citrate lyase (ACL) is utilized to
References
vs
Flux balance
analysis
(FBA) Extracellular
flux data
(ECAR/OCR)
Predicted and validated data
in brown adipose
Glucose, glutamine and pyruvate uptake
Ammonia secreon / urea secreon
GABA transaminase reacon
Figure 1. Integration of Flux Measurements
(ECAR/OCR) and Metabolic Models (FBA) in
Adipocytes, for Metabolic Predictions. Abbre-
viations: ECAR, extracellular acidification rate; OCR,
oxygen consumption rate; GABA transaminase, 4-
aminobutyrate transaminase.
or metabolomics data can illuminate
many processes, these remain insufficient
for flux estimation. Ramirez et al. offer a
new method to squeeze more flux esti-
mation out of extracellular flux analyzers.
What remains to be deciphered is how the
magnitude of the observed differences in
extracellular flux can be used with whole-
genome metabolic modeling to predict
differential fluxes in cells and tissues with
more subtle differences in metabolic func-
tionality. Regardless of the future potential
of this method, it provides more informa-
tion from currently used assays about the
flux of fat, and should be also utilized to
query metabolic flux regulation, and new
targets mediating the impact of insulin
resistance, in other tissues.
1
Section for Integrative Physiology, Novo Nordisk
Foundation Center for Basic Metabolic Research,
University of Copenhagen, Copenhagen, Denmark
2
Research Division, Joslin Diabetes Center, and Harvard
Medical School, Boston, MA, USA
*Correspondence:
MaryElizabeth.Patti@joslin.harvard.edu (M.-E. Patti).
https://doi.org/10.1016/j.tem.2018.01.005
202 Trends in Endocrinology & Metabolism, April 2018, Vol. 29, No. 4
1. Ramirez, A. et al. (2017) Integrating extracellular flux meas-
urements and genome-scale modeling reveals differences
between brown and white adipocytes. Cell Rep. 21, 3040–
3048
2. Orth, J. et al. (2010) What is flux balance analysis? Nat.
Biotechnol. 28, 245–248
3. Covert, M. et al. (2004) Integrating high-throughput and
computational data elucidates bacterial networks. Nature
429, 92–96
4. Dreyfuss, J. et al. (2013) Reconstruction and validation of a
genome-scale metabolic model for the filamentous fungus
Neurospora crassa using FARM. PLoS Comput. Biol. 9,
e1003126
5. Frezza, C. et al. (2011) Haem oxygenase is synthetically
lethal with the tumour suppressor fumarate hydratase.
Nature 477, 225–228
6. Nogiec, C. et al. (2015) Metabolic modeling of muscle
metabolism identifies key reactions linked to insulin resis-
tance phenotypes. Mol. Metab. 4, 151–163
7. Thiele, I. et al. (2005) Candidate metabolic network states
in human mitochondria. Impact of diabetes, ischemia, and
diet. J. Biol. Chem. 280, 11683–11695
8. McKnight, J.R. et al. (2010) Beneficial effects of L-arginine
on reducing obesity: potential mechanisms and important
implications for human health. Amino Acids 39, 349–357
9. Newgard, C.B. et al. (2009) A branched-chain amino acid-
related metabolic signature that differentiates obese and
lean humans and contributes to insulin resistance. Cell
Metab. 9, 311–326
10. Lerin, C. et al. (2016) Defects in muscle branched-chain
amino acid oxidation contribute to impaired lipid metabo-
lism. Mol. Metab. 5, 926–936
11. Lynch, C.J. and Adams, S.H. (2014) Branched-chain
amino acids in metabolic signalling and insulin resistance.
Nat. Rev. Endocrinol. 10, 723–736
Spotlight
ATP Citrate Lyase: A
New Player Linking
Skeletal Muscle
Metabolism and
Epigenetics
1 traction are energy-consuming pro-
Haisen Li and
Vittorio Sartorelli1,*
Intermediates generated in several
metabolic processes are used to
regulate transcription through
covalent histone and DNA modifi-
cations. In Cell Reports, Das et al.
show that acetyl-coenzyme A
(acetyl-CoA) generated by ATP
acetylate histone H3 at MyoD reg-
ulatory regions, resulting in
increased MyoD expression and
improved muscle regeneration
after injury.
Increasing evidence shows that, in addi-
tion to providing essential energy, meta-
bolic flux actively participates in numerous
processes, including development, stem
cell homeostasis, and regeneration [1].
Metabolic dysregulation is closely associ-
ated with disorders such as obesity and
cancer [2]. Acetyl-CoA, a metabolic inter-
mediate used in mitochondria energy pro-
duction, is required for the de novo
synthesis of cholesterol and fatty acid in
the cytosol because it provides a carbon
source. It is also used in histone and other
protein acetylation by providing acetyl
groups [3,4]. ACL is the enzyme that cat-
alyzes the generation of acetyl-CoA and
oxaloacetate from citrate in the presence
of ATP and CoA. This reaction is respon-
sible for the extramitochondrial acetyl-
CoA production [3]. By linking glucose
metabolism to macromolecular biosyn-
thesis and epigenetics, ACL has been
described to be involved in embryonic
growth, liver homeostasis, and cancer cell
proliferation, as well as metabolic disor-
ders, including hyperlipidemia [5]. How-
ever, whether ACL functions in nonliver
tissues, such as skeletal muscle, is still
poorly understood.
Skeletal muscle strengthening and con-
cesses, and skeletal muscle mass is
directly linked with muscle metabolism.
Exercise is often helpful for improving
muscle function by increasing metabolic
capacity, indicating that metabolic
changes somehow regulate muscle func-
tion. Interestingly, ACL activation induced
through the IGF1/PI3K/AKT pathway
increases cardiolipin synthesis and mito-
chondrial supercomplex activity, which
 Cytoplasm

