2017 Guide of Histone H3K36 methylation and acetylation antibodies

1. Previous study of Histone H3K36
Histone side chains are post-translationally modified at multiple sites, including at Lys36 on histone H3 (H3K36). Several enzymes from yeast and humans, including the methyltransferases SET domain-containing 2 (Set2) and nuclear receptor SET domain-containing 1 (NSD1), respectively, alter the methylation status of H3K36, and significant progress has been made in understanding how they affect chromatin structure and function. Although H3K36 methylation is most commonly associated with the transcription of active euchromatin, it has also been implicated in (1):

1.1 Alternative splicing
In fission yeast, where alternative splicing via exon skipping is rare, H3K36me3 is nevertheless enriched over exons, particularly in poorly expressed genes. Thus, this mark may facilitate proper splice site pairing via intron definition as well as exon definition by modulating the rate of Pol II elongation.(2)

1.2 Dosage compensation
H3K36me3 marks the body of all active genes yet is utilized in a chromosome-specific manner to enhance histone acetylation at sites of dosage compensation.(3)

1.3 Transcriptional repression
Generation of an H3 Lys36 antiserum reveals that Set2 is the only SET domain-containing protein in S. cerevisiae responsible for mediating methylation at this site. Finally, tethering experiments show that in vivo, Set2 functions as a transcriptional repressor that mediates its repression partially through the SET domain.(4)

1.4 DNA repair and recombination
H3K36 modification is cell cycle regulated with Set2-dependent H3K36 methylation peaking in G1 when NHEJ occurs, while Gcn5-dependent H3K36 acetylation peaks in S/G2 when HR prevails. These findings support an H3K36 chromatin switch in regulating DSB repair pathway choice.(5)

2. Modification of H3K36 Methylation and Actylation

2.1 Methlation: H3K36me1, H3K36me2, and H3K36me3

2.1.1 H3K36me1:
(i)K36me1 increases at replication origins upon binding of Cdc45, suggesting a positive function for K36me1 during initiation of DNA replication. (6)
(ii)H3K36me1 is catalysed by Ash1 enzyme and is known to be a mark of actively transcribing genes. (7)

2.1.2 H3K36me2:
(i)H3K36me2 has a role in double-strand break repair. H3K36me2 is deposited near the double-strand breaks early, and then serves to recruit early repair factors such as NBS1 and Ku70. (8)
(ii)K36me2 is sufficient for recruiting Rpd3S in vivo and for maintaining a functional Set2-Rpd3S pathway. (9)

2.1.3 H3K36me3:
H3K36me3 is deposited on histones as they are displaced by RNA polymerase II (RNAPII) during transcription. H3K36me3 then serves as a mark for HDACs to bind and deacetylate the histones, preventing run-away transcription in the wake of RNAPII. (10)

2.2 Actylation

2.2.1 H3K36ac
H3K36 acetylation shows a robust peak at the transcription start site (TSS) of active and poised genes. (11)

Check 2017 ChIP Validated Histone H3k36me antibodies from Epicypher validated Abcam OEM supplier: 

More details about the supplier

Point 1
Validated Original manufacturer.

ABclonal Inc. is one of the original manufactures which is famous for its Epigenetics antibodies such as H3K4me antibody and H3K9me antibody. It is the long-term OEM supplier for many top10 antibody companies and we also visited their factory for double confirmation.

Point 2
Lot number management

Lot number is unique for each batch of antibody and it can be taken as identity number of antibody.  ABclonal has effective batch management and it helps you maximize the reproducibility. We will share everything about the antibodies basing on Lot number.

Point 3
Antibody validation for each batch.

ABclonal is performing strict antibody validation for each batch. WB, IHC, IF, DB and ChIP are performed to make sure each Histone antibody has strong specificity and no cross-reactivity for multiple applications. It is the only one of 52 Histone antibody suppliers which passed ChIP test by EpiCypher in 2017. (Paper to be published)



3. Related protein study of H3K36me

 

