Báo cáo khoa học: The fabp4 gene of zebrafish (Danio rerio) ) genomic homology with the mammalian FABP4 and divergence from the zebrafish fabp3 in developmental expression pot

The fabp4 gene of zebrafish (Danio rerio ) ) genomic
homology with the mammalian FABP4 and divergence
from the zebrafish fabp3 in developmental expression
Rong-Zong Liu
1
, Vishal Saxena
1
, Mukesh K. Sharma
1
, Christine Thisse
2
, Bernard Thisse
2
,
Eileen M. Denovan-Wright
3
and Jonathan M. Wright
1
1 Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
2 Institut de Ge
´
ne
´
tique et Biologie Mole
´
culaire et Cellulaire, Department of Developmental Biology, CU de Strasbourg, Illkirch, France
3 Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada
Fatty acid-binding proteins (FABPs) are encoded by a
multigene family termed the intracellular lipid-binding
protein (iLBP) genes [1,2]. In vertebrates, at least 16
paralogous iLBPs, including 10 FABPs and six cellular

retinoid-binding proteins, have been identified [3].
Each iLBP gene shows a specific pattern of expression
during development and in adulthood of mammals
[4,5]. Despite several iLBP gene-knockout experiments
in mice that have attempted to provide direct evidence
for the biological function(s) of FABPs [6–8], the pre-
cise physiologic role(s) of each iLBP is far from being
resolved. The proposed functions of iLBPs include cel-
lular uptake and transport of long-chain fatty acids
and retinoids, interaction with other transport and
enzyme systems, regulation of gene transcription, and
protection of cells against the detergent effects of
excess fatty acids [4,5,9].
Phylogenetic analysis suggests that the vertebrate
iLBP multigene family may have arisen from a single
ancestral gene encoding a universal hydrophobic
Keywords
brain vasculature; conserved synteny; gene
phylogeny; linkage mapping; whole mount
in situ hybridization
Correspondence
J. M. Wright, Department of Biology,
Dalhousie University, Halifax, Nova Scotia,
Canada, B3H 4J1
Fax: +1 902 494 3736
Tel: +1 902 494 6468
E-mail:
Website: />(Received 1 December 2006, revised 15
January 2007, accepted 19 January 2007)
doi:10.1111/j.1742-4658.2007.05711.x

Teleost fishes differ from mammals in their fat deposition and distribution.
The gene for adipocyte-type fatty acid-binding protein (A-FABP or
FABP4) has not been identified thus far in fishes. We have determined the
cDNA sequence and defined the structure of a fatty acid-binding protein
gene (designated fabp4) from the zebrafish genome. The polypeptide
sequence encoded by zebrafish fabp4 showed highest identity to the H
ad
-
FABP or H6-FABP from Antarctic fishes and the putative orthologs from
other teleost fishes (83–88%). Phylogenetic analysis clustered the zebrafish
FABP4 with all Antarctic fish H6-FABPs and putative FABP4s from other
fishes in a single clade, and then with the mammalian FABP4s in an exten-
ded clade. Zebrafish fabp4 was assigned to linkage group 19 at a distinct
locus from fabp3. A number of closely linked syntenic genes surrounding
the zebrafish fabp4 locus were found to be conserved with human FABP4.
The zebrafish fabp4 transcripts showed sequential distribution in the devel-
oping eye, diencephalon and brain vascular system, from the middle somit-
ogenesis stage to 48 h postfertilization, whereas fabp3 mRNA was located
widely in the embryonic and ⁄ or larval central nervous system, retina, myo-
tomes, pancreas and liver from middle somitogenesis to 5 days postfertili-
zation. Differentiation in developmental regulation of zebrafish fabp4 and
fabp3 gene transcription suggests distinct functions for these two paralo-
gous genes in vertebrate development.
Abbreviations
dpf, days postfertilization; EST, expressed sequence tag; FABP, fatty acid-binding protein; hpf, hours postfertilization; iLBP, intracellular lipid-
binding protein; LG, linkage group; 5¢-RLM-RACE, 5¢-RNA ligase-mediated RACE.
FEBS Journal 274 (2007) 1621–1633 ª 2007 The Authors Journal compilation ª 2007 FEBS 1621
ligand-binding protein that underwent a series of gene
duplications, starting some 900 million years ago [3].
Among the iLBP multigene family, FABP3 and

FABP4, together with FABP5, FABP7, FABP8 and
FABP9, form the largest subfamily, subfamily IV [10].
Mammalian FABP4, also known as the adipocyte-type
FABP gene (A-FABP), the adipocyte P2 gene (aP2)or
the adipocyte lipid-binding protein gene (ALBP), was
first described in mice almost two decades ago [11].
Mammalian FABP3 and FABP4 are both expressed in
various tissues, with the transcripts and protein of
FABP3 being most abundant in heart and skeletal
muscle [12,13], and those of FABP4 being most abun-
dant in adipose tissue [14]. A protein similar to FABP3
(H-FABP) was isolated from the bovine mammary
gland, and initially termed mammary-derived growth
inhibitor [15]; it was later shown to be a mixture of
FABP3 and FABP4 (A-FABP) [16]. Two FABP
cDNAs, named H
h
-FABP and H
ad
-FABP, have been
isolated from mRNA extracted from the heart vent-
ricle of four Antarctic teleost fishes [17]. H
h
-FABP and
H
ad
-FABP cDNAs code for the proteins H8-FABP
and H6-FABP, respectively. Whereas the Antarctic fish
H6-FABP showed the highest sequence similarity to
FABP4, fabp4 has not, thus far, been formally repor-

