-
Články
- Časopisy
- Kurzy
- Témy
- Kongresy
- Videa
- Podcasty
A Sustained Dietary Change Increases Epigenetic Variation in Isogenic
Mice
Epigenetic changes can be induced by adverse environmental exposures, such as
nutritional imbalance, but little is known about the nature or extent of these
changes. Here we have explored the epigenomic effects of a sustained nutritional
change, excess dietary methyl donors, by assessing genomic CpG methylation
patterns in isogenic mice exposed for one or six generations. We find stochastic
variation in methylation levels at many loci; exposure to methyl donors
increases the magnitude of this variation and the number of variable loci.
Several gene ontology categories are significantly overrepresented in genes
proximal to these methylation-variable loci, suggesting that certain pathways
are susceptible to environmental influence on their epigenetic states. Long-term
exposure to the diet (six generations) results in a larger number of loci
exhibiting epigenetic variability, suggesting that some of the induced changes
are heritable. This finding presents the possibility that epigenetic variation
within populations can be induced by environmental change, providing a vehicle
for disease predisposition and possibly a substrate for natural selection.
Vyšlo v časopise: A Sustained Dietary Change Increases Epigenetic Variation in Isogenic Mice. PLoS Genet 7(4): e32767. doi:10.1371/journal.pgen.1001380
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1001380Souhrn
Epigenetic changes can be induced by adverse environmental exposures, such as
nutritional imbalance, but little is known about the nature or extent of these
changes. Here we have explored the epigenomic effects of a sustained nutritional
change, excess dietary methyl donors, by assessing genomic CpG methylation
patterns in isogenic mice exposed for one or six generations. We find stochastic
variation in methylation levels at many loci; exposure to methyl donors
increases the magnitude of this variation and the number of variable loci.
Several gene ontology categories are significantly overrepresented in genes
proximal to these methylation-variable loci, suggesting that certain pathways
are susceptible to environmental influence on their epigenetic states. Long-term
exposure to the diet (six generations) results in a larger number of loci
exhibiting epigenetic variability, suggesting that some of the induced changes
are heritable. This finding presents the possibility that epigenetic variation
within populations can be induced by environmental change, providing a vehicle
for disease predisposition and possibly a substrate for natural selection.
Zdroje
1. Anway
MD
Cupp
AS
Uzumcu
M
Skinner
MK
2005
Epigenetic transgenerational actions of endocrine disruptors and
male fertility.
Science
308
1466
1469
2. Weaver
ICG
Cervoni
N
Champagne
FA
Alessio
ACD
Sharma
S
2004
Epigenetic programming by maternal behaviour.
Nature Neuroscience
7
847
854
3. Young
LE
Fernandes
K
McEnvoy
TG
Butterwith
SC
Broadbent
PJ
2001
Epigenetic change in IGF2R is associated with fetal overgrowth
after sheep embryo culture.
Nature Genetics
27
153
154
4. Cooney
CA
Dave
AA
Wolff
GL
2002
Maternal methyl supplements in mice affect epigenetic variation
and DNA methylation in offspring.
The Journal of Nutrition
132
2393S
2400S
5. Cropley
JE
Suter
CM
Beckman
KB
Martin
DIK
2006
Germ-line epigenetic modification of the murine Avy allele by
nutritional supplementation.
Proceedings of the National Academy of Sciences of the United States of
America
103
17308
17312
6. Dolinoy
DC
Weidman
JR
Waterland
RA
Jirtle
RL
2006
Maternal genistein alters coat color and protects Avy mouse
offspring from obesity by modifying the fetal epigenome.
Environmental Health Perspectives
114
567
572
7. Lillycrop
KA
Phillips
ES
Jackson
AA
Hanson
MA
Burdge
GC
2005
Dietary protein restriction of pregnant rats induces and folic
acid supplementation prevents epigenetic modification of hepatic gene
expression in the offspring.
Journal of Nutrition
135
1382
1386
8. Sinclair
KD
Allegrucci
C
Singh
R
Gardner
DS
Sebastian
S
2007
DNA methylation, insulin resistance and blood pressure in
offspring determined by maternal periconceptional B vitamin and methionine
status.
Proceedings of the National Academy of Sciences of the United States of
America
104
19351
19356
9. Waterland
RA
Jirtle
RL
2003
Transposable elements: targets for early nutritional effects on
epigenetic gene regulation.
Molecular and Cellular Biology
23
5293
5300
10. Waterland
RA
Lin
JR
Smith
CA
Jirtle
RL
2006
Post-weaning diet affects genomic imprinting at the insulin-like
growth factor 2 (Igf2) locus.
Human Molecular Genetics
15
705
716
11. Zhang
S
Rattanatray
L
Maclaughlin
SM
Cropley
JE
Suter
CM
2010
Periconceptional undernutrition in normal and overweight ewes
leads to increased adrenal growth and epigenetic changes in adrenal IGF2/H19
gene in offspring.
