New mechanisms of epigenetic regulation through the cell identity regulator TET2

Understanding the molecular mechanisms that govern cell identity of each cellular type in our body is still one of the biggest challenges in biomedical research. Specifically, those pathways that are affected at the cellular level, and give rise to a specific pathology, are of special interest for therapeutics. Numerous epigenetic mechanisms have been shown to be deregulated in a variety of human diseases, including metabolic alterations, neurodegenerative disorders and cancer. Epigenetics can be defined as the chemical modifications that take place in histones, DNA and RNA molecules, and that define the transcriptional landscapes of each cell type. This regulatory mechanism endows that different cell types (i.e. a neuron and a hepatocyte) from the same individual, with identical genetic material, can have such different functions.

Methylation of cytosines in DNA (5mC) is among the epigenetic modifications identified up to date. 5mC levels are critical for transcriptional regulation and seem to be altered in several human diseases such as cancer. Nevertheless, in spite of its key role in gene expression, it was not until recently that the TET proteins, capable of removing 5mC from DNA, were discovered (Tahiliani et al., 2009). The TET (Ten-eleven-translocation) proteins can oxidize the methyl groups from cytosines, to give rise to intermediates such as 5-hydroximethylcytosine (5hmC), that will ultimately lead to the removal of the 5mC repressive mark from DNA. Among the three members of the TET family, TET2 stands out for its roles in embryonic stem cell identity regulation (Fidalgo et al., 2016) and for being deregulated in cancers, such as leukemia (Bowman and Levine, 2017).

Albeit of its importance, the mechanisms by which TET2 is recruited to chromatin to exert its function, remain unknown. For that reason, we decided to identify the proteins that interact with TET2, and that could mediate its specific localization at the chromatin level. Among all the identified candidates, the protein PSPC1, that can bind both DNA and RNA, caught our attention (Guallar et al, 2018). Interestingly, we found that PSPC1 is not only responsible for TET2 binding to chromatin, but also that this recruitment is dependent on PSPC1 ability to interact with RNA. In that sense, our study supports recent work that proposes the existence of feedback regulatory loops between epigenetics and transcription.

Molecular structure of TET2 interaction DNA. Imagen: RSCB PDB 5DEU.

On the other hand, our analysis determined that the TET2-PSPC1 complex is able to chemically modify the RNA molecules it interacted with, through oxidation of 5-methyl to 5-hydroxymethyl groups in cytosines. This discovery highlights the existence of a new epigenetic regulatory mechanism to balance 5mC and 5hmC levels in RNA, and was supported by a study performed by an independent laboratory (Shen et al., 2018). Surprisingly, we found endogenous retrovirus (ERVs) among TET2-PSPC1 bound RNA species. These repetitive DNA fragments account for more than 20% of our genome, and their deregulation has been correlated with illnesses related to the ageing process (i.e. Alzheimer, ALS and cancer) (Pal and Tyler, 2016). In our study, we find that TET2 regulates ERV RNAs at a post-transcriptional level. In particular, TET2 interaction with ERV RNA species through PSPC1, leads to the oxidation of 5mC, and their ultimate destabilization, therefore involving TET2-PSPC1 complex in the strict regulation of these parasitic elements.

The relevance of this finding comes from the observation that the deregulation of these parasitic elements can interfere with the correct functioning of the host cell at different levels. On the one hand, genomic insertion of new copies of ERVs can affect the expression of genes surrounding the site of integration at the host genome. On the other, some of these RNAs have retained their coding potential, therefore leading to the expression of viral proteins that can interfere with cellular decisions. Because each cell type of our organism requires such an exquisite regulation of ERV expression, we were not surprised to find that TET2-PSPC1 contribute to retrovirus regulation through a second layer of epigenetic repression by recruiting histone deacetylases (HDAC1/2) to chromatin. Our results place TET2 as a master regulator of these parasitic DNA elements at the cellular level.

Overall, our study shows for the first time that TET2, which was only regarded as a key protein for DNA methylation regulation, has the ability to modify RNA through deposition of the 5-hydroxymethylcitosine. Considering the reversible nature of epigenetic modifications, our findings position TET2, as well as PSPC1, as potential therapeutic targets that will need to be carefully examined in pathologies where a deregulation of endogenous retrovirus has been observed. Moreover, the characterization of TET2 RNA targets in several cellular contexts of homeostasis and pathogenesis will be key to understand how the deregulation of this epigenetic factor contributes to the onset of diseases with high negative impact in our societies.

Reference

Guallar, et al. RNA-dependent chromatin targeting of TET2 for endogenous retrovirus control in pluripotent stem cells. Nat Genet. 2018 Feb 26. doi: 10.1038/s41588-018-0060-9. [Epub ahead of print]

Bibliography

Bowman, R.L., and Levine, R.L. (2017). TET2 in Normal and Malignant Hematopoiesis. Cold Spring Harb. Perspect. Med. 7, a026518.

Fidalgo, M., Huang, X., Guallar, D., Sanchez-Priego, C., Valdes, V.J., Saunders, A., Ding, J., Wu, W.S., Clavel, C., and Wang, J. (2016). Zfp281 Coordinates Opposing Functions of Tet1 and Tet2 in Pluripotent States. Cell Stem Cell 19, 355–369.

Pal, S., and Tyler, J.K. (2016). Epigenetics and aging. Sci. Adv. 2, e1600584.

Shen, Q., Zhang, Q., Shi, Y., Shi, Q., Jiang, Y., Gu, Y., Li, Z., Li, X., Zhao, K., Wang, C., et al. (2018). Tet2 promotes pathogen infection-induced myelopoiesis through mRNA oxidation. Nature 554, 123–127.

Tahiliani, M., Koh, K.P., Shen, Y., Pastor, W.A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L.M., Liu, D.R., Aravind, L., et al. (2009). Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science (80-. ). 324, 930–935.

Imagen superior: Epigenetics endows that different cell types from same individual, with identical genetic material hav different functions. Imagen: Darryl Leja, National Human Genome Research institute (www.genome.gov)

Diana Guallar ¹ and Miguel Fidalgo ¹.

¹CiMUS, Universidade de Santiago de Compostela–Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain.