Cloning, chromosomal localization and characterization
of the murine mucin gene orthologous to human
MUC4
Jean-Luc Desseyn, Isabelle Clavereau and Anne Laine
Unite
´
560 INSERM, Place de Verdun, Lille, France
We report here the full coding sequence of a novel mouse
putative membrane-associated mucin containing three
extracellular EGF-like motifs and a mucin-like domain
consisting of at least 20 tandem repeats of 124–126 amino
acids. Screening a cosmid and a BAC libraries allowed to
isolate several genomic clones. Genomic and cDNA
sequence comparisons showed that the gene consists of 25
exons and 24 introns covering a genomic region of  52 kb.
The first intron is  16 kb in length and is followed by an
unusually large exon ( 9.5 kb) encoding Ser/Thr-rich
tandemly repeated sequences. Radiation hybrid mapping
localized this new gene to a mouse region of chromo-
some 16, which is the orthologous region of human chro-
mosome 3q29 encompassing the large membrane-anchored
mucin MUC4. Contigs analysis of the Human Genome
Project did not reveal any other mucin on chromosome 3q29
and, interestingly, our analysis allowed the determination of
the genomic organization of the human MUC4 and showed
that its exon/intron structure is identical to that of the mouse
gene we cloned. Furthermore, the human MUC4 shares
considerable homologies with the mouse gene. Based on
these data, we concluded that we isolated the mouse ortho-
log of MUC4 we propose as Muc4. Expression studies
showed that Muc4 is ubiquitous like SMC and MUC4, with

malignancy. Furthermore, SMC seems to be implicated in
the metastasis and in the resistance of SMC-expressing cells
to natural killer cells [9,10].
More recently, cloning and sequencing human MUC4
cDNAs showed similarities between MUC4 and SMC at
the N- and C-terminal portions of the molecules [11,12].
Although less is known about other large membrane-bound
mucins, it has been suggested that MUC4 is a homolog of
SMC.
Cloning a complete mucin cDNA and/or a complete
mucin gene is not an easy task for several reasons: (a) the
RNA messenger is very large (>10 kb) and often expressed
in low abundance in normal tissues; (b) the highly repetitive
sequence of the central portion makes it difficult to map,
subclone and sequence; (c) 5¢ and 3¢ ends are usually very
similar between genes from the same class; and (d) clones
may show instability presumably due to the repetitive
structure of sequences and this may explain that BAC and
YAC clones covering mucin genes clusters are still lacking in
the Human Genome Project.
In an effort to determine by genetic strategies, the specific
functions of large membrane-associated mucins, we cloned
and determined the complete cDNA and genomic sequences
of a new large putative membrane-bound mouse mucin.
This gene was assigned to mouse chromosome 16. RT-PCR
experiments showed high expression of Muc4 in trachea,
duodenum and intestine in contrast with a lower expression
in stomach, in salivary glands, in liver and gallbladder, and
in kidney. Chromosomal localization, sequence and expres-
sion analyses provide strong evidence that the human

kidney by using guanidine hydrochloride as previously
described [13].
RT-PCR amplifications
Single-stranded cDNA was generated from 1 lgoftotal
RNA using random hexamers or oligo(dT) primer. Several
oligonucleotides (Fig. 1) were designed by comparison of
the similar regions in the 3¢ regions of the gene coding for the
rat SMC and of the human MUC4 gene. The two sense
oligonucleotides NAU728 (5¢-TCCACTATCTGAACAA
CCAACT-3¢) and NAU727 (5¢-ATGCTGATTTCTCTAG
CTCCA-3¢) and the two antisense oligonucleotides NAU
726 (5¢-AACTTGTTCATGGAGCAGCCGC-3¢)and
NAU729 (5¢-AGTTGGTTGTTCAGATAGTGGA-3¢)
were designed from the SMC sequence (GenBank accession
number M91662). The sense oligonucleotide NAU576
(5¢-CCCCACATCACCACCTTGGAT-3¢) and the anti-
sense oligonucleotide NAU484 (5¢-AGAGAAACAGGGC
ATAGGACC-3¢) have been chosen from the human
MUC4 cDNA sequence (GenBank accession number
AJ000281). The antisense oligonucleotides NAU750
(5¢-CTACATTTCTTGGAGAGGCTGAGT-3¢)and
NAU762 (5¢-TGGAGCTAGAGAAATCAGCAT-3¢)
were designed from our mouse cDNA sequences.
NAU762 was used in RT-PCRs with the sense oligonucleo-
tide NAU941 from within the repeat region (see further) to
obtain the cDNA corresponding to the end of the repeat
region. The sense oligonucleotide NAU972 (5¢-GAGCTGC
CTGTGTTCTTGCCTCCT-3¢) was designed from the
sequence coding for the signal peptide of SMC (GenBank
accession number U06746) and used in RT-PCR experi-

