Alternative titles; symbols
HGNC Approved Gene Symbol: PHF7
Cytogenetic location: 3p21.1 Genomic coordinates (GRCh38) : 3:52,410,660-52,423,641 (from NCBI)
PHF7 is an epigenetic reader that binds methylated histones and functions as an E3 ubiquitin ligase to control male germline sexual determination (Yang et al., 2012; Wang et al., 2019; Kim et al., 2020).
Xiao et al. (2002) cloned PHF7, which they called NYD-SP6, from a human testis cDNA library. The deduced 381-amino acid protein contains 2 PHD finger domains. PHF7 is highly conserved, with human PHF7 sharing 84 and 35% amino acid identity with its mouse and Drosophila orthologs, respectively. Northern blot analysis showed that PHF7 was highly expressed in human testis, pancreas, placenta, spleen, white blood cells, and brain, whereas it was absent in heart, skeletal muscle, and prostate. PCR analysis with mouse testis suggested that Phf7 expression was development dependent. In situ hybridization revealed that PHF7 expression was confined to Sertoli cells, but not germ cells, in mouse and human testis. Fluorescence-tagged PHF7 localized to nuclei of transfected CHO cells, and mutation analysis suggested that the N-terminal region of PHF7 may act as a nuclear localization signal.
Using RT-PCR analysis, Yang et al. (2012) found that Phf7 expression was exclusive to gonads in Drosophila and was strongly biased toward testis. At the protein level, Phf7 expression was specific to the male germline and was regulated both extrinsically by the somatic gonad and intrinsically by the germline sex chromosome constitution.
By quantitative PCR and Western blot analyses, Wang et al. (2019) showed that Phf7 was specifically expressed in mouse testis. In testis, Phf7 was expressed in developing sperm, but not in spermatogonial stem cells or Sertoli cells. Immunofluorescence analysis showed that Phf7 localized specifically in nuclei of haploid mouse spermatids.
Xiao et al. (2002) determined that the PHF7 gene contains 11 exons.
By sequence analysis, Xiao et al. (2002) mapped the PHF7 gene to chromosome 3p24.3.
Gross (2022) mapped the PHF7 gene to chromosome 3p21.1 based on an alignment of the PHF7 sequence (GenBank AF151060) with the genomic sequence (GRCh38).
Yang et al. (2012) found that expression of human PHF7 could rescue the fecundity defect in male Phf7 -/- Drosophila (see ANIMAL MODEL). Human and Drosophila PHF7 functioned as a nuclear chromatin-associated factor that bound modified histone H3 (see 602810), specifically H3 with a dimethylated lys4 (H3K4me2).
Garry et al. (2021) identified Phf7 as a cardiac epigenetic reader that helped overcome epigenetic barriers to induce cardiac reprogramming by harnessing chromatin remodeling and transcriptional complexes in mouse and human fibroblasts. Analysis with mouse tail-tip fibroblasts and embryonic fibroblasts showed that Phf7 globally activated the cardiac transcriptome and reprogrammed fibroblasts to a cardiac fate in the absence of the cardiac transcription factor Gata4 (600576). Phf7 localized to cardiac regulatory regions in fibroblasts through its ability to read and bind directly to H3K4me2 and H3K4me3 modifications, and it bound activated cardiac reprogramming factors to dictate cardiac cell identity in the absence of Gata4. In addition, Phf7 interacted with Smarcd3 (601737), a subunit of the SWI/SNF complex, for chromatin remodeling. By cooperating with the SWI/SNF complex, Phf7 increased chromatin accessibility and transcription factors at cardiac enhancers, thereby informing expression of cardiac gene programs in cardiac fibroblasts.
Yang et al. (2012) found that Phf7 -/- Drosophila were viable, but that males showed substantially impaired fecundity compared with controls. Female fertility was normal in the absence of Phf7. Genetic mosaic clonal analysis revealed that Phf7 acted germline autonomously to regulate maintenance of male germline stem cells (GSCs) and development of spermatogonia in Drosophila. Loss of Phf7 resulted in feminization of GSCs, whereas ectopic expression of Phf7 led to ablation of female germ cells and made germ cells become GSCs, as Phf7 interfered with an early stage of the germ cell developmental program.
