Identification of target genes for spermatogenic cell-specific KRAB transcription factor ZFP819 in a male germ cell line
© The Author(s) 2017
Received: 25 August 2016
Accepted: 21 December 2016
Published: 3 January 2017
Zfp819, a member of the Krüppel-associated box (KRAB) family, encodes a spermatogenic cell-specific transcription factor. Zfp819-overexpression induces apoptosis and inhibits proliferation in somatic cell lines.
In the present study, we examined the cellular effects of Zfp819 in a male germ cell line (GC-2 cells). Overexpression of Zfp819 demonstrated an increase in the number of apoptotic cells, leading to inhibition of proliferation in GC-2 cells. We further investigated genes regulated by ZFP819 using microarray analysis and chromatin-immunoprecipitation combined with microarray analysis (ChIP-chip) in GC-2 cells. We identified 118 downregulated genes in Zfp819-overexpressing GC-2 cells using microarray analysis. ChIP-chip assay revealed that 1011 promoter sites (corresponding to 262 genes) were specifically enriched in GC-2 cells transfected with Zfp819. Two genes (trinucleotide repeat containing 6b and annexin A11) were commonly found when we compared the data between microarray and ChIP-chip analyses. Consistent with these results, Zfp819 overexpression significantly reduced the transcript levels of the two genes by binding to their promoter regions. Tissue distribution analysis indicated that both genes were predominantly expressed in testis. It has been reported that these two genes function in apoptosis.
Collectively, our study provides inclusive information on germ cell-specific gene regulation by ZFP819, which is involved in apoptosis, to maintain the integrity of spermatogenesis.
Spermatogenesis is a unique and highly elaborated process that requires a highly organized and tightly regulated network of genes, many of which are spermatogenic-cell-specific. Previous reports investigated gene expression profiles in mouse spermatocytes and round spermatids and found that the proportions of testis-specific genes in spermatocytes and round spermatids were 11% (230 genes) and 22% (467 genes), respectively [1, 2]. Despite the presence of many unique genes expressed in spermatogenic cells, the characteristics of their associated transcriptional network(s) are largely unknown.
The Krüppel-associated box and C2H2-type zinc finger motifs (KRAB-ZF) family, one of the largest transcription factor groups in vertebrates has a transcriptional repressive activity by binding to DNA in a sequence-specific manner . The members of KRAB-ZF family are generally expressed in various tissues and are involved in diverse processes including apoptosis, cell proliferation, and tumorigenesis . It has been reported that a number of the KRAB-ZF genes on a certain chromosome are abundantly expressed in testis and fetal brain and may have important functions in these tissues . Previously, we comprehensively identified and characterized the KRAB-ZF genes in the reproductive tissues (testis or ovary) . Three KRAB-ZF genes were specifically or predominantly expressed in the gonads. Of them, Zfp819, which was specific to spermatogenic cells, was analyzed in detail. We found that the overexpression of Zfp819 affected cell proliferation and induced apoptosis in somatic cell lines. The overexpression of Zfp819 changed the expression of B cell lymphoma protein-2 (BCL-2) and poly(ADP-ribose) polymerase (PARP) .
To date, the target genes of only a few KRAB-ZF members have been discovered [6–9]. In the present study, we investigated the transcriptional network of Zfp819 through genome-wide approaches in a germ cell line. We found that the overexpression of Zfp819 affected cell proliferation and induced apoptosis in GC-2 cells. Microarray analysis revealed 1737 differentially expressed genes in Zfp819-overexpressing cells compared with mock-transfected cells, and of them, 118 genes were down-regulated by ZFP819. In addition, chromatin immunoprecipitation (ChIP)-chip analysis revealed 1011 promoter sites enriched by ZFP819. Interestingly, two genes encoding trinucleotide repeat containing 6b (TNRC6B) and annexin A11 (ANXA11) were found to overlap between the microarray and ChIP results. These genes were verified by ChIP-PCR and promoter assays. They also demonstrated a predominant expression in testis and were previously reported to have important functions in apoptosis. Collectively, our results revealed for the first time to the best of our knowledge using GC-2 cells a germ cell-specific gene regulation by ZFP819 that is involved in apoptosis.