H3K36me Writer Find Antibodies Introduction Reference
SETD2  SETD2 antibody Setd2 is known as a histone-H3K36-specific methyltransferase. However, its role in physiological function remains unclear. In this study, we show that Setd2 mainly regulates differentiation of murine embryonic stem cells (mESCs) toward primitive endoderm. Furthermore, we show that downregulated endoderm-related genes in Setd2(-/-) mESCs are associated with an aberrantly low level of Erk activity and that enforced expression of Fgfr3 can rescue the defective Erk pathway in Setd2(-/-) mESCs. Interestingly, the transcriptional initiation of Fgfr3 is directly regulated through histone H3K36me3 modification in its distal promoter region by Setd2.  Zhang, Y., Xie, S., Zhou, Y., Xie, Y., Liu, P., Sun, M. Xiao, H., Jin, Y.Sun, X., Chen, Z., Huang, Q., and Chen, S. (2014) H3K36 histone methyltransferase Setd2 is required for murine embryonic stem cell differentiation toward endoderm. Cell Rep. 2014 Sep 25;8(6):1989-2002
NSD1,NSD2  NSD1 antibody

NSD2 antibody

The K36M substitution and NSD1 defects converge on altering methylation of histone H3 at K36 (H3K36), subsequently blocking cellular differentiation and promoting oncogenesis. dimethylation of histone H3 at lysine 36 (H3K36me2) is the principal chromatin-regulatory activity of NSD2. Catalysis of H3K36me2 by NSD2 is sufficient for gene activation. Papillon-Cavanagh et al. (2017). Impaired H3K36 Methylation Defines a Subset of Head and Neck Squamous Cell Carcinomas. Nat Genet 49 (2), 180-185.
Smyd2  Smyd2 antibody SET domain of Smyd2 mediates H3K36 di-methylation and that Smyd2 represses transcription from an SV40-luciferase reporter. Smyd2 associates specifically with the Sin3A histone deacetylase complex, which was recently linked to H3K36 methylation within the coding regions of active genes in yeast. Mark, A.B., Robert, J.S., Paul, D.G., and Philip, W. T., (2006) Identification and characterization of Smyd2: a split SET/MYND domain-containing histone H3 lysine 36-specific methyltransferase that interacts with the Sin3 histone deacetylase complex. Mol Cancer. 2006; 5: 26.
Ash1  Ash1 antibody the controversial histone lysine methyltransferase Ash1, a known Trithorax group protein that antagonizes Polycomb silencing in vivo, is an H3K36-specific dimethylase, not an H3K4 methylase, further supporting the role of H3K36 methylation in antagonizing PRC2-mediated H3K27 methylation. Yan, Y., Xu, M., Huang, C., Liu, N., Chen, S., and Zhu, B., (2011) H3K36 Methylation Antagonizes PRC2-mediated H3K27 Methylation. The Journal of Biological Chemistry 286, 7983-7989.
SETMAR  SETMAR antibody SETMAR has been associated with di-methylation of histone H3 lysine 36 (H3K36) at sites of DNA damage. However, SETMAR does not methylate H3K36 in vitro. This and the observation that SETMAR is not active on nucleosomes suggest that H3K36 methylation is not a physiologically relevant activity. Scott, M.C., Kaitlyn, E.M., Saumya, M.S., Nicolas, R.Joshua, E.E., and Or, G. (2015). A Proteomic Strategy Identifies Lysine Methylation of Splicing Factor snRNP70 by the SETMAR Enzyme. Journal of Biological Chemistry 290:12040.
H3K36me Erasers Find Antibodies Introduction Reference
KDM2A   KDM2A targets monomethylated and di-methylated Lys36 at histone H3 (H3K36me and H3K36me2, respectively), histone marks that are associated with active transcription; however, its substrate specificity is not fully understood. Eytan, Z. (2014) Structure–function analysis of KDM2A. Nature Reviews Molecular Cell Biology 15, 630–631
KDM4A  KDM4A antibody KDM4A is a histone demethylase that targets tri- and di-methylation marks on histone H3 lysines 9 and 36. While the abundance of KDM4A oscillates in the cell cycle, little is known how this enzyme is regulated to achieve targeted effects on specific histone residues in chromatin. Tan, M.K.M., Lim, H.J., and Harper, J.W., (2011) SCFFBXO22 Regulates Histone H3 Lysine 9 and 36 Methylation Levels by Targeting Histone Demethylase KDM4A for Ubiquitin-Mediated Proteasomal Degradation. Mol Cell Biol. 31(18): 3687–3699.
