Alterations in methionine metabolism affect histone methylation in a dynamic and reversible manner. Methionine depletion decreases histone H3 lysine 4 trimethylation (H3K4me3) globally and around the transcription start sites of specific genes, including colon cancer genes, decreasing their expression. This suggests a physiological feedback mechanism. Experiments in mice found alterations in methionine metabolism and histone methylation in the liver during methionine restriction, indicating this is a relevant in vivo mechanism for sensing and responding to one-carbon metabolism.

1. Histone
Methyla.on
Dynamics
and
Gene
Regula.on
Occur
Through
the
Sensing
of
One-­‐Carbon
Metabolism
Samantha
J.
Mentch
Locasale
Lab
Pharmacology
&
Cancer
Biology
Departmental
Retreat
September
18,
2015

2. The
Methionine
Cycle
and
Methyla.on
SAM:
S-­‐adenosylmethionine
SAH:
S-­‐adenosylhomocysteine
HMT:
Histone
methyltransferase
Transsulfura.on
pathway
me
Folate
Metabolism
or
Betaine
Cell
Membrane
HMT

3. Histone
methylaIon
and
gene
expression
me3
me3
me3
me3
me3
me3
me3
me3
me3
me3
me3
me3
H3K4me3
AcIve
promoters
Open
chromaIn
H3K27me3
H3K9me3
Closed
chromaIn
HeterochromaIn
HP1
Pol
II
Vermeulen,
et
al.
(2007)
Cell.
Nichibushi
and
Nakayama
(2014)
Lee
and
Mahadevan.
(2009)
J.
Cell.
Biochem.
Barth,
T.
K.,
and
Imhof,
A.
(2010)
Trends
Biochem.
Sci

4. Ques.ons
• Do
alteraIons
in
methionine
metabolism
affect
histone
methylaIon?
• How
are
specific
genes
affected
by
alteraIons
in
methionine
metabolism?
• Is
this
a
physiological
mechanism?
1.
2.
3.

5. Ques.ons
• Do
alteraIons
in
methionine
metabolism
affect
histone
methylaIon?
• Are
specific
genes
affected
by
alteraIons
in
methionine
metabolism?
• Is
this
a
physiological
mechanism?
1.
2.
3.

6. Do
altera.ons
in
methionine
metabolism
affect
histone
methyla.on?
1.
Methods:
Liquid
Chromatography
coupled
to
Mass
Spectrometry
(LC-­‐MS)
Liu,
et
al
(2014)
Analy6cal
Chem

7. Do
altera.ons
in
methionine
metabolism
affect
histone
methyla.on?
1.
Ques.on:
Can
methionine
restric.on
affect
methionine
metabolism
and
histone
methyla.on?
Results:
Methionine
restric.on
alters
methionine
cycle
flux
and
decreases
H3K4me3
M
ET
SA
M
SA
H
hC
ystB
etaine
D
M
G
G
LY
SER
-8
-6
-4
-2
0
2
4
Log2(-MET/+MET)

8. Do
altera.ons
in
methionine
metabolism
affect
histone
methyla.on?
1.
0 1 2 3 4 5 6 7 8
0.0
0.5
1.0
1.5
Time (Hours)
RelativeAbundance
SAH
MET
SAM
Ques.on:
How
dynamic
are
the
changes
in
methionine
metabolism
and
histone
methyla.on
during
methionine
restric.on?
Results:
Changes
in
methionine
cycle
metabolism
occur
in
minutes
followed
by
changes
in
histone
methyla.on

9. Do
altera.ons
in
methionine
metabolism
affect
histone
methyla.on?
1.
Ques.on:
Are
altera.ons
in
methionine
metabolism
and
histone
methyla.on
reversible
aWer
methionine
deple.on?
Results:
Decreases
in
methionine
cycle
flux
and
histone
methyla.on
are
reversible

10. Ques.ons
• Do
alteraIons
in
methionine
metabolism
affect
histone
methylaIon?
• Are
specific
genes
affected
by
alteraIons
in
methionine
metabolism?
• Is
this
a
physiological
mechanism?
1.
2.
3.

11. Ques.ons
• Do
alteraIons
in
methionine
metabolism
affect
histone
methylaIon?
• Are
specific
genes
affected
by
alteraIons
in
methionine
metabolism?
• Is
this
a
physiological
mechanism?
1.
2.
3.