involving a second round amplification using the antisense
oligonucleotide NAU1123 (5¢-CTGCTGGAAAGGGACA
TGGGT-3¢) and the anchor primer was carried out with
1 lL of the reaction mixture obtained from the previous
round of PCR as template. A major band of 230 bp was
amplified, cloned and sequenced.
Screening of genomic libraries
The mouse cDNA probe 1719 was generated by reverse-
transcription PCR using the two oligonucleotides NAU728
and NAU726 and used to screen a mouse pWE15 cosmid
library (Stratagene). Four clones were obtained and studied
but their analysis showed that they did not contain the
central region or the 5¢ end of the gene. The cosmid clone
containing the longest part of the new gene was named
CAR1 and studied. The 1719 probe and a cDNA probe
(1820) obtained by RT-PCR using the two oligonucleotides
NAU727 and NAU484 were then used to screen a mouse
BAC (bacterial artificial chromosome) library (Incyte
Genomics, Inc.). Filters were prehybridized, hybridized
and washed according to the manufacturer’s instructions
and one positive clone was obtained and named BAC4.
Fig. 1. Muc4 cDNA (A) and genomic (B) cloning strategy, and protein
domains organization (C). (A,B) Several cDNA clones and DNA
fragments are indicated with their numbers. Some primers and their
directions are indicated (not to scale) by horizontal arrows and their
NAU (N) numbers. Restriction enzymes: N, NdeI; B, BamHI; K,
KpnI. The hatched part corresponds to the repeat region. (C) Box with
dashes represents the signal peptide; dense dots, Ser/Thr-rich non-
repetitive sequence domain; diagonal lines, repetitive domain; square
blocks, first Cys-rich region; wavy lines, domain rich both in Ser/Thr

scriptII KS(+) vector (Stratagene). Genomic fragments of
interest obtained by PCR on cosmid CAR1 DNA and on
the clone BAC4 DNA using oligonucleotides designed
from cDNA sequences were cloned in pCR2-1 vector.
Large fragments of interest were cut from BAC4,
electrophoresed on a 0.8% agarose gel, electroeluted and
cloned to be sequenced and further digested and sub-
cloned into pBluescriptII KS(+) vector (Stratagene). To
determine the sequences of the 5¢ and 3¢ ends of intron 1,
we performed PCR experiments using BAC4 DNA as
template, the sense oligonucleotide NAU972 (located in
exon 1) and NAU1126 (located in exon 2), respectively,
and a mixture of hexamers used as second primer. PCR
products were subcloned into pCR4-TOPO vector (Invi-
trogen Ltd).
Plasmid inserts were sequenced on both strands several
times on LI-COR 4000 and computer analyses were
performed using
PC
/
GENE
Software. The mouse cDNA
and genomic sequences reported in this paper have been
deposited in the GenBank with accession numbers
AF441785 and AF441786, respectively.
BLAST
searches
of the human draft sequence using the MUC4 cDNA
(GenBank accession numbers AJ000281 and AJ010901)
and the Ensembl Genome Server (http://www.ensem-

Radiation hybrid (RH) mapping
The chromosomal localization of the new gene was
performed by PCR analysis using the T31 mouse/hamster
RH panel (Research Genetics) [14]. Primers NAU726
(antisense, see above) and NAU764 (sense 5¢-AAGTATGC
TGGAGGAGTACTT-3¢) located within the 3¢ end of the
mouse gene were tested on mouse and hamster DNA. These
oligonucleotides allow the amplification of a mouse DNA
fragment of 1182 bp without amplification from hamster
genomic template. The PCR reaction (50 lL) consists of
25 ng of DNA template, 15 pmol of each primer, 1.5 m
M
MgCl
2
,25l
M
of each dNTP and 2 U of Taq DNA
polymerase (Roche). The cycling conditions were: 2 min at
94 °C, 38 cycles of 15 s at 95 °C, 40 s at 56 °Cand90sat
72 °C followed by a final extension at 72 °Cfor7min.PCR
products were electrophoresed through a 1% agarose gel,
transferred overnight to membranes and hybridized with an
internal
32
P-labeled oligonucleotide NAU914 (5¢-GCTGCC
TAAGAATGGATACCCT-3¢). Logarithm of odds (lod)
scores were analyzed using the Jackson Laboratory mouse
RH data base (http://www.jax.org).
RESULTS
Isolation and sequencing of cDNAs

