Histone Modification Table Description

The nucleosome, made up of four core histone proteins (H2A, H2B, H3, and H4), and linker histone H1 are the primary building blocks of chromatin. 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 that regulate chromatin condensation and DNA accessibility. For example, acetylation of lysine residues has long been associated with histone deposition and transcriptional activation, and more recently found to be associated with DNA repair. Phosphorylation of serine and threonine residues facilitates chromatin condensation during mitosis and transcriptional activation of immediate-early genes. Methylation of lysine and arginine residues function as a major determinant for formation of transcriptionally active and inactive regions of chromatin and is crucial for proper programming of the genome during development. This table provides a referenced list of many known histone modifications, the associated modifying enzymes, and proposed functions.

Acetylation

Histone Site Histone-modifying Enzymes Proposed Function Ref. #
H2A Lys4 (S. cerevisiae) Esa1 transcriptional activation (1)
Lys5 (mammals) Tip60, p300/CBP transcriptional activation (2, 3)
Lys7 (S. cerevisiae) Hat1 unknown (4)
Esa1 transcriptional activation (1)
H2B Lys5 p300, ATF2 transcriptional activation (3, 5)
Lys11 (S. cerevisiae) Gcn5 transcriptional activation (6)
Lys12 (mammals) p300/CBP, ATF2 transcriptional activation (3, 5)
Lys15 (mammals) p300/CBP, ATF2 transcriptional activation (3, 5)
Lys16 (S. cerevisiae) Gcn5, Esa1 transcriptional activation (6)
Lys20 p300 transcriptional activation (3)
H3 Lys4 (S. cerevisiae) Esa1 transcriptional activation (1)
Hpa2 unknown (7)
Lys9 unknown histone deposition (8)
Gcn5, SRC-1 transcriptional activation (9, 10)
Lys14 unknown histone deposition (8)
Gcn5, PCAF transcriptional activation (3, 11)
Esal, Tip60 transcriptional activation (1, 2)
DNA repair (11, 12)
SRC-1 transcriptional activation (10)
Elp3 transcriptional activation (elongation) (13)
Hpa2 unknown (7)
hTFIIIC90 RNA polymerase III transcription (14)
TAF1 RNA polymerase II transcription (15)
Sas2 euchromatin (16)
Sas3 transcriptional activation (elongation) (17)
p300 transcriptional activation (3)
Lys18 Gcn5 transcriptional activation, DNA repair (9)
p300/CBP DNA replication, transcriptional activation (3, 18)
Lys23 unknown histone deposition (8)
Gcn5 transcriptional activation, DNA repair (9)
Sas3 transcriptional activation (elongation) (17)
p300/CBP transcriptional activation (3, 18)
Lys27 Gcn5 transcriptional activation (6)
Lys56 (S. cerevisiae) Spt10 transcriptional activation (19)
DNA repair (20)
H4 Lys5 Hat1 histone deposition (21)
Esal, Tip60 transcriptional activation (1, 2)
DNA repair (11, 12)
ATF2 transcriptional activation (5)
Hpa2 unknown (7)
p300 transcriptional activation (3)
Lys8 Gcn5, PCAF transcriptional activation (3, 22)
Esal, Tip60 transcriptional activation (1, 2)
DNA repair (11, 12)
ATF2 transcriptional activation (5)
Elp3 transcriptional activation (elongation) (13)
p300 transcriptional activation (3)
Lys12 Hat1 histone deposition (21)
telomeric silencing (23)
Esal, Tip60 transcriptional activation (1, 2)
DNA repair (11, 12)
Hpa2 unknown (7)
p300 transcriptional activation (3)
Lys16 Gcn5 transcriptional activation (22)
MOF (D. melanogaster) transcriptional activation (24)
Esal, Tip60 transcriptional activation (1, 2)
DNA repair (11, 12)
ATF2 transcriptional activation (5)
Sas2 euchromatin (2, 6)
Lys91 (S. cerevisiae) Hat1/Hat2 chromatin assembly (25)

