Gene Expression II

What is gene regulation?

how a cell controls which genes are expressed to produce RNA and protein

How does differential gene expression allow for unique activities of different cells and tissues?

different cells can express different sets of genes which directly gives the cell it’s unique properties

How are most proteins controlled?

transcriptional control

What are 2 examples of how transcription is controlled?

regulatory transcription factors and epigenetic regulation (methylation)

What are 2 examples of post-transcriptional control?

regulation of mRNA, RNA interference, and regulation of translation initiation

How can mRNA be regulated to change how much protein is synthesized from that mRNA?

the lifetime of the mRNA (RNA stability), and if translation machinery has access to the mRNA

How can mRNA stability be changed?

miRNA’s, they are hairpin shaped then processed further and bound to a multiprotein complex called RISC (RNA-induced silencing complex) that matches with an mRNA that matches the miRNA sequence. Once bound the mRNA is cleaved and destroyed. If the miRNA sequence is partially matched the mRNA is not destroyed but can have limited translation

How is transcription initiated?

TATA box in promoter is recognized by general transcription factors that recruit RNA polymerase, DNA unwinds to reveal template for RNA polymerase

How can transcription be increased or decreased?

by increasing or decreasing the access of initiation machinery to the mRNA

What is the purpose of regulatory transcription factors?

to activate or repress the initiation of transcription

What are transcription factors and their structure?

proteins that activate or repress initiation of transcription, have a DNA-binding domain, effector domain, and sometimes one or more regulatory domains

What does the DNA-binding domain do?

associates with DNA sequences outside of the promoter (control elements)

How does the DNA-binding domain recognize DNA?

it has sequence specific recognition

What does the effector domain do?

allows for alteration of chromatin structure and/or impacts the assembly of the general transcription machinery with other proteins

What do regulatory transcription factor that are activators do?

bind to DNA sequences (enhancers), attract and position general transcription factors and RNA polymerase so transcription can begin, some can recruit proteins that modify chromatin to be more accessible

What do repressor regulatory transcription factors do?

bind to DNA sequences (silencers), can block general transcription factors and RNA polymerase, antagonists of activators, can block activator proteins, and/or recruit proteins to modify chromatin

What are the two functional types of regulatory transcription factors?

activators and repressors

What is a mediator?

complex of proteins (in eukaryotes) that serves as an intermediary between the gene regulatory proteins, general transcription factors, and RNA polymerase to stabilize and initiate transcription

Can there be multiple inputs at the promoter region?

yes, can have multiple activators and/or repressors that allows for varied gene expression. This is called combinatorial control

What does the regulatory domain of the regulatory transcription factor do?

facilitate regulation of transcription factor activity by ligand binding, phosphorylation, hetero/homo-dimerization with other transcription factors and-coregulators, and more

What is epigenetic regulation?

heritable changes in gene expression that don’t alter underlying DNA sequence, histones, methylation of DNA, etc. They can work together with transcription factors to regulate transcription

What are the main types of epigenetic modification?

chemical DNA, histone, chromatin, and non-coding RNA

What are chemical DNA modifications?

DNA methylation of cytosine groups

What results from DNA methylation?

generally, repression of transcription through the blocking of activator binding and/or recruitment of chromatin-remodeling complexes to make DNA harder to access

What is histone modification in relation to epigenetic regulation?

acetylation, methylation, and phosphorylation of histone tails to alter chromatin density

What results from histone acetylation?

neutralization of positive charges on histones that loosens DNA binding and can activate transcription

What results from histone deacetylation?

restoration of positive charges which tightens DNA binding and silences transcription

What are chromatin remodeling epigenetic regualtions?

ATP-dependent repositioning of nucleosomes

What results from repositioning of nucleosomes?

promoter regions can be hidden or exposed to activate or repress trascription

What are non-coding RNA epigenetic regulations?

regulation of epigenetic machinery via miRNA or long non-coding RNA action

What do noncoding RNA’s do?

direct and tune epigenetic modifications and can alter chromatin accessibility

How is translation initiation regulated?

phosphorylation of elF2, when phosphorylated elF2 cannot associate with ribosome and translation is blocked, when not phosphorylated translation occurs. When the cell is starved elF-2 becomes phosphorylated not allowing translation and conserving resources

What is post-translational regulation?

chemical modification of protein activity

What are the general classes of mutations?

mutations that affect regulatory transcription factors, and those that can change the DNA sequence of regulatory elements, including promoters, enhancers, and silencer sequences

What is p53?

transcription factor that tightly regulates cell growth and proliferation in response to various cues, nearly half of all cancers have mutated p53

What is miRNA?

small, non-coding RNA molecules that regulate gene expression by binding to mRNA

How can miRNA be used as biomarkers?

expression of miRNA is highly regulated, and they act to regulate tissue function. Expression of miRNA changes during onset and progression of disease so we can use them to identify/detect certain diseases