. Author manuscript; available in PMC: 2012 Jan 20.

Published in final edited form as: Nat Rev Cancer. 2010 Jul;10(7):457–469. doi: 10.1038/nrc2876

Table 2.

List of PHD finger-containing proteins that specifically 'read' H3K4me3/2.

Gene ID^†	H3K4me3/2 reading motif	Known function and disease relevance	Ref.
BPTF	The second PHD finger	Component of a chromatin remodeling complex NURF, which contains a SWI/SNF family helicase/ATPase SMARCA1	^{12, 14}
ING1	PHD finger	Component of HDAC-Sin3A transcriptional repressive complexes	^{13, 70, 73}
ING2	PHD finger	Component of HDAC-Sin3A transcriptional repressive complexes	^{13, 70, 76}
ING3	PHD finger	Form a transcriptional activation complex with a histone acetyltransferase (HAT) Tip60	^{70, 76}
ING4	PHD finger	Form an HBO-containing transcriptional activation complex	^{70, 74–76}
ING5	PHD finger	Component of a transcriptional activation complex that contains a HAT protein, either HBO or MOZ/MORF	⁷⁶
JARID1A	The third PHD finger	H3K4me3/2-specific histone demethylase	²¹
JARID1B	The third PHD finger	H3K4me3/2-specific histone demethylase	^{18, 21}^*
MLL	The third PHD finger	Histone methyltransferase, specific for H3K4	⁵^*
PHF2	PHD finger	Putative histone demethylase	⁵^*
PHF8	PHD finger	Putative histone demethylase; PHF8 mutation associates with X-linked mental retardation.	^{5, 18}^*
PHF13	PHD finger	Unknown function	^{5, 18}^*
PHF23	PHD finger	Unknown function	²¹
Pygo	PHD finger	Pygo1/2 interacts with a cofactor BCL9, and is required for Wnt/β-catenin induced transcriptional activation.	^87–89
RAG2	PHD finger	A V(D)J recombinase critical for the development and maturation of B and T cells. Loss-of-function mutations of the RAG2 PHD finger lead to severe combined immunodeficiency and Omenn syndrome.	²⁰
TAF3	PHD finger	Component of RNA polymerase II-associated general transcription factor machinery TFIID, which contains TATA-binding protein (TBP) and 12–13 additional TBP-associated factors, TAF1–14.	^{18, 19}

^†

Gene full name shown as follows: BPTF, bromodomain PHD finger transcription factor; PHF, PHD finger protein; RAG2, recombination activating gene 2; TAF3, TATA box binding protein (TBP)-associated factor, 140kDa.

The H3K4me3-binding property was predicted based on domain homology⁵.