Transcript Epigenetics-2015

Establishment of Cell Identity in Drosophila Embryos
Segment identity is established by sequential
spatially-localized expression of specific genes
Regulatory genes are expressed transiently
Transcriptional memory is
maintained throughout development
from Lodish et al., Molecular Cell Biology, 5th ed. Fig 15-24
Misexpression of Homeotic Genes Lead to Morphological Abominations
from Lodish et al., Molecular Cell Biology, 5th ed. Fig 15-25
Polycomb and Trithorax Complexes
Prevents changes in cell identity by preserving transcription patterns
Chromatin is altered in a heritable manner
Polycomb-group Proteins
Maintains a silenced state
Prevents chromatin remodelling
Trithorax-group Proteins
Maintains an active state
Counteracts the action of PcG proteins
Memory system composed of PcG and trxG complexes is linked to the histone code
Polycomb Group Complexes on Chromatin in Drosophila
PcG proteins are recruited to
Polycomb response elements
E(z) of PRC2 trimethylates H3K27
Pc of PRC1 is recruited to H3K27me3
dRING on PRC1 ubiquitylates H2AK119
from Bantignies and Cavalli, Trends Genet. 27, 454 (2011)
H3K27me3 is segregated to
both daughter chromosomes
to maintain repression
Recruitment of PRC2 to Chromatin in Mammals
PRC2 can be recruited to a PRE by
transcription factors or long ncRNAs
from Morey and Helin, Trends Biochem.Sci. 35, 323 (2010)
PRC1 and PRC2 Promote Chromatin Compaction
from Bantignies and Cavalli, Trends Genet. 27, 454 (2011)
Chromatin compaction reinforces PcG silencing and maintains repressive domains
Co-suppression
Increase in gene copy number
results in decreased expression
Dependent on PcG genes
PcG complexes interact in trans
from Pirrotta, Cell 93, 333 (1998)
Formation of a Repressive Chromatin Hub
PREs and promoters make
contact and form chromatin loops
CTCF and cohesin stabilize loops
Chromatin loops are enriched
in visible PcG bodies
Loops could reinforce the
memory of the silenced state
from Bantignies and Cavalli, Trends Genet. 27, 454 (2011)
Chromosome Kissing
PcG proteins mediate longrange chromatin contacts
Distant complexes of chromosome
loops can interact with eath other
from Bantignies and Cavalli, Trends Genet. 27, 454 (2011)
Segment-specific Localization of Genes in PcG Bodies
PcG genes maintain the regional
identity of segments by repressing
Hox genes in specific regions
Hox genes are organized in
two clusters in Drosophila
PcG bodies are subdomains of the nucleus
that correlate with gene repression
Antp and AbdB genes are
silenced in the head (B)
from Hodgson and Brock, Cell 144, 170 (2011)
Antp and Ubx are silenced
in the posterior (C)
Role of Long-Range Chromosome Interactions in Obesity
Single-nucleotide changes in an
intron of the FTO gene have a
strong association with obesity
Expression of IRX3 correlates
with body weight
from Gorkin and Ren, Nature 507, 309 (2014)
An enhancer in the FTO intron
interacts with the IRX3 promoter
Sequence changes in the FTO
enhancer alters IRX3 expression
HOTAIR Represses Genes in trans
HOTAIR is a lncRNA expressed
by the HOXC locus
HOTAIR associates with
PRC2 and LSD1 and recruits
the complex to the HOXD locus
from Kugel, Trends Biochem.Sci. 37, 144 (2012)
HOTAIR acts in trans to repress the
HOXD locus on a different chromosome
ncRNA Recruits PRC2 to Control Flowering
Vernalization – Many plants flower in
spring after prolonged low temperatures
FLC represses genes required for flowering
and is highly expressed in the fall
COOLAIR is an antisense RNA
that inhibits FLC transcription
COLDAIR is a ncRNA that is induced
by prolonged low temperatures
from Heo and Sung, Epigenetics 6, 433 (2011)
COLDAIR acts in cis and recruits
PRC2, promotes H3K27me3, and
stably represses FLC
Propagation of H3K27 Methylation
EED2 (ESC) binds H3K27me3
and enhances methylation activity
of EZH2 [E(Z)] on a separate histone
EZH2 [E(Z)] methylates H3K27
on adjoining nucleosomes and
newly replicated chromatin
from Richly et al., BioEssays 32, 669 (2010)
Demethylation of H3K27me3 Promotes Gene Activation
PRC2 is recruited to H3K27me3
to mediate gene repression
UTX and JMJD3 are recruited to
Hox promoters and reverse repression
Change in cell fate is mediated by
H3K27 demethylation and H3K4
methylation, whose activities are
present in the same complex
from Rivenbark and Strahl, Science 318, 403 (2007)
Trithorax-group Protein Mechanism of Action
TrxG proteins maintain an active transcriptional state
TrxG proteins promote H3K4me
Effect of Transcription on Epigenetic Modifications
Transcription factor binding leads
to histone modifications that promotes
expression of neighboring genes
from Furey and Sethupathy, Science 342, 705 (2013)
The Viable Yellow Agouti Locus
Agouti promotes yellow pigment
formation on black hair shaft
Wild-type mice have brown fur
due to Agouti expression from
hair cell-specific promoter
Avy contains an IAP insertion that
contains a promoter expressed in all cells
from Dolinoy, Nutr.Rev. 22 (Suppl. 1), S7 (2008)
Avy is a Metastable Epiallele
Avy can be modified in a
variable and reversible manner
Methylation status of IAP determines
the activity of the ectopic promoter
Ectopic Agouti expression causes yellow
fur, obesity, diabetes and tumorigenesis
Avy can be used as an epigenetic biosensor
to study the nutritional and environmental
influences on the fetal epigenome
from Jirtle and Skinner, Nature Rev.Genet. 8, 253 (2007)
Maternal Nutrition Alters Gene Expression by Epigenetic Modification
Feeding of pregnant Avy/a mice with methyl-rich
supplements repress the ectopic Avy promoter
Offspring of diet-supplemented mice
have brown coat color and methylated IAP
from Jirtle and Skinner, Nature Rev.Genet. 8, 253 (2007)
Epigenetic Inheritance in Mammals?
