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Rumen-protected methyl donors
and the genome: beyond
nutrigenomics
Juan J. Loor, Zheng Zhou, and Mario Vailati-Riboni
Department of Animal Sciences, Division of Nutritional Sciences,
and Illinois Informatics Institute
University of Illinois, Urbana-Champaign, USA
XXI ASPA Congress
June 9‐12, 2015
Milan, Italy
Outline
• Brief “history”
• Nutritional and physiological context
• Nutrigenomics
 Met and choline
• Beyond nutrigenomics
 Can we “prime” cow and calf??
Nutritionally‐important methyl donors
Choline
Betaine
(Tri-Methyl glycine)
Methionine
5-methyl-tetrahydrofolate
(“folic acid”)
MAT1A
BHMTMTR GNMT
CBS
CTH
Antioxidants
Biochemistry of methyl donors is interrelated
[Modified from Mato et al. (2008)]
P-Ethanolamine
P-Choline
PEMT
SAH
SAHH
DNMT
Substrate =  e.g. CpG site
SAM = S‐adenosylmethionine
DNMT = DNA methyl 
transferase
Methyl donor cycle regulation: non‐ruminants
MAT1A
+
+
‐
ATP
MAT1A control:
Genome level
Promoter methylation (Huh‐7 cells) (Tomasi et al., 2012)
Certain microRNA  ↓ mRNA (Yang et al., 2012)
Enzyme level
Feed‐forward activation by Met (sheep) (Xue and Snoswell, 1989)
Feed‐back inhibition by SAM (sheep) (Xue and Snoswell, 1989)
(e.g. GNMT, DNMT)
ROM
‐
↑ Metabolism
↑ Oxidative stress
BHMT+MTR +
Glutathione+
Oxidase
Methyl donor requirements differ during the life 
stages of ruminants
(Pinoti et al., 2002)
Adult ruminant  greater requirements due to 
ruminal degradation of dietary sources
Use of “rumen‐protection” technology important
(MTR)
(MTR)
History of rumen‐protection: amino acids and choline
Journal of Dairy Science papers:
1968 ‐ First paper in JDS: Griel, Patton, McCarthy and Chandler “Milk production 
response to feeding methionine‐hydroxy analog (MHA) to lactating cows”
1970: Broderick, Kowalzyk and Satter “Milk production response to supplementation 
with encapsulated methionine per os or casein per abomasum” (Delmar Chemical, 
Ontario)
2006: Rulquin et al. “Effect of different forms of methionine on lactation 
performance of dairy cows”
2007: Cooke et al. “Supplemental choline for prevention and alleviation of fatty liver 
in dairy cattle”
2011: Chen et al. “Effect of feeding different sources of rumen protected methionine 
on milk production and N utilization in lactating dairy cows”
2011: Zom et al. “Effect of rumen‐protected choline on performance, blood 
metabolites, and hepatic triacylglycerols of periparturient dairy cattle”
Also,
Noftsger and St‐Pierre (2003), Noftsger et al. (2005), Socha et al. (2005), 
St‐Pierre and Sylvester (2005), Ordway et al. (2009), Appuhamy et al. (2011), 