363 and 366 bp surrounding a unique sequence. 5¢ RACE
PCR was then performed and we cloned and sequenced a
major 230-bp band (named 2359). Within this unique
sequence is an ATG with a Kozak consensus sequence [15]
suggesting that it represents the codon for initiation of
translation and, therefore, codes for the N-terminus of the
protein. This fragment contains a 105-bp fragment of 5¢
untranslated sequence upstream of the putative start site
ATG.
Characterization of the cosmid clones
and sequencing strategy
Four positive cosmid clones were obtained by screening a
mouse cosmid library using the cDNA probe 1719. The
clone that contains the longest part of the new gene, CAR1,
was studied. Two adjacent KpnI–KpnI fragments of 5 and
4 kb (named 1941 and 1956, respectively, Fig. 1B) overlap-
ping the 3¢ end of the cDNA were subcloned. We also
performed PCR using the CAR1 DNA as template and the
oligonucleotides we used previously to clone the cDNAs.
All PCR products were subcloned into pCR2.1 vector and
sequenced on both strands. We then obtained the complete
genomic sequence of the 3¢ part of the gene encompassing
17 kb. Three poly(A) signals were found after the stop
codon. Analysis of the four cosmid clones by PCR revealed
that they do not contain any sequence upstream of the
oligonucleotide NAU484.
Characterization of the BAC genomic clone
and sequencing strategy
We screened a BAC library using the cDNA probe 1820 and
one clone, BAC4, was obtained and studied. PCR amplifi-

experiments. The last exon is composed of a coding
sequence of 193 bp and of an untranslated region of at
least 131 bp. The size of the 24 introns ranges from 79 bp to
about 16 kb. The size of the largest intron was determined
by restriction mapping. Each intron begins with a GT and
ends with an AG. The gene spans  52 kb from the
initiation ATG codon to the stop codon. Three poly(A)
signals are present located 122, 191 and 361 bp downstream
of the stop codon.
BLAST
searches showed homologies with
SMC and the human MUC4 mucin. Sequence similarity
searches using the MUC4 cDNA identified two clones on
human chromosome 3 from the evolving working draft
sequence. The clone RP11-423B7 is  173 kb and consists
of 16 ordered pieces and the clone RP11-171N2 is  164 kb
and consists of 29 unordered pieces. Multiple alignments of
genomic sequence pieces with the MUC4 cDNA allow for
the first time determination of the complete exon–intron
structure of this large membrane-bound mucin gene.
Because several differences exist between the human cDNA
and the two human genomic sequences, exons sizes given in
the Table 1 for the human MUC4 gene correspond to the
sizes deduced from the cDNA sequence. All introns have
the same classes and positions in MUC4 and in the mouse
gene we describe here.
Chromosomal localization
Using the T31 mouse/hamster RH panel that consists of 100
hybrid cell lines [14], the new gene was mapped by PCR
screening on the chromosome 16 with highest lod score of

1
Human 1 >110
a
CCCAGgtaagtgatg 1 >2008 1
Mouse 2  9500
b
tttcaagaagATGCT CTCAGgtgagtcagc 2 223 1
Human 2 >15 432
c
ttcactccagGAACC ATCAGgtagctgcca 2 334 1
Mouse 3 129
ccatgtccagGATTG TCAGGgtaagtgata 3 1669 1
Human 3 153
acgtgtccagGAATG GAGAGgtgaggccat 3 >2579
c
1
Mouse 4 134
ccttgtctagGCATT TCTACgtgagtctct 4 761 0
Human 4 134
cctggcccagGAGTT TCTACgtgagtccgg 4 >2147
c
0
Mouse 5 165
ttgtgctcagGTTAC ACCAGgtgagtcatt 5 945 0
Human 5 165
atgtgctcagTTCAC ATCAGgtgagccttt 5 1629 0
Mouse 6 156 cctttcctagGAATA TTGGGgtgagtggat 6 1102 0
Human 6 156
cctttcctagGAATA TCGGGgtgagtagac 6 1063 0
Mouse 7 131

