2017 Histone H3K9 methylation antibodies and relating products


1. Introuduction of H3K9me1, H3K9me2 and H3K9me3

H3K9 methylation is the mark of heterochromatin. Heterochromatin is the condensed, transcriptionally inactive state of chromatin. It can be facultative or constitutive. Mono, di, and tri H3K9 methylations each have very distinct distributions. H3K9me1 is enriched at the transcriptional start site of active genes (Barski et al., 2007). The same study found that H3K9me2 and 3 were both found more often at silenced genes. However it is important to note that for all these methylations that the correlations were modest, with many highly active genes showing strong H3K9me2/3 enrichment at their promoters. In mammals, these covalent modifications are catalyzed by five members of the SET-domain containing family of methyltransferases. SETDB1 and the related enzymes SUV39H1 and SUV39H2 contribute to both H3K9me2 and H3K9me3, while GLP and G9a (also called EHMT1 and EHMT2, respectively) catalyze H3K9me1 and H3K9me2. H3K9me2 and me3 are bound by the chromo-domain of Heterochromatin protein 1 (HP1, three isoforms in mammals), which can self-oligomerize and recruit repressive histone modifiers, contributing to heterochromatin compaction and spread. The methyltransferases that deposit H3K9me2 and H3K9me3 are required to establish high levels of DNA methylation at CpG dinucleotides and low levels of histone acetylation, two other hallmarks of heterochromatin. Kallestad et al. (2014) showed that H3K9me2/me3 was observed when transcription was inhibited during active replication. This process did not require the presence of H3K9me1, which appears to have a highly specific function and is a less commonly explored feature of the epigenome. Relatedly, Pinheiro et al. (2012) identified very important characteristics of H3K9me1. These authors revealed that the lysine-specific HMTs Prdm3 and Prdm16 are responsible for direct H3K9 mono-methylation in the cytoplasm. Then, in the nucleus, H3K9me1 is converted to H3K9me3 by the Suv39h1 enzyme, promoting hetero-chromatinization.


Check 2017 ChIP Validated Histone H4k20me antibodies. 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)



2. Related protein study of H3K9me


The H3K9me protein study has three parts, including writers, erasers and readers.

Suv39H1, SUV39H2, G9a, SETDB1, Ash1, KMT1D, CLL8, RIZ1 are writers,
LSD1, KMD3A, KMD3B, KMD4A, KMD4B, KMD4C, KMD4D, TRIP8, PHF8 are erasers and
L3MBTL1, Tip60, SFMBT, HP1, CDY1, PC1, MPP8, CBX1-8, Np95, JARID1C, ATRX are readers.

 