ted in fishes, the largest and most diverse group of ver-
tebrates, with distinct physiologic features in fat
deposition and distribution [18]. Owing to these differ-
ences in fat deposition and distribution, the role(s) of
orthologous FABPs in fishes and mammals may differ
markedly.
Two important questions need to be answered. First,
is there a functional fabp4 in teleost fish genomes
orthologous to mammalian FABP4? Second, if there is
a fish fabp4, how does the fish fabp4 differ functionally
from the paralogous fabp3? To date, there has been no
detailed comparative functional analysis of these two
closely related paralogous genes in mammals, or any
other species. Here we report the identification of a
zebrafish gene transcript encoding a polypeptide with
highest sequence identity to H
ad
-FABP or H6-FABP
from four Antarctic fishes [17]. On the basis of gene
structure, phylogeny and conserved synteny, we deter-
mined that this zebrafish fabp is the ortholog of the
mammalian FABP4, and it is therefore hereafter
referred to as zebrafish fabp4. Taking advantage of the
qualities of the zebrafish as a model system for study-
ing gene expression during vertebrate development, we
provide, for the first time in vertebrates, a detailed spa-
tiotemporal expression profile for fabp4 during embry-
onic and larval development, and compare this pattern
of gene expression with that of zebrafish fabp3, a gene
encoding a polypeptide showing greatest sequence

identity to H
h
-FABP or H8-FABP from Antarctic
fishes [17]. The differential patterns of distribution for
the fabp3 and fabp4 transcripts in zebrafish embryos
and larvae suggest distinct functions for these two
paralogous genes during vertebrate development.
Results
cDNA sequence and gene structure of zebrafish
fabp4
A blastn search using a previously cloned zebrafish
fabp3 cDNA sequence [19] identified an expressed
sequence tag (EST) from GenBank exhibiting sequence
similarity to an fabp3 cDNA (accession number:
CN511548). 3¢-RACE and 5¢-RNA ligase-mediated
(RLM)-RACE generated a cDNA sequence (accession
number: AY628221) with a complete coding capacity
for an FABP, hereafter referred to as FABP4. The
cDNA contained a 64-nucleotide 5¢-UTR, a 205-nuc-
leotide 3¢-UTR, and a 405-nucleotide ORF that codes
for a polypeptide of 134 amino acids. The deduced
amino acid sequence had a theoretical molecular mass
of 15.1 kDa and an isoelectric point of 7.8. A consen-
sus polyadenylation signal (AATAAA) was located 19
nucleotides upstream of the poly(A) sequence.
The genomic sequence of zebrafish fabp4 was identi-
fied in a zebrafish genomic DNA assembly sequence
(accession number CR759777) in GenBank through a
tblastn search. The sequence of fabp4 spanned
2459 bp and consisted of four exons (137 bp, 176 bp,

102 bp, and 258 bp) separated by three introns
(217 bp, 101 bp, and 1468 bp) (Fig. 1), a gene struc-
ture common to all FABP genes identified in verte-
brates thus far (Fig. 2), with the exception of zebrafish
fabp1a, which contains an additional intron in the 5¢-
UTR [20]. The nucleotides at the splice site of each
exon–intron junction of zebrafish fabp4 conform to the
GT–AG rule [21]. Alignment of the cDNA sequence
with the coding sequence of zebrafish fabp4 showed
one nucleotide difference in the coding region of exon
2, resulting in an alteration of the ninth codon of this
exon from GTT to GTC without changing the encoded
amino acid. The genomic sequence and several EST
sequences from GenBank (CN511548, CN168379,
BC081489) had GTT at this position, whereas the ze-
brafish fabp4 cDNA sequence reported here and
another EST (CK355002) had GTC, suggesting that
this T–C transition most likely represents an allelic
variation.
5¢-RLM-RACE generated a single product for the
5¢-end of the cDNA using zebrafish fabp4 cDNA-speci-
fic nested antisense primers (data not shown). Align-
fabp4 gene in zebrafish R Z. Liu et al.
1622 FEBS Journal 274 (2007) 1621–1633 ª 2007 The Authors Journal compilation ª 2007 FEBS
ment of the nucleotide sequences of the cloned 5¢-
RLM-RACE product with the genomic sequence
assigned the transcription start site to a position 64 bp
upstream of the initiation codon (Fig. 1). The length
of the 5¢-UTR of zebrafish fabp4 is similar to that of
mouse Fabp4 (previously termed aP2) (67 bp) [11]. A