RT-PCR and qRT-PCR
Mouse adult tissues and GC-2 cells transfected with pcDNA3.1/myc or pcDNA3.1/myc-Zfp819 were assessed. All animal investigations were conducted according to the guidelines of the Animal Care and Use of the Gwangju Institute of Science and Technology. Total RNA samples were extracted using TRIzol™ Reagent (MRC) according to manufacturer’s protocol, and reverse transcribed with Omniscript reverse transcriptase (Qiagen). Complementary DNA samples prepared from mouse adult tissues were amplified with primers specific for each of the reproductive KRAB-ZF genes (Additional file 1: Table S1). Quantitative real-time PCR (qRT-PCR) was performed using SYBR Green Taq polymerase mix (TaKaRa Bio, Inc.). All of the reactions contained 10 µl of SYBR Green Master Mix and 50–100 ng of template cDNA. Glyceraldehyde 3-phosphate dehydrogenase (Gapdh) was used as an internal control.
Dual-luciferase reporter assay
GC-2 cells (4.0 × 105 cells/well) were seeded onto 24-well plates and incubated at 37 °C for 24 h. For repressive activity of Zfp819-KRAB, when the cells reached approximately 80–90% confluence, they were co-transfected with 250 ng of pcDNA3.1/myc-Zfp819-KRAB, 250 ng of a firefly luciferase-encoding vector (pGL3-promoter, Invitrogen), and 5 ng of pRL-TK (Renilla used as an internal control for normalization of transfection efficiency in the absence and presence of Zfp819 overexpression). After 24 h, the cells were lysed with passive lysis buffer (Promega), dual luciferase assays were performed with a Luciferase Reporter Assay kit (Promega), and the luciferase activity was measured using a Centro LB 960 DLReady microplate illuminometer (Berthold Technologies). GAL4-DBD was used as a basic control, and KOX1-DBD was used as a positive control. For promoter activity of Zfp819, Tnrc6b or Anxa11 promoter regions were inserted into pGL-promoter (Invitrogen). When the cells reached approximately 80–90% confluence, they were co-transfected with 250 ng of pcDNA3.1/myc-Zfp819 or pcDNA3.1/myc, 250 ng of a firefly luciferase-encoding vector (pGL3-promoter, Invitrogen), and 5 ng of pRL-TK (Renilla). Each experiment was repeated three independent times in triplicate.
Cell proliferation assay using MTT
Cell proliferation was measured using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. In brief, GC-2 cells were grown in 6-well plates for 1 day at a density of 3.0 × 105cells/well. After an additional 24 h, cells were transfected with pcDNA3.1/myc or pcDNA3.1/myc-Zfp819 plasmids using Lipofectamine 2000 (Invitrogen; 10 µl reagent per 5 µg DNA). After 48 h, the cells were exposed to 1 ml/well MTT solution (1.5 mg/ml) at 37 °C for 1.5 h in medium. The medium was removed, 0.04 N isopropanol in HCl was added to solubilize the formazan crystals, and the plates were gently agitated at room temperature for 10 min in the darkness. Cell proliferation was measured at 570 and 650 nm using an ELISA reader. Each experiment was performed three independent times in triplicate.
Flow cytometry and TUNEL assay
Cells were transfected with pcDNA3.1/myc (empty vector) or pcDNA3.1/myc-Zfp819 plasmids and incubated at 37 °C for 24 h. For the analysis of cell cycle distribution, GC-2 cells were seeded (3.0 × 105 cells/well) in 6-well plates for 24 h, harvested with trypsin–EDTA (TE, Gibco), and fixed with 70% ethanol for 1.5 h on ice in the dark. The cells were then collected by centrifugation, washed once with ice-cold PBS, and incubated with 500 µl of propidium iodide (PI) solution (50 µg/ml) for 30 min at 37 °C in the dark. Finally, the cells were resuspended in PBS then analyzed by flow cytometry. For the detection of apoptotic cells, the TUNEL assay was performed with an Apop Tag® Plus Peroxidase In Situ Apoptosis Detection kit (Chemicon). Cells (3.0 × 105 cells/well) were plated in 6-well plates, transfected as indicated for 48 h, and then fixed with 4% formaldehyde at room temperature for 10 min. The cells were then washed with PBS, mixed with 55 µl/well of TdT enzyme, and incubated at 37 °C in a humidified chamber for 1 h. The reaction was stopped with stop/wash buffer, DNA was counterstained with Hoechst 33,342 (Sigma), and the cells were visualized by confocal microscopy. Each experiment was performed three times in triplicate.
The transfected cell lysates were prepared with 1% sodium dodecyl sulfate (SDS). Equal amounts of protein (30 µg) were separated by 8% SDS–polyacrylamide gel electrophoresis and transferred onto a polyvinylidene difluoride (PVDF) membranes (Millipore corporation). Membranes were hybridized for 17 h at 4 °C or 1 h at room temperature with primary antibodies including: anti-Myc (1:1000, Cell signaling), anti-TNRC6B (1:1000, Millipore), anti-ɑ-tubulin (1:1000, Millipore), and anti-GAPDH (1:1000, Bio-RAD) antibodies. Bound IgG was detected following 1 h incubation with horseradish peroxidase-conjugated secondary antibodies (Jackson ImmunoResearch Laboratories) and the Luminol and Stable peroxidase solutions (ThermoFisher scientific).
GC-2 cells were transfected with pcDNA3.1/myc (empty vector) or pcDNA3.1/myc-Zfp819 using Lipofectamine 2000 reagent (Invitrogen). Total RNA was extracted using RNeasy columns (Qiagen) according to the manufacturer’s instructions. For control and test RNAs, the synthesis of target cRNA probes and hybridization were performed using Agilent’s LowInput QuickAmp Labeling Kit (Agilent Technology, USA) as per the manufacturer’s instructions. The hybridized microarrays were washed as per the manufacturer’s washing protocol (Agilent Technology). This analysis was repeated three times.
ChIP assay was performed using the Chromatin Immunoprecipitation Assay Kit (Millipore Upstate) as previously described . In brief, GC-2 cells transfected with pcDNA3.1/myc (mock without protein expression) or pcDNA3.1/myc-Zfp819 plasmids were cross-linked by adding 1% formaldehyde (37%) for 10 min in the humidified chamber (at 37 °C with 5% CO2), followed by a quenching step with 125 mM glycine. Cells were rinsed twice with 1× PBS and resuspended in 1% SDS lysis buffer containing protease inhibitor cocktail (PIC). Sonicated chromatin was immunoprecipitated with α-myc antibody (Cell Signaling). Antibody-bound chromatin complexes were then captured with protein A agarose beads blocked with salmon sperm DNA, and eluted in SDS buffer. Formaldehyde crosslinking was reversed, followed by DNA purification by phenol–chloroform extraction. The immunoprecipitated and input DNA were amplified using a whole genome amplification kit (GenomePlex® Complete Whole Genome Amplification Kit) as recommended by the manufacturer. Each 2.5–5 µg of cyanine 3-labeled and cyanine 5-labeled DNA target were mixed and then resuspended with 2× hybridization buffer, Cot-1 DNA, and Agilent 10× blocking agent. Before hybridization to the array, the 260 µl hybridization mixtures were denatured at 95 °C or 3 min and incubated at 37 °C for 30 min. The hybridization mixtures were centrifuged at 17,900×g for 1 min and directly pipetted onto the Mouse Promoter 2 × 400 K microarray. This array covers 415,814 probes (~19,000 genes as represented by RefSeq, probes are spaced 93 bp apart). The arrays hybridized at 65 °C for 40 h in an Agilent Hybridization oven (Agilent Technology). The hybridized microarrays were washed as per the manufacturer’s washing protocol (Agilent Technology).
Gene silencing using siRNAs
siRNA-mediated gene silencing of Tnrc6b and Anxa11 was performed using siRNA duplexes (Bioneer). The target sequences of siRNAs were ACU UCU GGA GAC UAU CGA A(dTdT) (Anxa11) and CUG GUU ACC UGC CAA AUC U(dTdT) (Tnrc6b). In brief, GC-2 cells were grown in 6-well plates for 1 day at a density of 6.0 × 105 cells/well. After an additional 24 h, cells were transfected with of control siRNA, Tnrc6b siRNA, or Anxa11 siRNA (25 nM) using Lipofectamine 2000 (Invitrogen; 6.25 µl reagent). After 48 h, total RNA was extracted using TRIzol™ Reagent (MRC) according to manufacturer’s protocol, and reverse transcribed with Omniscript reverse transcriptase (Qiagen). The knockdown efficiency was confirmed by RT-PCR with primers specific for Tnrc6b and Anxa11.
Each experiment was performed three times. Each time, measurements were conducted on three samples with the same design and averaged. Data are represented as mean ± standard error of mean (mean ± SEM.). Statistical analysis was calculated by Student’s t test.
Repressive activity of Zfp819 in germ cell line (GC-2 cell)
Inhibition of proliferation and induction of apoptosis in Zfp819-overexpressing cells
We used TUNEL assays to determine whether the alterations in the cell populations and cell cycle distributions in Zfp819-overexpressing cells were related to apoptosis, and observed more TUNEL-positive (i.e., apoptotic) signals in Zfp819-overexpressing cells than in controls (Fig. 2e). Our quantitative analysis demonstrated that Zfp819 overexpression increased the number of apoptotic cells by approximately threefold compared with controls (Fig. 2f).
