Table 2.

Histone modifications in Arabidopsis

Modification	Location	Effect	Transcription	Established by	Removed by
Ubiquitination
H2BK143ub1	Eu-chromatin	open	activation	Ring-Type E3 ligases HUB1, HUB2[52,53]	Deubiquitinases SUP32/UBP26[54]
Methylation
H3K4me*	Eu-chromatin	open	activation	trxG class of histone methyltransferases (HMTs)[55]	LSD1-type of histone demethylases (HDMs)[3,8] FLD[28]
H3K4me1	Eu-chromatin	open
H3K4me2	Eu-chromatin	open	activation intron1[38]	ATX1[56]
H3K4me3	Eu-chromatin	open	activation proximal promoter[55]; 5′end gene[57]	ATX1[56] EFS/SDG8[57]
H3K9me*	Both	closed		Su(var) class of HMTs[55]	JmjC-domain and LSD1-type HDMs[3,8]
H3K9me1	Hetero-chromatin	closed		SUVH2[58] SUVH4, SUVH6[59] SUVH5[60]
H3K9me2	Hetero-chromatin	closed		SUVH2[58] SUVH4, SUVH6[59] SUVR4[61]
H3K9me3	Eu-hromatin	closed	repression proximal promoter, 5′ end gene, gene[11]
H3K27me*	Both	closed	repression	E(Z) class of HMTs (PRC2 complex)[55]
H3K27me1	Hetero-chromatin	closed
H3K27me2	Hetero-chromatin	closed
H3K27me3	Eu-chromatin	closed	repression promoter, 5′end gene, gene[11-13]	CLF, SWN, MEA [12,13]
H3K36me*	Eu-chromatin	open	activation	Set domain HMTs	JmjC-domain HDMs. Possibly REF6[28,62]
H3K36me1	Eu-chromatin	open
H3K36me2	Both	open	activation intron1[63]	EFS/SDG8[63]
H3K36me3	Eu-chromatin	open
H4K20me*		closed			JmjC domain HDMs
H4K20me1	Hetero-chromatin			SUVH2[58]
H4K20me2	Eu-chromatin
H4K20me3	Eu-chromatin
H4R3sme2	Eu-chromatin	closed	repression promoter[64]	Arginine methyltransferases SKB1/AtPRMT5[64,65]	Deimination[8]
Acetylation
H3K* ac/H4K* ac	Both	open	activation promoter, 5′end gene[33,38,66]	Histone acetyltransferases (HATs)[25] GNAT family: GCN5/HAG1[30,34,42] CBP/p300 family: HAC1, HAC5, HAC12[26,67,68] TAFII family: HAF2/TAF1[30]	Histone Deacetylases (HDACs)[25] RDP3 family: HDA19[27,30,37, 42,69] HDA6[70] HDA1 family: HDA18[71] HD2 family: HD2A, HD2B[72], HD2C[73]
Phosphorylation2
H3S10ph H3S28ph H2T11ph	Both	open	activation	Kinases[74]	Phosphatases[74]

Histone modifications, their locations in the genome and their effects on chromatin (open/closed) as well as on transcription (where known) are listed. Also listed are the enzymes known to add and remove each modification. Plant histone modifiers are listed in bold type.

^*denotes all modifications of a certain type, for example, H3K9me* denotes mono, di, and trimethylation of lysine nine of histone H3, while H3*ac denotes general acetylation of lysines in histone H3.

¹These introns contain cis regulatory elements important for transcriptional regulation.

²The role of histone phosphorylation in the cell cycle is described elsewhere[24,74].