ctccttccagGTCCA CGGAGgtaggttggg 13 820 1
Mouse 14 168
tgtcttccagTCTTA TCTGGgtaagatgca 14 445 1
Human 14 168
gatgctccagGCCAG CCTGGgtgagggcgg 14 501 1
Mouse 15 102
tgtctcacagGAGTG GACATgtgagtctgg 15 351 1
Human 15 102
tgtccctcagGGGTC GACCTgtgagtctgg 15 366 1
Mouse 16 234 tgtgttacagGGCAC CCTCAgtaagtgaca 16 1133 1
Human 16 234
tgtgttacagGGCAG CCTCAgtaagtggcc 16 2059 1
Mouse 17 138
tctgtttcagATCAG CTTTGgtatgaatct 17 3067 1
Human 17 138
tgtgtttcagATCAG CTTTGgtaggactat 17 1806 1
Mouse 18 182
ctctggacagAAAAC TTGAGgtgagtagtg 18 838 0
Human 18 182
cccggggcagAGAAT TGGAGgtgagtgttg 18 >2683
c
0
Mouse 19 160
tgtcattcagGTGAC TGCAGgtgagtgtgg 19 862 1
Human 19 160
cctcctccagGTGGC TGCGGgtgagccggg 19 982 1
Mouse 20 174
ccctttacagCTCTG TACGGgtatggctaa 20 695 1
Human 20 180
cactctgcagCTCTG CCTAGgtaccgccag 20 1659 1

Two different sizes depending on the contig considered.
3154 J L. Desseyn et al. (Eur. J. Biochem. 269) Ó FEBS 2002
(S + T ¼ 28.7%). According to the results of restriction
mapping, the whole repeat region encompasses  8.3 kb, of
which more than 4 kb have been sequenced. Amino-acid
repeats are aligned in Fig. 2A and the comparison of the
126 amino acids consensus sequence with the consensus
sequence of SMC repeats is shown (Fig. 2B). A unique
sequence of 119 amino acids is inserted between the first two
repeats a1 and a2. A
32
P-labelled oligonucleotide designed
from this unique sequence was hybridized to a Southern
blot of the BAC4 DNA digested with various restriction
enzymes and revealed a single HpaI–HpaIbandof1.5kb
suggesting that this sequence is unique (data not shown).
The order of the repeats b1-b2, c1-c2 and d1 is unknown.
There is at least one potential N-glycosylation site (Asn-
X-Ser/Thr where X is any amino acid except Pro) in each
repeat. The tandem repeat array ends with the e1-e8 repeats.
The second Ser/Thr rich region starts at a AWTFGDPH
peptide and consists of 374 amino acids (S + T ¼ 21.1%).
Moreover, it contains 14 potential N-glycosylation sites.
The GDPH sequence is conserved in human MUC4 [11]
and in SMC [17]. It has previously been shown that SMC is
cleaved early in the pathway to the cell surface [7] at this site.
Comparison with SMC and MUC4 and domains analysis
using
SMART
N-Terminal parts of Muc4, SMC and MUC4 were aligned

A comparison of the consensus sequence of Muc4 tandem
repeats with the consensus sequence of SMC tandem
repeats published previously [19] demonstrated that there is
a good degree of sequence identity (67%) between the two
Fig. 2. Alignment of the amino-acid sequences of the Muc4 repeats (A) and comparison of the repeat consensus sequences of Muc4 and SMC (B).
(A) Under the consensus sequence, the repeats are numbered in order of appearance from N- to C-terminal. The order of the repeats (b–d) is
unknown. Repeats e1–e8 are the last eight repeats. Dots indicate exact sequence matches with the consensus sequence and dashes gaps in the
sequence. A unique sequence inserted between repeats a1 and a2 is observed. The potential N-glycosylation sites are underlined. (B) Conserved
amino acids are shaded. Dash indicates a gap.
Fig. 3. Alignment of the amino-terminal
sequences of mouse Muc4, rat SMC and human
MUC4. The dashes indicate gaps in the
sequence. Identical sequences are shaded.
Ó FEBS 2002 The mouse mucin gene Muc4 (Eur. J. Biochem. 269) 3155
rodent species (Fig. 2B). We then hybridized an interspecies
Zoo blot containing EcoRI-digested DNA from human,
monkey, rat, mouse (Balb/c), dog, cow, rabbit, chicken and
yeast with the probe 2155 corresponding to one-and-a-half
repeats. This showed a 20-kb faint band with the rat DNA
while a very strong signal at 18 kb is observed for the mouse
DNA supporting that Muc4 and SMC are orthologs. No
signal is observed for other species (Fig. 5).
Tissue specific expression of
Muc4
The tissue distribution of Muc4 was determined by
RT-PCR using total RNA from various tissues. PCR
amplifications were analyzed by ethidium bromide staining
(Fig. 6) and Southern blotting using an internal primer as a
probe. Strong expression of Muc4 is shown in trachea,
duodenum and intestine, while a much weaker expression is

