms

what are the 4 levels of gene regulation in euks?

1. epigenetic

2. transcriptional

3. post transcriptional

4. translational/post translational

mitochondrial dna comes from

mom

mRNA is synthesized where

nucleus

mRNA moves into the cytoplasm via

nuclear pore

where does translation occur?

cytoplasm

what is an epigenetic factor that can tag DNA and activate or repress genes?

methyl group

how are methyl groups added to DNA?

DNA methylation

what are 2 methods of epigenetic regulation

DNA methylation

DNA acetylation

DNA methylation occurs when the gene is

inactive (genes are tightly coiled around histones)

DNA acetylation occurs when the gene is

active (genes are loosely coiled around histones)

what is histone modification?

binding of epigenetic factors ot histone tails --> alters how DNA is wrapped around histones and the availability of genes to be activated

when genes are tightly wound around histones and the dna is inaccesible, the gene is

inactive

is dna methylation and histone acetylation reversible?

yes

epigenetic regulation of a gene is the process by which the activity of a particular gene is controlled by

the structure of nearby chromatin (allows access to DNA)

what are 3 epigenetic mechanisms of gene regulation

1. DNA methylation

2. Chromatin/Nucleosome Remodeling

3. noncoding RNA

what are tightly coiled DNA around proteins during cell division?

chromosomes

what are loosely packed DNA around proteins?

chromatin

what is the protein in which DNA is wrapped around?

histones

describe heterochromatin

tightly packed chromatin

inaccesible DNA

non transcribing

inactive

describe euchromatin

looser packed chromatin

transcription occurs

does gene regulation occur on heterochromatin or euchromatin?

euchromatin

what is the opening process of DNA for regulation is

chromatin/nucleosome remodeling

post translational modifications of histone

what are the 5 families of remodeling facotrs that result in chromatin/nucleosome remodeling

SWI/SNF

ISWI

Mi-2/NuD/CHD

INO80

SWR1

what is the main family of remodeling factors involved in chromatin/nucleosome remodeling?

SWI/SNF

what is the function of SWI/SNF

interacts with acetylated histones and many transcription factors

function of ISWI in nucleosome remodeling?

binds methylated histones

regulates transcription

function of Mi-2/NuD/CHD in nucleosome remodeling?

binds acetylated/methylated histone for positive regulation

function of INO80 in nucleosome remodeling?

histone deubiquintylation

function of SWR1 in nucleosome remodeling?

brings H2Az to promoter and regulates transcription

chromatin/nucleosome remodeling depends on

ATP

making DNA accessible to RNA polymerase and transcription factors

how does nucleosome/chromatin remodeling change DNA accessibility for transcription factors and RNA polymerase?

1. Nucleosome Sliding (moves/ejects nucleosome)

2. Histone exchange (position change)

3. Nucleosome Assembly

4. Restructures the spacing between nucleosomes

how many types of posttranslational modifications are there?

13

histone acetylation results in

activation of gene expression

deacetylated or unacetylated histones do what

inhibit gene transcription

histone modification impacts what other epigenetic modification mechanism?

chromatin remodeling

dna methylation blocks

RNA polymerase from doing job, blocking transcription

what epigenetic regulation in eukaryotic genes is critical in X-chromosome inactivation, gene imprinting, cancer and epigenetic regulation of many biological and pathological events?

dna methylation

dna methylation results in the

binding and recruitment of repressors to the promoter--> inhibiting transcription in eukaryotes

can epigenetic changes from dna methylation be passed from parent to child?

yes

is epigenetic inheritance controlled by base sequences?

no

what can explain abnormal or unexpected DNA expression often seen in identical twins?

dna methylation

DNA methylation deactivates

one homologous chromosome

unmethylated DNA and acetylated histones are found in

euchromatin

methylated NA and deacetylated histones are found in

heterochromatin

what is a non coding RNA (ncRNA)

functional RNA molecule that is transcribed from DNA but not translated into proteins

what are epigenetic related non coding RNAs?

microRNAs

short interfering RNAs

piwi interacting RNAs

long noncoding RNAs

do noncoding RNA's code for proteins?

no

are noncoding RNA's transcribed from the genome?

yes

noncoding RNA's regulate gene expression at what levels

transcriptional

post transcriptional

noncoding RNA's are critical for

gene imprinting, maintaining genome integrity

* which RNA polymerase transcribes most rRNA genes?

