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https://www.abbs.info ISSN 0582-9879 |
Identification
of a Novel Human Zinc Finger Protein Gene ZNF313
MA
Yong-Xin, ZHANG Si-Zhong*,
HOU Yi-Ping, HUANG Xin-Li1, WU Qia-Qing, SUN Yan
( The Key Laboratory of Biotherapy, Ministry of
Education; Department of Medical Genetics, West China Hospital, Sichuan
University, Chengdu 610041, China; 1Center for Human
Genetics, Boston University, Boston, MA 02118, USA )
Abstract A
novel human zinc finger protein gene that contains both ring finger and C
domain was first isolated by mRNA differential display between the testes of
fertile adults and azoospermic patients followed by rapid amplification of cDNA
ends (RACE). Total 6 exons of the human gene span a 17 484 bp genomic DNA
sequence that was mapped to chromosome 20q13 by fluorescence in situ
hybridization. The mature processed mRNA encodes a 228-amino acid protein with
a C
domains. Genomic analysis of the human gene identified two polyadenylation
signals in exon 6 resulting in alternative 3′-untranslated regions. Results of
Northern blot and RT-PCR of RNAs extracted from multiple tissues revealed that
the gene has two transcripts of which the shorter transcript was expressed
abundantly in fertile adult testes, but much less in testes of azoospermic
patient, fetus as well as other human tissues. These data suggest that the gene
may play a role in human spermatogenesis and male fertility.
Key words human ZNF313 gene; spermatogenesis; male
infertility; alternative polyadenylation signals
Idiopathic azoospermia or severe
oligozoospermia is observed in about 20% of all infertile men[1]. In these
cases, systematic analysis of molecular deletions of Y chromosome indicates
that three non-overlapping regions, AZFa, AZFb and AZFc, in band Yq11 are
involved in male spematogenesis[2]. A series of genes including DAZ and RBM
genes have been identified in these AZF regions as candidate genes for
azoospermia. They are categorized as a testis-specific type and a
multiple-tissue expression type[3–5]. However, gene-specific mutations causing
the azoospermia phenotype have only been found in the USP9Y gene[3,6]. Some
autosomal genes are also associated with spermatogenesis in mouse and man
including DAZLA (the autosomal DAZ gene homologue), CREM, and HSP70-2 with its
human homologue HSPA2[7–10].
The products of many genes are essential for spermatogenesis,
but a small number affect spermatogenesis exclusively. Identification of these
genes and their role is important in understanding the biology of
spermatogenesis[11]. Using mRNA differential display (mRNA-DD) between the mRNA
transcription pool of the testicular tissues of two healthy fertile adults and
two patients with meiotic spermatogenic disruptions at the spermatocyte phase,
we have identified a series of known and novel transcripts expressed
specifically or in high concentrations in normal testicular tissues. Among
these, a transcription product has proved to be a part of the previously
uncharacterized zinc finger protein gene, ZNF313, which is expressed highly in
testicular tissues of fertile adults.
More than 20 different zinc finger protein encoding
genes located both on sex chromosomes and on autosomes have been proposed to
play a regulatory role in mammalian spermatogenesis including the genes ZNF76,
Sperizin, ZFY and ZFX[12–14], which are usually expressed ubiquitously,
function primarily during meiosis and early spermatid development. In contrast,
zinc finger protein genes encoding both ring finger and C2H2 domains are rare.
Cloning and characterization of ZNF313 may provide an important clue.
1 Materials
and Methods
1.1 Subjects and RNA preparation
Fresh testicular tissues of two normal adults who
died in accidents and two six-month human fetal testicular tissues were
obtained from the West China Hospital, Sichuan University with the consent of
their relatives. Testis bioptic material of azoospermic patients came from the
Department of Urology, Sichuan College of Genital Health. The diagnosis of
azoospermia was made by sperm counting and confirmed by pathohistological
examination of testis. The spermatogenesis was arrested at spermatocyte stage.
Total RNA of testicular tissues were prepared by using RNeasy mini Kit (Qiagen)
and treated with DNase I(RNase-free, Boehringer-Mannheim) to eliminate DNA
contamination. Pellets of the total RNA were resuspended in DEPC-treated water
and stored at -80 ℃ until use.