KDM4B  KDM4B antibody The KDM4/JMJD2 Jumonji C-containing histone lysine demethylases (KDM4A-KDM4D), which selectively remove the methyl group(s) from tri/dimethylated lysine 9/36 of H3, modulate transcriptional activation and genome stability. Chu, C.H., Wang, L.Y., Hsu, K.C., Chen, C.C., Cheng, H. H., Wang, S.M., Wu, C.M., Chen, T.J., Li, L.T., Liu, R., Hung, C.L., Yang J.M., Kung H.J., and Wang, W.C. (2014) KDM4B as a target for prostate cancer: structural analysis and selective inhibition by a novel inhibitor. J Med Chem. 57(14):5975-85.
KDM4C  KDM4C antibody KDM4C, also known as JMJD2C/GASC1, is a member of the KDM4 subgroup of JmjC domain-containing proteins which catalyzes the demethylation of tri- and dimethylated lysine 9 and lysine 36 on histone H3. Yuan, X., Kong, J.Y., Ma, Z.K., Li, N., Jia, R.N., Liu, Y.W., Zhou, F.Y., Zhan, Q.M., Liu, G., and Gao, S.G. (2016). KDM4C, a H3K9me3 Histone Demethylase, is Involved in the Maintenance of Human ESCC-Initiating Cells by Epigenetically Enhancing SOX2 Expression. Neoplasia. 18(10): 594–609.
NO66   The Jumonji C (JmjC)-domain-containing NO66 is a histone demethylase with specificity for methylated histone H3K4 and H3K36. NO66 binds to the transcription factor Osterix (Osx) and inhibits its transcriptional activity in promoter assays. Chen, Q., Sinha, K., Deng, J.M., Yasuda, H., Krahe, R., Behringer, R.R., and de Crombrugghe, B., (2015). Mesenchymal Deletion of Histone Demethylase NO66 in Mice Promotes Bone Formation. J Bone Miner Res. 30(9):1608-17.
H3K36me Readers Find Antibodies Introduction Reference
MSL3   When MSL complex is ectopically localized to an autosome, histone H3K36 trimethylation (H3K36me3) is a strong predictor of MSL binding. We isolated mutants lacking Set2, the H3K36me3 methyltransferase, and found that Set2 is an essential gene in both sexes of Drosophila. Larschan, E., Alekseyenko, A.A., Gortchakov, A.A., Peng, S., Li, B., Yang, P., Workman, J.L., Park, P.J., and Kuroda, M.I. (2007) MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. Mol Cell. 2007 Oct 12;28(1):121-33.
MRG15  MRG15 (MORF4L1 ) antibody In vitro binding assay results indicate that the MRG15 chromo domain can bind to methylated Lys36 (H3K36), but not methylated Lys4, Lys9 and Lys27 of histone H3. Zhang, P., Du, J.M., Sun, B.F., Dong, X.C., Xu, G.L., Zhou, J.Q., Huang, Q.Q., Liu, Q., Hao, Q., and Ding, J.P. (2006) Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3. Nucleic Acids Res. 2006 Dec; 34(22): 6621–6628.
PHF19  PHF19 antibody Phf19 binds to a subset of PRC2 targets in mouse embryonic stem cells and that this is required for their repression and for H3K27me3 deposition. These findings show that the interaction of Phf19 with H3K36me2 and H3K36me3 is essential for PRC2 complex activity and for proper regulation of gene repression in embryonic stem cells. Ballare, C., Lange, M., Lapinaite, A., Martin, G.M., Morey, L., Pascual, G., Liefke, R., Simon, B., Shi, Y., Gozani, O., Carlomagno, T., Benitah, S.A., and Croce, L.D. (2012) Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity. Nat Struct Mol Biol. 2012 Dec; 19(12): 1257–1265.
PHF1  PHF1 antibody Ectopically expressed PHF1 induced Tudor-dependent stabilization of PRC2 complexes on bulk chromatin and mediated spreading of PRC2 and H3K27me3 into H3K36me3-containing chromatin regions. In murine pluripotent stem cells, we identified coexistence of H3K36me3, H3K27me3, and PHF19/PCL3 at a subset of poised developmental genes and demonstrated that PHF19/PCL3 Tudor function is required for optimal H3K27me3 and repression of these loci. Cai, L., Rothbart, S.B., Lu, R., Xu, B., Chen, W.Y.,Tripathy, A. Rochowitz, S., Zheng, D., Ratel D.J., Allis, C.D.,Strahl B.D., Song, J., and Wang, G.G., (2013) An H3K36 methylation-engaging Tudor motif of polycomb-like proteins mediates PRC2 complex targeting. Mol Cell. 2013 Feb 7;49(3):571-82.
GCN5  GCN5 antibody Set2-dependent H3K36 methylation reduces chromatin accessibility, reduces resection and promotes NHEJ, while antagonistic Gcn5-dependent H3K36 acetylation increases chromatin accessibility, increases resection and promotes HR Pai, C.C., Deegan, R.S., Subramanian, L., Gal, C., Sarkar, S., Blaikley, E.J., Walker, C., Hulme, L., Bernhard, E., Codlin, S., Bahler, J., Allshire, R., Whitehall, S., and Humphrey, T.C., (2014) A histone H3K36 chromatin switch coordinates DNA double-strand break repair pathway choice. Nat Commun. 2014 Jun 9;5:4091.

