~ ) Pergamon
PII:
Int. J. DevlNeuroscience, Vol. 15, No. 4/5, pp. 585-594, 1997
Copyright © 1997 ISDN. Published by Elsevier Science Ltd
Printed in Great Britain. All rights reserved
0736-5748/97 $17.00+0.00
S0736-5748(96)00113-X
NOVEL GENES EXPRESSED
IN THE CHICK OTOCYST DURING
DEVELOPMENT:
IDENTIFICATION
USING DIFFERENTIAL
DISPLAY OF RNA
TZY-WEN
L. G O N G , t
ADRIAN
D. HEGEMAN,'~
JOOYOUNG
J. S H I N , I "
KENDRA
H. LINDBERG,*
KATE F. BARALD:~ and MARGARET
I. L O M A X I " : ~ §
tKresge Heating Research Institute, Department of Otolaryngology/Head-Neck Surgery, University of Michigan Medical
School, Ann Arbor, MI 48109-0648, U.S.A.; :~Department of Anatomy and Cell Biology, University of Michigan Medical
School, Ann Arbor, MI 48109-0616, U.S.A.
Abstract--Differential display of mRNA is a technique that enables the researcher to compare genes
expressed in two or more different tissues or in the same tissue or cell under different conditions. The
method is based on polymerase chain reaction amplification and comparison of specific subsets of mRNA.
We have used this method to clone partial complementary DNAs (cDNAs; amplicons) for genes expressed
in the otocyst in order to identify genes that may be involved in development of the inner ear. A full length
cDNA was isolated from an embryonic quail head library with an amplicon (KH121) obtained from the
otocyst. This avian cDNA encoded a novel, 172-amino acid acidic protein and detected a major transcript
of ca 0.8 kb in RNA from chick embryos and several neonatal chick tissues. The full length avian cDNA
had high sequence identity to several human cDNAs (expressed sequence tags) from human fetal tissues,
including cochlea, brain, liver/spleen and lung, and from placenta. The human homologue of the avian
gene encoded a protein that was 183 amino acids long and had 75.6% amino acid sequence identity to the
avian protein. These results identified both the avian and human homologues of an evolutionarily conserved
gene encoding a small acidic protein of unknown function; however, expression of this gene was not
restricted to otocysts. © 1997 ISDN
Key words: differential display; human EST; acidic domain.
Birds provide an ideal model system for two types of studies in the auditory system: development
of the ear, 18 and repair and regeneration of the auditory epithelium after noise trauma. '°'43"44"49'5°
Development of the ear involves a genetic cascade, that is, a programmed series of sequential gene
activation and inactivation. TM Genetic analysis of embryonic lethal mutations in D r o s o p h i l a , 41'53
identified a large class of genes involved in the early events of vertebrate development, for example,
axis specification, segmentation, and pattern formation. Many of these genes are transiently expressed during embryonic development and encode transcription factors containing either homeodomains (HOX genes) or paired domains (PAX genes8). These transcription factors regulate the
expression of many as yet unidentified target genes. The DNA-binding domain of Hox and Pax genes
has been conserved throughout evolution, permitting the isolation of the vertebrate homologues by
using the Drosophila gene as a hybridization probe. One example of a transcription factor involved
in patterning the early events in ear development is Pax2. The Pax2 gene is expressed in the
otocyst6'4° and presumably activates the expression of additional target genes required for correct
ear development. This genetic approach cannot be used, however, to identify genes involved in the
later stages of development of vertebrate embryonic structures such as the ear, since no comparable
structures exist in invertebrates.
The second type of study that can be performed in birds involves repair and regeneration of the
auditory epithelium after acoustic overstimulation. Regeneration of the auditory epithelium after
damage by noise or ototoxic drugs occurs in birds but not mammals. This process has been examined
both histologically and physiologically. It has been clearly demonstrated in birds that hair cells in
the auditory system can regenerate if lost due to trauma. 1o,43.44Such regeneration not only repopulates
the damaged auditory epithelium with immature hair cells, but also restores its f u n c t i o n s . 35'39'49'5°
§To whom all correspondence should be addressed.
Abbreviations: BSA, bovine serum albumin; cDNA, complementary DNA; EDTA, ethylenediaminetetra-acetic acid; EST,
expressed sequence tag; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GTC, guanidinium isothiocyanate; mRNA,
messenger RNA; PCR, polymerase chain reaction; pI, isoelectric point; SSC, standard saline citrate.