Microarray and ChIP-chip analyses of Zfp819-overexpressing GC-2 cells
Down-regulated genes involved in apoptosis by microarray (anti-apoptotic function)
Carnitine palmitoyltransferase 1c
Lipid metabolic process
Negative regulation of apoptotic process
Sebaceous gland development
Negative regulation of apoptotic process
Splicing factor 3b, subunit 1
Blastocyst formation, RNA splicing
ELKS/RAB6-interacting/CAST family member 1
Retrograde transport, endosome to Golgi
F-box and WD-40 domain protein 11
Negative regulation of NF-kappaB import into nucleus
Intersectin 1 (SH3 domain protein 1A)
Negative regulation of neuron apoptotic process
Ring finger protein, LIM domain interacting
Regulation of dosage compensation by inactivation of X chromosome
Dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1b
Ring finger protein 121
ER-associated ubiquitin-dependent protein catabolic process
To further investigate genomic targets regulated by Zfp819, we applied ChIP-chip assay using mock or Zfp819-overexpressing GC-2 cells. For the purpose of this assay, GC-2 cells were transfected with the Zfp819 plasmid, and the ChIP assay was performed at 24 h post-transfection. Western blotting confirmed the efficient immunoprecipitation of ZFP819 in Zfp819-transfected cells compared with mock-transfected cells (Fig. 3c). Subsequently, the immunoprecipitated DNAs were hybridized on Agilent’s mouse promoter array (400 K), which covers over 400,000 promoter sites, and then analyzed through Agilent’s DNA microarray scanner. As the first step for selecting significant data, we collected probes satisfying two criteria (p < 0.05 and E-score > 3) using the Peak Shape Detection V2.1 Model (Fig. 3b). In this process, genes demonstrating low signals on a chip and random selection were removed. As a result, 3565 probes were selected as probes bound by ZFP819 (Fig. 3b). Of these 3565 probes, we found out that the majority of them (53.2%, 1897 probes) were located in promoter regions, whereas 46.8% of the bound probes were located within genes (Fig. 3d). Of the 1897 probes located in promoter regions, we considered those with log ratio (>1) to search for high potential targets of ZFP819. Finally, we identified a total of 1011 probes corresponding to 262 genes as targets bound by ZFP819 in GC-2 cells (p < 0.05, E-score > 3, log ratio > 1) (Additional file 1: Table S3, Additional file 2: Figure S3). Binding of ZFP819 to the targets was confirmed in several randomly selected genes by ChIP-PCR (Additional file 2: Figure S4). We further analyzed characteristics of these probes in several ways.
Identification of genes directly regulated by ZFP819
Direct targets of ZFP819 by ChIP-chip and microarray
ChIP-chip (log ratio)
Microarray (expression level)
Trinucleotide repeat containing 6b
Gene silencing by RNA, Regulation of translation
Response to calcium ion
Expression of Tnrc6b and Anxa11 in Zfp819-overexpressing GC2-cells
Here, we investigated the transcriptional network influenced by Zfp819 in a germ cell line. We previously identified the downstream genes of Zfp819 in NIH 3T3 cells by overexpression-microarray analysis . Because of some advantages, such as low cytotoxicity, minimal optimization, and high transfection efficiency, we used the NIH 3T3 cell line in the previous study. However, we needed to assess the transcriptional mechanism of Zfp819 in germ cells due to the specific expression of Zfp819. GC-2 cells, originally from mouse spermatocytes, have features in common with morphological differentiation at the early spermatid stages . However, these features were not observed in another germ cell line, GC-1 cells derived from spermatogonia. Thus, the GC-2 cell line is an essential tool to study cellular effects that occur in spermatocytes. The functions of several transcription factors have been studied in GC-2 cells [12, 13]. On the basis of these facts, we investigated the genomic targets of Zfp819 using GC-2 cells, thereby looking into the actual downstream genes of Zfp819 in a system as close to germ cells as possible. It should be noted that most of the differentially expressed genes were found to be upregulated in the microarray analysis. We do not know how the overexpression of Zfp819 leads to the larger number of upregulated genes, considering that ZFP819 is a transcriptional repressor. Perhaps, some of these genes were indirectly upregulated by the downregulated genes. Alternatively, the upregulated genes could be the result of compensatory response of cells undergoing changes by the overexpression of Zfp819. We focused on the downregulated genes to identify and investigate genes directly regulated by ZFP819.
