UHRF1 In Cancer: Role In DNA Methylation And Histone Modification

Oncogenic Properties of UHRF1

Discuss about the epigenetic integrator UHRF1 (Ubiquitin-like with PHD and RING Finger domains 1)

I. The role of UHRF1 in cancer
II. The role of UHRF1 in DNA methylation
III. The role of UHRF1 in Histone modifications
IV. Targeting of UHRF1 in cancer

UHRF1 or ubiquitin-like, containing PHD and RING finger domains, 1 belong to the RING-finger type subfamily of E3 ubiquitin ligase and are known to bind to hemi-methylated regions on the DNA during cell division (S-phase) and also recruits DNA methyltransferase gene for regulating gene expression and chromatin structure (Berkyurek et al., 2014). Owing to the fact that UHRF1 coordinates histone modification and DNA methylation, is considered as a primary regulator of the epigenome. Moreover, UHRF1 mediates silencing of several tumor suppressor genes. This chapter will illustrate on the role of UHRF1 in cancer, DNA methylation, histone modification and targeting it in cancer cells.

UHRF1 plays the role of a major oncogene that is over-expressed in a range of haematological or solid tumors (Mudbhary et al., 2014).  High levels of expression of URHF1 are found to be associated with reduced expression of a range of tumor suppressor genes, such as, BRCA1, p16 ^INK4A, KiSS1, and PPARG. UHRF1 leads to the formation of multiple coordinated dialogue that exist between histone post-translation modification and changes in DNA-methylation, thereby leading to silencing of tumor suppressor genes in an epigenetic way, which in turn facilitates the cancer cells to escape the process of apoptosis (Nishiyama et al., 2013).  The tumor suppressor gene p16 ^INK4A participates in the G1/S cell cycle checkpoint. Loss of expression of this gene often results in inhibition of apoptosis and enhances cellular proliferation. UHRF1 uses the SRA domain, and forms an interaction with DNMT1 and histone deacetylase 1 (HDAC1), at methylated promoter sites of the TSGs (Guan et al., 2013). UHRF1 overexpression have also been demonstrated in colorectal cancer and are associated with its progression (Zhu et al., 2015). In addition, overexpression of UHRF1 in primary non-small cell lung cancer (NSCLC) is related with an elevation of DNMT3A, DNMT1, and DNMT3B expression, which in turn is associated with hypermethylation of the p16 ^INK4A promoter.

DNA methylation refers to the problem that involves addition of methyl groups to DNA molecules. This results in bringing about a change in DNA segment activity, without alteration of the major sequence. Gametogenesis in mammals and subsequent preimplantation development often encompasses dynamic reprogramming that leads to CG methylation. Research evidences have shown significant effects of low expression of UHRF1 during mouse germ cell development that resulted in removal of CG methylation. The KO region of UHRF1 exert effects on proliferating embryonic lethal somatic cells and lead to genomic hypomethylation. Furthermore, the SRA domain of UHRF1 also recognizes the hemimethylated CG sites and leads to ubiqutination of H3K23 and HSK18 that is mediated by the E3 ubiquitin ligase activity of the RING finger domain of UHRF1 (Cheng et al., 2013). According to research evidences, UHRF1 is found to colocalize throughout the S phase of cell cycle, with DNMT1, commonly known as the maintenance DNA methyltransferase protein.

Epigenetic Silencing of Tumor Suppressor Genes

Moreover, UHRF1 has also shown significant effects on tethering of DNMT1 to its chromatin, by facilitating a direct interaction with the protein DNMT1 (Liu et al., 2013). Furthermore, a methyl DNA binding domain or site is located in UHRF1, commonly termed as the SET and RING associated (SRA) domain, which plays an important role in creating strong preferential bonds with the hemi-methylated CG sites. These sites act in the form of physiological substrate for the DNMT1 protein (Bronner, Krifa & Mousli, 2013). In other words, UHRF1 recruits DNMT1 to the hemi-methylated DNA regions for facilitating maintenance of DNA methylation.

UHRF1 is considered as an epigenetic hub protein, which facilitates crosstalk between histone modification and DNA methylation. The Plant HomeoDomain (PHD) brings about specific binding between UHRF1 to the histone proteins by recognizing unmodified lysine (K4) and arginine (R2) that are present on H3 protein. Crystallographic studies have provided evidences for the cooperation of PHD with TTD for contributing to pericentric heterochromatin organization of the UHRF1 protein (Cheng et al., 2013). Evidences hint at the role of UHRF1 in reading H3K9me2/3, present in the parental histone molecule. This is followed by recruitment or direction of G9a for writing H3K9me2/3 on a separate newly-deposited histone molecule. Histone modifications and DNA methylation have been found to act together, with the aim of influencing gene expression due to alterations in the chromatin structure (Llovet et al., 2015). This interaction is most commonly observed during gene silencing that involves H3K9 methylation, H3 hypo-acetylation, and DNA methylation (Guan et al., 2013). Owing to the fact that DNA methylation is a late event, role of UHRF1 has been demonstrated by research studies in the events related to histone modification. Thus, UHRF1 brings about. histone methylation (by G9) histone deacetylation (by HDAC1), and DNA methylation (by DNMT1). 