1.2 mRNA differential display
Isolated RNA from the testicular tissues of two
fertile adults and two azoospermic patients were used for the mRNA differential
display performed according to the protocol of Liang and Pardee[15] using the
RNAimage Kit (Gene Hunter). The amplified fragments were separated on a 6%
polyacrylamide sequencing gel for differential analysis. Bands displayed in two
control lanes (N1,N2 ) but at a reduced or undetectable level in patients
(P1,P2) were cut out from the gel and the DNA fragments were recovered by QIAEX
II Gel Extraction Kit (Qiagen, Victoria, Australia) according to the
manufacturer’s instructions. The eluted fragments were reamplified with the
same set of primers used in the mRNA-DD experiment. The reamplified fragments
were cloned into the pGEM-T Easy Vector (Promega, Madison, WI, USA) as
described by the manufacturer, and sequenced with Thermo Sequenase Cycle
Sequencing Kit (Amersham Pharmacia) using an ALF express Automatic DNA
Sequencer (Pharmacia, Ontaria, Canada).
1.3 Rapid amplification of cDNA ends
(5′-RACE)
5′-RACE experiments were performed using the SMART
RACE cDNA Construction Kit (Clontech). Briefly, 5′-RACE-Ready cDNA was obtained
by reverse transcription using total RNA from testicular tissues of healthy
fertile adults as templates. Universal primer mix (UPM) provided by the kit and
gene specific primers based on the sequence of the fragments obtained from
mRNA-DD were used for the 5′-RACE experiments. The touch-down PCR amplification
profile was 94℃ for 2 min; 94 ℃ for 30 s, 68–0.5 ℃/cycle for 30 s, 72 ℃ for 3
min,10 cycles; 94 ℃ for 30 s, 63 ℃ for 30 s, 72 ℃ for 3 min, 22 cycles;
followed by a final extension at 72 ℃ for 10 min. The PCR products were
recovered using QIAEX II Gel Extraction Kit (Qiagen) and cloned as described
above. Clones with the inserts of the expected size were identified by EcoRI
digestion and sequenced as described above.
1.4 Northern blot
Multiple Tissue Northern (MTN) Blot Membranes
(Clontech cat#7759-1 and 7760-1) with mRNA from 16 tissues were used to
determine the tissue expression pattern of ZNF313 gene. A clone contained
ZNF313 gene insert was digested with EcoRI, separated on a 1.5% agarose gel and
the insert was recovered as a cDNA probe. The probe was labeled with [32P]dCTP
with Random Primed DNA Labeling Kit (Roche, Indianapolis, IN,USA) according to
the manual’s protocol and purified with NucleoTrap PCR Purification Kit
(Clontech). Northern hybridization was then performed as described by the
manual and human β-actin gene as a control.
1.5 Cloning of 2.4 kb transcript of ZNF313
gene
Based on the result of Northern blot, the ZNF313 gene
has a 2.4 kb transcript in addition to the expected 0.75 kb transcript. During
the homology analysis of the sequence of the 0.75 kb transcript, we found a
1852 bp sequence AF131742 without a detectable open reading frame. Because this
sequence overlaps the 0.75 kb fragment by 143 bp, five primers were designed to
confirm the existence of the 2.4 kb transcript in testis. The sequences of the
three pair of primers were(Table 1): P4F3: 5′-TCCGTGCTTGC-TATCTGTCTCATG-3′ and
P4R3: 5′-GCATTTAAGA-CTGAACCAGTGAACTC-3′; P4F4:
5′-GAGTTCACT-GGTTCAGTCTTAAATGC-3′ and P4R4: 5′-CAGATT-AGGCTGACAGCTCTTGGAC-3′;
P4F5: 5′-GTCCAA-GAGCTGTCAGCCTAATCTG-3′ and CDSIII/3′PCR primer delivered by the
SMART RACE cDNA Construction Kit. The PCR products were then cloned into pGEM-T
easy vector and sequenced.
