(22) CH 20 - Additional Mechanisms of gene regulation in Eukaryotes

Ch 20 - epigenetic; DNA methylation and genomic imprinting

transcription factors interact with

cis-acting DNA regions to control rates of transcription initiation

basal factors bind to the promoter (at

TATA box binding site) to initiate basal gene expression levels

activators and repressors bind to

enhancers (usually, some pressers bind to promoter) to up regulate, down regulate, or prevent upregualitonof basal gene expression levels

direct effects of transcription factors:

through bind to DNA

• basal factors

• activators and repressors

indirect effect of transcription factors:

through protein-protein interactions

• co-activators and co-repressors

eukaryotes can use miRNAs to

down-regulate expression of target genes post-transcriptionally

two methods that eukaryotic cells use to regulate transcription initiation

• binding of transcription factors to enhancers

• DNA methylation in promoter region

binding of transcription factors to enhancers - this modulates the

spatial and temporal expression of many genes that are expressed only in particular tissues at specific times during development

DNA methylation in promoter region - a biochemical modification of DNA itself

a methyl (-CH3) groups is added to the fifth carbon of the cytosine base in a 5’CpG 3’ dinucleotide pair on one strand of the double helix

• the “p” in CpG stands for phosphate

the DNA sequence in genes is not the

only carrier of genetic information

epigenetic phenomena

heritable self-perpetuating changes in gene expression not caused by base pair sequence changes

epigenetic phenomena usually involves

modified cytosine residues, modified histone tails in chromatin, small RNAs

epigenetic factors that determine whether a gene is

“on” or “off” can change

transgenerational epigenetic inheritance -

when an environmentally induced trait (not caused by a base pair mutation) appears in an individual’s descendants whose DNA was no directly exposed to the environmental trigger (not well demonstrated yet in mammals)

chromatin structure can affect

transcription

• histone modification and DNA methylation

• chromatin remodeling and hyper condensation

nucleosomes can make

promoters inaccessible

epigenetic changes -

changes in chromatin structure that are inherited from one generation to the next

• DNA sequence is not altered

but particular cells with altered chromatin will have altered

gene expression, and this can be inherited from one cell generation not the next (e.g., in a given tissue type)

chromatin reduces

transcription

chromatin remodeling can change

accessibility for transcription factors

SWI-SNF are proteins that

remodel chromatin structure with the help of ATP; they are examples “remodeling proteins'“

note this contrasts with prokaryotes, which require

active repression via binding of repressors to cis-elements for transcriptional modulation

DNA methylation -

a methyl group is added to the cytosine base in a 5’ CpG 3’ dinucleotide by DNA methyl transferases (DMNTs)

in the human genome, 70% of the C residues in CpG dinucleotides are methylated, implying

DNA methylation is important for transcription regulation

transcription is active near

unmethylated CpG islands

CpG islands are regions with

a high concentration of CpG dinucleotides

CpG islands near genes are usually unmethylated because

an activator binds and blocks access by DNMTs

the chromatin is open and transcription is activated when

CpGs are unmethylated

DNA methylation at CpG islands silences

gene expression

DNA methylation at CpG islands usually

inhibits transcription of eukaryotic genes

in the absence of activators, the CpG islands become

methylated

methyl-CpG-binding proteins (MeCPs) bind and

close the chromatin structure

• closed chromatin = no transcription

C. elegans and yeast -

no DNA methylation

other invertebrates and lower eukaryotes -

very little DNA methylation

drosophila -

disagreement in the literature as to where there is presence of absence of 5-methylcytosine

in bees, and many other invertebrates

methylation found only is CDS

regardless of this variation, DNA methylation at CpG islands is likely

very important to human health

cytosine methylation pattern is copied during

DNA replication

DNA methylation is a epigenetic phenomenon because it

can heritably alter gene expression without changing DNA sequence

dividing cells retain memory of cell fate:

faithful transmission of epigenetic marks like DNA methylation and histone modification help maintain “cell identity” as to what genes should be turned on/off

gene expression repression by DNA methylation is often

long-term, because the methylation pattern is maintained through numerous mitotic cell divisions

long-term repression through DNA methylation is called

silencing

DNA methylation is an epigenetic phenomenon because it can

heritably alter gene expression without changing DNA sequence

sex-specific DNA methylation is responsible for

genomic imprinting

medelian rule -

parental origin of alleles does not affect F1 phenotype (usually)

• for the vast majority of genes in plants and animals, this principle holds true

genomic imprinting

expression of a gene depends on whether it was inherited from the mother or father

• epigenetic effect (no change in DNA sequence)

genomic imprinting occurs at

gametogenesis at some genes in mammals

genomic imprinting reflects programmed methylation of DNA sequences called

imprinting control regions (ICRs)