585
586
T.-W. L. Gong et al.
Thus, although the process of regeneration has been studied at the morphological and electrophysiological levels, very little is known about the molecular signals that trigger hair cell regeneration, or the physiological processes involved during regeneration. We have recently demonstrated
that several genes encoding proteins involved in signal transduction are expressed at higher levels
in the chicken basilar papilla after acoustic trauma. 22
We are also interested in the molecular events involved in early ear development and in repair
and regeneration of the auditory epithelium after acoustic overstimulation. In several organ systems,
notably skeletal muscle54 and liver, 7 genes that are expressed during development are re-expressed
during regeneration. Our hypothesis is that some genes that are expressed in the developing ear
(otocyst and associated neuronal structures) may be re-expressed during regeneration of the auditory
epithelium and thus provide important markers for molecular analysis of both ear development and
regeneration. A corollary of this hypothesis is that genes activated during regeneration may represent
previously unidentified genes important in development. To test this hypothesis, it will be necessary
to identify genes expressed in the otocyst during ear development. Very little is known about the
process at the molecular level, and what is known is summarized in our recent review. ~8 The
molecular mechanisms involved in mesodermal and neuronal induction of otic placode and otocyst
are not well understood. Neither are the genetic repertoires of placode cells or otocyst epithelia well
characterized. However, in recent years, gene expression studies have revealed that both the placode
and the developing otocyst have unique patterns of gene expression that restrict some genes and
their protein products to specific cells at critical periods in the developmental process. These genes
include: dix3,13 dix4, 3 o t x l , 3°'51, m s x D , 13 GH6, 52 Nkx5.1, 45 Pax2, 6'33"4° SOHo-1,12 9oosecoid, 2° and
secreted growth factors such as FGF3, 38 wnt3, 26 Xwnt4, 37 and B M P 4 , 57 receptor tyrosine kinases,
including ret, 46 and sekl,45 and Delta, which is a membrane-bound ligand in the Notch signaling
system (reviewed in Refs 5,1 7).
As a first step in identifying molecular events involved in later stages of development of the inner
ear, we have applied the method of differential display of messenger RNA (mRNA) 31'32'36to isolate
genes expressed in the otocyst during development, since the otocyst is the embryonic precursor of
the vertebrate ear. ~ In this paper we describe the results of differential display analysis of genes
expressed in the otocyst. One of these complementary DNAs (cDNAs) and its mammalian homologue have been completely sequenced and the expression pattern examined.
1. EXPERIMENTAL PROCEDURES
1.1. Isolation o f R N A
Total RNA was isolated by the acid-phenol method. 9 For differential display experiments, chick
embryonic RNA was isolated from Hamburger and Hamilton (HH) 24 stage 23-24 (3.5d-4d) chick
embryos. Embryos were aseptically removed from the eggs and rinsed in sterile phosphate buffered
saline (PBS)+Ca 2+ (Dulbecco's formulation; Life Technologies). Otocysts were dissected from
embryos and placed immediately into guanidinium isothiocyanate (GTC) solution. From ca 250
otocysts we obtained 30 #g of total RNA. After the otocysts were dissected, everything in the head
remaining rostral to visceral arch III and caudal to the mandibular arch, referred to hereafter as
hindbrain region, was removed and placed in GTC solution for RNA isolation. From ca 40 embryonic
hindbrain regions, we obtained 40 #g of total RNA, which was treated with RNase-free DNase I to
reduce DNA contamination, extracted with acid-phenol, and ethanol precipitated.
For construction of an embryonic quail head cDNA library, heads were dissected from 42
embryos at stage 19 and from 75 embryos at stage 21-22 for RNA isolation. Total RNA from both
stages was combined. Poly(A) + RNA was isolated from 572 #g RNA by the magnetic bead method,
with a Poly A-Tract mRNA isolation kit (Promega, Madison, WI). The yield was 2.8 #g. For
Northern blot analysis, total RNA was isolated from 1-week-old white Leghorn hatchling chickens
or from 2-month-old mice. Tissues were dissected, placed immediately into GTC solution and
disrupted with a Polytron (Brinkman) prior to total RNA isolation. Poly(A) + RNA was isolated
as described above.