Fig. 1. Nucleotide sequence of zebrafish fabp4 and its proximal 5¢-upstream region. Exons are shown in upper-case letters, with the coding
sequences of each exon underlined and the deduced amino acid sequence indicated below. Numbers on the right indicate nucleotide posi-
tions in the gene sequence. The initiation site for transcription is numbered + 1. A putative polyadenylation signal is highlighted in bold and
underlined. PCR primers (s1, as1, as2) used in this study are double underlined and indicated. A putative TATA box, two 5¢-upstream
AP1-binding sites and two CCAAT box sequences are boxed and indicated. A variation between the cDNA sequence and the genomic
DNA sequence within exon 2 is highlighted in bold, with the variation indicated above. Zebrafish fabp4 and its 5¢-upstream sequence were
identified from a Danio rerio DNA sequence assembly deposited in GenBank (accession number CR759777) by The Wellcome Trust Sanger
Institute.
R Z. Liu et al. fabp4 gene in zebrafish
FEBS Journal 274 (2007) 1621–1633 ª 2007 The Authors Journal compilation ª 2007 FEBS 1623
TATA box-like element (TTGAAAA) is located at nu-
cleotides ) 26 to ) 32 (Fig. 1). The position of this
putative TATA box of zebrafish fabp4 is identical to
that of the TATA box (TTTAAAA) of mouse Fabp4
relative to their transcription start sites [11]. Inspection
of the upstream sequence of zebrafish fabp4 using
motif search () identified two
AP1-binding sites and two CCAAT box elements
within 400 bp of the proximal promoter sequence
(Fig. 1). These cis elements have been shown to be
important in controlling the expression of mouse
Fabp4 during adipocyte differentiation [22].
Zebrafish fabp4 is the ortholog of mammalian
FABP4
The deduced amino acid sequence of zebrafish FABP4
showed highest sequence identity to H
ad
-FABP (H6-
FABP) from Antarctic teleost fishes (83–84%, Fig. 3)
and to the putative orthologs of other teleost fishes,

including Takifugu rubripes (85%, deduced from a
cDNA sequence deposited in GenBank with accession
number AL837220), Oryzias latipes (84%, BJ899828)
and Cyprinus carpio (88%, CF661735). The second
highest identity of zebrafish FABP4 was to mammalian
FABP4 (51–53%), FABP3 (54–56%) and FABP7 (54–
55%). In contrast to the divergence in amino acid
sequence between fish FABP4s (83–88%) and mamma-
lian FABP4s (51–53%), zebrafish FABP3 exhibited
similar amino acid sequence identities to other fish
(71–72%) and mammalian (72–73%) FABP3s (Fig. 3).
Despite the divergence of their primary protein
sequence, residues R107, R127 and Y129 of zebrafish
FABP4 and Antarctic H
ad
-FABPs (H6-FABPs) are
conserved with residues R106, R126 and Y128 of
mammalian FABP4s (Fig. 3). These residues are
believed to play a critical role in the specificity and
affinity of ligand binding by mammalian FABP4 [23].
The phylogenetic relationship of zebrafish fabp4 and
the H6-FABP gene from Antarctic fishes was deter-
mined using amino acid sequences of members of the
FABP family from mammals and fishes (Fig. 4). A dis-
tinct clade consisting of zebrafish FABP4, the four
Antarctic fish H6-FABPs and putative FABP4 homo-
logs from three other teleost fishes was evident. The
teleost fish FABP4 (H6-FABP) clustered with mamma-
lian FABP4s in an extended clade (Fig. 4). Zebrafish
FABP3 and the four Antarctic fish H8-FABPs, along

with other fish and mammalian FABP3s, formed a
separate clade (Fig. 4). The phylogenetic analysis
resolved fish FABP4 (and H6-FABPs) and FABP3
(and H8-FABPs) as proteins encoded by distinct genes,
and suggested that these genes are orthologs of mam-
malian FABP4 and FABP3, respectively.
To further confirm that zebrafish fabp4 is indeed the
orthologous gene of mammalian FABP4, we first
mapped zebrafish fabp4 to a particular linkage group
(LG) in the zebrafish genome using the radiation
hybrid mapping panel LN54 [24], and then compared
its syntenic relationships with the mammalian FABP4s
(Table 1). Zebrafish fabp4 was assigned to LG 19 with
a mapping distance of 14.73 centi-Rads (cR) to the
genome framework marker fa04h09. Using a pair of
the closest flanking markers (fd60g10 and Z22532), ze-
brafish fabp4 was located between 50.8 and 53.1 cM
on the merged ZMAP. The syntenic relationship of 19
gene loci mapped so far surrounding fabp4 on zebra-
fish LG 19 was conserved with human FABP4 on
chromosome 8 (Table 1). The majority of these con-
served syntenies span a mapping distance of around
10 cM (46.86–57.80 cM) on zebrafish LG 19 and
8q21–8q24.3 on human chromosome 8 (Table 1). In
addition to sequence identities (Fig. 3) and the phylo-
genetic analysis (Fig. 4), the well-conserved synteny
provides compelling evidence that the putative zebra-
fish fabp4 and human FABP4 are orthologous genes.
Exon 1 Intron 1 Exon 2 Intron2 Exon 3 Intron 3 Exon 4
24 aa 217 bp 59 aa 101 bp 34 aa 1468 bp 17 aa