12. Are
specific
genes
affected
by
altera.ons
in
methionine
metabolism?
2.
Ques.on:
How
does
H3K4me3
distribu.on
change
genome-­‐wide?
Results:
Methionine
deple.on
alters
H3K4me3
peak
shape

13. Are
specific
genes
affected
by
altera.ons
in
methionine
metabolism?
2.
Ques.on:
Does
methionine
deple.on
affect
colon
cancer
genes?
Results:
Methionine
deple.on
decreases
H3K4me3
around
TSS
of
colon
cancer
genes
and
decreases
expression
D AKT1 MYC
TGFR1 MAPK1
RAC3 BIRC5
+M
-M
+M
-M
+M
-M
+M
-M
+M
-M
TGFR1 MAPK1
RAC3 BIRC5
RHOA AXIN2
-M
+M
-M
+M
-M
+M
-M
+M
-M
+M
-M
+M
-M
+M
-M
+Met H3K4me3 -Met H3K4me3 RNA-seq

14. Are
specific
genes
affected
by
altera.ons
in
methionine
metabolism?
2.
Ques.on:
Does
methionine
deple.on
demonstrate
regulatory
proper.es?
Results:
Methionine
deple.on
results
in
decreased
H3K4me3
and
gene
expression
sugges.ng
a
feedback
mechanism

15. Ques.ons
• Do
alteraIons
in
methionine
metabolism
affect
histone
methylaIon?
• Are
specific
genes
affected
by
alteraIons
in
methionine
metabolism?
• Is
this
relevant
in
vivo?
1.
2.
3.

16. Ques.ons
• Do
alteraIons
in
methionine
metabolism
affect
histone
methylaIon?
• Are
specific
genes
affected
by
alteraIons
in
methionine
metabolism?
• Is
this
a
physiological
mechanism?
1.
2.
3.

17. Is
this
a
physiological
mechanism?
3.
Liver
Control MET Restricted
0
1×107
2×107
3×107
4×107
MSIntensity
MET
p = N.S.
Control MET Restricted
0
2×105
4×105
6×105
8×105
MSIntensity
SAM
p = 0.0007
Control MET Restricted
0
2×105
4×105
6×105
MSIntensity
SAH
p = 0.015
SAM/SAH
Control MET Restricted
0.0
5.0×107
1.0×108
1.5×108
2.0×108
2.5×108
MSIntensity
Betaine
p = 0.003
Control MET Restricted
0
2×106
4×106
6×106
8×106
MSIntensity
DMG
p = 6.2 x 10-6
Control MET Restricted
0.0
5.0×105
1.0×106
1.5×106
MSIntensity
Cystathionine
p = 0.005
MTA
Control MET Restricted
0.0
5.0×106
1.0×107
1.5×107
2.0×107
MSIntensity
MET
p = 0.001
Control MET Restricted
0
1×104
2×104
3×104
4×104
5×104
MSIntensity
SAM
p = N.S.
Control MET Restricted
0.0
5.0×103
1.0×104
1.5×104
2.0×104
MSIntensity
SAH
p = N.S.
p = N.S.
SAM/SAH
Control MET Restricted
3×107
4×107
5×107
6×107
7×107
MSIntensity
Betaine
p = 0.007
Control MET Restricted
0.0
5.0×105
1.0×106
1.5×106
MSIntensity
DMG
p = 0.0002
Control MET Restricted
0.0
5.0×104
1.0×105
1.5×105
MSIntensity
Cystathionine
p = 0.006
KMTB
Plasma
H3K4me3/H3
H3K4me3
Total H3
Control MET Restricted
Results:
Methionine
deple.on
can
be
sustained
in
vivo
and
alter
histone
methyla.on
in
the
liver

18. Is
this
a
physiological
mechanism?
3.
0
10
20
30
40
[Methionine](µM)
Human
Serum
Samples
D
iet
N
on-diet
D
ietx
N
on-diet
U
nexplained
0.0
0.1
0.2
0.3
0.4
0.5
Varianceexplained
Results:
High
varia.on
in
methionine
explained
in
part
by
diet
and
commensurate
with
levels
necessary
for
altered
H3K4me3
methyla.on

19. Summary
• Decreasing
methionine
availability
decreases
methionine
cycle
flux
and
H3K4me3
• Decreased
H3K4me3
and
gene
expression
of
colon
cancer
genes
• Feedback
mechanism
regulaIng
methionine
metabolic
genes
• AlteraIons
in
methionine
metabolism
can
be
sustained
by
diet
in
vivo
Mentch,
et
al.
(2015)
Cell
Metabolism

20. Acknowledgements
CommiZee
Members
Jason
Locasale
Sylvia
Lee
Chris
Fromme
Locasale
Lab
Xiaojing
Liu
Ahmad
Cluntun
Mahya
Mehrmohamadi
Lei
Huang
Marc
Warmoes
Maria
LiberI
Elena
Turner
Louis
Vergara
Collaborators
Saliendra
Nichenametla
Dwight
Maeocks
Gene
Ables
Thalacker-­‐Mercer
Lab
(Anna,
Diwakar,
Heather)
Lee
Lab
(Erin,
MinIe)
Cores
Cornell
InsItute
for
Biotechnology
–
Genomics
Core
Weill
Cornell
Epigenomics
Core
Funding
Duke
University
School
of
Medicine
NIH

21. Ques.ons?