Lee et al. (2012), Osorio et al. (2013), Osorio et al. (2014ab)
Dietary methyl‐donors in dairy cows
SAM
SAH
Homocysteine
Cysteine
Diet
Tissues
Milk
Liver health
DNA methylation
Epigenetics
VLDLPC
Vit. B12 CH3
PE
rRNA complex
Protein synthesis initiation
Choline
Betaine
Dimethylglycine
Diet
5-MTHF
Methionine
Diet
Folate
+ + +
Cooke et al. 2007
Zom et al. 2011
+
Glutathione
Antioxidants
Taurine
+
Embryo
Fetus
Pre‐calving Post‐calving
~3‐4 wk ~3‐4 wkCalving
(Block et al., 2001)
Energy balance
Body condition score
Energy intake
4% Fat corrected milk
(Ingvartsen, 2006)
Transition period
Tissue mobilization
(Komaragiri and Erdman, 1997)
Both body fat and protein are mobilized
Increased milk by 3 kg/d 
with no change in intake
‐46
‐21
‐61
‐21
(Bertoni and Trevisi, 2013)
Inflammation and oxidative 
stress occur during transition
• Acidosis
• Metritis
• Retained placenta
• High NEFA and
BHBA
(++)
Physiological context for rumen‐protected methyl 
donors
NEFA
Metabolism
Oxidative
Stress
Cell 
Damage
Inflammation
Nutrigenomics
Nutriepigenomics
Met, Choline
Production
Health
Fertility
Practical 
outcomes
Mechanistic 
outcomes
DMI (kg/d)
Day relative to calving Day relative to calving
Diet P = 0.67
Time P <.001
DxT P = 0.42
Diet P = 0.18
Time P <.001
DxT P = 0.78
Met P = 0.06 
Control
MetaSmart
Smartamine
Met = Control vs MetaSmart + Smartamine
~7 g Met/d supplemented ~10 g Met/d supplemented
Better performance with Methionine
Parameter
Diet
SE
P‐value
Control MetaSmart Smartamine Diet Met Par Time D×T
Milk yield (kg/d) 35.7 38.1 40.0 1.6 0.15 0.08 ‐‐ <0.01 0.86
Milk fat (%) 4.27 4.68 4.09 0.22 0.59 0.36 .05 <0.01 0.01
Milk protein (%) 3.04 3.26 3.19 0.08 0.13 0.05 ‐‐ <0.01 0.23
Milk fat
yield (kg/d) 1.64 1.84 1.81 0.08 0.11 0.04 ‐‐ 0.04 0.01
Milk  protein
Yield (kg/d) 1.11 1.23 1.24 0.05 0.08 0.03 ‐‐ 0.02 0.14
ECM (kg/d) 41.0 44.8 45.0 1.55 0.09 0.03 ‐‐ <0.01 0.07
Milk yield and components
Met = Control vs MetaSmart + Smartamine
(Osorio et al., 2013)
Day after parturition
0 5 10 15 20 25 30 35
kg/d
10
12
14
16
18
20
22
24
26
Control
Methionine
Choline
Recent experiment confirms the benefit of 
rumen‐protected Methionine
• Dry matter intake during last 3 wk prepartum
greater (1‐2 kg/d) with Methionine 
• Milk protein % greater with Methionine
• Lower inflammatory and oxidative stress status
Day aftyer parturition
0 5 10 15 20 25 30 35
kg/d
20
25
30
35
40
45
50
55
Control
Methionine
Choline
Dry matter intakeMilk productionMet P = 0.03
Chol P = 0.41
Day P < 0.01
Met P = 0.02
Chol P = 0.90
Day P < 0.01
(Zhou et al., 2015 Abs. 455, JAM Orlando, FL, USA)
Nutri....what??!!