Dr fabp4
24 aa 1241 bp 58 aa 224 bp 34 aa 1284 bp 16 aa
Gg fabp4
24 aa 2496 bp 58 aa 968 bp 34 aa 500 bp 16 aa
Hs FABP4
24 aa 2316 bp 58 aa 607 bp 34 aa 670 bp 16 aa
M
m Fabp4
Fig. 2. Comparison of the gene structure of zebrafish fabp4 and its chicken and mammalian orthologous genes. Exons are shown as solid
boxes, introns as open boxes, and the UTRs of the first and fourth exon as dotted boxes. The number of amino acids encoded by each exon
is shown above each box. The size of each intron is indicated in bp. The D. rerio (Dr), Gallus gallus (Gg), Homo sapiens (Hs) and Mus muscu-
lus (Mm) FABP4 sequences were obtained from GenBank (accession numbers CR759777, NC_006089, NC_000008 and NC_000069,
respectively).
fabp4 gene in zebrafish R Z. Liu et al.
1624 FEBS Journal 274 (2007) 1621–1633 ª 2007 The Authors Journal compilation ª 2007 FEBS
Differential distribution of the zebrafish fabp3
and fabp4 transcripts during embryonic and
larval development
The spatiotemporal distribution of the fabp4 and fabp3
transcripts during zebrafish embryonic and larval
development was analyzed by whole mount in situ
hybridization [25] using probes generated from their
specific cDNA sequences (Figs 5 and 6). At middle
somitogenesis [17 h postfertilization (hpf)], fabp4 tran-
scripts were detected only in the proximal region of
the retina, whereas fabp3 transcripts were distributed
in several structures, including the diencephalon, hind-
brain, spinal cord, and somites (Fig. 5A). At 24 hpf,
the fabp4 transcripts were abundant in the lens and in
the dorsal diencephalon, and visible in the choroid fis-

sure. The pattern of expression of fabp3 in the devel-
oping brain was similar at 17 hpf and 24 hpf. Levels
of fabp3 transcripts, however, were higher at 24 hpf
than at 17 hpf. In addition, at 24 hpf, fabp3 transcripts
were detected in the retina, tectum, and posterior bran-
chial arches (Fig. 5B). At the 36 hpf larval stage, the
A
B
Fig. 3. Alignment of zebrafish FABP4 and FABP3 with the orthologous protein sequences from other teleost fishes and mammals. (A) D. re-
rio (Dr) FABP4 (GenBank accession number AY628221) was aligned with Chaenocephalus aceratus (Cha, AAC60350), Cryodraco antarcticus
(Ca, AAC60351), Gobionotothen gibberifrons (Gog, AAC60354), Notothenia coriiceps (Nc, AAC60352), H. sapiens (Hs, CAG33184) and
M. musculus (Mm, AAH02148) FABP4s. (B) D. rerio FABP3 (Dr, AAL40832) was aligned with Ch. aceratus (AAC60356), Cr. antarcticus
(AAC60357), Go. gibberifrons (AAC60359), N. coriiceps (AAC60358), H. sapiens (CAG33148) and M. musculus (AAH89542) FABP3s. Dots
indicate amino acid identity, and dashes represent gaps. Positions of amino acids are marked and numbered. Three residues implicated in
ligand-binding specificity and affinity and conserved among the zebrafish, Antarctic fish and mammalian FABP4s are boxed. Amino acid
sequence identity values between the zebrafish FABP4 or FABP3 and the Antarctic fish, human and mouse FABP4s or FABP3s are indicated
at the end of each alignment.
R Z. Liu et al. fabp4 gene in zebrafish
FEBS Journal 274 (2007) 1621–1633 ª 2007 The Authors Journal compilation ª 2007 FEBS 1625
Fig. 4. Phylogenetic relationship of the zebrafish and other teleost fish FABP4s and FABP3s in the FABP family. The bootstrap neighbor-join-
ing phylogenetic tree was constructed with
CLUSTALX [43] using H. sapiens LCN1 (GenBank accession number NP_002288) as an outgroup.
The bootstrap values (based on number per 1000 replicates) are indicated above or under each node. Amino acid sequences used in this
analysis include: D. rerio (Dr) FABP4 (derived from AY628221), FABP3 (AAL40832), FABP2 (AAP93851), FABP7a (AAH55621), FABP7b
(AAQ92970), and FABP10 (AAH76219); H. sapiens (Hs) FABP1 (CAG46887), FABP2 (AAH69617), FABP3 (CAG33148), FABP4 (CAG33184),
FABP5 (AAH70303), FABP6 (AAH22489), FABP7 (CAG33338), and FABP8 (AAH34997); M. musculus (Mm) FABP1 (NP_059095), FABP2
(AAS00550), FABP3 (AAH89542), FABP4 (AAH02148), FABP5 (NP_034764), FABP6 (NP_032401), FABP7 (NP_067247), FABP8 (XP_485204),
and FABP9 (NP_035728); Rattus norvegicus (Rn) FABP1 (NP_036688), FABP2 (NP_037200), FABP3 (NP_077076), FABP4 (NP_445817),
FABP5 (NP_665885), FABP6 (NP_058794), FABP7 (NP_110459), and FABP9 (NP_074045); Sus scrofa (Ss) FABP4 (CAC95166); Ga. gallus
(Gg) FABP4 (NP_989621); Ch. aceratus (Cha) FABP4 (H6-FABP, AAC60350) and FABP3 (H8-FABP, AAC60356); Cr. antarcticus (Ca) FABP4