A comparison between the data of microarrays revealed that there were hardly overlapped genes in two cell lines (NIH 3T3 and GC-2) , even though Zfp819 overexpression showed the same phenotype (induction of apoptosis). This suggests that Zfp819 regulates different upstream genes in different pathways, eventually involved in apoptosis. Intriguingly, however, the different genes of TNRC6 family showed down-regulation in Zfp819-overexpressing cells, which are Tnrc6b and Tnrc6a in GC-2 and NIH 3T3 cells, respectively. The members of TNRC6 family (also GW182, glycine-tryptophan repeats) are well known as the major components in miRNAs-mediated gene silencing . For the functions, they interact with Argonautes (AGOs) which is the central effectors [14, 15]. The TNRC6 members have the functional redundancy , and thus, been speculated about playing a role in a tissue-or cell-specific manner . We suppose that Zfp819 regulates gene expression of members in TNRC6 family, each different members in different cell lines.
Of 118 down-regulated genes by microarray, we found 10 genes showing an anti-apoptotic function in the previous studies (Table 1). Two (Ctsh, and Mtdh) of them regulate expression of proteins belonging to Bcl-2 family [18, 19]. Cbx7 as a component of polycom repressive complex 1 has functions in cancer cell development and extension of cellular life span . A recent paper demonstrated that apoptotic cells increased via expression of tumor necrosis factor-related-apoptosis-inducing ligand (TRAIL) in Cbx7-silenced condition . Fbxw11 and Itsn1 are involved in apoptosis by modulating expression of downstream genes in mitogen-activated protein kinases (MAPK) family [21, 22]. On the other hand, seven genes selected by microarray in NIH 3T3 cells play a role in apoptosis by affecting the expression of downstream effectors of p53 or depending on p53 [5, 23–25]. Thus, the selected genes in both cell lines control the expression of multiple steps in apoptosis, ultimately activating Caspase-3 or PARP, although they individually regulate several proteins in different pathways.
Furthermore, we defined the genomic target sites of Zfp819 by ChIP-chip technique in GC-2 cells. Of the enriched 1011 promoter sites (262 genes) by Zfp819, surprisingly, only two genes (Tnrc6b and Anxa11) were selected by two different genome-wide approaches (microarray and ChIP-chip). This suggests that most of the down-regulated genes in the microarray analysis are indirectly regulated by Zfp819. Alternatively, it is possible that transfection efficiency of Zfp819 influences on expression of downstream genes, in spite of the same condition in two different experiments. In addition, ChIP-chip technique sometimes generates a high ratio of signal-to-noise, thereby selecting a large number of peaks . These results were also obtained in other similar studies [27–29].
So far, apoptosis has been considered an important process at every stages during spermatogenesis . As undergoing mitosis, meiosis, and post-meiosis sequentially, cells need to keep a balance between proliferation and apoptosis for producing normal sperm. There is high possibility of occurring many of errors for mitosis and meiosis, and cell death by apoptosis is necessary to remove those cells with generic defects. In terminal differentiation, apoptosis generally occurs to remove cytoplasmic components, producing highly specialized cells.
Both Tnrc6b and Anxa11 are heavily involved in apoptosis. As mentioned the above, TNRC6B is an interacting partner of Ago2 and forms a complex with miRNA induced-silencing complex (miRISC) [15, 31]. This complex participates in two different ways for silencing of mRNA: mRNA decay and translational repression . In these processes, miRNAs have an important role by recognizing their mRNA targets. MiRNAs are essential to control the temporal and spatial gene expression at every stages during spermatogenesis as well . For example, miR-34c, expressed from pachytene spermatocyte, promotes the apoptosis of germ cells via balancing expressions between the Bcl-2 and BCL2 associated X protein (Bax) genes . Additionally, miR-34c activates the expression of transcription factor 1 (Atf1), and then decreases Bax expression in knockdown of Atf1, consequently, inducing germ cell apoptosis .
Anxa11 encodes a calcium-dependent phospholipid-binding protein. During cell cycle, ANXA11 shows a dynamic pattern from nucleus to nuclear envelop with co-localization of S100A6, a small calcium binding protein [35, 36]. In Anxa11-silenced condition, the siRNA-transfected cells appeared the incompletion of cytokinesis generating many of binucleate cells, thereby leading to apoptosis by increasing the expression of PARP . So far, the mechanism that Anxa11 is involved in apoptosis exactly has not been discovered. A recent study indicated that the knockdown of Anxa11 decreased proliferation and survival of hepatocarcinoma cells by increasing expression of thymoma viral proto-oncogene 2 (AKT2) and phospholylated forkhead box O1 (FOXO1) . Thus, this suggests that Anxa11 is involved in cell survival or apoptosis in different cell types.