• works the same in every individual

paternally imprinted gene is

transcriptionally silenced if it was transmitted from the father

• maternally inherited allele is expressed

maternally imprinted gene is transcriptionally silenced if it was

transmitted from the mother

• paternally inherited alleles is expressed

imprinted =

silenced

sex-specific DNA methylation mediates

imprinting

in somatic cells, the genomic imprint is maintained during

mitosis; so the imprinting markers remain throughout the life of the mammal

in germ cells, genomic imprints are reset during

meiosis before being passed on to the next generation

• DNA methylation is removed during early meiosis

• and new sex-specific DNA methylation is generated before final gamete formation

the resetting of genomic imprints during

meiosis

sex-specific methylation remain in the somatic cells throughout

the life of this individual

• imprints are erased during meiosis of germ-line cells

• accompanied by heavy methylation to rest sex-specific imprinting

imprinting (silencing) caused by methylation, but methylation not always

at a silenced gene

knowing that a gene is paternally or maternally imprinted tells you which

alleles is transcriptionally active and which is silenced

imprinting does not tell you which

allele is methylated necessarily

methylation of one imprinting control region (ICR) can turn

a gene off, whereas methylation of another ICR can turn a gene on

in some cases, the imprinted (silenced) allele is

one that is not methylated

methylation at imprinting control regions (ICRs) affects

gene expression

in ncRNA based imprinting, ICR contains a

noncoding RNA whose transcription is controlled by CpG islands

ncRNA Air in turn controlled transcription of

Igfr2 gene (insulin growth factor receptor 2)

the air ncRNA prevents

expression of lgfr2

methylated maternal CpG islands prevents production of Air;

transcription of lgfr2 is active

nonmethylated paternal CpG islands allows production of

Air ncRNA; transcription of lgfr2 is silenced

insulators can have CpGs, and methylation at imprinting control regions (ICRs) affects gene expression by

altering TADs

• ICR is an insulator that controls transcription of lgf2 gene

maternal chromosome - unmethylated insulators is functional

it binds CTCF and the enhancer on the maternal chromsome cannot interact with the promoter of lgf2 because they are in different TADs → maternal lgf2 copy is silenced

paternal chromosome - insulator is methylated, which prevents is from binding to

CTCF → paternal lgf2 promoter and enhancer are in the same TAD and transcription is active

sex specific imprinting - effects of deletion depends on

whether it is present of paternal or maternal copy of the chromosome

Prader-Willi syndrome

C expressed normally but no A or B expression because of maternal imprinting

angel man syndrome

A and B expressed normally but no C expression because of paternal imprinting

inheritance patterns with imprinting - the sex of the parent carrying the mutant allele determines

offspring phenotype, not sex of offspring

inheritance patterns with imprinting - a mutant in a maternally imprinted gene will never show up

along a strictly female line

• mother’s copy is always silenced, and father contributes normal copy

imprinting occurs only in

placental mammals

most imprinted genes control

prenatal growth

parental conflict hypothesis -

mother’s best interest for her baby to be small; father’s interest for his baby to be large and robust

lgf2 promotes growth when it

bins to a receptor

• maternal imprinting would silence one copy of lgf2 and thus keeps the fetus small

igf2 encodes a different

receptor for lgf2 that represses growth

• paternal imprinting and silencing of lgf2 could help fetuses get larger

other epigenetic phenomena transmit information of silenced state to subsequent cells through

mitosis, but not through the gametes

memory of cell fate - all cells in multicellular organisms have the

same genes and cell types are different because of gene expression

memory of cell fate - cells “remember” fate through mitosis in part because

histone modifications that repression transcription of certain are copied at replication

epialleles are alleles of genes that can

be silenced spontaneously by methylation

epialleles more common in

plants than mammals (plants don’t erase methylation during gametogenesis)

expression status of epiallels can be transmitted

insatiably based on environmental influence nvire

environmentally acquired trait - agouti genet in mice

• yellow phenotype only apparent if the Avy allele is unmethylated

• methylated Avy alleles behave as WT

agouti gene in mice - Avy allele was generated when a

retrotransposon containing a promoter region and CpG island jumped upstream of agouti

agouti gene in mice - when CpG island is unmethylated high levels of

agouti mRNA are transcribed from retrotransposon promoter - yellow coat

agouti gene in mice - when CpG island is methylated,

transcription occurs from the normal agouti promoter - gray coat

agouti gene in mice - yellow phenotype only apparent is

CpG island in retrotransposon promoter upstream of agouti gene is unmethylated

agouti gene in mice - Avy allele produces

an unstable phenotype

agouti gene in mice - degree of CpG methylation of the

TE insertion correlated with coat color

intergenerational transmission of an environmentally induced phenotype

maternal diet affects coat color - Avy a mice whose mothers were fed a diet rich in methyl groups were darker on average

• exposure of mother and developing offspring = intergenerational , not true transgenerational