“Nutrigenomics attempts to study the
genome‐wide influences of nutrition. From a
nutrigenomics perspective, nutrients are
dietary signals that are detected by the cellular
sensor systems that influence gene and
protein expression and, subsequently,
metabolite production”
Müller and Kersten, Nature Review, 2003
“Is a sub‐specialty of nutrition science which aims to 
understand how genome‐diet interactions influence 
individuals’ and populations’ responses to food, 
disease susceptibility, and population health” 
The Omics Ethics Research Group
genome‐wide
nutrients
dietary signals
sensor systems
Definition of nutrigenomics
DNA
mRNA
Transcription
mRNA editing
(splicing)
mRNA
Translation
Ribosomes
(build proteins based on 
information in mRNA)
Protein
synthesis
Newly‐formed
protein
Specific function inside 
(or outside) the cell
Enzymatic
Structural
Signaling
Transcription regulator
Transport
-10.0 7.0 21.0 -10.0 7.0 21.0 -10.0 7.0 21.0
CO MS SM
1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
2
3
4
5
-10.0 7.0 21.0 -10.0 7.0 21.0 -10.0 7.0 21.0
CO MS SM
1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
2
3
4
5
Smartamine +
Control
MetaSmart +
Control
Control
(higher-energy,
“close-up” to calving)
Rumen-protected Methionine alters the liver transcriptome
2,663 genes with diet  time effect
(Osorio et al., 2013)
The 12 most-impacted metabolic pathways with
rumen-protected Methionine
Impact
0 200 400 600 800 1000 1200 1400 1600
Cyanoamino acid metabolism
Taurine and hypotaurine metabolism
Lipoic acid metabolism
Propanoate metabolism
Pyruvate metabolism
Cysteine and methionine metabolism
Glyoxylate and dicarboxylate metabolism
Riboflavin metabolism
Valine, leucine and isoleucine biosynthesis
Glutathione metabolism
Glycolysis and gluconeogenesis
Citrate cycle (TCA cycle)
Carbohydrate
metabolism
Antioxidants
**These are key pathways responsible for the adaptations in liver to parturition
and rumen‐protected Methionine supplementation
1-Carbon
metabolism
pathway
Taurine
Transcription regulator Function Frequency
FBJ osteosarcoma oncogene (FOS) Regulates cell proliferation, 
differentiation, and transformation
Associated with apoptosis
7 of 18
Ets homologous factor (EHF) Repressor of cellular differentiation 6 of 18
Kruppel‐like factor 4 (KLF4) Repressor of cellular proliferation
Promotes cell survival
6 of 18
Kruppel‐like factor 5 (KLF4) Transcriptional activator
Promotes and suppresses cell 
proliferation and cell growth
6 of 18
v‐myc avian myelocytomatosis viral 
oncogene homolog (MYC)
Regulates cell cycle progression, 
apoptosis, and cellular transformation
6 of 18
Top 5 most-frequently affected transcription
regulators with rumen-protected Methionine
(Zhou et al., in review)
At day 7 postpartum
EHF down-regulated 2.4-fold in
cows fed Methionine vs. control
Biological meaning of transcription regulator
networks?
At day 7 vs. -10 d postpartum
EHF down-regulated 1.7-fold in
cows fed Methionine
• Methionine could have direct anti-
inflammatory role through EHF
Methionine, choline
Calf metabolism
Can methyl donors affect the developing calf 
in utero?
Or can they elicit an effect through colostrum?
Bioinformatics analysis revealed unique 
biological responses to rumen‐protected Met
Immune func on ↓ 
Nutrient metabolism ↑
Endocrine signaling ↓
• Functional outcome 
still unknown
• Epigenomic
alterations??
Methionine and mTOR signalling
Met?
Potential mechanisms:
• Binding directly to
regulatory site on
mTOR
• Binding to a co-
regulator of mTOR
(indirect)
• Stimulating a protein
kinase
Not only protein‐coding genes...
Epigenetic/epigenomic = “above” the genome
Epigenetic modifications are reversible modifications of DNA or 
histones that affect gene expression without altering the DNA 
sequence
Histone modifications
DNA methylation
microRNA target and repress mRNA
Targeted analysis of methylation status
“Hypo‐methylation” or “Hyper‐methylation” status
Transcription regulators and target genes: PPARalpha (76 CpG sites)
Methylation status
mRNA expression
• These were newborn piglets
• Functional outcome on gluconeogenic flux was small
• Longer-term study needed  e.g. through weaning transition
• Findings indicate a physiological benefit of 
supplementing rumen‐protected Met during the 
transition period
• Underscore the importance of maintaining an 
adequate Met:Lys balance
• Clear nutrigenomics effects 
• Likely epigenomic effects
Met : Lys
Conclusions
Perspectives
• Interchangeable roles and interactions 
between methyl donors (e.g. choline, Met, 
betaine) should be further investigated at 
various life stages
• Molecular techniques will help  
Perspectives
• Functional effects of increasing the 
methylation capacity through rumen‐
protected Met or Choline supplementation 
need to be studied in cow and calf
Acknowledgements
Thank you
jloor@illinois.edu

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