Identification of novel genes using RNA differential display
587
1.2. DNA probes and primers
DNA fragments used as hybridization probes were isolated in low melting point agarose and
were labeled by the random primer method 15'16with [~-32P]dCTP ( > 3000 Ci/mmol; DuPont-New
England Nuclear). All oligonucleotide primers were synthesized in the University of Michigan DNA
Synthesis Facility. The eDNA for human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) 14
was obtained from Maria Alexander-Bridges, Massachusetts General Hospital.
1.3. Differential display of mRNA
Differential display reactions were performed as described previously22 with the RNAmap kit
(GenHunter, Inc., Brookline, MA). MMLV reverse transcriptase and an anchored 3' primer
(dT)~2MdG (M = a mixture of dA, dC, and dG) were used to generate first strand cDNA from total
RNA. Aliquots of the resulting single-stranded eDNA population (first strand eDNA) were used
as template DNAs for polymerase chain reaction (PCR) amplification, as described by Liang et al. 3~
with the same anchored 3' primer (dT)~2MdG and five different 10-mer arbitrary primers (AP-1 to
AP-5; RNAmap kit) on RNA from both otocyst and hindbrain region. [~-35S]dATP was included
in the PCR reaction mixture to label the resulting cDNA fragments (amplicons). Bands representing
amplicons that were present in duplicate eDNA samples from otocysts, but not from the hindbrain
region, were isolated, re-amplified by identical PCR reactions containing only unlabeled dNTPs,
and subcloned into plasmid vectors as described previously. 22 Plasmid DNA was prepared using a
modification of the alkaline lysis method. 48 These amplicons were presumed to be derived from
genes that were differentially expressed in otocysts compared to hindbrain region. However, as
indicated in Section 2, that was not always the case.
1.4. Construction and screenin9 of a eDNA library from embryonic quail head mRNA
A cDNA library from embryonic quail head mRNA was generated to provide a source of full
length cDNAs enriched in genes expressed in the otocyst. A unidirectional cDNA library was
constructed in 2UniZAP-XR (Stratagene, La Jolla, CA) from 1.5 #g poly(A) + RNA, according to
the manufacturer's instructions. Briefly, first strand cDNA synthesis was primed with an oligo(dT)
primer containing a XhoI adapter. The second strand eDNA was synthesized by using RNaseH to
nick the RNA strand of the R N A - D N A hybrid, followed by nick translation with Escherichia coli
DNA polymerase holoenzyme to generate the DNA duplex. Double-stranded cDNA was treated
with DNA polymerase to create blunt ends, ligated to EcoR1 adapters, and digested with XhoI. The
resulting cDNAs were passed over a Sephacryl S-400 column to isolate cDNAs longer than 500 bp,
which were ligated to 2UniZAP-XR vector arms at the EcoRI (5') and Xhol (3') sites within the
pBlueScript II plasmid vector. The resulting recombinant DNAs were packaged with Gigapack II
(Stratagene) and used to infect E. coli strain LE392. The primary library contained 1.5 x l 0 6 plaque
forming units (p.f.u.). One round of amplification generated a secondary library with an estimated
titer of 1 x 10J°p.f.u./ml. The fraction of nonrecombinant plaques (3%) was estimated from the
number of blue LacZ + plaques on plates containing X-gal, a chromogenic/~-galactoside. An aliquot
of the library was plated and screened by plaque hybridization 48with a chick/%actin cDNA probe. 27
The library contained 1.5% fl-actin cDNAs, an appropriate percentage of cDNAs for this highly
abundant mRNA. Therefore, we could conclude that this library has a high probability of containing
moderately abundant mRNAs.
The secondary (amplified) embryonic quail head eDNA library was screened for full length
cDNAs by plaque hybridization. 48 A total of 5 x 105 p.f.u, was plated on E. coli and transferred to
nitrocellulose membranes (BA85; Schleicher & Schuell, Keene, NH). Plaque hybridization was
performed at 60°C overnight in 5 × standard saline citrate (SSC=0.15 M NaC1, 0.015 M sodium
citrate, pH 7.0), 5 x Denhardt's solution (1 x = 0.2% each Ficoll, polyvinylpyrrolidone, and bovine
serum albumin; BSA), 0.1% sodium dodecyl sulfate (SDS), and sheared, denatured fish sperm DNA
(100 pg/ml). Hybridization solutions contained 5 x 105c.p.m./ml of denatured cDNA probe. The
most stringent post-hybridization washes were performed in 0.2 × SSC, 0.1% SDS at 60°C. Positive
plaques were purified by successive rounds of hybridization. The plasmids contained within the
2UniZAP-XR DNA were excised in vivo, as described previously25 by co-infecting cells with both
lambda phage and helper M13 phage and plating the infected cells on ampicillin plates to select
cells containing the excised plasmid.