(H6-FABP, AAC60351) and FABP3 (H8-FABP, AAC60357); Go. gibberifrons (Gog) FABP4 (H6-FABP, AAC60354) and FABP3 (H8-FABP,
AAC60359); N. coriiceps (Nc) FABP4 (H6-FABP, AAC60352) and FABP3 (H8-FABP, AAC60358); Parachaenichthys charcoti (Pc) FABP4 (H6-
FABP, AAC60355); Ta. rubripes (Tf) FABP4 (deduced from AL837220); Tetraodon nigroviridis (Tn) FABP4 (deduced from CR723700); Or. lati-
pes (Ol) FABP4 (deduced from BJ899828); and Cy. carpio (Cc) FABP4 (deduced from CF661735). Scale bar ¼ 0.1 substitutions per site.
fabp4 gene in zebrafish R Z. Liu et al.
1626 FEBS Journal 274 (2007) 1621–1633 ª 2007 The Authors Journal compilation ª 2007 FEBS
hybridization signal for fabp4 transcripts was detected
in the head vasculature system and remained in the
lens and dorsal diencephalon (Fig. 6B). In comparison,
the distribution of fabp3 transcripts was similar to that
of the 24 hpf stage, with the exception of a slightly
decreased intensity of hybridization signal in the spinal
cord and the appearance of transcripts at the level of
myosepta in muscle pioneers (Fig. 6A). At 48 hpf, in
addition to their continued presence in the lens and
dorsal diencephalon, fabp4 transcripts were elevated in
the head vasculature and detected at low levels in the
intersegmental blood vessels and in the aorta wall
(Fig. 6B). The relative levels of fabp3 transcripts, as
indicated by the hybridization signal, were dramatic-
ally reduced in most of the structures at 48 hpf as
compared to those at 36 hpf, with the fabp3 transcripts
being first detected in the liver, intestinal bulb, pan-
creas and one cranial ganglion (posterior lateral line
Table 1. Conserved syntenies of the zebrafish fabp4 with human FABP4. –, data not available.
Gene name
Zebrafish
a
Human
b

Gene symbol
Linkage roup
position
(cM) Mapping panel Gene symbol Chromosomal location
Mitochondrial folate
transporter ⁄ carrier
mftc 19, 46.86 LN54 MFTC 8q22.3
Growth differentiation
factor 6
gdf6b 19, 47.30 HS GDF6 8q22.1
Sperm-associated
antigen 1
spag1 19, 49.00 T51 SPAG1 8q22.2
Zinc finger protein,
multitype 2
zfpm2b 19, 49.00 T51 ZFPM2 8q23
Protein tyrosine
phosphatase type IVA,
member 3
ptp4a3 19, 50.25 HS PTP4A3 8q24.3
Ribonucleotide
reductase M2 b
rrm2b 19, 50.60 T51 RRM2B 8q23.1
Hairy ⁄ enhancer-of-split
related to YRPW motif 1
Hey1 19, 50.80 LN54 HEY1 8q21
Ribosomal protein L30 rpl30 19, 50.80 LN54 RPL30 8q22
Lysosomal-associated
protein
transmembrane 4b

laptm4b 19, 50.80 LN54 LAPTM4B 8q22.1
Fatty acid-binding
protein 4, adipocyte
fabp4 19, 50.80–53.10
c
LN54 FABP4 8q21
Angiopoietin 2 angpt2 19, 50.80–57.80
c
LN54 ANGPT2 8q23.1
Serine ⁄ threonine
kinase 3
stk3 19, 51.88 T51 STK3 8q22.2
Metadherin lyricl 19, 51.95 T51 MTDH
(LYRIC)
8q22.1
Antizyme inhibitor 1 azin1 19, 53.30 T51 AZIN1 8q22.2
N-myc downstream
regulated gene 1
ndrg1 19, 55.13 LN54 NDRG1 8q24.3
Trichorhinophalangeal
syndrome I
trps1 19, 78.10 LN54 TRPS1 8q24.12
Angiopoietin 1 angpt1 19, 81.93 T51 ANGPT1 8q22.3–q23
ATPase, H
+
transporting, lysosomal
42 kDa, V1 subunit C1
atp6v1c1l 19 – ATP6V1C1 8q22.3
Brain and acute
leukemia, cytoplasmic

Baalc 19 – BAALC 8q22.3
PTK2 protein tyrosine
kinase 2
ptk2.2 19 – PTK2 8q24-q
ter
a
Mapping information derived from the merged genetic map at the ZFIN website: :6070.
b
Mapping information
derived from NCBI at .
c
Location defined by flanking framework markers on zebrafish linkage group 19.
R Z. Liu et al. fabp4 gene in zebrafish
FEBS Journal 274 (2007) 1621–1633 ª 2007 The Authors Journal compilation ª 2007 FEBS 1627
ganglion) at this stage (Fig. 6A). Strong hybridization
signals for fabp3 transcripts remained in the liver, pan-
creas and posterior optic tectum of 5-day-old larvae
(Fig. 6C). The zebrafish fabp4 transcripts were unde-
tectable at the 5 days postfertilization (dpf) larval stage
(data not shown).
Adult tissue-specific distribution of fabp3 and
fabp4 transcripts detected by RT-PCR
RT-PCR was employed to detect the presence of fabp3
and fabp4 transcripts in adult zebrafish tissues. Both
fabp3 and fabp4 mRNA were detected by the highly
sensitive technique of RT-PCR in all the adult tissues
examined, which included the ovary, liver, skin, intes-
tine, brain, heart, testis, and muscle (Fig. 7). It is of
note that fabp3 transcripts had only been detected pre-
viously in adult zebrafish ovary and liver by the less