FASEB J
12. Waterland
RA
Dolinoy
DC
Lin
JR
Smith
CA
Shi
X
2006
Maternal methyl supplements increase offspring DNA methylation at
Axin Fused.
Genesis
44
401
406
13. McMillen
IC
Robinson
JS
2005
Developmental origins of the metabolic syndrome: prediction,
plasticity and programming.
Physiological Reviews
85
571
633
14. Gallou-Kabani
C
Junien
C
2005
Nutritional epigenomics of metabolic syndrome: new perspective
against the epidemic.
Diabetes
54
1899
1906
15. Thompson
RF
Einstein
FH
2010
Epigenetic basis for fetal origins of age-related
disease.
Journal of Women's Health
19
581
587
16. Cropley
JE
Suter
CM
2008
An epigenetic basis for fetal programming.
Highlights
16
22
25
17. Waterland
RA
Garza
C
1999
Potential mechanisms of metabolic imprinting that lead to chronic
disease.
American Journal of Clinical Nutrition
69
179
197
18. Burdge
GC
Slater-Jefferies
J
Torrens
C
Phillips
ES
Hanson
MA
2007
Dietary protein restriction of pregnant rats in the F0 generation
induces altered methylation of hepatic gene promoters in the adult male
offspring in the F1 and F2 generations.
British Journal of Nutrition
97
435
439
19. Tobi
EW
Lumey
LH
Talens
RP
Kremer
D
Putter
H
2009
DNA methylation differences after exposure to prenatal famine are
common and timing - and sex specific.
Human Molecular Genetics
18
4046
4053
20. Heijmans
BT
Tobi
EW
Stein
AD
Putter
H
Blauw
GJ
2008
Persistent epigenetic differences associated with prenatal
exposure to famine in humans.
Proceedings of the National Academy of Sciences of the United States of
America
105
17046
17049
21. Gemma
C
Sookoian
S
Alvariñas
J
García
SI
Quintana
L
2009
Maternal pregestational BMI is associated with methylation of the
PPARGC1A promoter in newborns.
Obesity
17
1032
1039
22. Einstein
F
Thompson
RF
Bhagat
TD
Fazzari
MJ
Verma
A
2010
Cytosine Methylation Dysregulation in Neonates Following
Intrauterine Growth Restriction.
PLoS ONE
5
e8887
doi:10.1371/journal.pone.0008887
23. Thompson
RF
Fazzari
MJ
Niu
H
Barzilai
N
Simmons
RA
2010
Experimental intrauterine growth restriction induces alterations
in DNA methylation and gene expression in pancreatic islets of
rats.
Journal of Biological Chemistry
285
15111
15118
24. Schumacher
A
Weinhausl
A
Petronis
A
2008
Application of microarrays for DNA methylation
profiling.
Methods in Molecular Biology
439
109
129
25. Schumacher
A
Kapranov
P
Kaminsky
Z
Flanagan
J
Assadzadeh
A
2006
Microarray-based DNA methylation profiling: technology and
applications.
Nucleic Acids Research
34
528
542
26. Weber
M
Hellmann
I
Stadler
MB
Ramos
L
Paabo
S
2007
Distribution, silencing potential and evolutionary impact of
promoter DNA methylation in the human genome.
Nature Genetics
39
457
466
27. Irizarry
RA
Ladd-Acosta
C
Carvalho
B
Wu
H
Brandenburg
SA
2008
Comprehensive high-throughput arrays for relative methylation
(CHARM).
Genome Research
18
780
790
28. Cropley
JE
Suter
CM
Beckman
KB
Martin
DIK
2010
CpG methylation of a silent controlling element in the murine
A(vy) allele is incomplete and unresponsive to methyl donor
supplementation.
PLoS ONE
5
e9055
doi:10.1371/journal.pone.0009055
29. Flanagan
JM
Popendikyte
V
Pozdniakovaite
N
Sobolev
M
Assadzadeh
A
2006
Intra - and interindividual epigenetic variation in human germ
cells.
American Journal of Human Genetics
79
67
84
30. Mill
J
Tang
T
Kaminsky
Z
Khare
T
Yazdanpanah
S
2008
Epigenomic profiling reveals DNA-methylation changes associated
with major psychosis.
American Journal of Human Genetics
82
696
711
31. Beissbarth
T
Speed
TP
2004
GOstat: find statistically overrepresented Gene Ontologies within
a group of genes.
Bioinformatics
20
1464
1465
32. Feinberg
AP
Irizarry
RA
2010
Stochastic epigenetic variation as a driving force of
development, evolutionary adaptation, and disease.
