Lecture 10: Heterochromatin, Euchromatin, and Epigenetics

Epigenetic Changes

Non-genetic changes in histones or DNA that alter gene function without altering the DNA sequence

Epigenetic Inheritance

Heritable modifications in gene function not due to changes in DNA sequence

stable inheritance from cell to cell and stable inheritance from parent to child

There are two types of epigenetic inheritance:

Transgenerational Inheritance

Persistance of inheritance across multiple generations

Intergenerational Inheritance

Transmission of traits or epigenetic changes from one generation to the next

intergenerational

If a pregnant female is exposed to an environmental condition the same condition can affect the female parent, the F1 generation, and the F1’s germ cells simultaneously— even though the F2 generation is affected, this is still considered…

Euchromatin

Chromatin containing active genes and is thought of as less compacted; weak staining

Heterochromatin

Chromatin containing repressed genes and is thought of as more compacted; strong DNA staining

Constitutive Heterochromatin

Heterochromatin marked with H3K9me3 and is bound by HP1

Facultative Heterochromatin

Heterochromatin marked by H3K27me3 and is bound by polycomb

silencers, closed chromatin states, recruiting histone methyltransferases

Polycomb binds _____ and promotes _____ via _____

polycomb, trithorax, PRE/TRE

____ and ____ bind to the same cis-regulatory module (_____, which encodes a non-coding RNA)

H3K27me3, closed chromatin, maintenance during replication

Polycomb is recruited by ______ and is involved in the formation of ______ and for _______

PRE

Cis-regulatory module that is nucleosome-depleted

TRE

Cis-regulatory module that overlaps with or is identical to PRE

PHO-RC

DNA-binding protein that contains a zinc finger among other elements; pleiohomeotic repressive element

PRC2

Writer protein that harbours the SET-domain-containing “enhancer of Zeste” protein

H3K27me3

PRC2 marks _____ which PRC1 reads

PRC1

Reader protein that harbours the polycomb chromodomain

PRC2 binding, spreading H3K27me3

PRC1 binds to allow for additional _____, serving as a positive feedback mechanism allowing for _______

HP1 only, PcG only, both, or neither

Several types of heterochromatin exist, including those bound by…

nucleation point, silenced, insulator elements

Heterochromatin can spread from a ______ and genes within heterochromatin are _____. _____ can stop the spread of heterochromatin

Su(var)3-9

Methylates H3K9 which allows for HP1 recruitment

chromodomain, more Su(var)3-9, HDACs

HP1 contains a _____ which is necessary for recognising H3K9 methylation. Upon binding HP1 recruits _____ as well as _____ to drive heterochromatin formation forwards

Position Effect Variegation

A gene’s expression changes depending on its location on a chromosome, specifically when it is near heterochromatin

more red than white, heterochromatin spreading is suppressed so less w+ is silenced

w^m4 with mutations in Su(var) result in _____ because _____

more white than red, heterochromatin spreading is enhanced so more w+ is silenced

w^m4 with mutations in E(var) result in _____ because ______

w^-

Drosophila mutant, white eyes

w⁺

Drosophila wild-type, red-eyed

Su(var)

Suppressor of position effect variegation

E(var)

Enhancer of position effect variegation

suppresses

Mutations in HP1 _____ position effect variegation (PEV)

ATP-binding cassette (ABC) transporter, formation of red pigmented eyes

The Drosophila w+ (white) gene encodes a _______ that is required for ______

inversion placing the allele physically close to heterochromatin

PEV is found in w^m4 flies due to….

varies from cell to cell, fluctuates, irregular distribution of red-pigmented cells in the eye

The extent by which heterochromatin spreads into neighbouring regions ______ therefore w^m4 expression ______ resulting in _____

Insulator

Blocks enhancer function and spreading of heterochromatin

5, CpG dinucleotides, maintained, imprinting, MeCP2, CpG dinucleotides

DNA methylation occurs at the ___ position of cytosines. 90% of methylated cytosines are found in ______ and the methylation pattern is ____ through cell division. This pattern constitutes an epigenetic mark and causes ______. _____ binds _____ as an efficient form of gene repression

major groove, DNA-binding for many transcription factors, 5-methylcytosine binding proteins, MeCP2 (methyl-CpG-binding protein 2)

The methyl group of 5-methylcytosine is in the _____ and impairs/blocks _______. It attracts ________, for example ______

sugar-phosphate backbone, two adjacent C/G base pairs

The “p” in CpG refers to ___, indicating _____

Protamine

Small, arginine-rich nuclear proteins that replace histones in late spermatogenesis

allowing extremely compact chromatin, sperm are very small

Protamines are essential in sperm for ______ as protamines are _____ than nucleosomes. This is needed because ______

DNMT3A/B

Recognise unmethylated DNA and add methyl groups on appropriate cytosines in the genome on both strands, referred to as de novo methylation

DNMT

____ is prevented from entering the oocyte to allow for methylation dilution to occur

Passive Demethylation

Demethylation that occurs as a result of replication

Maintenance Methylation

Methylation of hemi-methylated DNA strands created by replication

DNMT1

Protein that conducts maintenance methylation

DNMT1 is not imported into the nucleus to allow for full methylation dilution

As the embryo begins dividing newly formed DNA is not methylated because…

Dnmt3 gene repression, less methylation

Royal jelly or siRNAs cause ______ which causes _____, resulting in a queen bee as queen characteristic genes are not repressed

IGF2

Imprinted gene that stimulates fetal growth

active, repressed

Igf2 is _____ in the paternal allele and ____ in the maternal allele

CTCF, ICR, H19, IGF2

On the maternal chromosome, ____ blocks the _____, therefore the enhancer works on ____ but not ____ and Igf2 is off

CTCF, ICR, ICR, H19

On the paternal chromosome, _____ does not block the ____. ____ and ____ are methylated and therefore the enhancer works on Igf2

demethylated

Imprinted loci are not _____ in the zygote— in the male, histones remain which ensure this

no functional consequence

Mutations in the imprinted allele have…

Rett Syndrome

Caused by mutations in MeCP2 that appears as severe autism in females and is neonatal lethal in males

Fragile X Syndrome

Caused by trinucleotide repeats resulting in methylation and gene silencing of FMR1

Beckwith-Wiedermann Syndrome

Caused by loss of CTCF binding to the maternal ICR which affects Igf2/H19 imprinting therefore Igf2 expression is biallelic and H19 is off. Appears as organ overgrowth/Wilm’s tumours