In summary, we herein investigate cellular effects and target genes influenced by Zfp819 in GC-2 cells. The overexpression of Zfp819 induced apoptosis and inhibited cellular proliferation. We identified two genes regulated by Zfp819 by microarray and ChIP-chip analysis. Interestingly, both of two genes showed the predominant expression in testis. Previously, these genes were found to play an important role in apoptosis. Taken together, our study provides new information about germ cell-specific gene regulation by Zfp819 which potentially functions in maintaining the integrity of spermatogenesis through apoptosis.
SJ and CC conceived and designed the experiments; SJ performed the experiments; SJ and CC analyzed the data; HC, JTK, JK, JJ, JK, and SH contributed reagents/materials/analysis tools; SJ and CC wrote the paper. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Availability of data and supporting materials section
The datasets supporting the conclusions of this article are included within the article.
This work was supported by Mid-career Researcher Program through NRF grant funded by the MEST (NRF-2015R1A2A2A01005300), the Bio & Medical Technology Development Program of the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning (NRF 2013M3A9A7046297) and GIST Systems Biology Infrastructure Establishment grant.
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- Hong S, Choi I, Woo JM, Oh J, Kim T, Choi E, Kim TW, Jung YK, Kim DH, Sun CH, et al. Identification and integrative analysis of 28 novel genes specifically expressed and developmentally regulated in murine spermatogenic cells. J Biol Chem. 2005;280(9):7685–93.View ArticlePubMedGoogle Scholar
- Choi E, Lee J, Oh J, Park I, Han C, Yi C, Kim do H, Cho BN, Eddy EM, Cho C. Integrative characterization of germ cell-specific genes from mouse spermatocyte UniGene library. BMC Genom. 2007;8:256.View ArticleGoogle Scholar
- Urrutia R. KRAB-containing zinc-finger repressor proteins. Genome Biol. 2003;4(10):231.View ArticlePubMedPubMed CentralGoogle Scholar
- Lorenz PDS, Wilhelm T, Koczan D, Autran S, Gad S, Wen G, Ding G, Li Y, Rousseau-Merck MF, Thiesen HJ. The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues. BMC Genom. 2010;11:206.View ArticleGoogle Scholar
- Jin S, Choi H, Kwon JT, Kim J, Jeong J, Kim J, Ham S, Cho BN, Yoo YJ, Cho C. Identification and characterization of reproductive KRAB-ZF genes in mice. Gene. 2015;565(1):45–55.View ArticlePubMedGoogle Scholar
- Hallen L, Klein H, Stoschek C, Wehrmeyer S, Nonhoff U, Ralser M, Wilde J, Rohr C, Schweiger MR, Zatloukal K, et al. The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2. Hum Mol Genet. 2011;20(1):104–14.View ArticlePubMedGoogle Scholar
- He Z, Cai J, Lim JW, Kroll K, Ma L. A novel KRAB domain-containing zinc finger transcription factor ZNF431 directly represses Patched1 transcription. J Biol Chem. 2011;286(9):7279–89.View ArticlePubMedGoogle Scholar
- Shin JH, Ko HS, Kang H, Lee Y, Lee YI, Pletinkova O, Troconso JC, Dawson VL, Dawson TM. PARIS (ZNF746) repression of PGC-1 alpha contributes to neurodegeneration in Parkinson’s disease. Cell. 2011;144(5):689–702.View ArticlePubMedPubMed CentralGoogle Scholar
- Wang S, Cheng Y, Du W, Lu L, Zhou L, Wang H, Kang W, Li X, Tao Q, Sung JJ, et al. Zinc-finger protein 545 is a novel tumour suppressor that acts by inhibiting ribosomal RNA transcription in gastric cancer. Gut. 2013;62(6):833–41.View ArticlePubMedGoogle Scholar
- Fujita N, Wade PA. Use of bifunctional cross-linking reagents in mapping genomic distribution of chromatin remodeling complexes. Methods. 2004;33(1):81–5.View ArticlePubMedGoogle Scholar
