PHF2, a novel PHD finger gene located on human Chromosome 9q22
Brian P. Chadwick,* Thomas Theil,
** Stephanie K. Heath,
David G. Wilkinson,
Molecular Analysis of Mammalian Mutation, Imperial Cancer Research Fund, London WC2A 3PX, UK
Division of Developmental Neurobiology, National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
Received: 9 July 1998 / Accepted: 16 October 1998
Abstract. We have isolated and characterized a novel PHD finger
gene, PHF2, which maps to human Chromosome (Chr) 9q22 close
to D9S196. Its mouse homolog was also characterized and mapped
to the syntenic region on mouse Chr 13. The predicted human and
mouse proteins are 98% identical and contain a PHD finger do-
main, eight possible nuclear localization signals, two potential
PEST sequences, and a novel conserved hydrophobic domain.
Northern analysis shows widespread expression of PHF2 in adult
tissues, while in situ hybridization on mouse embryos reveals
staining in the neural tube and dorsal root ganglia significantly
above a ubiquitous low level expression signal. From its expres-
sion pattern and its chromosomal localization, PHF2 is a candidate
gene for hereditary sensory neuropathy type I, HSN1.
When a disease gene is localized to a particular region, candidate
genes are considered for mutation analysis on the basis of criteria
such as functional motifs, homology to known genes, and expres-
sion pattern. Transcriptional regulators, such as the zinc finger
family of transcription factors, are one class of genes commonly
mutated in human disease (Engelkamp and van Heyningen 1996).
The PHD (plant homeodomain)/ LAP (leukemia-associated pro-
tein) finger has been identified in more than 40 proteins (Aasland
et al. 1995; Saha et al. 1995). It consists of eight ligands (Cys/His)
in a unique Cys
pattern spanning approximately 50–80
residues, and is distinct from other classes of zinc finger motifs
such as the RING finger and LIM domain. PHD finger genes are
thought to belong to a diverse group of transcriptional regulators
possibly affecting eukaryotic gene expression by influencing chro-
matin structure. This influence might involve protein/protein or
protein/nucleic acid interactions mediated by the PHD finger.
We report here the identification and expression pattern of the
human and murine homolog of a novel gene, PHF2, that contains
a PHD finger domain. The PHD finger is not the only recognizable
motif within these genes; the predicted proteins also contain two
potential PEST sequences [sequences of high proline (P), glutamic
acid (E), serine (S), and threonine (T) content], several potential
nuclear localization signals, and a novel conserved domain of un-
known function. The presence of the combination of the known
motifs suggests that PHF2 may function as a transcriptional regu-
PHF2 was isolated from a human cDNA library enriched for
transcripts from 9q22. Further analysis showed that the genetic
marker D9S196 on Chr 9q22 is located close to or within this gene;
therefore, PHF2 lies in the candidate region for hereditary sensory
neuropathy type I, HSN1 (Nicholson et al. 1996; Blair et al. 1997)
and multiple self-healing squamous epithelioma, ESS1 (Goudie et
Materials and methods
cDNA selection was performed as described previously
(Chadwick et al. 1997), based on the method of Korn and associates
(1992). For the construction of the selected cDNA library, human foreskin
fibroblast (HFF) poly(A)
RNA was used.
Isolation and sequencing of cDNA clones.
HFF1H10, a 600-bp clone,
was isolated from the selected cDNA library. Using HFF1H10 as a probe,
clone Ker57B18 (3.6 kb) and clone K1 (1.4 kb) were isolated from a
human keratinocyte library (B. Lin unpublished) and a Jurkat 6 T cell
library (M. Owen; Dunne et al. 1995) respectively. Hybridization of a
mouse thymus cDNA library (David Simmons) with HFF1H10 resulted in
the isolation of nine different cDNA clones. Two cDNA clones with the
largest inserts, E11 (1.5 kb) and E17 (1.5 kb), were analyzed further. EST
clones corresponding to the PHF2 transcript (I.M.A.G.E. ID) human:
290233 and murine: 304334, 35100, 789877, 763234 were obtained from
the Human Genome Mapping Project Resource Centre (HGMP, Hinxton,
UK). We have since been informed that clone 304334 may be of rat origin
All cDNA clones mentioned above were completely sequenced.
Genomic library screening.
A Lawrence Livermore Chr 9-specific li-
brary, LL09Nc01 (constructed at the Biomedical Sciences Division,
Lawrence Livermore National Laboratory, Livermore, Calif.) under the
auspices of the National Laboratory Gene Library Project sponsored by the
US Department of Energy, and the 129/4 mouse cosmid library (Frischauf,
unpublished) were screened by standard protocols.
First-strand cDNA was synthesized with 1 g
RNA from a human lymphoblast cell line and G5P22 (CTCAG-
CAAAAAACTCGTATAAATG), a primer from the 3Ј untranslated region
of PHF2 (from EST 290233) with Superscript Reverse Transcriptase
(Gilco BRL) as recommended by the manufacturer. For amplification of
PHF2, the primer pair G5PAdirect (CTGACCACGAATATACAGCAG)
and G5P21 (GTTCGCCAGGCTCCGGTG) was used. The resulting PCR
fragment was sequenced with the primers IP2 (CGGGGGTCCTGAG-
CAGAGC) and G5P24 (CATCCCCCAACAACACTGC).
Northern blot analysis.
A human multiple tissue Northern blot (Clon-
tech, 7759-1) was hybridized with the insert from IMAGE clone 290233
(1.4 kb), and a mouse multiple tissue Northern blot (Clontech 7762-1) with
the insert from IMAGE clone 789877 (389bp). Hybridizations were per-
formed according to manufacturer’s instructions.
In situ hybridization analysis.
In situ hybridizations on whole-mount
mouse embryos were performed as described by Xu and Wilkinson (1998).
The RNA probe for Phf2 was derived from the IMAGE clone 789877 (389
bp). Sense-strand controls were also carried out. For expression analysis on
* Present address: Institute of Human Genetics, Harvard Medical School,
Boston, MA 02115, USA.
** Present address: Medical University Hannover, Institute of Microbiol-
ogy, OE 5250, Carl-Neuberg-Strasse 1, 30659 Hannover, Germany.
Correspondence to: A.-M. Frischauf
Mammalian Genome 10, 294–298 (1999).
© Springer-Verlag New York Inc. 1999