expression of SMC is believed to mask antigens at the tumor
cell surface. The precise function of the SMC transmem-
brane subunit is poorly understood due to the large size of
the molecule and the presence of several domains. In order
to further investigate the biological roles of large mem-
brane-bound mucins, we cloned a new mouse gene using
primers designed from the cDNA sequence of SMC and
human MUC4. Cloning and sequencing the human MUC4
had shown substantial similarities between MUC4 and
SMC at the N- and C-terminal portions of the molecules
[11,12] but such similarities may exist with rat and human
mucin cDNAs that still remain to be cloned. The work we
present in this paper provides strong evidence that the
mouse gene we cloned, characterized and suggested as
Muc4, is the ortholog of SMC and MUC4:(a)thethree
molecules show high sequence similarities; (b) the region of
mouse chromosome 16 on which we mapped the gene
exhibits synteny with human chromosome 3q where the
human MUC4 gene has been mapped; (c) Muc4 and MUC4
have a similar pattern of expression; (d) the tandem repeat
sequences of Muc4 share homology with the tandem repeat
sequences of SMC; and (e)
BLAST
searches and multiple
alignments allowed to determine the complete genomic
organization of MUC4 and this clearly shows that the two
genes are very close.
Based on sequence similarities we believe that we cloned
the complete coding sequence from the ATG initiator to the
stop codon of Muc4 which is followed by three poly(A)

did not succeed in cloning and sequencing the full repetitive
region but we can assume by restriction mapping experi-
ments that exon 2 is  9.5 kb in length and codes for two
Ser/Thr-rich regions flanking 20 or 21 imperfect mucin-type
repeats of 124 or 126 amino acids. An unusually large exon
coding for tandem repeats rich in Ser/Thr is a common
feature of mucins [23–25] and this suggests that the tandem
repeat array arose through internal duplications rather than
through exon shuffling. Alignment of repeat sequences
(Fig. 2A) shows an insertion of a unique peptide of
119 amino acids between repeats a1 and a2. This sequence
is unrelated to the three insertion sequences of 33, 43 and 94
amino acids described previously between tandem repeats of
SMC [19]. It is interesting to note that all the repeats of
Muc4 contain at least one potential N-glycosylation site, an
uncommon feature in mucin, contained only by the mouse
submandibular small mucin [26].
The consensus sequence of the Muc4 tandem repeat is
very close to that of SMC. Nevertheless, the tandem repeat
domain of Muc4 does not show significant identity with the
human MUC4 except that they are both rich in serine and
threonine. It is known that tandem repeats differ in
sequence and size between the two species and different
mucins [5]. Previous work on rat Muc5ac [27], and mouse
Muc3 [28], together with this work, clearly shows that rat
and mouse tandem repeats are conserved suggesting a high
pressure of selection on the tandem repeat sequences of
rodents.
The derived amino-acid sequence was used to search a
collection of gapped alignments of domains using the

epithelial morphogenesis [31]. The significance of this
domain in membrane-bound mucins is unclear. EGF-like
motifs are found in numerous growth factors and extracel-
lular proteins involved in formation of extracellular matrix,
cell adhesion, chemotaxis and wound healing [4]. These
motifs may allow exposure of ligand-binding sites outside of
the cell. To date, no ligand has been identified for MUC3
but SMC has been shown to bind the erbB2 receptor
tyrosine kinase through one of the EGF-like domains of
Ó FEBS 2002 The mouse mucin gene Muc4 (Eur. J. Biochem. 269) 3157
SMC and this interaction modulates the receptor tyrosine
kinase activity [8]. According to these authors, SMC
interacting directly with ErbB2 extracellular domain
through its EGF1 domain potentiates signaling through
the ErbB receptor network.
Expression of epithelial mucins is tissue-specific and
several mucins may be expressed in each tissue [5]. MUC4 is
expressed in numerous normal tissues including ocular,
salivary glands, trachea, lung, stomach, colon, ovary, uterus,
prostate, and endocervix [32–34]. There is no detectable
expression in normal pancreas while there is an abnormal
expression of MUC4 in pancreatic tumors [35,36]. The
mouse Muc4 seems to have a similar pattern of expression as
MUC4. It is also expressed in numerous epithelial tissues
with the highest expression in trachea, duodenum and
intestine while a lower expression is observed in submaxil-
lary glands, salivary glands, liver, gallbladder and in kidney.
Abnormal expression of MUC4 has been reported in
several human epithelial cancers [35,37,38] and it has been
shown that SMC contributes to tumor progression [8]. The

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