A controlled organ homeostasis is essential to sustain the integrity of any living organism. This homeostasis relies on stem cells, which maintain themselves and give rise to the various types of differentiated cells. It is well established that the differentiation of pluripotent embryonic stem cells (ESCs) depends on major changes in transcriptional programs. Covalent modifications of DNA, RNA and proteins are instrumental in setting up the genetic programs associated with cell fates. Another important mechanism for regulation of gene expression is protein localisation and stability. In addition to ubiquitination, SUMOylation and phosphorylation, methylation of proteins is an important determinant of their properties.
Our current understanding of the biological significance of protein methylation comes from studies of histones. Methylation of histones is catalysed by enzymes containing a conserved amino acid motif collectively named the Su(var)3-9, Enhancer of zeste [E(z)], Tritorax (SET) domain (1). First characterized as a novel methyltransferase modifying histone 3 at lysine 4 (2), SETD7 interacts with and methylates a large number of proteins, including transcription factors BRG1 (3), E2F1 (4), SMAD3 (5), SOX2 (6), TATA box-binding protein associated factor 10 (7) and DNMT1 DNA methyltransferase (8). In some instances, SETD7-dependent methylation reduces protein stability, for example of SOX2, DNMT1 and E2F1. In other cases, SETD7-mediated methylation facilitates recruitment of transcription factors to chromatin (9,10). Finally, methylation of proteins by SETD7 affects protein-protein interaction both in the nucleus and cytoplasm (7,11,12).
SETD7 is absent in pluripotent ESCs (11). Its expression is activated once cells transit from pluripotent to multipotent state and further maintained in post-mitotic differentiated cells (11). Interestingly, the expression of SETD7 is lost in epithelial tumours (13,14). The levels of SETD7 expression negatively correlate with the degree of cancer progression. It is not clear whether SETD7 is silenced upon neoplastic transformation or SETD7-negative cells represent the adult somatic stem/progenitor pool, which is expanded in neoplastic tissues. Similar to ESCs, SETD7 is not expressed in quiescent adult muscle stem cells but is rapidly activated once cells enter the cell cycle (12). This suggests that the primary function of SETD7 is to promote differentiation of lineage-committed progenies. Indeed, SETD7 is required for mes-endoderm specification as well as for the differentiation of cardiomyocytes, endothelial cells, hepatocytes and neuron precursor cells in vitro (11). Notably, the methyltransferase activity is not required during these processes. How does SETD7 regulate its dynamic sets of target genes during each step of differentiation? It does so by changing its binding partners.
In mesodermal progenitors, SETD7 interacts with components of SWI/SNF chromatin-remodelling complex, including BRG1, and recruits them to the promoters of the mesoderm specific genes (11). Once mesodermal progenitors are committed towards the cardiac lineage, the expression of BRG1 is downregulated (15). In contrast, the expression of cardiac lineage genes, including NKX2-5 is upregulated. SETD7 interacts with NKX2-5 (11). Both SETD7, NKX2-5 and other cardiac specific transcription factors co-occupy the promoters of genes promoting differentiation of cardiomyocytes. It remains to be determined whether SETD7 is required for the recruitment of NKX2-5 to its target genes.
In contrast to transcription factors or the members of SWI/SNF complex, SETD7 is associated not only with the promoters but also with the gene body of the target genes, in a pattern reminiscent of H3K36me3 (11). Histone H3K36 is co-transcriptionally tri-methylated by SETD2 methyltransferase during RNA polymerase II (RNA pol II) transcription elongation (16). H3K36me3 serves as a recruitment platform for several chromatin-modifying proteins, including DNA methyltransferase 3a (17) and the member of Rpd3S deacetylase complex Eaf3Jeny (18-20). Using SETD2 knock-down human ES cells, co-immunoprecipitation and peptide arrays, Lee et al., showed that H3K36me3 directly interacts with SETD7 and is required for the recruitment of the protein to the gene bodies (11). While the loss of SETD7 does not affect the distribution of H3K36me3, it reduces the occupancy of the elongating form of RNA pol II along the target genes. The biological significance of SETD7 dual distribution, at the promoters and the gene bodies, is not clear. In contrast to SETD7 mutants, lacking the protein at the both promoters and gene bodies, loss of SETD7 at the gene bodies has little or no effect on the expression of the few tested target genes (11).
Interestingly, Setd7 mutant mice are viable and do not show any defects in either mesoderm or cardiomyocyte specification (21,22). The different requirement for SETD7 between mouse and human can be attributed to the presence of the species-specific factor(s) acting redundantly with Setd7 in mice. Alternatively, the cell culture conditions used for differentiation of human ESCs towards cardiomyocytes lack paracrine signals present within the developing embryos in vivo.
Although Setd7 is dispensable during mouse embryogenesis, it is required for the differentiation of adult muscle stem cells/satellite cells upon injury (12). In the absence of Setd7, quiescent satellite cells enter the cell cycle and give rise to myogenic progenitors. Yet, those progenitors do not differentiate further and do not form muscle fibres. In both satellite cells and myogenic progenitors, Setd7 is localized in the cytoplasm, where it binds and methylates β-catenin. Upon stimulation of myogenic progenitors with Wnt ligands, β-catenin translocates to the nucleus and activates the transcription of its target genes (23). Inhibition of Setd7 methyltransferase activity blocks the translocation of β-catenin to the nucleus and disrupts the myogenic programme. Setd7 regulates Wnt/β-catenin dependent gene expression not only in skeletal muscles but also in intestinal epithelial tumours (24). ApcMin/+ mice deficient for Setd7 develop twice fewer polyps compared to the controls. Yet, in this biological context Setd7 promotes proliferation and inhibits differentiation of neoplastic cells. In summary, the requirement for Setd7 in multiple contexts both during differentiation of adult progenitors and ESCs highlights the importance of understanding how its two functions as methyltransferase in the cytoplasm and chromatin binding factor in the nucleus are integrated and how their impaired activity leads to diseases.
