MCB 010 Topic 5: Regulation of Gene Expression

gene regulation makes cells different

-controls which genes are "turned on" (expressed)

-each cell type has a different set of active genes

-different patterns of gene expression make different proteins, which allow for cell specialization

How do cells decide what to express?

-cell type

-info from inside the cell: inherited proteins, damaged DNA, ATP

-info from outside the cell: chemical signals from other cells, mechanical signals, and nutrient levels

types of gene expression and regulation

-chromatin accessibility

-transcription

-RNA processing

-RNA stability

-translation

-protein activity

***main one is transcription

chromatin accessibility (gene expression & regulation)

the structure of chromatin can be regulated. More open or "relaxed" makes a gene more available for transcription.

-Euchromatin

-Heterochromatin

chromatin

-DNA wrapped around histone proteins

-state of DNA in humans (& other eukaryotic)

transcription (gene expression & regulation)

-regulating whether transcription initiation occurs

-most regulated step b/c the cell could potentially waste a lot of resources allowing transcription to happen

-chromatin (epigenetics)

-transcription factors

RNA processing (gene expression & regulation)

Can be regulated...

-splicing

-capping

-adding poly-A tail

-what exits the nucleus

-alternative splicing

RNA stability (gene expression & regulation)

the lifetime of a mRNA molecule in the cytosol affects how many proteins can be made from it. Small regulatory RNAs called miRNAs can bind to the target mRNAs and cause them to be chopped up

translation (gene expression & regulation)

can be increased or inhibited by regulators

-miRNAs block translation of target mRNAs

-amount of protein made

protein activity (gene expression & regulation)

variety of modifications--chopped up or tagged with chemical groups

-affect the activity or behavior of the protein

transcription factors

proteins that regulate the transcription of genes--that is their copying into RNA, on the way to making a protein

-ensures that the right genes are expressed at the right time

-bind to DNA (& other proteins) in a sequence specific manner (lock and key)

gene expression

when a gene is turned on & used to make the protein it specifies

-not all genes are on a the same time or in the same cells or parts of the body

What is the key on/off control point for many genes

transcription

-if a genes is not transcribed then it will not make a protein

-if it is transcribed then it will make a protein and it will be expressed

-the more a gene is transcribed the more protein is made

transcription factors and regulation

-transcription factors are necessary for RNA polymerase to attach to the DNA and start transcribing

-large class that controls the expression of specific, individual genes

How transcription factors regulate

-once a transcription factor binds to the DNA at the target sequence it makes it easier or harder for the RNA polymerase to bind to the promoter of the gen

-activators

-repressors

-binding sites

activators

activate transcription

-help general transcription factors and or RNA polymerase bind to the promoter

repressors

repress transcription

block general transcription factors and or RNA polymerase from binding to the promoter

binding sites

often close to gene's promoter. However they can also be found in other parts of the DNA, sometimes very far away from the promoter, and still affect the transcription of the gene

differences in _________________________ result in cellular diversity within an organism. Different cells have the same _____________ genes but different _____________ and _________.

gene expression

proteins, mRNA

gene expression

-transcription and translation of a gene

-producing mRNA and proteins of what the gene encodes

when a gene is "on"

-expressed

-transcription and translation

when a gene is "off"

-not expressed

-no transcription or no translation

-end product is not made

What determines a cell's identity/function?

the amount and types of mRNA (& the proteins made from it)

transcription factors (gene expression & regulation)

sets of transcription factor proteins bind to specific DNA sequences in or near a gene and promote or repress its transcription into an RNA

nucleosome

double stranded DNA wrapped around 8 histone proteins; basic unit of chromatin

Euchromatin

-"open chromatin"

-loosely packed nucleosomes

-genes on

-spacing of nucleosomes would make it more accessible

Heterochromatin

-"closed chromatin"

-genes off

general transciption factors (GTF)

-bind to promoter sequency (TATA) and help recruit RNA polymerase

-required for transciption to occur for all genes

-basal TFs

specific transcription factors

-bind to regulatory DNA sequences called either enhancer sequences or silencer sequences and function to activate or repress transcription initiation

-specific to a set of genes, cell type, tissue type, or development time

many transcription factors can regulate expression of the same gene

true

far away sequences can be close together in the 3D, especially when DNA is wrapped up

true

gene regulation cascade

master transcription factor

top of a gene regulation cascade to drive a developmental fate or differentiation

-Oct4, Sox2, Nanog

-repress differentiation

stem cell

special type of cell that has the ability to 1) replicate (mitosis) & make more cells 2) ability to differentiate into different cell types

-undifferentiated

what helps regulate differentiation

transcription factors

differentiation changes

what genes are expressed

embryonic stem cells (ESCs)

Harvested from blastocysts; used to regenerate tissues and organs

Pluripotent—can generate most types of cells

blastocyst

the developing zygote, with cells surrounding a fluid-filled core, contains embryonic stem cells and the cells that will become the placenta

blastocyst parts

1. Inner cell mass/embryoblast

- where embryo develops from, embryonic stem cells

2. Trophoblast

- Outer layer of blastocyst

- Take part in placenta formation

totipotent

can give rise to all human cell types

-"all" & "powerful"

pluripotent

give rise to most human cell types but not all

-not placenta cells

fertilized eggs are...

totipotent

the blastocyst, specifically the inner mass cells are...

pluripotent

multipotent

can give rise to more than one cell type, but limited

(endoderm, mesoderm, ectoderm)

unipotent

can only give rise to one cell type

-lung cell, heart cell, liver cell

cause of differentiation

-changes in gene expression, caused by transcription factors

you can take a differentiated cell and make it into a stem cell by adding...

-"pluripotency" factors

-master transcription factors: Oct4, Sox2, Nanog

-called "induced pluripotent stem cells" (iPS)

there are high levels of master transcription factors (Oct4, Sox2, Nanog) in embryonic stem cells

true, the inhibit differentiation, allowing the stems cells to stay stem cells and not specialize

master transcription factors induce differentiation

false!!

they repress it, allowing stem cells to stay stem cells

induced pluripotent stem cells (iPS)

-differentiated adult somatic cell + master transcription factors

-pluripotent

embryonic stem cells vs induced pluripotent stem cells

-ethical reasons

-immune rejection