The prototypical Plant HomeoDomain finger (PHD) (sometimes referred to as HB-PHD) was first identified in 1993 as a 'Cys4HisCys3' zinc finger motif in the homeodomain protein HAT3.1 in Arabidopsis thaliana (Schindler et al., 1993, Aasland et al., 1995). The HAT3.1 shows a preference for the sequence T(A/G)(A/C)ACCA, different from those bound by other homeodomains (Viola et al., 2007).

Since then, dozens of PHD fingers have been reported to express histone-binding activities (Lee et al., 2009). The present data support one notion that the histone H3 N-terminal segment, notably the 'NH2-ARTKQTARK' motif is virtually the major target for most histone-binding PHD fingers. On the other hand, the 'readership' of each particular PHD finger is deliberately 'twisted' to interpret the message encoded by different histone post-translational modifications within the flexible histone N-terminal tails. PHD family proteins have been shown to act as readers for many different histone post translational modifications (Li et al., 2012, Qian et al., 2021).

The PHD domain (PFAM domain PF00628l) folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains (Pascual et al., 2000).

In maize sixty-seven PHD-finger genes were identified and further divided into ten groups according to phylogenetic analysis that was supported by motif and intron/exon analysis. These genes were unevenly distributed on ten chromosomes and contained 12 segmental duplication events, suggesting that segmental duplications were the major contributors in expansion of the maize PHD family (Wang et al., 2015). In the hexaploid wheat at least 244 PHD genes have been identified (Pang et al., 2022). In rice the Baymax1 (BM1), gene encodes a MYB protein that physically interacts with bHLH protein TIP2, EAT1, and PHD (plant homeodomain)-finger member TIP3, respectively,  to affect the expression of several known genes related to tapetum and microspore development (Xiang et al., 2021).

Last updated June 2023 by John Gray

References:

Aasland R, Gibson TJ, Stewart AF. The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci. 1995 Feb;20(2):56-9. doi: 10.1016/s0968-0004(00)88957-4. PMID: 7701562.

Schindler U, Beckmann H, Cashmore AR. HAT3.1, a novel Arabidopsis homeodomain protein containing a conserved cysteine-rich region. Plant J. 1993 Jul;4(1):137-50. doi: 10.1046/j.1365-313x.1993.04010137.x. PMID: 8106082.

Li Y, Li H. Many keys to push: diversifying the 'readership' of plant homeodomain fingers. Acta Biochim Biophys Sin (Shanghai). 2012 Jan;44(1):28-39. doi: 10.1093/abbs/gmr117. PMID: 22194011.

Pascual J, Martinez-Yamout M, Dyson HJ, Wright PE. Structure of the PHD zinc finger from human Williams-Beuren syndrome transcription factor. J Mol Biol. 2000 Dec 15;304(5):723-9. doi: 10.1006/jmbi.2000.4308. PMID: 11124022.

Wang Q, Liu J, Wang Y, Zhao Y, Jiang H, Cheng B. Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response. Int J Mol Sci. 2015 Sep 30;16(10):23517-44. doi: 10.3390/ijms161023517. PMID: 26437398; PMCID: PMC4632711.

Pang F, Niu J, Solanki MK, Nosheen S, Liu Z, Wang Z. PHD-finger family genes in wheat (Triticum aestivum L.): Evolutionary conservatism, functional diversification, and active expression in abiotic stress. Front Plant Sci. 2022 Dec 12;13:1016831. doi: 10.3389/fpls.2022.1016831. PMID: 36578331; PMCID: PMC9791960.

Viola IL, Gonzalez DH. Interaction of the PHD-finger homeodomain protein HAT3.1 from Arabidopsis thaliana with DNA. Specific DNA binding by a homeodomain with histidine at position 51. Biochemistry. 2007 Jun 26;46(25):7416-25. doi: 10.1021/bi602657e. Epub 2007 May 26. PMID: 17530779.

Lee WY, Lee D, Chung WI, Kwon CS. Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers. Plant J. 2009 May;58(3):511-24. doi: 10.1111/j.1365-313X.2009.03795.x. Epub 2009 Jan 18. PMID: 19154204.

Qian F, Zhao QY, Zhang TN, Li YL, Su YN, Li L, Sui JH, Chen S, He XJ. A histone H3K27me3 reader cooperates with a family of PHD finger-containing proteins to regulate flowering time in Arabidopsis. J Integr Plant Biol. 2021 Apr;63(4):787-802. doi: 10.1111/jipb.13067. Epub 2021 Mar 4. PMID: 33433058.

Xiang XJ, Sun LP, Yu P, Yang ZF, Zhang PP, Zhang YX, Wu WX, Chen DB, Zhan XD, Khan RM, Abbas A, Cheng SH, Cao LY. The MYB transcription factor Baymax1 plays a critical role in rice male fertility. Theor Appl Genet. 2021 Feb;134(2):453-471. doi: 10.1007/s00122-020-03706-w. Epub 2020 Oct 21. PMID: 33089345.