RNA polymerase I

* which RNA polymerase transcribes genes encoding protein (mRNA), most snRNAs and microRNAs?

RNA Polymerase II

* which RNA polymerase transcribes 5s rRNA, tRNA and other small RNA's

RNA polymerase III

mRNA is transcribed by which RNA polymerase?

RNA Polymerase iI

the genetic mechanism of transcription regulation is dependent on

genetic DNA sequences via interaction of transcription factors with specific cis elements

what are the essential cis elements of transcription regulation?

GC rich sequence in all TATA box-less promoters

TATA box

TSS- transcription start site

enhancers are cis-elements involved in transcription regulation that

interact with activators and positively regulate transcription

silencers are cis-elements involved in transcription regulation that

interact with repressors and negatively regulate transcription

insulators are cis-elements involved in transcription regulation that

separate promoters for different genes in the genome

transcription is regulated by cis-elements or trans-factors?

both

what are the two types of trans factors involved in transcription?

1. General Transcription Factors of RNA Poymerase II

2. Sequence Specific Transcription factors (Activator, repressor)

transcription factors are proteins that bind cis-elements and they are similar to

trans regulators

can cofactors bind to DNA directly?

no

Cofactors interact with

DNA bound proteins and modulate transcription

how do cofactors alter the transcription rate

they can increase or repress it

* what are the three methods of eukaryotic post transcriptional gene regulation

1. RNA shuttling

2. Alternative RNA splicing

3. Noncoding RNA

what are the methods of RNA shuttling post transcriptional gene regulation

RNA capping

Polyadenylation

RNA capping and polyadenylation do what

stabilize mRNA for translation

what is RNA capping?

a methylated guanine is added to the 5' of recently transcribed mRNA

what is polyadenylation?

poly A tail of adenines is added to the 3' end of recently transcribed mRNA next to the noncoding sequence

what is the function of RNA splicing?

remove introns

what is the advantage of alternative splicing?

increase diversity w/o increasing genome size

different isoforms can express in different tissue and at different stages of development

what is an isoform?

proteins from the same gene that were splice differently

do prokaryotes have introns/noncoding regions?

no

*what do micro RNA's do?

degrade mRNA

block translation

* which type of RNA causes mRNA to fold on itself and base pair creating dsRNA which is then digested with an enzyme

microRNA

microRNA is ____ stranded

single

short interferring RNA (siRNA) is ___ stranded

double

what does short interferring RNA (siRNA) do?

degrade mRNA and block translation (RNA interference (RNAi))

Short Interferring RNA (siRNA) and microRNA (miRNA) are both ____RNA

noncoding RNA

microRNA binds to ______ of ____mRNA and degrade it

binds to noncoding regions of premature mRNA and degrade it

small RNA interfere with the ___ and ____ of mRNA

function and stability

what is the first mechanism of RNAi (RNA interference/blocking translation)

siRNA

what is the second mechanism of RNAi (RNA interference/blocking translation)

miRNA, small RNA

one miRNA have ___ mRNA targets

multiple

how many nucleotides in miRNA

19-25

miRNA matured from

longer pre-miRNA with structured hairpins that were derived from longer pri-miRNA

miRNA binds target mRNA on ____ inhibiting translation and/or inducing mRNA degradation

3' UTR

one mRNA may be the target of ___ miRNA

multiple

mis-expression of miRNA can cause

pathology/cancer

post translational modifications are also called

protein modifications

2 examples of post translational modification

protein folding

protein modification and degradation

what are 3 important protein modifications

Phosphorylation

Glycosylation

Ubiquitination

What occurs during phosphorylation

adds a phosphate to serine, threonine or tyrosine

this changes the conformation

what occurs during glycosylation

attaches a sugar, usually to an "N" or "O" in an amino acid side chain

what occurs during ubiquitination

adds a ubiquitin to lysine residue of a target protein for degradation

ubiquitination is also called a

lysosome tag

what do proteosomes do

break apart proteins into smaller peptide units

proteins to be degraded are tagged with

ubiquitin

proteins that are tagged with ubiquitin go where

into the proteasome