CST Guide:

Section I: Research Areas
Protein Acetylation
Histone
Acetylation
Protein
Acetylation
GCN5L2
Cell Cycle
Rb
Stability
DNA Damage
SRC-3
Tip60
ATM
DNA
Repair
TF
CBP/
p300
TF
HDAC Classes
Class I: HDAC1-3, 8
Class II: HDAC4-7, 9, 10
Class III: SIRT1-7
Class IV: HDAC11
p53
TF
Stability
Acetylases
PCAF
Su
Sirtuins
Regulatory
Signaling Pathways
DNA
Damage
AceCS1
PEPCK
PGC-1α
Idh2
TFIID
TFIIA TBP
HDAC
NuRD
NcoR
Sin3
26 For Research Use Only. Not For Use in Diagnostic Procedures. See pages 302 & 303 for Pathway Diagrams, Application, and Reactivity keys.
Tip60
Histones
Signaling Pathways
Metabolism
Deacetylases
SirT1
Tip60
SirT1
SirT3
Cytoskeletal Regulation Ribosomal Proteins
Chaperones
BRCA1
TATA
RNA Splicing
Acetylation
Acetyl
Transferases
ATF-2 MORF
CBP MOZ
CDY p300
PCAF CLOCK PCAF
CBP/
p300
EWI p/CIP
Su
Elp3 SRC-1
SRC-3
GCN5L2 SRC-3
GRIP hTAF II
250
α-Importin
HAT1 TFIIB
HBO1 Tip60
MCM3AP
Nuclear Transport
Transcription
TFIIH
Pluripotency
TFIIF
Development
TFIIB
RNA Pol II Differentiation of
Neural Stem Cells
TFIIE
BMP, Wnt, Notch
AceCS1
PEPCK
PGC-1α
Idh2
Deacetylation
Fatty Acid Synthesis
Histone Acetylation
Gluconeogenesis
Expression of
Gluconeogenic Genes
NADPH
Lysine acetylation is a reversible post-translational modification that plays a crucial role in regulating protein function, chromatin structure, and gene expression. Many
transcriptional coactivators possess intrinsic acetylase activity, while transcriptional corepressors are associated with deacetylase activity. Acetylation complexes (such as CBP/
p300 and PCAF) or deacetylation complexes (such as Sin3, NuRD, NcoR, and SMRT) are recruited to DNA-bound transcription factors (TFs) in response to signaling pathways.
Histone hyperacetylation by histone acetyltransferases (HATs) is associated with transcriptional activation, whereas histone deacetylation by histone deacetylases (HDACs) is
associated with transcriptional repression. Histone acetylation stimulates transcription by remodeling higher order chromatin structure, weakening histone-DNA interactions,
and providing binding sites for transcriptional activation complexes containing proteins that possess bromodomains, which bind acetylated lysine. Histone deacetylation
represses transcription through an inverse mechanism involving the assembly of compact higher order chromatin and the exclusion of bromodomain-containing transcription
activation complexes. Histone hypoacetylation is a hallmark of silent heterochromatin. Site-specific acetylation of a growing number of non-histone proteins has been shown
to regulate their activity, localization, specific interactions, and stability/degradation. Remarkably, recent advances in mass spectrometry technologies allowed high resolution
mapping of most of the acetylation sites in all the proteome. These studies demonstrated that the “acetylome” encompasses nearly ~3600 acetylation sites in roughly ~1750
proteins, suggesting that this modification is one of the most abundant chemical modifications in nature. Indeed, it appears that this mark can influence the activity of proteins
in diverse biological processes, including chromatin remodeling, cell cycle, splicing, nuclear transport, mitochondrial biology, and actin nucleation. At an organismal level,
acetylation plays an important role in immunity, circadian rhythmicity, and memory formation. Protein acetylation is becoming a favorable target in drug design for numerous
disease conditions.