Glucose

Acetyl-CoA Acetyl-CoA

P300 ACL

Ph
Nucleus

os
ph
or
y la
Ac Ac Ac Ac Ac Ac

tio
n
Pyruvate Akt
Muscle-specific
gene acƟvaƟon

Citrate
IGF1 recptor

Mitochondria IGF1

Figure 1. Model of the IGF1/AKT/ATP citrate lyase (ACL)/Acetyl-Coenzyme A (Acetyl-CoA) Pathway Regulating Gene Expression in Skeletal Muscle
Cells. Citrate is generated from glucose-derived pyruvate through the tricarboxylic acid (TCA) cycle in mitochondria, and transported into the
cytoplasm. After being phosphorylated by IGF1/AKT signaling, ACL converts citrate into acetyl-CoA, which is utilized for p300-mediated histone
acetylation. This acetylation induces muscle-specific gene expression, resulting in satellite cell (SC) differentiation.

ultimately enhances mitochondrial func-
tion in skeletal muscle [6]. However,
whether muscle stem cells, also known
as satellite cells (SCs), and muscle regen-
eration are affected by ACL remains to be
determined. A recent paper by Das et al.
sheds light on ACL specific functions in
skeletal muscle by revealing that ACL/
acetyl-CoA modulates SC differentiation
and muscle regeneration by affecting his-
tone acetylation level at gene regulatory
regions [7].
In both mouse and human myoblasts,
Das et al. observed that reducing ACL
selectively decreased fast myosin (fast
MyHC, MYH1) expression and increased
slow myosin (slow MyHC, MYH7) expres-
sion. In ex vivo experiments, overexpres-
sion of ACL did not alter SC proliferation,
but rather promoted their differentiation,
resulting in increased fast myosin expres-
sion and myotube size. By contrast, ACL
knockdown inhibited SC differentiation
(Figure 1).
Suspecting that ACL might regulate the
expression or activity of myogenic tran-
scription factors, Das et al. knocked down
MyoD and found that such intervention
abolished the effect of ACL on fast MyHC
expression and that, conversely, MyoD
overexpression partially rescued reduced
fast MyHC expression caused by ACL inhi-
bition. ACL knockdown resulted in a gen-
eralized reduction of histone H3 acetylation
and prompted the authors to evaluate H3
acetylation at the MyoD regulatory regions.