Wang et al. (2019) found that Phf7 -/- mice had normal growth and morphology, but that Phf7 -/- males were infertile. Phf7 -/- testis and epididymis had normal weight, but sperm count in mutant epididymis was drastically reduced, and mutant sperm showed little motility and forward progression. Further analysis revealed that depletion of Phf7 caused defective spermatogenesis at a later stage of spermiogenesis in a germ cell-autonomous manner. Meiosis was normal in round spermatids, but Phf7 deletion caused abnormal histone removal, as histone-to-protamine exchange was impeded during spermiogenesis, leading to reduced chromatin compaction in Phf7 -/- sperm. Mechanistically, Phf7 functioned as an E3 ligase that bound to H3Kme3/me2 via its PHD and simultaneously ubiquitylated H2A (see 613499) via its RING domain in spermatids during the histone-to-protamine exchange process.
Kim et al. (2020) found that mice with testicular germ cell-specific deletion of Phf7 were infertile due to defects in histone-to-protamine exchange during spermiogenesis. Mutant mice had decreased sperm count in cauda epididymis and abnormal sperm morphology and motility. Further analysis identified Phf7 as an E3 ubiquitin ligase for histone H3 at lys14 and indicated that both the PHD domain and RING domain of PHF7 were required for histone H3 ubiquitination. Characterization of knockin mice carrying an enzymatically dead C160A mutation in the RING domain of Phf7 confirmed that the E3 ubiquitin ligase activity of Phf7 was crucial for histone-to-protamine exchange and H3 ubiquitination during spermiogenesis. Furthermore, the E3 ubiquitin ligase activity of Phf7 was required for histone removal following H4 (see 602822) hyperacetylation, an epigenetic event that takes place prior to histone-to-protamine exchange in elongating spermatids and induces histone removal and reduction of H4 acetylation level. H4 acetylation derived from incomplete histone removal during spermiogenesis was abnormally retained in condensing/condensed spermatids of Phf7-deficient mice. Mechanistically, loss of Phf7 caused downregulation of Brdt (602144), a histone removal factor that recognizes H4 acetylation, in step-12 spermatids, leading to incomplete histone removal. Phf7 attenuated ubiquitination of Brdt via histone ubiquitination, which maintained Brdt stability by reducing its degradation by Spop (602650) in early condensing spermatids.
Garry, G. A., Bezprozvannaya, S., Chen, K., Zhou, H., Hashimoto, H., Morales, M. G., Liu, N., Bassel-Duby, R., Olson, E. N. The histone reader PHF7 cooperates with the SWI/SNF complex at cardiac super enhancers to promote direct reprogramming. Nat. Cell Biol. 23: 467-475, 2021. [PubMed: 33941892] [Full Text: https://doi.org/10.1038/s41556-021-00668-z]
Gross, M. B. Personal Communication. Baltimore, Md. 9/28/2022.
Kim, C. R., Noda, T., Kim, H., Kim, G., Park, S., Na, Y., Oura, S., Shimada, K., Bang, I., Ahn, J. Y., Kim, Y. R., Oh, S. K., Choi, H. J., Kim, J. S., Jung, I., Lee, H., Okada, Y., Ikawa, M., Baek, S. H. PHF7 modulates BRDT stability and histone-to-protamine exchange during spermiogenesis. Cell Rep. 32: 107950, 2020. [PubMed: 32726616] [Full Text: https://doi.org/10.1016/j.celrep.2020.107950]
Wang, X., Kang, J. Y., Wei, L., Yang, X., Sun, H., Yang, S., Lu, L., Yan, M., Bai, M., Chen, Y., Long, J., Li, N., and 9 others. PHF7 is a novel histone H2A E3 ligase prior to histone-to-protamine exchange during spermiogenesis. Development 146: dev175547, 2019. Note: Erratum: Development 147: dev191445, 2020. [PubMed: 31189663] [Full Text: https://doi.org/10.1242/dev.175547]
Xiao, J., Xu, M., Li, J., Chang Chan, H., Lin, M., Zhu, H., Zhang, W., Zhou, Z., Zhao, B., Sha, J. NYD-SP6, a novel gene potentially involved in regulating testicular development/spermatogenesis. Biochem. Biophys. Res. Commun. 291: 101-110, 2002. [PubMed: 11829468] [Full Text: https://doi.org/10.1006/bbrc.2002.6396]
Yang, S. Y., Baxter, E. M., Van Doren, M. Phf7 controls male sex determination in the Drosophila germline. Dev. Cell 22: 1041-1051, 2012. [PubMed: 22595675] [Full Text: https://doi.org/10.1016/j.devcel.2012.04.013]