Select Reviews:
Albaugh, B.N., Arnold, K.M., and Denu, J.M. (2011) Chem. Bio. Chem. 12, 290–298. • Choudhary, C., Kumar, C., Gnad, F., Nielsen, M.L., Rehman, M., Walther, T.C.,
Olsen, J.V., and Mann, M. (2009) Science 325, 834–840. • Dali-Youcef, N., Lagouge, M., Froelich, S. et al. (2007) Ann. Med. 39, 335–345. • Finkel, T., Deng, C.H., and
Mostoslavsky, R. (2009) Nature 460, 587–591. • Haberland, M., Montgomery, R.L., and Olson, E.N. (2009) Nat. Rev. Genet. 10, 32–42. • Peng, L. and Seto, E. (2011)
Handbook Exp. Pharmac. 206, 39–56. • Spange, S., Wagner, T., Heinzel, T., and Krämer, O.H. (2009) Int. J. Biochem. Cell Biol. 41, 185–198. • Yang, X.J. and Seto, E.
(2007) Oncogene 26, 5310–5318. • Yang, X.J. and Seto, E. (2008) Mol. Cell 31, 449–461.
© 2002–2015 Cell Signaling Technology, Inc. • We would like to thank Prof. Raul Mostoslavsky, Harvard Medical School, Boston, MA, for reviewing this diagram.
H4K20me
Methylases:
SET8/KMT5A (+)
NSD1/KMT3B (+,†)
ASH1L/KMT2H (+,†,‡)
SUV420H1/KMT5B (†,‡)
SUV420H2/KMT5C (†,‡)
NSD2/KMT3G (+,†)
Demethylases:
JHDM1D/KDM7A (+,†)
PHF8/KDM7B (+,†)
H3K9me
Methylases:
PRDM3/KMT8E (+)
PPRDM16/KMT8F (+)
G9a/EHMT2/KMT1C (+,†)
EHMT1/KMT1D (+,†)
ASH1L/KMT2H (+,†,‡)
PRDM2/KMT8A (+,†,‡)
PRDM8/KMT8D (†)
SUV39H1/KMT1A (†,‡)
SUV39H2/KMT1B (†,‡)
ESET/KMT1E (†,‡)
CLLD8/KMT1F (†,‡)
Demethylases:
AOF1/KDM1B (+,†)
JMJD1A/KDM3A (+,†)
JMJD1B/KDM3B (+,†)
JMJD1C/KDM3C (+,†)
JHDM1D/KDM7A (+,†)
PHF8/KDM7B (+,†)
JMJD2A/KDM4B (†,‡)
JMJD2B/KDM4B (†,‡)
JMJD2C/KDM4C (†,‡)
JMJD2D/KDM4D (†,‡)
KDM4E/KDM4DL (†,‡)
H3K27me
Methylases:
Ezh2/KMT6 (+,†,‡)
NSD2/KMT3G (+,†,‡)
NSD3/KMT3F (†,‡)
Demethylases:
JHDM1D/KDM7A (+,†)
PHF8/KDM7B (+,†)
UTX/KDM6A (†,‡)
JMJD3/KDM6B (†,‡)
Histone Lysine Methylation
SUV
39h
HP1
Me
Me
Transcriptionally Inactive
Chromatin
SUV
39h
PRC1
PC
Me
PRC1
PC
Me
HP1
Me
Me
SUV
39h
HP1
Me
Me
SUV
39h
HP1
Me
Pericentric Heterochromatin
Inactive X Chromosome
Rb-Mediated Repression
PRC1
PC
Me
PRC1
PC
Me
Me
Pericentric Heterochromatin
Inactive X Chromosome
Hox Gene Repression
Methylation
H4K20me
Demethylation
Methylation
H3K9me
Demethylation
Methylation Degree: + Mono † Di ‡ Tri
Methylation
H3K27me
Demethylation
chapter 01: GENE EXPRESSION, EPIGENETICS, AND NUCLEAR FUNCTION
Methylation
Methylation
Demethylation
Methylation
H3K79me
Demethylation
H3K4me
Demethylation
H3K36me
Transcriptionally Active
Chromatin
NURF
BPTF
Me
Me
Me
Me
NURF
BPTF
Me
Me
Me
Me
Me
Anti-Silencing
Me
Me
Transcription Initiation
Me
Transcription Elongation
The nucleosome is the primary building block of chromatin containing a histone octamer composed of two sets of H3-H4 and H2A-H2B dimers.