Proceedings of the National Academy of Sciences of the United States of
America
107
1757
1764
33. Kaminsky
Z
Tang
T
Wang
S
Ptak
C
Oh
GHT
2009
DNA methylation profiles in monozygotic and dizygotic
twins.
Nature Genetics
41
240
245
34. Fraga
MF
Ballestar
E
Paz
MF
Ropero
S
Setein
F
2005
Epigenetic differences arise during the lifetime of monozygotic
twins.
Proceedings of the National Academy of Sciences of the United States of
America
102
10604
10609
35. Jablonka
E
Lamb
MJ
1989
The inheritance of acquired epigenetic
variations.
Journal of Theoretical Biology
139
69
83
36. Monk
M
1995
Epigenetic programming of differential gene expression in
development and evolution.
Developmental Genetics
17
188
197
37. Guerrero-Bosagna
C
Sabat
P
Valladares
L
2005
Environmental signaling and evolutionary change: can exposure of
pregnant mammals to environmental estrogens lead to epigenetically induced
evolutionary changes in embryos?
Evolution and Development
7
341
350
38. Skinner
MK
Manikkam
M
Guerrero-Bosagna
C
2010
Epigenetic transgenerational actions of environmental factors in
disease etiology.
Trends in Endocrinology and Metabolism
21
214
222
39. Sved
J
Bird
A
1990
The expected equilibrium of the CpG dinucleotide in vertebrate
genomes under a mutation model.
Proceedings of the National Academy of Sciences of the United States of
America
87
4692
4696
40. Park
JH
Stoffers
DA
Nicholls
RD
Simmons
RA
2008
Development of type 2 diabetes following intrauterine growth
retardation in rats in associated with progressive epigenetic silencing of
Pdx1.
The Journal of Clinical Investigation
118
2316
2324
41. Kovacheva
VP
Mellot
TJ
Davison
JM
Wagner
N
Lopez-Coviella
I
2007
Gestational choline deficiency causes global and Igf2 gene DNA
hypermethylation by upregulation of Dnmt1 expression.
Journal of Biological Chemistry
282
31777
31788
42. Pham
TD
MacLennan
NK
Chiu
CT
Laksana
GS
Hsu
JL
2003
Uteroplacental insufficiency increases apoptosis and alters p53
gene methylation in the full-term IUGR rat kidney.
American Journal of Physiology - Regulatory Integrative &
Comparative Physiology
285
962
970
43. Cubas
P
Vincent
C
Coen
E
1999
An epigenetic mutation responsible for natural variation in
floral symmetry.
Nature
401
157
161
44. Crain
PF
1990
Preparation and enzymatic hydrolysis of DNA and RNA for mass
spectrometry.
Methods in Enzymology
193
782
790
45. Kovacheva
VP
Mellott
TJ
Davison
JM
Wagner
N
Lopez-Coviella
I
2007
Gestational choline deficiency causes global and Igf2 gene DNA
hypermethylation by up-regulation of Dnmt1 expression.
Journal of Biological Chemistry
282
31777
31788
46. Ihaka
R
Gentleman
R
1996
R: A Language for Data Analysis and Graphics.
Journal of Computational and Graphical Statistics
5
299
314
47. Clark
SJ
Harrison
J
Paul
CL
Frommer
M
1994
High sensitivity mapping of methylated cytosines.
Nucleic Acids Research
22
2990
2997
48. Goecks
J
Nekrutenko
A
Taylor
J
Team
G
2010
Galaxy: a comprehensive approach for supporting accessible,
reproducible, and transparent computational research in the life
sciences.
Genome Biology
11
R86
49. Kent
WJ
Sugnet
CW
Furey
TS
Roskin
KM
Pringle
TH
2002
The human genome browser at UCSC.
Genome Research
12
996
1006
50. van Heeringen
SJ
Veenstra
GJ
2011
GimmeMotifs: a de novo motif prediction pipeline for
ChIP-sequencing experiments.
Bioinformatics
27
270
271
51. Frith
MC
Fu
Y
Yu
L
Chen
JF
Hansen
U
2004
Detection of functional DNA motifs via statistical
over-representation.