Research evidence suggest that presence of UHRF1-mediated epigenetic silencing of major tumor suppressor genes primarily occur due to presence of the SET- and RING-associated domains. This SRA domain helps in the development of an interaction of UHRF1 with HDAC1 and DNMT1, thereby inhibiting tumor suppressor genes. Furthermore, other functional domains present in UHRF1 have also been found to significantly contribute inhibition of TSGs that includes the tandem Tudor domain (TTD), ubiquitin-like domain, and PHD and RING domain (Rothbart et al., 2013). Two key mechanisms have also been identified that mediate the role of UHRF1 in carcinogenesis, namely onset and maintenance of cancer. Furthermore, researchers have been successful in establishing the role of increased expression of UHRF1 in colorectal, gastric, bladder, breast and blood cancer. Thus, all of these evidences confirm the role of UHRF1 in cell cycle progression through G1/S phase of cell cycle via the p16INK4A-dependent pathway (Choudhry et al., 2018). Thus, use of miRNA in targeting UHRF1 has been considered as a novel kind of cancer therapy.

Role in DNA Methylation

DNA methylation is a major epigenetic modification involved in several cellular processes that encompass transposon silencing, cell differentiaton, carcinogenesis, and genomic imprinting.  The process of epigenetic silencing of major tumor suppressor genes (TSGs) occur through the process of histone alterations and DNA methylation, which in turn are regarded as the primary hallmark of cancer. Thus, the aforementioned evidences suggest that mitotic binding of the UHRF1 protein to methylated regions of chromatin are imperative for bringing about stability of DNMT1, as well as DNA methylation maintenance. Thus, UHRF1 can be considered as essential targets for treatment of cancer.

References

Berkyurek, A. C., Suetake, I., Arita, K., Takeshita, K., Nakagawa, A., Shirakawa, M., & Tajima, S. (2014). The DNA methyltransferase Dnmt1 directly interacts with the SET and RING finger-associated (SRA) domain of the multifunctional protein Uhrf1 to facilitate accession of the catalytic center to hemi-methylated DNA. Journal of Biological Chemistry, 289(1), 379-386.

Bronner, C., Krifa, M., & Mousli, M. (2013). Increasing role of UHRF1 in the reading and inheritance of the epigenetic code as well as in tumorogenesis. Biochemical pharmacology, 86(12), 1643-1649.

Cheng, J., Yang, Y., Fang, J., Xiao, J., Zhu, T., Chen, F., ... & Xu, Y. (2013). Structural insight into coordinated recognition of trimethylated histone H3 lysine 9 (H3K9me3) by the plant homeodomain (PHD) and tandem tudor domain (TTD) of UHRF1 (ubiquitin-like, containing PHD and RING finger domains, 1) protein. Journal of Biological Chemistry, 288(2), 1329-1339.

Choudhry, H., Zamzami, M. A., Omran, Z., Wu, W., Mousli, M., Bronner, C., & Alhosin, M. (2018). Targeting microRNA/UHRF1 pathways as a novel strategy for cancer therapy. Oncology letters, 15(1), 3-10.

Guan, D., Factor, D., Liu, Y., Wang, Z., & Kao, H. Y. (2013). The epigenetic regulator UHRF1 promotes ubiquitination-mediated degradation of the tumor-suppressor protein promyelocytic leukemia protein. Oncogene, 32(33), 3819.

Liu, X., Gao, Q., Li, P., Zhao, Q., Zhang, J., Li, J., ... & Wong, J. (2013). UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9. Nature communications, 4, 1563.

Llovet, J. M., Villanueva, A., Lachenmayer, A., & Finn, R. S. (2015). Advances in targeted therapies for hepatocellular carcinoma in the genomic era. Nature reviews Clinical oncology, 12(7), 408.

Mudbhary, R., Hoshida, Y., Chernyavskaya, Y., Jacob, V., Villanueva, A., Fiel, M. I., ... & Lachenmayer, A. (2014). UHRF1 overexpression drives DNA hypomethylation and hepatocellular carcinoma. Cancer cell, 25(2), 196-209.

Nishiyama, A., Yamaguchi, L., Sharif, J., Johmura, Y., Kawamura, T., Nakanishi, K., ... & Koseki, H. (2013). Uhrf1-dependent H3K23 ubiquitylation couples maintenance DNA methylation and replication. Nature, 502(7470), 249.

Rothbart, S. B., Dickson, B. M., Ong, M. S., Krajewski, K., Houliston, S., Kireev, D. B., ... & Strahl, B. D. (2013). Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylation. Genes & development, 27(11), 1288-1298.

Zhu, M., Xu, Y., Ge, M., Gui, Z., & Yan, F. (2015). Regulation of UHRF1 by microRNA?9 modulates colorectal cancer cell proliferation and apoptosis. Cancer science, 106(7), 833-839.