BIOMG 1350 - Lecture 19

Regulation of Gene Expression II

Transcriptional regulators

Can generate many cell types during development.

• Can regulate the expression of dozens or even hundreds of genes.

• Different combinations can achieve many different cell types with unique behaviors.

Organoids key

• Knowing the right combination of signaling pathways and transcriptional regulators is key

Organoids

Are made of a collection of organ-specified cell types that are development in vitro and have some of the spatial organization and function of the actual organ.

Master Regulator Formation

• Single transcription factor can lead to the formation of an entire organ

Master Regulator

• expressed at the beginning of a developmental lineage

• participates in the specification of the lineage by regulation multiple downstream genes

• When mis-expressed (a “move-it” experiment), has the ability to respecify the fate of cells destined to form other lineage

Eyeless Gene

• A master regulator for eye development

Eyeless Gene Facts

• It encodes a transcriptional regulator that initiates eye development

• It activates the expression of genes needed to build eyes

• Eyeless alone is sufficient for eye development

Function of the eyeless gene in eye development is evolutionarily conserved.

Lose it (homolog in mice)

• Eye gets smaller or no eye

Move It (Mouse eye in fly eye)

• Ectopic eye (different location)

Tightly packed chromatin

Inhibits transcription so we need a way to loosen/tighten chromatin to make genes more accessible/inaccessible for transcription.

Chromatin remodeling complexes “loosen” the DNA

• DNA that is less accessible to other proteins inhibits transcription

• DNA that is more accessible to other proteins facilitate transcription, because transcriptional machinery can access regulatory sequences.

• Use the energy of ATP to loosen the DNA wrapped around nucleosomes

Chromatin Remodeling Complexes Know Where to Go

• This information is on the histone tails

Histone Tails

Can be modified by adding chemical marks to the tail to communicate if it packed into chromatin or more decondenses

• reversible process

Histone Tails Directly

By altering the affinity of tails for an adjacent nucleosome

Histone Tails Indirectly

By attracting general transcription regulators and chromatin remodeling complexes

Histone modifying enzymes

• add/remove covalent modification on the core of the histone tail

Some histone modifications allow heterochromatin to form and spread

Reader-writer complex recognizes modified histone

• Spreads heterochromatin-specific histone tail modifications; other heterochromatin specific proteins bind

• Heterochromatin spreads until it encounters a barrier DNA sequence

Some histone modifications can lead to gene expression

• TATA box is recognized by the chromatin-remodeling complex

• Or another enzyme can interpret the transcription regulator and will add pro transcription histone modification on the neighboring nucleosomes which is a way to decondense DNA

• Makes space for different proteins needed at the promoter to initiate transcription.

DNA methylation

Prevents gene expression

• can only occur on cytosine (C) that are next to guanine (G) in the 5’-3’ direction

• Doesn’t affect DNA base pairing

CpG island in mammals

Are areas of the genome that have high prevalence of 5’ CG 3’ dinucleotide sequences

• 70% of human genes have a CpG island near their promoter

unmethylated CpG island

• recruit proteins that decondense chromatin

• activate gene expressions

methylated CpG island

• recruit proteins that condense chromatin

• repress gene expression

Cell Memory Positive Feedback

• Protein A activates transcription of itself (positive feedback) and other genes that control cell fate

Cell Memory Positive Feedback Step 1

Transient signal turns on expression of Gene A

Cell Memory Positive Feedback Step 2

Gene a continues to be transcribed in absence of initial signal

Cell Memory Positive Feedback Step 3

Continued cell memory

Cell memory via histone modifications step 1

parental nucleosomes with modified histone

Cell memory via histone modifications step 2

When DNA divides only half of the daughter nucleosomes are inherited parental modified histones

• some have modifications and some dont

Cell memory via histone modifications step 3

parental pattern of histone modification reestablished by enzymes that recognize the same modifications they catalyze.

Cell memory via DNA methylation

Can be passed onto the daughter cells by action of maintenance methyltransferase.

Cell memory via DNA methylation Step 1

DNA replication

Cell memory via DNA methylation Step 2

New DNA Strands through methylation of newly synthesized strand

Epigenetic inheritance

Dosage Compensation

Dosage Compensation

• Equalizes the amount of expression for X chromosome gene for XX and XY individual

• In most mammals, this is via random inactivation of one of the X chromosomes in XX individuals

• X inactivation is irreversible and via epigenetic mechanism

X inactivation

• Randomly chooses which x chromosome will be inactivated

• Dosage Compensation

  • Cat fur