sensitive technique of tissue section in situ hybridiza-
tion [19]. No hybridization signal for fabp4 mRNA
was observed in any of the adult tissues using the
method of tissue section in situ hybridization (data not
shown), suggesting the presence of low levels of fabp4
transcripts in adult zebrafish tissues.
Discussion
In the vertebrate iLBP multigene family, fabp3 and
fabp4 are grouped in the same subfamily, subfamily IV
[10]. Their primary amino acid sequences share high
identities (63–68% between mammalian FABP3s and
FABP4s). Besides the common three-dimensional fold
of the protein backbone, mammalian FABP3 and
FABP4 show additional similarities in their tertiary
structures, related to their ligand-binding specificity
and affinity [10]. In addition to the similar three-
dimensional structure and ligand-binding specificity
and affinity of FABP3 and FABP4, the transcripts and
proteins of the two paralogous genes exist in multiple
tissues and are colocalized in several mammalian tis-
sues, including mammary gland [16], heart [17], skel-
etal muscle [26], and adipose tissue [27]. In earlier
studies, the gene products from these two paralogs
were not readily resolved. For example, bovine FABP3
and FABP4 were once regarded as a single protein,
termed mammary-derived growth inhibitor when it
was first isolated from the bovine mammary gland
[15]. Mammary-derived growth inhibitor was later
shown to be a mixture of FABP3 and FABP4 [16].
Vayda et al. [17] isolated two fabp gene transcripts,

termed H
h
-FABP, coding for H8-FABP, and H
ad
-
FABP, coding for H6-FABP, from the heart ventricle
of four Antarctic fishes. On the basis of sequence
Fig. 5. Spatiotemporal distribution of zebrafish fabp3 and fabp4
transcripts during development at 17 and 24 hpf. (A) Distribution of
fabp3 transcripts (A1, A2) in the diencephalon (Di), hindbrain (Hb),
spinal cord (Sc), and somites (So), and fabp4 transcripts (A3, A4) in
the retina (Re) of 17 hpf embryos. (A1, A3) Lateral view, head to
the left. (A2, A4) Dorsal view, head to the left. (B) Comparison of
the distribution of fabp3 and fabp4 transcripts at 24 hpf. Abundant
fabp3 mRNA was present in the diencephalon (Di), retina (Re), tec-
tum (Te), hindbrain (Hb), spinal cord (Sc), and myotomes. fabp4
mRNA was restricted to the dorsal diencephalon, lens (Le) and
choroid fissure (Cf) of 24 hpf embryos. (B1, B4) Lateral view, head
to the left. (B3, B6) Dorsal view, head to the left. (B2) Magnified
lateral view of the tail. (B5) Magnified lateral view of the head.
fabp4 gene in zebrafish R Z. Liu et al.
1628 FEBS Journal 274 (2007) 1621–1633 ª 2007 The Authors Journal compilation ª 2007 FEBS
comparison and phylogenetic analysis, these two fabp
cDNAs, present as mRNA transcripts in cardiac tissue
of Antarctic fishes, were proposed to be products of
distinct genes, and their encoded proteins were thought
to be homologous to mammalian adipose FABP and
heart FABP [17]. However, Vayda et al. [17] did not
explore further the genomic relationship of these Ant-
arctic fish FABPs with their mammalian orthologs. In

Fig. 6. Comparison of the distribution of fabp3 and fabp4 transcripts at 36 hpf, 48 hpf and 5 dpf. (A) fabp3 mRNA was detected in the tec-
tum (Te, 36–48 hpf), retina (Re, 36–48 hpf), hindbrain (Hb, 36 hpf), spinal cord (Sc, 36–48 hpf), branchial arches (Ba, 36 hpf), muscle pioneers
at the level of the longitudinal myosepta (Mys, 36 hpf), cranial ganglion (Cg, 48 hpf), liver (Li, 48 hpf), intestine (In, 48 hpf), and intestinal
bulb (Inb, 48 hpf). The relative positions of the notochord (No) and otic vesicle (Ov) are indicated in red (A5, A10). (B) fabp4 mRNA was dis-
tributed in the diencephalon (Di, 36–48 hpf), lens (Le, 36–48 hpf), head vasculature (B1–B5, arrowheads, 36–48 hpf) intersegmental blood
vessels (B6, arrows, 48 hpf), and aorta wall. (C) Detection of fabp3 mRNA in the posterior tectum (Te), liver (Li) and pancreas (Pa) of 5 dpf
larvae. (A1, A6, A8, B1, B3, B4, C1) Lateral view, head to the left. (A2, A7, B2, B5) Dorsal view, head to the left. (A3, A4, A9, B6) Magnified
lateral view of the tail. (A5) Magnified view of the tail, cross-section. (C2, C3) Magnified lateral view of the liver and pancreas.
R Z. Liu et al. fabp4 gene in zebrafish
FEBS Journal 274 (2007) 1621–1633 ª 2007 The Authors Journal compilation ª 2007 FEBS 1629
the present study, we have determined the cDNA
sequence and the structure of a gene coding for a pro-
tein similar to the Antarctic teleost H
ad
-FABPs (or
H6-FABPs). In addition to the evidence from sequence
identity and gene phylogeny, the conserved syntenic
relationship of this zebrafish fabp with human FABP4
strongly suggests that we have identified a gene ortho-
logous with mammalian FABP4 and distinct from
zebrafish fabp3. We concluded that zebrafish fabp4,
along with the Antarctic teleost genes for H
ad
-FABPs
(or H6-FABPs), and zebrafish fabp3, along with the
Antarctic teleost genes for H
h
-FABP (or H8-FABP),
are orthologous with mammalian FABP4 and FABP3,
respectively.