- Hofmann MC, Hess RA, Goldberg E, Millan JL. Immortalized germ cells undergo meiosis in vitro. Proc Natl Acad Sci USA. 1994;91(12):5533–7.View ArticlePubMedPubMed CentralGoogle Scholar
- Chen H, Fok KL, Jiang X, Jiang J, Chen Z, Gui Y, Chan HC, Cai Z. CD147 regulates apoptosis in mouse spermatocytes but not spermatogonia. Hum Reprod. 2012;27(6):1568–76.View ArticlePubMedGoogle Scholar
- Zhou R, Wang R, Qin Y, Ji J, Xu M, Wu W, Chen M, Wu D, Song L, Shen H, et al. Mitochondria-related miR-151a-5p reduces cellular ATP production by targeting CYTB in asthenozoospermia. Sci Rep. 2015;5:17743.View ArticlePubMedPubMed CentralGoogle Scholar
- Eulalio A, Tritschler F, Izaurralde E. The GW182 protein family in animal cells: new insights into domains required for miRNA-mediated gene silencing. RNA. 2009;15(8):1433–42.View ArticlePubMedPubMed CentralGoogle Scholar
- Pfaff J, Meister G. Argonaute and GW182 proteins: an effective alliance in gene silencing. Biochem Soc Trans. 2013;41(4):855–60.View ArticlePubMedGoogle Scholar
- Lazzaretti D, Tournier I, Izaurralde E. The C-terminal domains of human TNRC6A, TNRC6B, and TNRC6C silence bound transcripts independently of Argonaute proteins. RNA. 2009;15(6):1059–66.View ArticlePubMedPubMed CentralGoogle Scholar
- Baillat D, Shiekhattar R. Functional dissection of the human TNRC6 (GW182-related) family of proteins. Mol Cell Biol. 2009;29(15):4144–55.View ArticlePubMedPubMed CentralGoogle Scholar
- Floyel T, Brorsson C, Nielsen LB, Miani M, Bang-Berthelsen CH, Friedrichsen M, Overgaard AJ, Berchtold LA, Wiberg A, Poulsen P, et al. CTSH regulates beta-cell function and disease progression in newly diagnosed type 1 diabetes patients. Proc Natl Acad Sci USA. 2014;111(28):10305–10.View ArticlePubMedPubMed CentralGoogle Scholar
- Zou Y, Qin X, Xiong H, Zhu F, Chen T, Wu H. Apoptosis of human non-small-cell lung cancer A549 cells triggered by evodiamine through MTDH-dependent signaling pathway. Tumour Biol. 2015;36(7):5187–93.View ArticlePubMedGoogle Scholar
- Shinjo K, Yamashita Y, Yamamoto E, Akatsuka S, Uno N, Kamiya A, Niimi K, Sakaguchi Y, Nagasaka T, Takahashi T, et al. Expression of chromobox homolog 7 (CBX7) is associated with poor prognosis in ovarian clear cell adenocarcinoma via TRAIL-induced apoptotic pathway regulation. Int J Cancer. 2014;135(2):308–18.View ArticlePubMedGoogle Scholar
- Soldatenkov VA, Dritschilo A, Ronai Z, Fuchs SY. Inhibition of homologue of Slimb (HOS) function sensitizes human melanoma cells for apoptosis. Cancer Res. 1999;59(20):5085–8.PubMedGoogle Scholar
- Predescu SA, Predescu DN, Knezevic I, Klein IK, Malik AB. Intersectin-1 s regulates the mitochondrial apoptotic pathway in endothelial cells. J Biol Chem. 2007;282(23):17166–78.View ArticlePubMedGoogle Scholar
- Devlin HL, Mack PC, Burich RA, Gumerlock PH, Kung HJ, Mudryj M. deVere White RW: Impairment of the DNA repair and growth arrest pathways by p53R2 silencing enhances DNA damage-induced apoptosis in a p53-dependent manner in prostate cancer cells. Mol Cancer Res. 2008;6(5):808–18.View ArticlePubMedGoogle Scholar
- Driskell I, Oda H, Blanco S, Nascimento E, Humphreys P, Frye M. The histone methyltransferase Setd8 acts in concert with c-Myc and is required to maintain skin. EMBO J. 2012;31(3):616–29.View ArticlePubMedGoogle Scholar
- Peschiaroli A, Scialpi F, Bernassola F, Pagano M, Melino G. The F-box protein FBXO45 promotes the proteasome-dependent degradation of p73. Oncogene. 2009;28(35):3157–66.View ArticlePubMedGoogle Scholar
- Ho JW, Bishop E, Karchenko PV, Negre N, White KP, Park PJ. ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genom. 2011;12:134.View ArticleGoogle Scholar
- Gorski JJ, Savage KI, Mulligan JM, McDade SS, Blayney JK, Ge Z, Harkin DP. Profiling of the BRCA1 transcriptome through microarray and ChIP-chip analysis. Nucleic Acids Res. 2011;39(22):9536–48.View ArticlePubMedPubMed CentralGoogle Scholar
