BIOL 303 - Ch. 14 - control of gene expression in eukaryotes

lindsey farris

DNase I hypersensitive sites are

regions of chromatin that become sensitive to digestion by the enzyme DNase I

DNase I hypersensitive sites are found near

the transcription start sites

What three processes affect gene regulation through chromatin structure

chromatin remodeling, modification of histone proteins, and DNA methylation

Chromatin remodeling complexes are

proteins that bind to specific sites on DNA and position the nucleosome so that transcription factors and RNA polymerase can bind and initiate transcription

What two things can chromatin remodeling cause?

The nucleosome to slide along DNA and a conformational change in the DNA and or the nucelosome

The 2 regions of a Histone

the globular domain and the positively charged tail

The histone code is

a series of modifications to histone proteins that affect how genes are expressed

Histone modification: Writers

enzymes that add modifications to histones

Histone modification: Readers

proteins that recognize and bind histone modifications

Histone modification: Erasers

enzymes that remove histone modifications

The methylation of histones can

repress or activate transcription

Histone methyltransferases

add the methylgroups, usually to K or R

Histone demthylases

remove methyl groups

What recruits histone modifying enzymes?

Sequence specific binding proteins, preexisting modifications, and RNA molecules

What does acetylation of histones cause?

Acetyl groups destabilize chromatin structure, allowing for transcription

Acetyltransferases

add acetyl groups to histones

deacetylases

remove acetyl groups from histones

Acetylation of Histones: What do transcription factors do?

They can have acetyltransferase activity themselves or attract the enzymes to DNA

Chromatin immunoprecipitation allows

researchers to determine locations in the genome where certain proteins interact with DNA

Chromatin immunoprecipitation: Crosslinked ChIP identifies

the binding sites for transcription factors

Chromatin immunoprecipitation: ChIP-Seq

determines sequences

DNA Methylation is the addition of

Methyl groups, CH3, to cytosines

DNA methylation creates

5 methyl cytosine

DNA methylation is associated with

transcription repression

CpG islands are

regions of DNA with many cytosines followed by a guanine

CpG are often found

near transcription start sites

Methylation attracts

deacetylases

Transcription factors are

proteins that regulate gene expression through the binding of specific DNA sequences

Transcription factors can either be

activators or repressors

promoters are regulated by

unique combination of transcription factors

Enhancers are

regulatory elements that stimulate transcription of distant genes

Enhancers are made up of

hundreds of base pairs and multiple TF binding sites

Enhancers cause

DNA to loop out, brining the promoter and enhancer close

A super enhancer is

several enhancers clustered together that stimulate high levels of transcription

Silencers are

regulatory elements that decrease transcription

Insulators are

DNA sequences that block the effects of enhancers

insulators are found

between the enhancer and promoter of a gene

Insulators might be

involved in topologically associated domain formation which allows or inhibits enhancer and promoter interaction

RNA Polymerase will

stall 24 to 50 nucleotides into transcription of specific genes

Heat shock proteins are

proteins that prevent damage by stressors where RNA polymerase stalling is observed

What factor binds to RNA pol to cause stalling?

Negative elongation factor

What relieves RNA pol stalling?

positive transcription elongation factor b

How does P-TEF b (positive transcription elongation factor b) work

by phosphorylating NELF and RNA pol

Response elements are

DNA sequences that are shared by promoters or enhancers of genes that regulatory proteins can bind to stimulate transcription

What promotes or represses the use of splice sites?

Exonic/ionic splicing enhancers and splicing enhancers

SR proteins are rich in what

serine and arginine

SR proteins are involved in

splice site selection

SR proteins contain

an RNA binding region and an alternating SR domain

SR proteins are though to

bind splicing enhancers and stimulate snRNP attachment

RNA is degraded by

ribonucleases or enzymes that break down RNA through various pathways

Degradation of RNA: Method one

poly A tail is shortened, 5’ cap is removed, and then 5’ to 3’ nucleotide removal

Degradation of RNA: Method 2

remove nucleotides in the 3’ to 5’ direction

Degradation of RNA: Method 3

involves mRNA cleavage at internal sites

RNA degradation takes place

in complexes called P bodies or processing bodies

The 4 mechanisms of RNAi

RNA cleavage, inhibition of translation, transcriptional silencing, and mRNA degradation

Mechanisms of RNAi: RNA cleavage

RISCs with an siRNA bind mRNA and cut, cleavage is carried out by slicer, and mRNA is further degraded afterwards

Mechanisms of RNAi: Inhibition of Translation

miRNAs inhibit translation in the initiation phase, by triggering ribosome stalling or premature termination

Mechanisms of RNAi: Transcriptional Silencing

siRNAs can alter chromatin structure, combine with protein complex RITS which attracts histone methyltransferases

Mechanisms of RNAi: mRNA degradation

short lived mRNAs with an AU rich 3’ UTR element, miRNA complementary to AU region, often found in cytokines

Boosting Translation: Exposure to an antigen, such as a virus, causes

an increase in availability of initiation factors which allows ribosomes to bind to mRNA and carry out translation