In this article, we provide for the first time the spa-
tiotemporal distribution of fabp4 and fabp3 transcripts
during development in vertebrates, using zebrafish as a
model system. Although a similar distribution of the
transcripts for these two genes has been observed in
adult tissues from Antarctic fishes by northern blot
analysis, we revealed strikingly different patterns of
expression for the fabp4 and fabp3 transcripts during
embryonic and larval development in zebrafish (Figs 5
and 6) that suggest distinct function(s) for these two
genes during vertebrate development. Although the
fabp4 and fabp3 cDNAs from four Antarctic fishes
were isolated from the heart, and both gene transcripts
were abundant in this tissue as determined by northern
blot analysis [17], a previous study by us did not detect
fabp3 transcripts in the adult zebrafish heart using tis-
sue section in situ hybridization [19]. In the present
study, we again did not observe hybridization signals
for fabp3 and fabp4 transcripts in the embryonic or
larval heart tissue. In contrast, zebrafish fabp3 mRNA
was abundant in the adult [19], embryonic and larval
liver, but the Antarctic fish fabp3 (H
ad
-FABP or H8-
FABP) is not present in the adult liver [17]. Consider-
ing that Antarctic teleost fishes and the tropical
zebrafish live in environments with extremely different
temperatures, the differences in the tissue expression
patterns of these two paralogous genes may reflect var-
iations in fatty acid metabolism, energy utilization and

storage between these two fish lineages. The expression
of fabp3 and fabp4 may be regulated by environmental
factors [27] and training [26]. We detected zebrafish
fabp4 transcripts in the early head vascular system at
36 hpf, and the intensity of the hybridization signal in
this structure had greatly increased at 48 hpf (Fig. 6).
The distribution pattern of fabp4 transcripts in the
developing brain vasculature system parallels the devel-
opment dynamic of this tissue in zebrafish [28]. Blood
circulation in zebrafish embryos starts at about
24–26 hpf through a single circulatory loop. Connec-
tion of simple blood vessel branches can be seen in the
head of the zebrafish embryos at 36 hpf (1.5 dpf), and
a rather complex head vascular system is formed at
48 hpf [28]. Our detection of the specific and dynamic
distribution of fabp4 transcripts in the early developing
vasculature of the zebrafish embryonic brain suggests a
function for this gene in brain angiogenesis. Our obser-
vation of the abundant distribution of the zebrafish
fabp4 transcripts in developing embryonic tissues
and low levels in adult tissues indicates a developmen-
tal role for this gene in zebrafish that has not been
well documented in the embryogenesis of mammalian
species.
The genes for FABP3 and FABP4 reside on different
chromosomes in human (chromosomes 1 and 8, respect-
ively) [29,30], mouse (chromosomes 4 and 3, respect-
ively) [31,32] and rat (chromosomes 5 and 2,
respectively) [33,34]. We assigned both fabp3 [19] and
fabp4, however, to a single LG, LG 19, of the zebrafish

genome using the same radiation hybrid mapping
panel, LN54 [24]. Different radiation hybrid scoring
vectors (Table 2) generated by gene-specific primers
assigned zebrafish fabp3 and fabp4 to different loci in
the same LG and confirmed that they are indeed dis-
tinct genes with divergent linkage relationships with the
genome markers. Interestingly, zebrafish LG 19 con-
tained both conserved syntenies surrounding the fabp3
[19] and fabp4 loci (Table 1) with the chromosomal seg-
ments harboring FABP3 and FABP4 on human chro-
mosomes 1 and 8, respectively. The conserved synteny
of zebrafish LG 19 to both human chromosomes 1 and
8 suggests chromosomal rearrangement after the diver-
gence of fish and mammals, which is estimated to have
occurred approximately 450 million years ago [35], and
which is an event revealed by extensive zebrafish–
human comparative genomic analyses [36–39]. In
humans, FABP4 (8q21) [30], FABP5 (8q21.13) and
Fig. 7. Zebrafish fabp3 and fabp4 transcripts detected by RT-PCR
in RNA extracted from adult tissues. RT-PCR products were gener-
ated from total RNA extracted from various adult zebrafish tissues
(indicated below the panel showing stained agarose gels), using
both fabp3 and fabp4 cDNA-specific primers. As a positive control,
rack1 transcripts were detected by RT-PCR in RNA extracted from
all adult tissues. A negative control (–) lacking RNA template gener-
ated no RT-PCR products.
fabp4 gene in zebrafish R Z. Liu et al.
1630 FEBS Journal 274 (2007) 1621–1633 ª 2007 The Authors Journal compilation ª 2007 FEBS
FABP8 (8q21.13-q22.1) [40] exhibit closely linked synt-
enies. The latter two genes, however, have not been