- Ladha J, Sinha S, Bhat V, Donakonda S, Rao SM. Identification of genomic targets of transcription factor AEBP1 and its role in survival of glioma cells. Mol Cancer Res. 2012;10(8):1039–51.View ArticlePubMedGoogle Scholar
- van der Deen M, Akech J, Lapointe D, Gupta S, Young DW, Montecino MA, Galindo M, Lian JB, Stein JL, Stein GS, et al. Genomic promoter occupancy of runt-related transcription factor RUNX2 in Osteosarcoma cells identifies genes involved in cell adhesion and motility. J Biol Chem. 2012;287(7):4503–17.View ArticlePubMedGoogle Scholar
- Shaha C, Tripathi R, Mishra DP. Male germ cell apoptosis: regulation and biology. Philos Trans R Soc Lond B Biol Sci. 2010;365(1546):1501–15.View ArticlePubMedPubMed CentralGoogle Scholar
- Meister G, Landthaler M, Peters L, Chen PY, Urlaub H, Luhrmann R, Tuschl T. Identification of novel argonaute-associated proteins. Curr Biol. 2005;15(23):2149–55.View ArticlePubMedGoogle Scholar
- Iwakawa HO, Tomari Y. The functions of MicroRNAs: mRNA decay and translational repression. Trends Cell Biol. 2015;25(11):651–65.View ArticlePubMedGoogle Scholar
- McIver SC, Roman SD, Nixon B, McLaughlin EA. miRNA and mammalian male germ cells. Hum Reprod Update. 2012;18(1):44–59.View ArticlePubMedGoogle Scholar
- Liang X, Zhou D, Wei C, Luo H, Liu J, Fu R, Cui S. MicroRNA-34c enhances murine male germ cell apoptosis through targeting ATF1. PLoS ONE. 2012;7(3):e33861.View ArticlePubMedPubMed CentralGoogle Scholar
- Tomas A, Moss SE. Calcium- and cell cycle-dependent association of annexin 11 with the nuclear envelope. J Biol Chem. 2003;278(22):20210–6.View ArticlePubMedGoogle Scholar
- Tomas A, Futter C, Moss SE. Annexin 11 is required for midbody formation and completion of the terminal phase of cytokinesis. J Cell Biol. 2004;165(6):813–22.View ArticlePubMedPubMed CentralGoogle Scholar
- Liu S, Wang J, Guo C, Qi H, Sun MZ. Annexin A11 knockdown inhibits in vitro proliferation and enhances survival of Hca-F cell via Akt2/FoxO1 pathway and MMP-9 expression. Biomed Pharmacother. 2015;70:58–63.View ArticlePubMedGoogle Scholar
- Zaugg K, Yao Y, Reilly PT, Kannan K, Kiarash R, Mason J, Huang P, Sawyer SK, Fuerth B, Faubert B, et al. Carnitine palmitoyltransferase 1C promotes cell survival and tumor growth under conditions of metabolic stress. Genes Dev. 2011;25(10):1041–51.View ArticlePubMedPubMed CentralGoogle Scholar
- Larrayoz M, Blakemore SJ, Dobson RC, Blunt MD, Rose-Zerilli MJ, Walewska R, Duncombe A, Oscier D, Koide K, Forconi F, et al. The SF3B1 inhibitor spliceostatin A (SSA) elicits apoptosis in chronic lymphocytic leukaemia cells through downregulation of Mcl-1. Leukemia. 2016;30(2):351–60.View ArticlePubMedGoogle Scholar
- Ducut Sigala JL, Bottero V, Young DB, Shevchenko A, Mercurio F, Verma IM. Activation of transcription factor NF-kappaB requires ELKS, an IkappaB kinase regulatory subunit. Science. 2004;304(5679):1963–7.View ArticlePubMedGoogle Scholar
- Jiao B, Ma H, Shokhirev MN, Drung A, Yang Q, Shin J, Lu S, Byron M, Kalantry S, Mercurio AM, et al. Paternal RLIM/Rnf12 is a survival factor for milk-producing alveolar cells. Cell. 2012;149(3):630–41.View ArticlePubMedPubMed CentralGoogle Scholar
- Li L, Liu Y, Zhang Q, Zhou H, Zhang Y, Yan B. Comparison of cancer cell survival triggered by microtubule damage after turning Dyrk1B kinase on and off. ACS Chem Biol. 2014;9(3):731–42.View ArticlePubMedGoogle Scholar
- Zhao Y, Hongdu B, Ma D, Chen Y. Really interesting new gene finger protein 121 is a novel Golgi-localized membrane protein that regulates apoptosis. Acta Biochim Biophys Sin. 2014;46(8):668–74.View ArticlePubMedGoogle Scholar