Dev Bio Module 06 - Differential Gene Expression

differential gene expression

process by which cells become different from one another based on a unique combination of genes that are expressed/active

• some housekeeping genes are expressed in all cells

• genes expressed by only one cell type make great markers / ideal for reporters

who demonstrated genome equivalence and how

john gurdon

enucleated xenopus egg, replaced with nucleus of epithelial cell from xenopus tadpole intestines, egg gave rise to tadpole which grew into a frog which was a clone of the frog who donated the nucelus

demonstration of genome equivalence in mammals

Ian Wilmut cloned dolly out of a cell

oocyte donor, nuclear donor

• enucleated oocyte donor, transferred udder cell to enucleated egg

• fused with electric current

• emrbyo cultured for 7 days, blastocyst transplanted into oocyte donor

• birth of dolly genetically identical to nuclear donor

what are the four levels of differential gene expression

1. differential transcription (chromatin modifications, epigenetic regulation)

2. differential splicing

3. what, when, if mRNA is translated

4. post translational modifications

nucleosomes

pack DNA, a nucleosome is one unit of chromatin

contains 2 loops of DNA around a histone octamer

euchromatin

open and active DNA, permissive

heterochromatin

closed and inactive, restrictive

chromatin

dna + protein making up a chromasome

components of a histone octamer

2 H2A units

2 H2B units

2 H3 units

2H4 units

(H1 closes the nucleosome, is not a part of the octamer)

histone tail

rich in lysine, amino terminal of the histone, subject to modification

what is one example of epigenetic changes that affect differential transcription

histone modification: opening and closing chromatin- modify histone protein NOT the DNA itself

histone acetyltransferase

add acetyl groups to histone (COCH3), tends to open the chromatin

histone deacetylase

removes acetyl groups from histone, tends to deactivate/close histones

histone methyltransferase and demethylase

add or remove a methyl (CH3) group, activation or inactivation depends on target

histone 3 modifications

K4, me1 is closed me3 is open

K27 ac is active, me3 silences/represses

DNA methylation / DNA methyltransferase

recognize seqeunce 5’-CpG-3’

DNMT3 - modifes untouched CpGs

DNMT1 - replicative maintenance, important so patterns of methylation are inherited

DNA methylation is mostly repressive

CpG islands are frequently found in the

promoter

pathway of dna methylation

1. dnmt3 recognizes and methylates CpG

   1. decrease tf binding

   2. attracts mecp2: methyl cpg binding protein 2

2. mecp2 recruits and activates histone modifying enzymes (HDAC3 - histone deacetylases)

3. triggers histone modification, triggers formation of heterochromatin, not accessible for RNA polymerase

structure of transcription factors - noncoding regulatory elements

1. protein-protein interaction domains: docking site for other transcription factors

2. dna binding domain

3. transactivation domain; recruits or activates RNA polymerase II

transcription factors are classified by family and are highly conserved through evolution