588
T.-W. L. Gong et al.
1.5. DNA sequence analysis
Purified plasmid DNA was sequenced either manually by the dideoxy-chain termination method
(Sequenase 2, Amersham) or on an Applied Biosystems, Inc. model 373A automated DNA sequencer
in the University of Michigan DNA Sequencing Core. DNA sequences were aligned with PC/GENE
sequence analysis programs (Intelligenetics, Campbell, CA). Nucleotide database searches were
performed with the FASTA program of the University of Wisconsin Genetics Computer Group
(GCG) and with the BLAST 4 search program at the National Center for Biotechnology Information
(NCBI) against GenBank, EMBL, dbEST [the database of expressed sequence tag (EST) sequences],
and nonredundant PDB databases. Protein sequences were analyzed for secondary structure predictions either with PC/GENE or G C G programs, including Prosite, Motif, and Blocks searches.
Protein searches were performed with FASTA via the GenQuest server at the Johns Hopkins
University against SwissProt (release 32), Genome Sequence Database (GSDB-LANL), PDB,
dbEST, and Genpept (release of Oct. 1995) databases and by BEAUTY searches.
1.6. Northern blot analysis
Chick hatchling poly(A) + RNA (1 #g) was subjected to electrophoresis through denaturing 1%
agarose-2.2 M formaldehyde gels in a buffer containing 0.02 M 3-(N-morpholino)propane sulfonic
acid (pH 7.0), 8 mM sodium acetate, and 1 mM ethylenediaminetetra-acetic acid (EDTA). RNA
was transferred to Nytran membranes (Schleicher & Schuell, Keene, NH) by capillary transfer in
10 × SSC and immobilized by baking at 80°C for 2hr in vacuo. The membrane was hybridized
overnight at 65°C in a buffer containing 5 × SSPE (1 × SSPE=0.15M sodium chloride, 0.05M
sodium phosphate, 5 mM EDTA, pH 7.4), 5 × Denhardt's, 1% SDS, and denatured fish sperm DNA
(100/~g/ml). DNA probes labeled by the random priming method were added to a final concentration
of 4 × 1 0 6 c.p.m./ml. The post-hybridization washes were performed 65°C in 0.2 × SSC-0.5% SDS.
2. RESULTS
2.1. Differential display analysis of genes expressed in the otocyst
To identify genes involved in the development of the vertebrate inner ear, our strategy was to use
differential display 31'32'36 to compare genes expressed in the otocyst with genes expressed in the
surrounding tissues (hindbrain region) (Fig. 1). We isolated and sequenced three PCR products
(amplicons) that, based on differential display gels, appeared to be present in RNA isolated from
otocysts, but were not present, or were present at very low levels, in RNA from the hindbrain
region. The DNA sequence of each of the three amplicons was compared with all sequences in the
GenBank database. One partial cDNA clone (KH119, 359 bp) had 97.8% sequence identity to a
known sequence in the database, the chick ND5 gene. The ND5 gene is located on mitochondrial
DNA and encodes a subunit of the mitochondrial enzyme NADH-dehydrogenase (ND). The two
remaining partial cDNAs, designated KH120 (268 bp) and KH121 (367bp), respectively, had no
significant sequence identity with any known DNA sequence in the database and were therefore
presumed to be derived from previously unidentified genes.
2.2. K H 121 identified an embryonic avian cD NA encodin9 a previously unidentified acidic protein
To determine the type of protein encoded by a novel gene, it is necessary to isolate and sequence
the full length cDNA, then translate the cDNA sequence to deduce the amino acid sequence.
