Epigenetics Exam II

types of embryo polarization

A-P, D-V, L-R

3 germ layers

ectoderm, mesoderm, endoderm

morphogen

can induce different cell fates depending on its concentration

body segmentation

repeated body parts/blocks

bicoid mRNA

maternally derived, anterior (A-P)

bicoid

homeobox gene; organises anterior body pattern of Drosophila

del bicoid

embryos fail to develop anterior segments including head/thorax

segments vary in __ composition and regulation.

transcription factor

homeosis

mutations in Hox genes (cause parts to form in wrong places)

PRC

polycomb repressive complex; repress Hox genes

TrxG

activates hox genes

PcG

polycomb group; represses Hox gene expression

PRE

polycomb response elements at Hox promoters; bound by PRC

PRC2

responsible for methylation of polycomb complex

PRC1 complex

methylation complex

PRC2 components

core, PRC2.1, PRC2.2

mechanisms of PcG recruitment to chromatin

DNA-based, histone PTM-based, RNA-based

PcG creates

H3K27 repressive mark

TrxG mutations

mimic Hox gene loss of function

TrxG active mark

H3K4

Ash1

histone methyltransferase

PRC1 binds

H3K27

ncRNA examples

rRNA, tRNA, snoRNA, snRNA, miRNA, siRNA, piRNA, lncRNA, eRNA

most cellular RNAs are ___.

assembled into ribosomes

siRNA

degradation of target mRNA

miRNA

inhibit translation

piRNA

control transposons

lncRNA

gene regulation in nucleus, 5’ cap

eRNA

from active enhancers; regulation

siRNA structure

19-21 nt duplex, 3’ overhang

RISC

RNA-induced silencing complex

miRNA synthesis

exportation, dicing, strand selection from duplex

lncRNA functions

transcriptional interference, chromatin remodelling, alternative splicing, protein activity, structure

lncRNA in cis

ANRIL, binds PRC2 and PRC1

lncRNA in trans

HOTAIR binds PRC2, silence HoxD

targetting of ncRNA

RNA-RNA interactions

localization of H3 modifications =

active transcription

transcription of eRNA (step 1)

transcription factors bind enhancer locus, recruit other transcription factors and complexes

transcription of eRNA (step 2)

P300 acetylates H3K27 to open enhancer locus, recruit RNAP II

transcription of eRNA (step 3)

CTD of RNAP II is phosphorylated, MLL methyltransferases recruited to start transcription

transcription of eRNA (step 4)

BRD4 facilitates elongation, H3K4 methylation — termination via polyadenylation, exosome degradation

eRNA functions

enhancer-promoter looping, histone mods, transcriptional interactions,

RAP

biotinylated probes hybridised to target RNA crosslinked to proteins and DNA- map lncRNA

chromatin decondensation in embryonic stem cells is caused by ___.

H1 depletion

maintenance of silent heterochromatin

HP1 binding to H3K9

boundary elements

insulators between chromatin domains

CTCF

insulator binding protein

TAD

topologically associating domains

3C

convert chromatin interactions into ligation products

Hi-C

crosslink DNA, cut, mark with biotin, ligate, purify and shear

dosage compensation

equalises level of expression of X-linked genes in the two sexes

dosage compensation discovered in

drosophila

MSL1,2

bind MSL to chromatin

MOF

H4K17Ac

MLA

helicase, ATPase, ssRNA binding

mammal dosage compensation

inactivate one X in female

Drosophila dosage compensation

double expression of X in male

C. elegans dosage compensation

halve expression of both X in female

X-inactivation extraembryonic

paternally imprinted

X-inactivation embryo

random

XIC

X-inactivation center

Xist

lncRNA, coats inactive X

Tsix

antisense to Xist; transcribed on active X

hnRNP U

localises Xist RNA

genomic imprinting

allelic expression of genes by parent

genomic imprinting consequence

difference between maternal and paternal genomes

blastocyst cell types

1x fetal, 2x extraembryonic

extraembryonic cells

trophectoderm, primitive endoderm

genomic imprinting is found in

placental mammals, marsupials, plant endosperm

imprinted gene locations

clustered, repetitive

imprinted clusters contain __.

ncRNA

imprinting diseases

Angelman, Prader-Willi, Beckwith-Weidemann

epigenetic imprinting mechanisms

differential chromatin modification, insulator binding proteins, ncRNA

pronuclei

separates gamete genomes for a few hours after fertilisation

paternal genome post-fertilisation

demethylated

PGC (germ cells)

derived from ectoderm, lots of 5mC

demethylation of the embryo occurs in

2-cell stage

remethylation of embryo occurs in

postimplantation

cell lineage is determined by

internal factors, external cues

cell lineage starts with

stem cells

symmetric division

produces two of the same cell

asymmetric division

produces two different cells

symmetric divisions can change lineages via

environmental cues

stem cell features

self-renewal, differentiation

fertilised egg potency

totipotent

EPSC potency

totipotent

IPSC potency

pluripotent

ESC potency

pluripotent

neural stem cell potency

multipotent

gastrulation

three germ layers

reprogramming of somatic cells

fusion of somatic cell to embryonic stem cell

heterokaryon

two nuclei

fibroblast to iPSC

viral transfection, self-excising vectors, non-integrating

EPSC in development

8-16 cell

ESC in development

early blastocyst

chromatin in pluripotent stem cells

open (euchromatin)

chromatin in differentiated cells

closed (heterochromatin)

LOCK

H3K9 methylation, HP1 binding

ESC histone modifications

bivalent