by Rein Aasland(1), Toby J. Gibson and A. Francis Stewart
EMBL, Meyerhofstrasse 1, D-69117 Heidelberg. Germany

Published in Trends Biochem. Sci. 20(2) 56-59 (1995)

Abstract

Using new tools for sequence searches based on profile analysis, we have found that the PHD-finger, a zinc finger-like motif ( Figure 1A), occurs in a set of proteins that includes members of the Drosophila Polycomb and trithorax group genes. These genes regulate the expression of the homeotic genes through a mechanism thought to involve some aspect of chromatin structure. Other proteins which have this motif (Table 1) also have additional domains or characteristics that support our suggestion that the PHD-finger is involved in chromatin-mediated gene regulation ( Figure 1B). One example is the human X-linked gene, XE169, which escapes X-inactivation, another process known to involve chromatin structure. The PHD-finger was recently identified in four related plant homeodomain proteins (see Table 1). We speculate that the PHD-fingers are protein-protein interaction domains or that they recognise a family of related targets in the nucleus such as the nucleosomal histone tails. The identification of PHD-fingers in this context forms the basis for designing experiments which may shed light on the mechanism of chromatin-mediated transcriptional regulation.

This page will have the alignment of the PHD-finger, and further information of how the alignment and the searches were performed as well as further details of how each PHD-finger was scored against different profiles.

Here is Figure 1A showing a ascii-version of the alignment of the PHD-fingers and here is Figure 1B showing how some PHD-fingers are positioned in various PHD-finger proteins. A description of each of the PHD-fingers can be viewd in Table 1 Here are the references to the paper.

NOTE Since the publication of this paper, several new PHD-finger proteins have been identified, including the transcriptional coactivators p300 / CBP and TIF1, the trx-G protein ash-1, and most recently, the putative chromatin-associated acetylase MOZ, encoded by a gene which was found fused [t(8;16)(p11;p14)] with the CBP gene in acute myeloid leukemia (Borrow et al., Nature Genet. 14:33 (1996)) A new analysis of the PHD-finger family is under way and will appear on these pages - but here is an partially updated cartoon of PHD finger proteins . And here is some recent news abut PHD fingers .

The sequence analysis for this work was carried out using the multiple sequence alignment program Clustal W and Ewan Birney's Profile search tools, WiseTools: SearchWise and PairWise. The actual profiles used can be found in the legend to Table 1.

(1) corresponding author, presently at:
Department of Molecular BIology
University of Bergen, HiB
Bergen, Norway

E-mail:  aasland@mbi.uib.no
Phone:   +47-5558-4531 
fax:     +47-5558-9683 

This work was carried out at the EMBL.

These pages were written by Rein Aasland, December1994. Last updated, December 9. 1997.