described to date in fishes. It would be interesting to
know whether functional fabp5 and fabp8 exist in the
zebrafish genome, and whether their syntenic relation-
ships with fabp4 are conserved in fishes.
In summary, we have determined the cDNA
sequence, defined the gene structure and mapped the ge-
nomic locus of a paralogous member of the iLBP multi-
gene family in zebrafish. Analysis of amino acid
sequence similarity, gene phylogeny, conserved synteny
and developmental expression of gene transcription
revealed that this newly identified fabp4, along with the
H6-FABP genes described earlier in Antarctic fishes
[17], is the ortholog of mammalian FABP4. We also
show that zebrafish fapb4 is paralogous to zebrafish
fabp3 [19], which is orthologous with the Antarctic fish
H8-FABP and mammalian FABP3 genes. We have fur-
ther demonstrated the different spatiotemporal distribu-
tion of the zebrafish fabp3 and fabp4 transcripts during
embryonic and larval development, which may provide
further insights into the potential physiologic role(s)
that these two genes play in vertebrate development.
Experimental procedures
Zebrafish culture and breeding
Zebrafish were purchased from a local aquarium store and
cultured in filtered, aerated water at 28.5 °C in 35 L aqua-
ria. Fish were maintained on a 24 h cycle of 14 h light and
10 h darkness. Fish were fed with a dry fish feed, TetraMin
Flakes (TetraWerke, Melle, Germany), in the morning, and
hatched brine shrimp (Artemia cysts from INVE, Grants-
ville, UT, USA) in the afternoon. Fish breeding and

embryo manipulation were conducted according to estab-
lished protocols [41].
Cloning of the zebrafish fabp4 cDNA
To obtain the complete cDNA sequence encoded by zebra-
fish fabp4, both 3¢-RACE and 5¢-RLM-RACE were
employed as previously described [19,42]. The sense and
antisense primers used for 3¢-RACE (s1, Fig. 1) and 5¢-
RLM-RACE (as1, as2, Fig. 1) were designed on the basis
of a zebrafish EST (GenBank accession number
CN511548). The 3¢-RACE cDNA and 5¢-RLM-RACE
products were cloned, and three clones for each product
were sequenced. The complete cDNA sequence coding for
zebrafish FABP4 was determined by aligning and combi-
ning all 3¢- and 5¢-cDNA end sequences.
Phylogenetic analysis
Phylogenetic analysis of zebrafish fabp4 and fabp3 and
other fish and mammalian FABP genes was performed
using clustalx [43]. The Antarctic fish H6-FABP and H8-
FABP sequences were included in this analysis, and the
putative FABP4 sequences from Ta. rubripes, Cy. carpio,
Oncorhynchus mykiss and Or. latipes were deduced from
the cDNA sequences deposited in GenBank (http://
www.ncbi.nlm.nih.gov/), which are similar to the zebrafish
fabp4 cDNA. A bootstrap neighbor-joining phylogenetic
tree was constructed using the Homo sapiens lipocalin 1
precursor (accession number NP_002288) as an outgroup.
LG assignment of zebrafish fabp4 using the
radiation hybrid mapping panel LN54
Genomic DNA from radiation hybrids of the LN54 panel
[24] was kindly provided by M Ekker, University of

Ottawa, and used to assign zebrafish fabp4 to a specific
LG. The sequences of the primers used to amplify the
genomic DNA from radiation hybrids of the LN54 panel
are shown in Fig. 1 (s1, as2). The PCR conditions have
been previously described [42].
Whole mount in situ hybridization to zebrafish
embryos
Digoxigenin-labeled RNA probes were transcribed from the
linearized fabp3 and fabp4 cDNAs generated by 3¢-RACE.
Whole mount in situ hybridization to zebrafish embryos
and larvae at different developmental stages (gastrula, early
somitogenesis, middle somitogenesis, 24 hpf, 36 hpf, 48 hpf,
and 5 dpf, respectively) was performed as previously
described [25].
RT-PCR
RT-PCR was employed to determine the tissue-specific dis-
tribution of fabp4 and fabp3 transcripts in adult zebrafish
according to Liu et al. [18]. Primers used in RT-PCR for
detection of fabp4 transcripts are shown in Fig. 1 (s1, as1).
Table 2. Comparison of the LN54 radiation hybrid mapping panel scoring data and gene location of the zebrafish fabp3 and fabp4.
Gene Location Scoring vector
a
fabp3 LG 19, 365.69 cR 000000011111100000210010000000000000000010000000000100010000000000000000100000100000000001000
fabp4 LG 19, 287.93 cR 000000000011000000000010100000011102000000000001010101010000001100100000100000100010011000010
a
1, positive hybrid; 0, negative hybrid; 2, missing or ambiguous hybrid data.
R Z. Liu et al. fabp4 gene in zebrafish
FEBS Journal 274 (2007) 1621–1633 ª 2007 The Authors Journal compilation ª 2007 FEBS 1631
The constitutively expressed gene for receptor for the activa-
ted C kinase 1 gene, rack1, was used as positive control for

all RT-PCRs. Conditions for detection of rack1 transcripts
were the same as those used for detection of fabp3 and fabp4
transcripts. The primers used for RT-PCR amplification of
fabp3 and rack1 mRNA are described in Liu et al. [19].
Acknowledgements
This work was supported by research grants from the
Natural Sciences and Engineering Research Council of
Canada (to J. M. Wright), the Canadian Institutes of
Health Research (to E. Denovan-Wright), and the
Institut National de la Sante
´
et de la Recherche Me
´
di-
cale, Centre National de la Recherche Scientifique,
Hoˆ pital Universitaire de Strasbourg, Association pour
la Recherche sur le Cancer, Ligue Nationale Contre le
Cancer, National Institute of Health (to C. Thisse and
B. Thisse), and Izaak Walton Killam Memorial Schol-
arships (to M. K. Sharma and R Z. Liu). We thank
Aline Lux and Vincent Heyer for help with whole
mount in situ hybridization experiments.
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