Trends in Endocrinology & Metabolism, April 2018, Vol. 29, No. 4 203

Chromatin immunoprecipitation with anti-
bodies directed against acetyl-H3(K9/K14)
revealed that reducing ACL decreased H3
acetylation at a MyoD enhancer (distal reg-
ulatory region; DRR) and promoter, and
prevented MyoD expression. Acetyl-H3
(K9/K14/K27) at a more distal MyoD
enhancer (core enhancer) was not
affected, indicating a role of ACL in the
H3 acetylation of specific MyoD regulatory
regions. Complementary experiments
revealed that ACL overexpression
increased H3 acetylation at the DRR and
MyoD promoter, and upregulated MyoD
expression. ACL-mediated increased H3
acetylation and MyoD expression were
counteracted by treatment of differentiat-
ing myoblasts with an inhibitor of the p300
histone acetyltransferase, confirming that
the effects of ACL on myogenesis are
mediated by acetylation. Das et al. previ-
ously reported that ACL activity is regulated
by the IGF1/PI3K/AKT pathway [6]. There-
fore, it was satisfying to observe that ACL
silencing blunted some of the well-known
effects of IGF1 on skeletal muscle, includ-
ing IGF1-induced histone acetylation
enrichment at the MyoD promoter.
Skeletal muscle regeneration relies on
SCs and, thus, provides an excellent
experimental perturbation with which to
investigate SC activation, proliferation,
and differentiation in vivo [8]. Das et al.
tested the role of ACL in injured tibialis
muscle by overexpressing it before injury.
Notably, ACL overexpression increased
muscle weight and average fiber cross-
sectional area, and led to formation of an
increased number of large myofibers dur-
ing muscle regeneration. ACL overex-
pression significantly enhanced the
expression of Pax7, MyoD, and Myf5,
as well as of Myh3, Myh8, Myh1, Myh2,
and Myh4. The increased MyoD expres-
sion correlated with augmented H3 acet-
ylation at the DRR and MyoD promoter.
These findings indicate that ACL, by influ-
encing histone acetylation, critically regu-
lates both SC activation and
204 Trends in Endocrinology & Metabolism, April 2018, Vol. 29, No. 4
differentiation and, in doing so, mediates
muscle repair after injury.
ACL inhibition dramatically reduces the
net amount of cellular acetyl-CoA in can-
cer cells [9]. Whether this also occurs in
normal mammalian cells has not yet been
tested. However, since glucose acts as
the major carbon source of acetyl-CoA,
ACL knockdown or overexpression is
likely to reduce or increase, respectively,
the net abundance of acetyl-CoA also in
normal muscle cells. The concomitant
upregulation of ACL expression and
increased acetyl-H3(K9/K14), but not
acetyl-H3(K27), during differentiation is
of interest and suggests that different his-
tone acetyltransferases have distinct sen-
sitivity for acetyl-CoA level alteration.
Overall, these findings indicate that the
ACL/acetyl-CoA/p300 pathway is a pre-
viously undescribed transduction arm for
IGF1 function.
Myogenesis is a process precisely con- Immunol. 17, 1016–1024
trolled by gene networks. The work of Das
et al. provides an additional mechanistic
explanation to how growth factors regu-
late myogenesis by providing evidence
that IGF1 activates the ACL/acetyl-CoA/ Spotlight
p300 pathway leading to SC differentia-
tion through transcriptional regulation of
master regulatory genes. Considering the
important roles exerted by IGF1 in muscle
physiology [10], manipulating ACL activity
might provide new ways to treat muscle
diseases and aging. Moreover, since ace-
tyl-H3(K9/27) acetylation-mediated gene
expression participates in the progress of Felicity E. Stubbs,
hematological malignancies, such as leu- Benjamin P. Flynn,1 and
kemia [11,12], the ACL/acetyl-CoA/H3 Becky L. Conway-Campbell1,*
acetylation pathway may have key roles
in hematological malignancies, and its In a recent study, Jubb et al.
manipulation could provide promising used 3D DNA FISH to assess glu-
therapeutic targets for combatting these cocorticoid-induced
diseases.
1
Laboratory of Muscle Stem Cells and Gene Regulation,
National Institute of Arthritis, Musculoskeletal and Skin
Diseases (NIAMS), National Institutes of Health, Bethesda,
MD 20892, USA
*Correspondence: sartorev@mail.nih.gov (V. Sartorelli).
https://doi.org/10.1016/j.tem.2018.01.006
References
1. Ryall, J.G. et al. (2015) Metabolic reprogramming of stem
cell epigenetics. Cell Stem Cell 17, 651–662
2. Koopman, R. et al. (2014) A metabolic link to skeletal
muscle wasting and regeneration. Front. Physiol. 5, 32
3. Pinkosky, S.L. et al. (2017) Targeting ATP-citrate lyase in
hyperlipidemia and metabolic disorders. Trends Mol. Med.
23, 1047–1063
4. Zhao, S. et al. (2016) ATP-citrate lyase controls a glucose-
to-acetate metabolic switch. Cell Rep. 17, 1037–1052
5. Burke, A.C. and Huff, M.W. (2017) ATP-citrate lyase:
genetics, molecular biology and therapeutic target for
dyslipidemia. Curr. Opin. Lipidol. 28, 193–200
6. Das, S. et al. (2015) ATP citrate lyase improves mitochon-
drial function in skeletal muscle. Cell Metab. 21, 868–876
7. Das, S. et al. (2017) ATP Citrate lyase regulates myofiber
differentiation and increases regeneration by altering his-
tone acetylation. Cell Rep. 21, 3003–3011
8. Relaix, F. and Zammit, P.S. (2012) Satellite cells are essen-
tial for skeletal muscle regeneration: the cell on the edge
returns centre stage. Development 139, 2845–2856
9. Hatzivassiliou, G. et al. (2005) ATP citrate lyase inhibition
can suppress tumor cell growth. Cancer Cell 8, 311–321
10. Velloso, C.P. (2008) Regulation of muscle mass by growth
hormone and IGF-I. Br. J. Pharmacol. 154, 557–568
11. Greenblatt, S.M. and Nimer, S.D. (2014) Chromatin modi-
fiers and the promise of epigenetic therapy in acute leuke-
mia. Leukemia 28, 1396–1406
12. Ntziachristos, P. et al. (2016) Emerging concepts of epi-
genetic dysregulation in hematological malignancies. Nat.
FISH-ing Novel
Dynamic Modes of
Glucocorticoid-Induced
Chromatin
Reorganization
1
‘chromatin
decompaction’ at multiple loci.
Determinants of the specificity,
speed, and duration of this phe-
nomenon further enhance our