There are several examples
of nongenetic germline transmission
of traits resulting from pesticides,
metabolic state, and behavior
The majority of sperm DNA
is repackaged by protamines
DNA is demethylated in
the single-celled embryo
DNA methylation is gradually
reestablished in the early embryo
from Hughes, Nature 507, 22 (2014)
A second round of DNA demethylation
occurs in the developing germline
The Link Between Intrauterine Growth Retardation and T2D
Infants born during the Dutch Hunger Winter had lower
birth rates, but had impaired glucose tolerance later in life
Progression of Epigenetic Changes in IUGR Rats
Pdx1 is a transcription factor
necessary for b-cell function
Intrauterine growth restriction
recruits histone deacetylases that
prevents USF-1 binding
Altered histone methylation
reinforces Pdx1 repression
Recruitment of DNMT3A
locks Pdx1 in a silent state
The result is defective glucose homeostasis
from Pinney and Simmons, Trends Endocrinol.Metab. 21, 223 (2009)
Parental Experiences Impact the Behavior of the Offspring
from D’Urso and Brickner, Trends Genet. 30, 230 (2014)
Stress reduces maternal care. Pups are more sensitive to stress and
display reduced maternal care, even in the absence of stress
The altered gene expression of target genes (GR in the hippocampus)
is mediated by DNA methylation and histone modifications
Expression patterns are inherited in future generations
Somatic Cell Reprogramming
Pleuripotency genes in somatic cells
have methylated CpG islands
Epigenetic marks must be
reset to generate induced
pleuripotent stem (iPS) cells
from Cedar and Bergman, Nature Rev.Genet. 10, 295 (2009) Repressive histone methylation
marks must be removed, followed
by removal of DNA methylation
which activates the gene
Prion Epigenetics
Prions template conformational conversion
of other molecules of the same protein
Prions are formed through an oligomeric
nucleus, and the elongating polymer is
severed by protein remodeling factors
Prions are disseminated to
daughter cells during cell division
from Halfmann and Lindquist, Science 330, 629 (2010)
Stress Accelerates Prion Appearance
Abrupt changes have consequences
for protein folding
Prion-free cells are adapted to
environment 1, but poorly
adapted to environment 2
Prion formation and disappearance
provide fitness advantages in
different environments
from Halfmann and Lindquist, Science 330, 629 (2010)
Prions connect environmental
conditions to acquisition and
inheritance of new traits
Epigenome Modification and Interpretation
Writers catalyze posttranslational
modifications on DNA or proteins
Erasers remove posttranslational
modifications and DNA methylation
Readers interpret the modifications
and alter chromatin structure
from Helin and Dhanak, Nature 502, 480 (2013)
The Metabolic State is Linked to Epigenetic Modifications
Most chromatin-modifying
enzymes use metabolites as co-factors
The metabolic status of a cell can
transduce a transcriptional response
from Gut and Verdin, Nature 502, 489 (2013)
Conversion of 5hmC from 5mC by TET
TET catalyzes oxidative
decarboxylation of a-ketoglutarate
TET-bound Fe(IV)-oxo intermediate
converts 5mC to 5hmC
from Kohli and Zhang, Nature 502, 472 (2013)
The Complete Demethylation Pathway of 5mC
5mC is oxidated iteratively by TET
5hmC is reverted to unmodified C by
passive dilution during DNA replication
Oxidative products are excised by thymine
DNA glycosylase and repaired by BER
from Kohli and Zhang, Nature 502, 472 (2013)
DNA Methylation Dynamics During Epigenetic Reprogramming
Epigenetic memory must be erased
for cells to achieve pleuripotency
Maternal DNA undergoes passive
demethylation in pre-implantation embryos
Paternal genome is actively
demethylated by TET3
DNA methylation patterns are re-established
by de novo DNMTs at the blastocyst stage
Primordial germ cells are demethylated
through a TET-independent and a
TET-mediated oxidative pathway
from Kohli and Zhang, Nature 502, 472 (2013)
DNA Methylation During Human Embryogenesis
from Reik and Kelsey, Nature 511, 540 (2014)
DNA methylation is largely lost after fertilization, mostly from the paternal genome
Demethylation of the maternal genome continues until the blastocyst stage
DNA becomes remethylated upon differentiation