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from Dolinoy, Nutr.Rev. 22 (Suppl. 1), S7 (2008)
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 Jirtle and Skinner, Nature Rev.Genet. 8, 253 (2007)
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
Avy can be used as an epigenetic biosensor to study the nutritional and environmental influences on the fetal epigenome
Ectopic Agouti expression causes yellow fur, obesity, diabetes and tumorigenesis
The Effect of Nutrition on the Epigenome
from Jirtle and Skinner, Nature Rev.Genet. 8, 253 (2007)
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
Progression of Epigenetic Changes in IUGR Rats
Pdx1 is a transcription factor necessary for -cell function
from Pinney and Simmons, Trends Endocrinol.Metab. 21, 223 (2009)
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
Imprinting
Expression of only one allele of a locus
Only ~100 genes in mammals are imprinted
Most imprinted genes are involved in growth control or postnatal behavior
Imprinted genes involves allele specific methylation and are resistant to genome-wide demethylation in germ cell development
Some clusters of imprinted genes contain long ncRNAs that control allele-specific expression
Some imprinted gene clusters are regulated by methylation-regulated insulators
Parthenogenesis is not possible in mammals due to incorrect expression of imprinted genes
Imprinted Expression of the H19 and Igf2 Genes
ICR is methylated in the male germ line
ICR is protected from methylation in the female germ line by CTCF
CTCF binds to the unmethylated ICR in females and forms an insulator that prevents the activation of Igf2 by a downstream enhancer
In males, the downstream enhancer activates Igf2 and H19 expression is repressed by DNA methylation
from Bartolomei, Genes Dev. 23, 2124 (2009)
from Bartolomei, Genes Dev. 23, 2124 (2009)
ICR in the Airn promoter is methylated in females
Airn is expressed in males and silences Igf2r, Slc22a2 and Slc22a3 in females
Airn is a long ncRNA that might associate with proteins that modify histones
A long ncRNA Controls Imprinting at the Igf2r Locus
from Ferguson-Smith and Surani, Science 293, 1086 (2001)
Imprinting of the PWS-AS Locus
The AS-ICR is required for methylation and inactivation of the PWS-ICR in females to repress nearby genes
The AS-ICR is nonfunctional in males allowing the PWS-ICR to activate nearby genes
The PWS-ICR promotes expression of an antisense Ube3a transcript in males
from Straub and Becker, Nature Rev.Genet. 8, 47 (2007)
Dosage Compensation Mechanisms
Genomes compensate for different numbers of sex chromosomes by adjusting gene expression levels
from Augui et al., Nature Rev.Genet. 12, 429 (2011)
X Chromosome Inactivation in Female Mouse Embryos
Xp is initiatially inactivated after fertilization due to a maternal imprint
A maternal pool of RNF12 initiates imprinted Xp inactivation
Xp is reprogrammed at the blastocyst stage
Random X chromosome inactivation takes place in the ICM due to reactivation of RNF12 from Xp
Xi reprogramming correlates with expression of pleuripotency factors
Monoallelic expression of Xist is maintained
Xi is reprogrammed in the female germ line
The X-Inactivation Center in Mouse
The XIC is the minimum region necessary to trigger X-chromosome inactivation
Xist is an RNA expressed from Xi that coats the X chromosome in cis
RNF12 activates Xist in a dose-dependent manner by ubiquitylating the REX1 transcription factor
REX1 activates Tsix and represses Xist
Tsix is an RNA expressed from the opposite strand from Xist that acts as an Xist repressor
from Augui et al., Nature Rev.Genet. 12, 429 (2011)
from Lee, Genes Dev. 23, 1831 (2009)
The Basic Events of X-inactivation
The two X chromosomes are brought together by CTCF, Tsix and Xite
Transcription factors stochastically shift to the future Xa
Tsix becomes monoallelically expressed
Differential chromatin modifications in Xist lead to its monoallelic expression
from Lee, Genes Dev. 23, 1831 (2009)