Nucleic Acids Research
32
1372
1381
Štítky
Genetika Reprodukčná medicína
Článek Incorporating Biological Pathways via a Markov Random Field Model in Genome-Wide Association StudiesČlánek Survival Motor Neuron Protein Regulates Stem Cell Division, Proliferation, and Differentiation inČlánek Epigenetic Regulation of Cell Type–Specific Expression Patterns in the Human Mammary Epithelium
Článok vyšiel v časopisePLOS Genetics
Najčítanejšie tento týždeň
2011 Číslo 4- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
-
Všetky články tohto čísla
- Is Co-Expressed with Closely Adjacent Uncharacterised Genes Spanning a Breast Cancer Susceptibility Locus at 6q25.1
- The Liberation of Embryonic Stem Cells
- Genome-Wide Meta-Analysis Identifies Regions on 7p21 () and 15q24 () As Determinants of Habitual Caffeine Consumption
- A Sustained Dietary Change Increases Epigenetic Variation in Isogenic Mice
- The Exocyst Protein Sec10 Interacts with Polycystin-2 and Knockdown Causes PKD-Phenotypes
- Incorporating Biological Pathways via a Markov Random Field Model in Genome-Wide Association Studies
- Survival Motor Neuron Protein Regulates Stem Cell Division, Proliferation, and Differentiation in
- Identification and Functional Validation of the Novel Antimalarial Resistance Locus in
- Does Positive Selection Drive Transcription Factor Binding Site Turnover? A Test with Drosophila Cis-Regulatory Modules
- Protein Phosphatase 2A Controls Ethylene Biosynthesis by Differentially Regulating the Turnover of ACC Synthase Isoforms
- Ribosomal DNA Deletions Modulate Genome-Wide Gene Expression: “–Sensitive” Genes and Natural Variation
- Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape
- Variable Pathogenicity Determines Individual Lifespan in
- Evolution of Vertebrate Transient Receptor Potential Vanilloid 3 Channels: Opposite Temperature Sensitivity between Mammals and Western Clawed Frogs
- Towards Establishment of a Rice Stress Response Interactome
- Mouse Genome-Wide Association and Systems Genetics Identify As a Regulator of Bone Mineral Density and Osteoclastogenesis
- Quantitative Fitness Analysis Shows That NMD Proteins and Many Other Protein Complexes Suppress or Enhance Distinct Telomere Cap Defects
- Highly Precise and Developmentally Programmed Genome Assembly in Requires Ligase IV–Dependent End Joining
- PDP-1 Links the TGF-β and IIS Pathways to Regulate Longevity, Development, and Metabolism
- Genome-Wide Association Study Using Extreme Truncate Selection Identifies Novel Genes Affecting Bone Mineral Density and Fracture Risk
- Eight Common Genetic Variants Associated with Serum DHEAS Levels Suggest a Key Role in Ageing Mechanisms
- 14-3-3 Proteins Regulate Exonuclease 1–Dependent Processing of Stalled Replication Forks
- HDA6 Regulates Locus-Directed Heterochromatin Silencing in Cooperation with MET1
- Epigenetic Regulation of Cell Type–Specific Expression Patterns in the Human Mammary Epithelium
- Enhanced Statistical Tests for GWAS in Admixed Populations: Assessment using African Americans from CARe and a Breast Cancer Consortium
- Beyond Missing Heritability: Prediction of Complex Traits
- An Evolutionary Genomic Approach to Identify Genes Involved in Human Birth Timing
- Long-Lost Relative Claims Orphan Gene: in a Wasp
- PTG Depletion Removes Lafora Bodies and Rescues the Fatal Epilepsy of Lafora Disease
- Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome
- GWAS of Follicular Lymphoma Reveals Allelic Heterogeneity at 6p21.32 and Suggests Shared Genetic Susceptibility with Diffuse Large B-cell Lymphoma
- Loss-of-Function Mutations in Cause Metachondromatosis, but Not Ollier Disease or Maffucci Syndrome
- DNA Damage, Somatic Aneuploidy, and Malignant Sarcoma Susceptibility in Muscular Dystrophies
- The Phylogenetic Origin of Coincided with the Origin of Maternally Provisioned Germ Plasm and Pole Cells at the Base of the Holometabola
- Genome Analysis Reveals Interplay between 5′UTR Introns and Nuclear mRNA Export for Secretory and Mitochondrial Genes
- Genome-Wide Association Analysis of Soluble ICAM-1 Concentration Reveals Novel Associations at the , , , and Loci
- The Complete Spectrum of Yeast Chromosome Instability Genes Identifies Candidate CIN Cancer Genes and Functional Roles for ASTRA Complex Components
- Dynamic Regulation of H3K27 Trimethylation during Differentiation
- Phosphorylation-Dependent Differential Regulation of Plant Growth, Cell Death, and Innate Immunity by the Regulatory Receptor-Like Kinase BAK1
- PLOS Genetics
- Archív čísel
- Aktuálne číslo
- Informácie o časopise
Najčítanejšie v tomto čísle- PTG Depletion Removes Lafora Bodies and Rescues the Fatal Epilepsy of Lafora Disease
- Survival Motor Neuron Protein Regulates Stem Cell Division, Proliferation, and Differentiation in
- An Evolutionary Genomic Approach to Identify Genes Involved in Human Birth Timing
- Loss-of-Function Mutations in Cause Metachondromatosis, but Not Ollier Disease or Maffucci Syndrome
Prihlásenie#ADS_BOTTOM_SCRIPTS#Zabudnuté hesloZadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.
- Časopisy