Therefore, we used both the 268-bp eDNA insert from KH120 and the 367-bp eDNA insert from
KH121 as hybridization probes to screen an embryonic quail head eDNA library constructed in
~UniZAP-XR. No full length eDNA was obtained with the KH 120 partial eDNA probe; therefore,
the nature of this gene is still unknown. We identified two plaques from the embryonic quail head
eDNA library that hybridized with the KH121 eDNA probe, excised the plasmids from the purified
phage in vivo, and determined the complete DNA sequence of one eDNA (KH210, 777 bp). This
cDNA encoded a novel protein: a small, 172 amino acid, acidic polypeptide (Fig. 2) with a predicted
molecular weight of 19 kDa. The deduced protein sequence contained many charged amino acid
residues and was particularly rich in acidic amino acids, yielding a calculated isoelectric point (pI)
of 5.13. There is no obvious hydrophobic, transmembrane domain. The theoretical protein sequence
Identification of novel genes using R N A differential display
0
R
C
0
R
589
C
m
-3SObp
KIt119-.
-aoo~
- KH 121
KH120-
Fig, 1. Identification of partial cDNAs (amplicons) KH 119, KH 120 and KH 121 by differential display of
mRNA. Total RNA from chick otocysts (O) and hindbrain region (R) was treated with RNase-free DNase
I to remove DNA and was subjected to the differential display procedure. First strand cDNA was generated
from RNA with MMLV reverse transcriptase and the (dT)12MdG anchored primer (see Section 1.3). PCR
amplification was performed using (dT)~2MdG and either the AP-4 (5'-GGTACTCCAC-3') or AP-5 (5'GTTGCGATCC-3') amplification primer (GenHunter RNAmap kit). PCR cycling conditions were 94°C
for 30 sec, 40°C for 2 min, 72°C for 30 sec, for a total of 40 cycles, followed by 72°C for 5 rain. PCR
products were analyzed by electrophoresis at 60 W for 3.5 hr on a denaturing 6% acrylamide-7 M urea gel.
The dried gel was exposed to X-Omat film overnight. Left panel, PCR products generated with the
(dT)12MdG and AP-4 primers. Right panel, PCR products generated with the (dT)I2MdG and AP-5
primers. Lanes: O, duplicate PCR reactions performed on RNA from otocysts; R, duplicate PCR reactions
performed on RNA from hindbrain region; C, control reactions containing no reverse transcriptase to test
for DNA contamination. The left control lane contained RNA from the O samples; the right control lane
contained RNA from the R samples. The arrows indicate three unique PCR products (amplicons), designated KH119, KH120, KHI21, that were observed in the duplicate O lanes, but not in the duplicate R
lanes.
d e d u c e d f r o m the e m b r y o n i c quail c D N A h a d no significant sequence i d e n t i t y to a n y k n o w n
p r o t e i n using the B L A S T P search a l g o r i t h m , n o r c o u l d we identify a n y k n o w n p r o t e i n m o t i f in the
e m b r y o n i c quail p r o t e i n sequence. W e c o n c l u d e d , therefore, t h a t the c D N A we isolated a n d
sequenced ( K H 2 1 0 ) was the t r a n s c r i p t o f a novel, p r e v i o u s l y unidentified gene e n c o d i n g a small,
highly acidic p r o t e i n o f u n k n o w n function.
2.3. Identification of a human homologue of the embryonic quail gene
It was i m p o r t a n t to d e t e r m i n e w h e t h e r o r n o t the h u m a n g e n o m e c o n t a i n e d a h o m o l o g u e o f the
novel a v i a n gene we identified b y differential display, since the presence o f a m a m m a l i a n h o m o l o g u e
m i g h t indicate t h a t the p r o t e i n was c o n s e r v e d t h r o u g h o u t v e r t e b r a t e evolution. W e used the B L A S T
a l g o r i t h m to search the G e n B a n k a n d d b E S T nucleic acid d a t a b a s e s for m a m m a l i a n c D N A s with
significant sequence i d e n t i t y to the full length quail c D N A (KH210). This search identified several
u n c h a r a c t e r i z e d h u m a n c D N A s , ESTs, 1.2 with high sequence i d e n t i t y to the e m b r y o n i c quail c D N A .
T.-W. L. Gong et al.
590
HUMAN
- MSAARESHP-HGVKRSASPDDDLGSSNWF_,AADLGNEERKQKFLRLMGAGK
li.ll.i
QUAIL
HUMAN
tl.11.tlll
II
MSSARDSQAQHGLKRAASPD---GSGSWQAADLGNEERKQKFLRLMGAGK
-
-
HUMAN
-
-
HUMAN
-
-
-97
CGLGFSEVEDHDGEGDVAGDDDDDDDDSPDPESPDDSESDSESEKEESAE
-149
-
I
CGLGFSEFQEVEEEA--AGH
II
i i II .Jill i.il .llli
.......