 

Reference

1. Wagner, E.J. and Carpenter, P.B., (2012) Understanding the language of Lys36 methylation at histone H3. Nature Reviews Molecular Cell Biology 13, 115-126
2. Zhou, H.L., Luo, G.B., Wise, J.A., and Lou, H., (2014) Regulation of alternative splicing by local histone modifications: potential roles for RNA-guided mechanisms. Nucleic Acids Res. 2014 Jan; 42(2): 701–713.
3. Bell, O., Conrad, T., Kind, J., Wirbelauer, C., Akhtar, A., and Schubeler, D., (2008) Transcription-Coupled Methylation of Histone H3 at Lysine 36 Regulates Dosage Compensation by Enhancing Recruitment of the MSL Complex in Drosophila melanogaster. Mol. Cell. Biol. May 2008 vol. 28 no. 10 3401-3409
4. Strahl BD, Grant PA, Briggs SD, et al. Set2 Is a Nucleosomal Histone H3-Selective Methyltransferase That Mediates Transcriptional Repression. Molecular and Cellular Biology. 2002;22(5):1298-1306.
5. Pai C-C, Deegan RS, Subramanian L, et al. A histone H3K36 chromatin switch coordinates DNA double-strand break repair pathway choice. Nature communications. 2014;5: 4091. doi:10.1038/ncomms5091.
6. Pryde F, Jain D, Kerr A, Curley R, Mariotti FR, et al. (2009) H3 K36 Methylation Helps Determine the Timing of Cdc45 Association with Replication Origins. PLoS ONE 4(6): e5882.
7. Tanaka, Y., Katagiri, Z., Kawahashi, K., Kioussis, D., and Kitajima, S., (2007) Trithorax-group protein ASH1 methylates histone H3 lysine 36. Gene. 2007 Aug 1;397(1-2):161-8.
8. Fnu, S., Williamson, E.A., De Haro, L.P., Brenneman, M., Wray, J., Shaheen, M., Radhakrishnan, K., Lee, S.H., Nickoloff, J.A., and Hromas, R. (2011). Methylation of histone H3 lysine 36 enhances DNA repair by nonhomologous end-joining. Proc. Natl. Acad. Sci. U. S. A. 108, 540-545.
9. Li, B., Jackson, J., Simon, M.D., Fleharty, B., Gogol, M., Seidel, C., Workman, J.L., and Shilatifard, A., (2009) Histone H3 Lysine 36 Dimethylation (H3K36me2) Is Sufficient to Recruit the Rpd3s Histone Deacetylase Complex and to Repress Spurious Transcription. The Journal of Biological Chemistry 284, 7970-7976.
10. Carrozza, M.J., Li, B., Florens, L., Suganuma, T., Swanson, S.K., Lee, K.K., Shia, W.J., Anderson, S., Yates, J., Washburn, M.P., and Workman, J.L. (2005). Histone H3 methylation by Set2 directs deacetylation of coding regions by Rpd3S to suppress spurious intragenic transcription. Cell 123, 581-592.
11. Wang Z, Zang C, Rosenfeld JA, et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nature genetics. 2008;40(7):897-903. doi:10.1038/ng.154.