The Mechanism of Pairing to Initiate X-inactivation
Stepwise Progression of X Inactivation in Differentiating ES Cells
from Brockdorff, Trends Genet. 18, 352 (2002)
One X chromosome is converted to facultative heterochromatin
Xist transcription off the inactive X initiates chromatin modification events
X inactivation is maintained epigenetically
Calico Cats
One of the genes controlling fur color is on the X chromosome
B – orangeb - black
Random X inactivation early in embryonic development leads to patchworks of skin cells expressing each allele
Female mammals are genetic mosaics
The Dosage Compensation Complex in Drosophila
from Gilfillan et al., FEBS Lett. 567, 8 (2004)
SXL in females prevents MSL2 translation
MSL2 in males stabilizes roX, MSL1, and MSL3
DCC binds to high affinity sites on X chromosome
DCC spreads to nearby sites on active chromatin
H4K16 acetylation impedes formation of condensed chromatin structure
from Straub and Becker, Nature Rev.Genet. 8, 47 (2007)
DCC is Localized to the X Chromosome
DCC localization is determined by staining of polytene chromosomes with anti-MSL1
DCC associates almost exclusively with transcribed regions
DNA Replicates by a Semiconservative Mechanism
Grow cells in 15N and transfer to 14N
Analyze DNA by equilibrium density gradient centrifugation
Presence of H-L DNA is indicative of semiconservative DNA replication
from Lodish et al., Molecular Cell Biology, 6th ed. Fig 4-29
The 11th Commandment
The Replicon Model
from Aladjem, Nature Rev.Genet. 5, 588 (2007)
Sequence elements determine where initiation initiates by interacting with trans-acting regulatory factors
Leading strand is synthesized continuously and lagging strand is synthesized as Okazaki fragments
Mechanics of DNA Replication in E. coli
The 5’ to 3’ exonuclease activity of Pol I removes the RNA primer and fills in the gap
DNA ligase joins adjacent completed fragments
from Lodish et al., Molecular Cell Biology, 4th ed. Fig 12-9
Initiation of DNA Replication in E. coli
DnaA binds to high affinity sites in oriB
DnaC loads DnaB helicase to single stranded regions
DnaB helicase unwinds the DNA away from the origin
DnaA facilitates the melting of DNA-unwinding element
from Mott and Berger, Nature Rev.Microbiol. 5, 343 (2007)
DnaB is an ATP-dependent Helicase
SSB proteins prevent the separated strands from reannealing
DnaB uses ATP hydrolysis to separate the strands
DnaB unwinds DNA in the 5’-3’ direction
from Lodish et al., Molecular Cell Biology, 4th ed. Fig 12-8
from Alberts et al., Molecular Biology of the Cell, 4th ed., Fig 5-12
RNA Primer Synthesis Does Not Require a 3’-OH
Primase is recruited to ssDNA by a DnaB hexamer
Coordination of Leading and Lagging Strand Synthesis
Two molecules of Pol III are bound at each growing fork and are held together by
The size of the DNA loop increases as lagging strand is synthesized
Lagging strand polymerase is displaced when Okazaki fragment is completed and rebinds to synthesize the next Okazaki fragment
from Lodish et al., Molecular Cell Biology, 4th ed. Fig 12-11
from Pomerantz and O’Donnell, Nature 456, 762 (2008)
Interruption of Leading Strand Synthesis by RNA Polymerase
Most transcription units in bacteria are encoded by the leading strand
Natural selection for co-directional collisions in the cell
from Pomerantz and O’Donnell, Nature 456, 762 (2008)
Replisome Bypass of a Co-directional RNA Polymerase
from Pomerantz and O’Donnell, Nature 456, 762 (2008)
Replication fork recruits the 3’-terminus of the mRNA to continue leading-strand synthesis
The leading strand is synthesized in a discontinuous fashion
Replisome Bypass of a Co-directional RNA Polymerase
Bidirectional Replication of SV40 DNA from a Single Origin
from Lodish et al., Molecular Cell Biology, 6th ed. Fig 4-32
Replication of SV40 DNA
T antigen binds to origin and melts duplex and RPA binds to ss DNA
Primase synthesizes RNA primer and Pol extends the primer
PCNA-Rfc-Pol extend the primer
from Lodish et al., Molecular Cell Biology, 6th ed. Fig 4-31