SSDHESSEDSESGSDSEQDESAE
ELQAAEHPDEVEDPKNKKDAKSNYKMMFVKSSGS
LIii11
QUAIL
-99
.llt Iii
KEHTGRLVIGDHRSTSHFRTC-EEDKKMNEELESQYQQSMDSTMSGRNRRH
iltlill
QUAIL
-47
KEHTGRLVIGDHKSTSHFRTGEEDKKINEELESQYQQSMDSKLSGRYRRH
[lililililil.lllliliililii.lllilllliillil
QUAIL
-49
I lllllilliliillillilll
LI.
-138
- 183
I III.Iii111ii111.iii
ELQAAEKHDEAAVPENKKEAKSNYKMMFVKASGS
- 172
Fig. 2. Comparison of the deduced amino acid sequences of the quail head and human proteins. The
deduced amino acid sequence of the embryonic quail protein was obtained by translating a full length
cDNA sequence(KH210, GenBankaccessionNo. U37722).The first ATG in the sequencewas surrounded
by a sequence with nine out of 11 matches to the Kozak consensus sequence for translation initiation,z8
Similarly,the human protein sequencewas deducedfrom a full length cDNA (KH25h GenBankaccession
No. U51678)from a human placental cDNA library. Protein sequenceswere aligned using the CLUSTAL
program of PC/GENE. Symbols: I, identical amino acids;., conservativesubstitutions; -, gap inserted to
optimize the amino acid alignment.
The D N A sequences of these ESTs were identical, indicating that all were derived from the same
human gene. The cDNAs that gave rise to the EST sequences were present in libraries from different
tissues, indicating that the gene was expressed in a wide range of cell types. We obtained and
completely sequenced one full length human c D N A (KH251; I. M.A.G.E. ClonelD 145052,
Research Genetics) identified by the I.M.A.G.E. Consortium 29 at Washington University. The
deduced human protein sequence was slightly longer than the avian protein (183 vs 172 amino acids
long and 20 kDa vs 19 kDa predicted molecular weight) (Fig. 2). The human protein had a high
proportion of charged amino acids and was particularly rich in acidic amino acids such as aspartate
(D = A s p ) and glutamate ( E = Glu), including a central region of the protein containing eight
contiguous Asp residues, resulting in a predicted pI of 4.57. Database searches with the deduced
human protein identified no known protein with significant sequence identity nor any known protein
motif. This lack of amino acid sequence identity supported the conclusion that these proteins and
the genes encoding them have not been described previously.
2.4. The novel quail and human proteins are highly conserved
Alignment of the quail and human protein sequences with the FSTPSCAN program of P C / G E N E
(Fig. 2) demonstrated 75.6% overall amino acid sequence identity between the quail and the human
protein sequences. The sequences are co-linear except for the single amino acid deletion in the
human protein at residue 10, the three amino acids inserted between codons 20-21, and eight
contiguous Asp residues in the central region of the protein, which are present only in the human
protein. Notably, there were two regions of sequence conservation: a region of high sequence
identity (73/78 amino acids) in the N-terminal half of the protein and a well conserved region at the
C-terminus. The amino acid sequence surrounding the eight contiguous Asp residues in the center
of the protein was not as well conserved and represents the region of greatest sequence divergence
between these two proteins. However, there are approximately the same number of negatively
charged amino acid residues (Asp or Glu) flanking this stretch of eight Asp residues. Thus, the most
important feature of this domain may be a high concentration of negatively charged amino acids,
not the exact amino acid sequence.
2.5. The gene encoding the embryonic quail cDNA is expressed in both embryonic and neonatal avian
tissues
Northern blot analysis of total R N A from whole chick embryos (4 days) or from various tissues
from hatchling chicks indicated that the gene encoding the novel acidic protein is widely expressed.
The KH210 c D N A probe detected a major transcript of ca 0.8 kb in total R N A from brain, heart,
Identification of novel genes using RNA differential display
591
eye, liver, kidney, and skeletal muscle of chick hatchlings, as well as in 4-day embryos (Fig. 3). The
same transcript is also present in 2- and 6-day chick embryos (data not shown). In addition, two
minor transcripts of ca 1.8 and 1.5 kb were detected in all tissues examined. These larger transcripts
appeared to be less abundant than the smaller 800 bp transcript. It is not clear whether these larger
transcripts represented an alternatively spliced m R N A or cross-hybridization to a transcript from
a related m e m b e r of a gene family. Preliminary in s i t u hybridization experiments with the quail
c D N A in whole chick embryos indicated that the gene was expressed in m a n y cell types and was
not restricted to the otocyst (Lewis and Barald, unpublished data).
The pattern of expression of the h u m a n homologue of the avian gene can also be deduced to
some extent from the distribution of the human EST sequences in c D N A libraries. ESTs with high
sequence identity to the quail head c D N A (KH210) were derived from c D N A s isolated from several
fetal tissue libraries (cochlea, brain, lung, placenta) and from neonatal or adult tissues (brain, lung,
white blood cells, melanocytes, and prostate gland). Expression in a wide variety of tissues is
consistent with the tissue distribution observed by Northern analysis in the chick. It also suggests
that expression m a y be higher in fetal tissues, since the c D N A was found primarily in fetal and
neonatal c D N A libraries. It should be noted that this novel gene is expressed in h u m a n fetal
cochleas, at least during the stage of fetal development at which the cochleas were isolated for
construction of the c D N A library. 47 The role of this protein during development of the inner ear
remains to be determined.
An additional question that we hope to address with these novel c D N A s is whether their genes
represent candidate genes for hereditary syndromic or nonsyndromic deafness. To answer this
question, we attempted to m a p the gene for the m a m m a l i a n homologue of KH121. Southern
hybridization analysis of a h u m a n chromosome mapping panel with the h u m a n c D N A identified
two genes, one on h u m a n chromosome 11, the other on chromosome 14 (data not shown). These
mapping results suggest that there are either two related expressed genes, or an expressed gene and
a pseudogene, in the h u m a n genome. F o u r nonsyndromic deafness genes have been mapped to
these two chromosomes: D F N A I 155 to 1 lq12.3-q21; DFNB223 to 1 lq13.5; DFNA934 to 14q12-q13;
and D F N B 5 ~9to 14q12. Isolation of the expressed gene will be required to distinguish between these
1 2 3 4 5
a.
--
2.8
kb
--
1.6 kb
--
1 . 0 kb
0 . 4 kb
b.
Fig. 3. Expression of the embryonic quail gene (KH210) in chicken tissues. Northern blot analysis was
performed on poly(A)÷ RNA (1/tg per lane) from 4-day chick embryos (lane 1) or tissues from 1-weekold hatchling chicks, including brain (lane 2), eye (lane 3), heart (lane 4), and skeletal muscle (lane 5). RNA
was subjected to electrophoresis on denaturing 1% agarose-2.2M formaldehyde gels and transferred to
Nytran membranes. (A) Northern blot hybridized with the KH210 cDNA probe. The most stringent posthybridization wash was carried out at 0.2 × SSC4).5% SDS at 65°C. The sizes of the mRNA transcripts,
estimated from the migration of RNA molecular weight standards, are ca 0.8 kb and 2.3 kb. (B) Northern
blot hybridized with the human GAPDH cDNA probe. The same membrane was stripped and reprobed
with a cDNA for GAPDH as a control for RNA loading. Final wash conditions were: 0.2 x SSC~0.5%
SDS at 65°C.
592
T.-W. L. Gong et al.
two genomic regions and to determine whether the expressed gene maps near, and is thus a candidate
for, a deafness gene on one of these two chromosomes.
3. DISCUSSION
Little is known at the molecular level about the processes involved in development of the inner
ear, or in regeneration of the auditory epithelium after noise trauma. To begin to fill this gap in
our knowledge, we have designed experiments to identify genes expressed in the otocyst during
development of the ear. In several organ systems, notably skeletal muscle54 and liver, 7 genes that
are expressed during development are re-expressed during regeneration. Genes that meet the criteria
of being differentially expressed in the otocyst will eventually be used to test our hypothesis that
such genes might be re-expressed in the avian basilar papilla during regeneration following acoustic
trauma; however, none of the genes isolated in this study meet the criteria of being differentially
expressed in the otocyst. Isolation of the ND5 gene encoding a subunit of the mitochondrial NADHdehydrogenase complex may indicate increased levels of mitochondrial biogenesis in the otocyst at
this stage of development. In view of the known effect of mitochondrial DNA mutations on
hearing, 56 this observation deserves further examination.
