Comparative genomic sequence analysis of the Williams syndrome
region (LIMK1-RFC2) of human Chromosome 7q11.23
Duane W. Martindale,
Michael D. Wilson,
Robert D. Burke,
Ben F. Koop
Department of Biology, Centre for Environmental Health, P.O. Box 3020, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada
Department of Medicine, Jack Bell Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
Received: 27 December 1999 / Accepted: 18 May 2000
Abstract. Williams syndrome (WS) is a complex neurodevelop-
mental disorder arising from a microdeletion at Chr band 7q11.23,
which results in a hemizygous condition for a number of genes.
Within this region we have completely characterized 200 kb con-
taining the genes LIMK1, WBSCR1, and RFC2. Evidence was
also found for WBSCR5 in this region, but not the previously
proposed genes WSCR2 and WSCR6. The syntenic region in
mouse was also sequenced (115 kb) and characterized, and a com-
parative sequence analysis with a percent identity plot (PIP) easily
allowed us to identify coding exons. This genomic region is GC
rich (50.1% human, 49.9% mouse) and contains an unusually high
abundance of repetitive elements consisting primarily of Alu
(45.4%, one of the highest levels identified to date) in human, and
the B family of SINES (30.6% of the total sequence) in mouse.
WBSCR1 corresponds to eukaryotic initiation factor 4H, identified
in rabbit, and is herein found to be constitutively expressed in both
human and mouse, with two RNA and protein products formed
(exon 5 is alternatively spliced). The transcription pattern of WB-
SCR5 was also examined and discussed along with its putative
amino acid sequence.
Williams syndrome (WS; also known as Williams-Beuren syn-
drome) is a genetic disorder affecting multiple physiological sys-
tems [Online Mendelian Inheritance in Man (OMIM) 194050;
http://www.ncbi.nlm.nih.gov/omim]. WS is characterized by a
characteristic craniofacial dysmorphology, cardiovascular disease,
hypertension, infantile hypercalcemia, dental abnormalities, her-
nias, and diverticuli, as well as a distinct cognitive and personality
profile (Morris et al. 1988; Bellugi et al. 1990; Keating 1997).
Although most WS individuals have a short attention span, re-
duced spatial skills, and mild mental retardation, many also tend to
have a good memory, expressive language, and musical talent. The
typical WS personality includes a combination of friendliness and
anxiety (Bellugi et al. 1999a, 1999b).
The genetic basis of WS is just beginning to be understood.
The starting point for much of the recent work stems from the
finding that WS results from hemizygous microdeletions at Chr
7q11.23 that include the elastin gene (ELN) (Ewart et al. 1993).
The commonly deleted interval includes the genes sequenced and
analyzed in this paper: LIMK1 (encoding LIM
giskakis et al. 1996; Osborne et al. 1996; Tassabehji et al. 1996);
illiam-Beuren syndrome critical region 1; originally
called WSCR1 and encoding eIF4H), (Osborne et al. 1996; Rich-
ter-Cook et al. 1998); WBSCR5 (originally called WSCR5 and
tentatively identified by an EST) (Osborne et al. 1996); and RFC2
eplication factor C subunit 2) (Osborne et al. 1996;
Peoples et al. 1996). See Fig. 1A for a schematic physical map
incorporating these genes and others within this region.
The size of the commonly deleted region associated with WS
has been found to span approximately 1.5–2 Mb of DNA (Osborne
et al. 1996; Perez Jurado et al. 1996; Robinson et al. 1996; Urban
et al. 1996; Wang et al. 1997; Meng et al. 1998; Wu et al. 1998;
Hockenhull et al. 1999). Recently, Botta et al. (1999) described
two patients with the full Williams syndrome phenotype who car-
ried deletions from just before the ELN gene to just past marker
D7S1870 within the GTF2I gene (Fig. 1A); this ‘minimal’ region
defines a region estimated to be approximately 850 kb. The se-
quences analyzed in this paper are within this smaller defined
The WS commonly deleted region at human Chr 7q11.23 has
been found to have conserved synteny to a region on the distal
portion of mouse Chr 5 (DeBry and Seldin 1996; DeSilva et al.
1999). Comparative physical mapping of the human and mouse
WS regions indicates that while the duplicated regions bounding
the human common deleted region are absent in mouse (DeSilva et
al. 1999), the expected genes residing between Eln and p47-phox
In this paper we report the sequence of both the human and
syntenic mouse regions containing the known genes LIMK1, WB-
SCR1, and RFC2 and a novel gene, WBSCR5. The transcription
patterns of WBSCR1 and WBSCR5 are examined and a brief
analysis of the product of the mouse Wbscr1 gene is included.
Alternative splicing is demonstrated for both of these genes. Un-
usual characteristics of this genomic region are noted and dis-
Materials and methods
DNA sequencing and analysis.
A sublibrary was constructed (Rowen
and Koop 1994) for each of the cosmids and the BAC clone (Fig. 1B,C).
Briefly, DNA from each cosmid or BAC was isolated and randomly
sheared by nebulization. The sheared DNA was then fractionated by aga-
rose gel electrophoresis, and fragments (2–4 kb) were collected, blunt-
ended, and cloned into M13mp19 by standard techniques. Random clones
from each sublibrary were sequenced with the aid of ABI 373 or 377
sequencing machines and fluorescently labeled primers (ABI, Amersham).
DNAStar software was used for gel trace analysis and contig assembly, as
well as DNA and protein alignments. DNA and protein sequences were
examined against available public databases by using the various Blast
programs available through the network server at the National Center for
Biotechnology. Repeat elements were characterized by using RepeatMas-
ker2 (A.F.A. Smit and P. Green; http://ftp.genome.washington.edu/cgi-bin/
RepeatMasker). Comparative sequence alignment was done with PipMaker
(http://globin.cse.psu.edu/cgi-bin/pipmaker), which produces the percent
Database Accession Numbers: U63721, AF045555, AF139987.
Correspondence to: Ben Koop; E-mail: email@example.com
Mammalian Genome 11, 890–898
© Springer-Verlag New York Inc. 2000