I thank T. Montavon for critical reading of manuscript.
Funding: N Soshnikova is supported by the Heisenberg Programme, DFG (SO1738/1).
Conflicts of Interest: The author has no conflicts of interest to declare.
Ethical Statement: The author is accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.
- Herz HM, Garruss A, Shilatifard A. SET for life: biochemical activities and biological functions of SET domain-containing proteins. Trends Biochem Sci 2013;38:621-39. [Crossref] [PubMed]
- Wang H, Cao R, Xia L, et al. Purification and functional characterization of a histone H3-lysine 4-specific methyltransferase. Mol Cell 2001;8:1207-17. [Crossref] [PubMed]
- Okabe J, Orlowski C, Balcerczyk A, et al. Distinguishing hyperglycemic changes by Set7 in vascular endothelial cells. Circ Res 2012;110:1067-76. [Crossref] [PubMed]
- Kontaki H, Talianidis I. Lysine methylation regulates E2F1-induced cell death. Mol Cell 2010;39:152-60. [Crossref] [PubMed]
- Shuttleworth VG, Gaughan L, Nawafa L, et al. The methyltransferase SET9 regulates TGFB1 activation of renal fibroblasts via interaction with SMAD3. J Cell Sci 2018;131. [Crossref] [PubMed]
- Zhang C, Hoang N, Leng F, et al. LSD1 demethylase and the methyl-binding protein PHF20L1 prevent SET7 methyltransferase-dependent proteolysis of the stem-cell protein SOX2. J Biol Chem 2018;293:3663-74. [Crossref] [PubMed]
- Kouskouti A, Scheer E, Staub A, et al. Gene-specific modulation of TAF10 function by SET9-mediated methylation. Mol. Cell 2004;14:175-82. [Crossref] [PubMed]
- Estève PO, Chin HG, Benner J, et al. Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells. Proc Natl Acad Sci U S A 2009;106:5076-81. [Crossref] [PubMed]
- Tuano NK, Okabe J, Ziemann M, et al. Set7 mediated interactions regulate transcriptional networks in embryonic stem cells. Nucleic Acids Res 2016;44:9206-17. [PubMed]
- Kassner I, Barandun M, Fey M, et al. Crosstalk between SET7/9-dependent methylation and ARTD1-mediated ADP-ribosylation of histone H1.4. Epigenetics Chromatin 2013;6:1. [Crossref] [PubMed]
- Lee J, Shao NY, Paik DT, et al. SETD7 Drives Cardiac Lineage Commitment through Stage-Specific Transcriptional Activation. Cell Stem Cell 2018;22:428-44.e5. [Crossref] [PubMed]
- Judson RN, Quarta M, Oudhoff MJ, et al. Inhibition of Methyltransferase Setd7 Allows the In Vitro Expansion of Myogenic Stem Cells with Improved Therapeutic Potential. Cell Stem Cell 2018;22:177-90.e7. [Crossref] [PubMed]
- Huang R, Li X, Yu Y, et al. SETD7 is a prognosis predicting factor of breast cancer and regulates redox homeostasis. Oncotarget 2017;8:94080-90. [Crossref] [PubMed]
- Guo T, Wen XZ, Li ZY, et al. ISL1 predicts poor outcomes for patients with gastric cancer and drives tumor progression through binding to the ZEB1 promoter together with SETD7. Cell Death Dis 2019;10:33. [Crossref] [PubMed]
- Alexander JM, Hota SK, He D, et al. Brg1 modulates enhancer activation in mesoderm lineage commitment. Development 2015;142:1418-30. [Crossref] [PubMed]
- Wagner EJ, Carpenter PB. Understanding the language of Lys36 methylation at histone H3. Nat Rev Mol Cell Biol 2012;13:115-26. [Crossref] [PubMed]
- Heyn P, Logan CV, Fluteau A, et al. Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions. Nat Genet 2019;51:96-105. [Crossref] [PubMed]
- Carrozza MJ, Li B, Florens L, et al. Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 2005;123:581-92. [Crossref] [PubMed]
- Keogh MC, Kurdistani SK, Morris SA, et al. Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex. Cell 2005;123:593-605. [Crossref] [PubMed]
- Joshi AA, Struhl K. Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. Mol Cell 2005;20:971-8. [Crossref] [PubMed]
- Campaner S, Spreafico F, Burgold T, et al. The methyltransferase Set7/9 (Setd7) is dispensable for the p53-mediated DNA damage response in vivo. Mol Cell 2011;43:681-8. [Crossref] [PubMed]
- Lehnertz B, Rogalski JC, Schulze FM, et al. p53-dependent transcription and tumor suppression are not affected in Set7/9-deficient mice. Mol Cell 2011;43:673-80. [Crossref] [PubMed]
- Rudolf A, Schirwis E, Giordani L, et al. β-Catenin Activation in Muscle Progenitor Cells Regulates Tissue Repair. Cell Rep 2016;15:1277-90. [Crossref] [PubMed]
- Oudhoff MJ, Braam MJS, Freeman SA, et al. SETD7 Controls Intestinal Regeneration and Tumorigenesis by Regulating Wnt/β-Catenin and Hippo/YAP Signaling. Dev Cell 2016;37:47-57. [Crossref] [PubMed]
Cite this article as: Soshnikova N. Functions of SETD7 during development, homeostasis and cancer. Stem Cell Investig 2019;6:26.