We were able to use the avian cDNA (KH121) identified by differential display analysis of chick
otocyst RNA to obtain a full length avian (quail) cDNA and subsequently to identify and sequence
the human homologue of this gene. These analyses indicated that the gene we had identified encoded
a novel protein that is highly conserved between mammals (human) and birds. FASTA and BLASTP
searches of the entire SwissProt database with either the entire protein sequence or the highly
conserved N-terminal region of the human and quail protein sequences did not reveal any protein
motif or any region of significant sequence homology to known proteins. Although the central,
acidic region of both the quail and human proteins (Fig. 2) showed some sequence similarity to
acidic activation domains found in several proteins with nucleotide binding properties, the sequence
identity could not be extended beyond this region. We concluded, therefore, that this gene encoded
a highly conserved novel protein of unknown function.
These results also illustrate the importance of the Human Genome Project, and in particular, the
EST project, 1'2'29 for gene discovery studies in other organisms such as birds. Database searches,
particularly with sequences from the 5' end of a cDNA, can demonstrate quickly that the human
genome contains a homologous gene. Furthermore, the pattern of expression of the human gene
can be deduced from the cDNA libraries that contain the EST sequence. The presence of the human
homologue of KH 121 in a human fetal cochlear cDNA library suggested that even though the gene
was not otocyst-specific, it may yet be shown to have an important function in development of the
ear. The challenge for studies of these novel genes will be to define the function of the protein, based
only on information on the primary structure (amino acid sequence). This is an area of biology that
lags far behind our ability to clone and sequence genes. 42
We were unable to identify full length cDNAs for KH120 in the embryonic quail head cDNA
library we constructed. This could be due to low levels of gene expression at the embryonic stages
used for constructing the library. Alternatively, there may have been high level expression in the
otocyst but not in other cell types, leading to dilution of the otocyst mRNA in RNA from total
head, which was used in the construction of the library. Clearly, the availability of an otocystspecific cDNA library, which has recently been constructed (D. Fekete, personal communication)
and made available to us, will enhance these types of studies by optimizing our ability to isolate full
length otocyst-specific cDNAs.
To test the corollary of our hypothesis, that is, that genes expressed during regeneration may
represent genes important for development, we have begun to identify genes expressed after acoustic
trauma and during regeneration of the basilar papilla in chickens. 22 In addition to several cDNAs
encoding proteins involved in signal transduction, one cDNA, KH129, was shown to be present at
higher concentrations after noise,22 but could not be identified because the cDNA sequence did not
have significant sequence identity to known genes in the GenBank database. This cDNA, and others
isolated during regeneration after acoustic trauma, will be tested for expression in the otocyst or in
later embryonic structures derived from the otocyst.
Identification o f novel genes using R N A differential display
593
We achieved only limited success in mapping the human homologue of the gene encoding the
KH121 c D N A (amplicon). We identified genomic regions on human chromosomes 1 ! and 14,
respectively; however, we do not know which chromosome contains the expressed gene. We have
successfully mapped the mouse homologue of KH12921 to a region of mouse chromosome 4 that is
syntenic with human chromosome lp36. Although the hereditary deafness gene DFNA2 has been
mapped to the short arm of human chromosome 1, ~1 these mapping studies on the mouse and
human genes for KKH12921 excluded this gene as a candidate for DFNA2. Such mapping studies
will be an important aspect of analyzing these novel cDNAs and determining whether or not the
gene is a candidate gene for a hereditary deafness.
Acknowledgements---We thank Dr Paul Fuchs, Johns Hopkins University, for the chick inner ear (cochlear) cDNA library;
support from the National Organization for Hearing Research, Narberth, PA to P. F. funded construction of this library.
Supported by grants from the Deafness Research Foundation, the National Organization for Hearing Research, and NIH
DC02492 to M. I.L., NIH Grant NS31641 and NSF Grant IBN19666 to K. F.B., and in part by a grant from the Oberkotter
Foundation to the Kresge Hearing Research Institute. Support for computing facilities provided in part by the General
Clinical Research Center (GCRC) at the University of Michigan, funded by grant MOIRR00042 from the National Center
for Research Resources, NIH, USPHS.
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