Table 1 The sequences of PCR primers used for ZNF313
amplification
|
Primer |
Sequence |
Position |
|
G4F1 |
5′-ATCCGGTCCCACGTGGCTACTTGTTCC-3′ |
313-339 |
|
P4 |
5′-TGCAGTGTTCCACAAGTCCTTCCT-3′ |
487-464 |
|
P4F3 |
5′-TCCGTGCTTGCTATCTGTCTCATG-3′ |
700-723 |
|
P4R3 |
5′-GCATTTAAGACTGAACCAGTGAACTC-3′ |
1322-1297 |
|
P4R4 |
5′-GAGTTCACTGGTTCAGTCTTAAATGC-3′ |
1297-1322 |
|
P4R4 |
5′-CAGATTAGGCTGACAGCTCTTGGAC-3′ |
1935-1911 |
|
P4F5 |
5′-GTCCAAGAGCTGTCAGCCTAATCTG-3′ |
1911-1935 |
|
G4R2 |
5′-GCGCGAGGTAGCACTTGCAGCCCCATC-3′ |
2031-2005 |
1.6 Chromosomal mapping
ZNF313 gene was mapped by fluorescence in situ
hybridization (FISH) of an 8.1 kb PCR amplified genomic DNA fragment to
metaphase human cell separated by standard protocols. The primers for the PCR
were G4F1 and G4R2: 5′-ATCCGGTCCCAC-GTGGCTACTTGTTCC-3′ and 5′-GCGCGAGGTAG-CACTTGCAGCCCCATC-3′.
The amplified genomic products was labeled with digoxigenin-11-dUTP (Enzo
Diagnosis) by nick-translation (Intergen, Purchase, NY, USA) and hybridized to
the denaturedchro-mosomes at a final concentration of 20 μg/L in 50% formamide,
10% dextran sulfate, 2 × SSC, 0.2 g/L Cot-1 DNA (Gibco BRL, Gathersburg, MD,
USA), 2 g/L salmon sperm DNA, and 2 g/L E.coli tRNA. The hybridized signals
were detected with anti-digoxigen-rhodamine (Boehringer Mannheim).Chromosomal
DNA were counterstained with DAPI II (4,6-diamidino-2-phenylindole) and the
slides were examined through a Zeiss fluorescent microscope with a integrating
CCD camera (Photometrics). These images were captured by a Cyto Vision-Ultra
Workstation (Applied Imaging, Santa Clara) using the Probe Software.
1.7 Genomic structure analysis
Exon-intron boundaries of the gene were identified by
aligning the cDNA sequences with corresponding genomic sequence (GenBank
accession No.AL 031685).
1.8 RT-PCR analysis
Total RNAs from the normal human tissues including
testis, skeletal muscle, lung, liver, brain, spleen, kidney and stomach were
extracted for RT-PCR analysis. A 175 bp fragment of ZNF313 was amplified by PCR
with primers G4F1 and P4. The sequence of primer P4 was:
5′-TGCAGTGTTCCAC-AAGTCCTTCCT-3′. As an internal control, the 401 bp β-actin
gene fragment was amplified with the following primers:
5′-GACCTGACTGACTACCTCATGA-3′ and 5′-TGATCTCCTTCTGCATCCTGTC-3′. The PCR reaction
profile was 94 ℃ for 2 min; 94 ℃ for 30 s, 63 ℃ for 30 s, 72 ℃ for 90 s,
totally 32 cycles, with final extension at 72 ℃ for 10 min. The PCR products
were then separated on 1.5% agarose gel and analyzed for RNA expression.
For comparison study of ZNF313 expression, RT-PCR
with RNAs extracted from the testicular tissues of two normal fertile adults,
two fetus and two azoospermic patients was carried out under the same condition
as described above.
2 Results
2.1
Transcription products displayed differen-tially in fertile and infertile men
include known and novel genes
Thirty-six fragments from the mRNA differential
display cDNA pool were obtained by polyacrylamide gel electrophoresis. 12 of
these between 200 bp and 600 bp in length were reamplified, cloned and
sequenced. The ESTs used for 5′-RACE reactions were renamed as EST DD1 to DD6,
and the other 6 ESTs were renamed as EST DD7 to DD12. BLAST analysis of
nucleotide sequences in the GenBank database revealed that these 12 ESTs could
be grouped into four categories: novel ESTs, ESTs homologous to those in the
testis library, known gene sequences and ubiquitously expressed ESTs. For
example, EST DD-7 and DD-8 is identical to the downstream region of a human
TCP1 gene and HsMCAK gene, respectively, and DD-9 is part of TnP1 gene. Finding
of these genes which are involved in or essential for spermatogenesis suggests
that our experimental approach for the isolation of novel human spermatogenesis
genes by mRNA-DD is successful.
For cloning of novel full length
cDNAs with a potential role in human spermatogenesis, 5 ESTs (DD-1, DD-2, DD-3,
DD-4 and DD-6) that have homologous ESTs from testis but not in full length and
1 novel ESTs (DD-5) were used as starting points to isolate the related full
length cDNA sequences by RACE technique. The DD-1-DD-6 differential display
products are displayed (Fig.1).