Originally thought to function as a static scaffold for DNA packaging, histones have more recently been shown to be dynamic proteins, undergoing
multiple types of post-translational modifications and impacting numerous nuclear functions. Lysine methylation is one such modification and is
a major determinant for genome organization and the formation of active and inactive regions of the genome. Lysines can have three different
methylation states (mono-, di-, and tri-) that are associated with different nuclear features and transcriptional states. In order to establish these
methylation states, cells have enzymes that both add (lysine methyltransferases- KMTs) and remove (lysine demethylases- KDMs) different degrees
of methylation from specific lysines within the histones. To date, all but one histone lysine methyltransferase (DOT1L/KMT4) has a conserved
catalytic SET domain that was originally identified in the Drosophila Su[var]3-9, Enhancer of zeste, and Trithorax proteins. In the case of the histone
lysine demethylases, there are two different classes: the FAD-dependent amine oxidases and the JmjC-containing enzymes. Both KMTs and KDMs
have specificity for specific lysine residues and degrees of methylation within the histone tails. Therefore, all KMTs and KDMs are not the same in
their biological functions or roles in transcriptional output.
Lysine methylation has been implicated in both transcriptional activation (H3K4, K36, K79) and silencing (H3K9, K27, H4K20). The degree of
methylation is associated with different outcomes. For example, H4K20 monomethyation (H4K20me1) is observed in the bodies of active genes,
while H4K20 trimethylation (H4K20me3) is affiliated with gene repression and compacted genomic regions. Gene regulation is also affected by
the location of the methylated lysine residue with respect to the DNA sequence. For example, H3K9me3 at promoters is associated with gene
repression, while some induced genes have H3K9me3 in the gene body. Since this modification is uncharged and chemically inert, the impact
these modifications have is through recognition by other proteins with binding motifs. Lysine methylation coordinates the recruitment of chromatin
modifying enzymes. Chromodomains (e.g., found in HP1, PRC1), PHD fingers (e.g., found in BPTF, ING2, SMCX/KDM5C), Tudor domains (e.g.,
found in 53BP1 and JMJD2A/KDM4A), PWWP domains (e.g., found in ZMYND11) and WD-40 domains (e.g., found in WDR5) are among a
growing list of methyl lysine binding modules found in histone acetyltransferases, deacetylases, methylases, demethylases and ATP-dependent
chromatin remodeling enzymes. Lysine methylation provides a binding surface for these enzymes, which then regulate chromatin condensation
and nucleosome mobility, active and inactive transcription as well as DNA repair and replication. In addition, lysine methylation can block binding
of proteins that interact with unmethylated histones or directly inhibit catalysis of other regulatory modifications on neighboring residues.
Histone methylation is crucial for proper programming of the genome during development and misregulation of the methylation machinery can
lead to diseased states such as cancer. In fact, cancer genome analyses have uncovered lysine mutations in H3K27 and H3K36. These sites are
enriched in subsets of cancer. Therefore, an entirely new therapeutic and biomarker space is emerging with the discovery of these enzymes, the
impact modifications have on the genome and disease associated mutations.
Select Reviews:
Black, J.C., Van Rechem, C., and Whetstine, J.R. (2012) Mol. Cell. 48, 491–507. • Greer, E.L. and Shi, Y. (2012) Nat. Rev. Genet. 13, 343–357.
• Herz, H.M., Garruss, A., and Shilatifard, A. (2013) Trends Biochem. Sci. 38, 621–639. • Kooistra, S.M. and Helin, K. (2012) Nat. Rev. Mol.
Cell Biol. 13, 297–311. • Tee, W.W. and Reinberg, D. (2014) Development 141, 2376–2390. • Van Rechem, C. and Whetstine, J.R. (2014)
Biophys. Acta. May 23 [Epub ahead of print].
© 2006–2015 Cell Signaling Technology, Inc. • We would like to thank Prof. Jonathan Whetstine for reviewing this diagram.
H3K4me H4K20me
Methylases: Methylases:
MLL1/KMT2A SET8/KMT5A (+,†,‡) (+)
MLL2/KMT2B NSD1/KMT3B (+,†,‡) (+,†)
MLL3/KMT2C ASH1L/KMT2H (+) (+,†,‡)
MLL4/KMT2D (+) SUV420H1/KMT5B (†,‡)
SET1A/KMT2F (+,†,‡)
SUV420H2/KMT5C (†,‡)
SET1B/KMT2G (+,†,‡)
NSD3/KMT3F NSD2/KMT3G (+,†) (+,†)
NSD2/KMT3G Demethylases: (+,†)
SET7/KMT7 JHDM1D/KDM7A (†) (+,†)
SMYD3/KMT3E PHF8/KDM7B (†,‡) (+,†)
ASH1L/KMT2H (+,†,‡)
PRDM9/KMT8B H3K9me (‡)
Demethylases:
Methylases:
LSD1/KDM1A (+,†)
PRDM3/KMT8E (+)
AOF1/KDM1B (+,†)
JARID1A/KDM5A PPRDM16/KMT8F (+) (†,‡)
JARID1B/KDM5B G9a/EHMT2/KMT1C (†,‡) (+,†)
JARID1C/KDM5C EHMT1/KMT1D (†,‡) (+,†)
JARID1D/KDM5D ASH1L/KMT2H (†,‡) (+,†,‡)
PRDM2/KMT8A (+,†,‡)
PRDM8/KMT8D (†)
H3K36me SUV39H1/KMT1A (†,‡)
Methylases:
SUV39H2/KMT1B (†,‡)
NSD1/KMT3B (+,†)
SMYD2/KMT3C ESET/KMT1E (+,†) (†,‡)
NSD2/KMT3G CLLD8/KMT1F (+,†) (†,‡)
SET2/KMT3A Demethylases: (‡)
Demethylases: AOF1/KDM1B (+,†)
JMJD1A/KDM2A JMJD1A/KDM3A (+,†) (+,†)
JMJD1B/KDM2B JMJD1B/KDM3B (+,†) (+,†)
JMJD2A/KDM4A (†,‡)
JMJD1C/KDM3C (+,†)
JMJD2B/KDM4B (†,‡)
JHDM1D/KDM7A (+,†)
JMJD2C/KDM4C (†,‡)
JMJD2D/KDM4D PHF8/KDM7B (†,‡) (+,†)
KDM4DL/KDM4E JMJD2A/KDM4B (†,‡) (†,‡)
JMJD2B/KDM4B (†,‡)
JMJD2C/KDM4C (†,‡)
JMJD2D/KDM4D (†,‡)
KDM4E/KDM4DL (†,‡)
H3K79me
Methylases:
H3K27me
DOTIL/KMT4 (+,†,‡)
Demethylases: Methylases:
Ezh2/KMT6 (+,†,‡)
NSD2/KMT3G (+,†,‡)
NSD3/KMT3F (†,‡)
Demethylases:
JHDM1D/KDM7A (+,†)
PHF8/KDM7B (+,†)
UTX/KDM6A (†,‡)
JMJD3/KDM6B (†,‡)
H3K4me
Methylases:
MLL1/KMT2A (+,†,‡)
MLL2/KMT2B (+,†,‡)
MLL3/KMT2C (+)
MLL4/KMT2D (+)
SET1A/KMT2F (+,†,‡)
SET1B/KMT2G (+,†,‡)
NSD3/KMT3F (+,†)
NSD2/KMT3G (+,†)
SET7/KMT7 (†)
SMYD3/KMT3E (†,‡)
ASH1L/KMT2H (+,†,‡)
PRDM9/KMT8B (‡)
Demethylases:
LSD1/KDM1A (+,†)
AOF1/KDM1B (+,†)
JARID1A/KDM5A (†,‡)
JARID1B/KDM5B (†,‡)
JARID1C/KDM5C (†,‡)
JARID1D/KDM5D (†,‡)
H3K36me
Methylases:
NSD1/KMT3B (+,†)
SMYD2/KMT3C (+,†)
NSD2/KMT3G (+,†)
SET2/KMT3A (‡)
Demethylases:
JMJD1A/KDM2A (+,†)
JMJD1B/KDM2B (+,†)
JMJD2A/KDM4A (†,‡)
JMJD2B/KDM4B (†,‡)
JMJD2C/KDM4C (†,‡)
JMJD2D/KDM4D (†,‡)
KDM4DL/KDM4E (†,‡)
H3K79me
Methylases:
DOTIL/KMT4 (+,†,‡)
Demethylases:
www.cellsignal.com/cstpathways 27