Genome stability and Chromosome Segregation: a Unique SET of Functions

Aliyah Weinstein, Ph.D.

hSET1, encoded by gene SETD1A, and also known as MLL, is a human lysine methyltransferase. hSET1 functions as a subunit of the histone H3K4 methyltransferase complex and is most functional within the COMPASS complex¹. hSET1 interacts with numerous other nuclear proteins to regulate transcription and cellular differentiation through H3K4 methylation, and this function is conserved in SET1 orthologs across eukaryotes including yeast, drosophila, mice, and humans^1-4.

Studies of SET1 in yeast identified that methylation of H3K4 is required for non-homologous end joining, a cellular mechanism that repairs double-stranded DNA breaks². In the yeast Saccharomyces cerevisiae, SET1 can demethylate or trimethylate H3K4, and these methylation states are found in regions of the genome that are actively being transcribed, but not in heterochromatic regions⁵. During transcription, SET1 plays a crucial role in maintaining genome stability through its interaction with BOD1L. Both SET1 and BOD1L function as replication fork protection factors that facilitate migration of histone proteins to stalled replication forks to protect them from degradation 6. SET1 also physically interacts with phosphorylated RNA polymerase II. This interaction facilitates trimethylation of H3K4 near the transcription start site⁷, and indicates that trimethylation of H3K4 may be a mark of recently transcribed regions of the genome⁸ and may functionally suppress the activity of RNA polymerase II⁹. The ability of SET1 to methylate H3K4 is nonredundant, as ablation of SET1, but not other proteins containing a SET domain, abrogates H3K4 methylation and that this methylation is required for normal cell growth and the regulation of transcription⁹. SET1 is additionally involved in regulating transcription in telomeric regions by maintaining the integrity of telomeres^10,11. In eukaryotes, SET1 silences the transcription of telomere associated satellite-like sequences^10,12. The interaction between SET1 and MEC3 is important for telomeric stability, as SET1 requires MEC3 to silence transcription of telomeres¹³.

Independent of its effects on genome stability, SET1 plays an important role in chromosome segregation during the cell division process in yeast. SET1 impacts chromosome segregation through methylation of the kinetochore protein, Dam1. A balance between methylation of Dam1 by SET1, and phosphorylation of Dam1 by Ip11 is required for proper segregation of chromosomes during mitosis¹⁴.

Histone methyltransferases that contain a SET domain have been implicated in several types of cancer 15. hSET1 is being investigated as a novel therapeutic target for colon carcinoma as it was observed that blockade of hSET1 selectively induced apoptosis of cancer cells and led to regression of a transplantable model of colon cancer in a mouse model 16. Rearrangement of the gene encoding MLL, the human homolog to yeast hSET1, has been observed in a variety of hematologic malignancies including B and T cell lymphomas and acute myeloid leukemia 17, 18. In breast cancer, duplication of the gene encoding hSET1 has been observed, and expression of hSET1 maintains the expression of several matrix metalloproteinases that are involved in cancer metastasis¹⁹.

Detection of human hSET1 (red) in FFPE ovarian carcinoma by IHC-IF.

Detection of human hSET1 by WB of immunoprecipitates from HEK293T lysate.

Detection of human hSET1 in FFPE lung carcinoma by IHC.

References

1. Shilatifard A (2006) Chromatin Modifications by Methylation and Ubiquitination: Implications in the Regulation of Gene Expression. Annu Rev Biochem 75:243–269 . doi: 10.1146/annurev.biochem.75.103004.142422

2. Faucher D, Wellinger RJ (2010) Methylated H3K4, a Transcription-Associated Histone Modification, Is Involved in the DNA Damage Response Pathway. PLoS Genet 6:e1001082 . doi: 10.1371/journal.pgen.1001082

3. Bernstein BE, Humphrey EL, Erlich RL, Schneider R, Bouman P, Liu JS, Kouzarides T, Schreiber SL (2002) Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci 99:8695–8700 . doi: 10.1073/pnas.082249499

4. Hanson RD, Hess JL, Yu BD, Ernst P, van Lohuizen M, Berns A, van der Lugt NM, Shashikant CS, Ruddle FH, Seto M, Korsmeyer SJ (1999) Mammalian Trithorax and polycomb-group homologues are antagonistic regulators of homeotic development. Proc Natl Acad Sci U S A 96:14372–7

5. Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NCT, Schreiber SL, Mellor J, Kouzarides T (2002) Active genes are tri-methylated at K4 of histone H3. Nature 419:407–411 . doi: 10.1038/nature01080

6. Higgs MR, Sato K, Reynolds JJ, Begum S, Bayley R, Goula A, Vernet A, Paquin KL, Skalnik DG, Kobayashi W, Takata M, Howlett NG, Kurumizaka H, Kimura H, Stewart GS (2018) Histone Methylation by SETD1A Protects Nascent DNA through the Nucleosome Chaperone Activity of FANCD2. Mol Cell 71:25–41.e6 . doi: 10.1016/j.molcel.2018.05.018

7. Sayou C, Millán-Zambrano G, Santos-Rosa H, Petfalski E, Robson S, Houseley J, Kouzarides T, Tollervey D (2017) RNA Binding by Histone Methyltransferases Set1 and Set2. Mol Cell Biol 37:e00165-17 . doi: 10.1128/MCB.00165-17

8. Ng HH, Robert F, Young RA, Struhl K (2003) Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol Cell 11:709–19

9. Briggs SD, Bryk M, Strahl BD, Cheung WL, Davie JK, Dent SY, Winston F, Allis CD (2001) Histone H3 lysine 4 methylation is mediated by Set1 and required for cell growth and rDNA silencing in Saccharomyces cerevisiae. Genes Dev 15:3286–3295 . doi: 10.1101/gad.940201

10. Nislow C, Ray E, Pillus L (1997) SET1 , A Yeast Member of the Trithorax Family, Functions in Transcriptional Silencing and Diverse Cellular Processes. Mol Biol Cell 8:2421–2436 . doi: 10.1091/mbc.8.12.2421

11. Roguev A, Schaft D, Shevchenko A, Pijnappel WW, Wilm M, Aasland R, Stewart AF (2001) The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4. EMBO J 20:7137–7148 . doi: 10.1093/emboj/20.24.7137

12. Doheny JG, Mottus R, Grigliatti TA (2008) Telomeric Position Effect—A Third Silencing Mechanism in Eukaryotes. PLoS One 3:e3864 . doi: 10.1371/journal.pone.0003864

13. Corda Y, Schramke V, Longhese MP, Smokvina T, Paciotti V, Brevet V, Gilson E, Géli V (1999) Interaction between Set1p and checkpoint protein Mec3p in DNA repairand telomere functions. Nat Genet 21:204–208 . doi: 10.1038/5991

14. Zhang K, Lin W, Latham JA, Riefler GM, Schumacher JM, Chan C, Tatchell K, Hawke DH, Kobayashi R, Dent SYR (2005) The Set1 methyltransferase opposes Ipl1 aurora kinase functions in chromosome segregation. Cell 122:723–34 . doi: 10.1016/j.cell.2005.06.021

15. Schneider R, Bannister AJ, Kouzarides T (2002) Unsafe SETs: histone lysine methyltransferases and cancer. Trends Biochem Sci 27:396–402 . doi: 10.1016/S0968-0004(02)02141-2

16. Yadav S, Singhal J, Singhal SS, Awasthi S (2009) hSET1: a novel approach for colon cancer therapy. Biochem Pharmacol 77:1635–41 . doi: 10.1016/j.bcp.2009.02.019

17. Tenney K, Shilatifard A (2005) A COMPASS in the voyage of defining the role of trithorax/MLL-containing complexes: Linking leukemogensis to covalent modifications of chromatin. J Cell Biochem 95:429–436 . doi: 10.1002/jcb.20421

18. Rowley JD (1998) THE CRITICAL ROLE OF CHROMOSOME TRANSLOCATIONS IN HUMAN LEUKEMIAS. Annu Rev Genet 32:495–519 . doi: 10.1146/annurev.genet.32.1.495

19. Salz T, Deng C, Pampo C, Siemann D, Qiu Y, Brown K, Huang S (2015) Histone Methyltransferase hSETD1A Is a Novel Regulator of Metastasis in Breast Cancer. Mol Cancer Res 13:461–469 . doi: 10.1158/1541-7786.MCR-14-0389