Methylation

Histone Site Histone-modifying Enzymes Proposed Function Ref. #
H1 Lys26 Ezh2 transcriptional silencing (48, 49)
H3 Lys4 Set1 (S. cerevisiae) permissive euchromatin (di-Me) (26)
Set7/9 (vertebrates) transcriptional activation (tri-Me) (27)
MLL, ALL-1 transcriptional activation (28, 29)
Ash1 (D. melanogaster) transcriptional activation (30)
Arg8 PRMT5 transcriptional repression (31)
Lys9 Suv39h,Clr4 transcriptional silencing (tri-Me) (32, 33)
G9a transcriptional repression genomic imprinting (34)
SETDB1 transcriptional repression (tri-Me) (35)
Dim-5 (N.crassa), Kryptonite (A. thaliana) DNA methylation (tri-Me) (36, 37)
Ash1 (D. melanogaster) transcriptional activation (30)
Arg17 CARM1 transcriptional activation (18)
Lys27 Ezh2 transcriptional silencing (38)
X inactivation (tri-Me)  
G9a transcriptional silencing (34)
Lys36 Set2 transcriptional activation (elongation) (39)
Lys79 Dot1 euchromatin (40)
transcriptional activation (elongation) (41)
checkpoint response (42)
H4 Arg3 PRMT1 transcriptional activation (43)
PRMT5 transcriptional repression (31)
Lys20 PR-Set7 transcriptional silencing (mono-Me) (44)
Suv4-20h heterochromatin (tri-Me) (45)
Ash1 (D. melanogaster) transcriptional activation (30)
Set9 (S. pombe) checkpoint response (46)
Lys59 unknown transcriptional silencing (47)

Phosphorylation

Histone Site Histone-modifying Enzymes Proposed Function Ref. #
H1 Ser27 unknown transcriptional activation, chromatin decondensation (48, 49)
H2A Ser1 unknown mitosis, chromatin assembly (50)
MSK1 transcriptional repression (51)
Thr119 (D. melanogaster) NHK1 mitosis (52)
Ser122 (S. cerevisiae) unknown DNA repair (53)
Ser129 (S. cerevisiae) Mec1, Tel1 DNA repair (54, 55)
Ser139 (mammalian H2A.X) ATR, ATM, DNA-PK DNA repair (56, 57, 58)
H2B Ser10 (S. cerevisiae) Ste20 apoptosis (59)
Ser14 (vertebrates) Mst1 apoptosis (60)
unknown DNA repair (61)
Ser33 (D. melanogaster) TAF1 transcriptional activation (62)
H3 Thr3 Haspin/Gsg2 mitosis (63)
Ser10 Aurora-B kinase mitosis, meiosis (64, 65)
MSK1, MSK2 immediate-early gene activation (66)
IKK-α transcriptional activation (67)
Snf1 transcriptional activation (68)
Thr11 (mammals) Dlk/Zip mitosis (69)
Ser28 (mammals) Aurora-B kinase mitosis (70)
MSK1, MSK2 immediate-early activation (66, 71)
H4 Ser1 unknown mitosis, chromatin assembly (50)
CK2 DNA repair (72)

Ubiquitylation

Histone Site Histone-modifying Enzymes Proposed Function Ref. #
H2A Lys119 (mammals) Ring2 spermatogenesis (73)
H2B Lys120 (mammals) UbcH6 meiosis (74)
Lys123 (S. cerevisiae) Rad6 transcriptional activation (75)
euchromatin

Sumoylation

Histone Site Histone-modifying Enzymes Proposed Function Ref. #
H2A Lys126 (S. cerevisiae) Ubc9 transcriptional repression (76)
H2B Lys6 or Lys7 (S. cerevisiae) Ubc9 transcriptional repression (76)
H4 N-terminal tail (S. cerevisiae) Ubc9 transcriptional repression (77)

Biotinylation

Histone Site Histone-modifying Enzymes Proposed Function Ref. #
H2A Lys9 biotinidase unknown (78)
Lys13 biotinidase unknown (78)
H3 Lys4 biotinidase gene expression (79)
Lys9 biotinidase gene expression (79)
Lys18 biotinidase gene expression (79)
H4 Lys12 biotinidase DNA damage response (80, 81)

CST would like to thank Prof. Craig Peterson, University of Massachusetts Medical School, Worcester, Massachusetts, for reviewing this table.

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created May 2007

revised November 2010