H3K9me Writers Find antibody Introduction Reference
Suv39H1  Suv39H1 antibody Sulforaphane stimulates ubiquitination and acetylation of SUV39H1 within a C-terminal nuclear localization signal peptide motif and coincides with its dissociation from chromatin and a decrease in global H3K9me3 levels. Exogenous SUV39H1 expression leads to an increase in H3K9me3 and decreases sulforaphane-induced apoptotic signaling. SUV39H1 is thus identified as a novel mediator of sulforaphane cytotoxicity in PC3 cells. Watson, GW; Wickramasekara, S; Palomera-Sanchez, Z; Black, C; Maier, CS; Williams, DE; Dashwood, RH; Ho, E. ONCOGENESIS; DEC, 2014; 3, Database: Science Citation Index
SUV39H2  Suv39H2 antibody-ChIP Grade SUV39H2 recognizes a long sequence on histone H3 comprising T6–K14.Additional SUV39H2 substrates besides H3K9 could not be identified.SUV39H2 prefers H3K9me0 and processively introduces two methyl groups. By Schuhmacher, Maren Kirstin; Kudithipudi, Srikanth; Kusevic, Denis; Weirich, Sara; Jeltsch, Albert. In BBA – Gene Regulatory Mechanisms. January 2015 1849(1):55-63 Language: English. DOI: 10.1016/j.bbagrm.2014.11.005, Database: ScienceDirect
G9a  G9a (EHMT2) antibody Activity of H3K9 histone methyltransferase G9a is reportedly induced by transforming growth factor-beta1 (TGF-beta1) and plays an important role in the progression of cancer and fibrosis. Inhibition of H3K9 methyltransferase G9a suppresses peritoneal fibrosis through a reduction of H3K9me1. Maeda, Kazuya; Doi, Shigehiro; Nakashima, Ayumu; Nagai, Takuo; Irifuku, Taisuke; Ueno, Toshinori; Masaki, Takao. PLoS ONE. 3/9/2017, Vol. 12 Issue 3, p1-13. 13p. DOI: 10.1371/journal.pone.0173706. , Database: Academic Search Complete
SETDB1  SETDB1 antibody H3K9 KMTase SETDB1 (ESET/KMT1E), which plays an important role in stem cell maintenance is required for H3K9me3 marking and silencing of several ERV subfamilies in mESCs. By Matsumura, Yoshihiro; Nakaki, Ryo; Inagaki, Takeshi; Yoshida, Ayano; Kano, Yuka; Kimura, Hiroshi; Tanaka, Toshiya; Tsutsumi, Shuichi; Nakao, Mitsuyoshi; Doi, Takefumi; Fukami, Kiyoko; Osborne, Timothy F.; Kodama, Tatsuhiko; Aburatani, Hiroyuki; Sakai, Juro. In Molecular Cell. 19 November 2015 60(4):584-596 Language: English. DOI: 10.1016/j.molcel.2015.10.025, Database: ScienceDirect
Ash1   Ash1 antibody Ash1 is a known H3K36-specific histone demethylase that is required for normal Hox gene expression and fertility in Drosophila and mammals. By: Cao, Zhaojun; Yin, Yue; Sun, Xuan; Han, Jun; Sun, Qing peng; Lu, Min; Pan, Jinbao; Wang, Weixiang. BioMed Research International. 9/26/2016, Vol. 2016, p1-9. 9p. DOI: 10.1155/2016/1575430. , Database: Academic Search Complete
RIZ1  RIZ1 (PRDM2) antibody H4K20me1-H3K9me1 trans-tail ‘histone code’. Here we show that PR-Set7 specifically and directly binds the C-terminus of the Riz1/PRDM2/KMT8 tumor suppressor and demonstrate that the N-terminal PR/SET domain of Riz1 preferentially monomethylates H3K9. Congdon, LM; Sims, JK; Tuzon, CT; Rice, JC. NUCLEIC ACIDS RESEARCH; APR, 2014; 42; 6; p3580-p3589, Database: Science Citation Index
H3K9me Readers Find antibody Introduction Reference
LSD1 KDM1 / LSD1 antibody – ChIP Grade Lysine specific demethylase 1: LSD1 is a kind of fiavin adenine dinucleotid FAD dependent amine oxidase and can specifically demethylate H3K4me2/me1 and H3K9me2/me1, thus it can regulate gene transcriptional activity. Recently, function study of LSD1 showed that by regulating the expression of target genes, LSD1 plays an important role in tumorigenesis, embryonic differentiation, and the formation of pluripotent stem cells and so on.  
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.
PHF8  PHF8 antibody PHF8 is localized in the nucleolus and may regulate rRNA transcription. Indeed, PHF8 bound to the promoter region of the rDNA gene. Knockdown of PHF8 reduced the expression of rRNA, and overexpression of the gene resulted in upregulation of rRNA transcript. Concomitantly, H3K9me2 level was elevated in the promoter region of the rDNA gene in PHF8 knockdown cells and reduced significantly when the wild type but not the catalytically inactive H247A mutant PHF8 was overexpressed. Zhu, ZQ; Wang, YR; Li, X; Wang, YQ; Xu, LY; Wang, X; Sun, TL; Dong, XB; Chen, LL; Mao, HL; Yu, Y; Li, JS; Chen, PA; Chen, CD. CELL RESEARCH; JUL, 2010; 20; 7; p794-p801, Database: Science Citation Index
H3K9me Erasers Find antibody Introduction Reference
Tip60  KAT5 / Tip60 antibody A function for H3K9me3 in coordinating activation of Tip60- dependent DNA repair pathways, and imply that aberrant patterns of histone methylation may contribute to cancer by altering the efficiency of DSB repair.  Sun, Yingli; Jiang, Xiaofeng; Xu, Ye; Ayrapetov, Marina K.; Moreau, Lisa A.; Whetstine, Johnathan R.; Price, Brendan D. Nature Cell Biology. Nov2009, Vol. 11 Issue 11, p1376-1382. 7p. 2 Color Photographs, 5 Black and White Photographs, 9 Graphs. DOI: 10.1038/ncb1982. , Database: Academic Search Complete
HP1   Distribution of HP1beta in the embryonic mouse brain is related to that of H3K9me1/me2 but not to that of H3K9me3. Kozubek, Stanislav. Histochemistry & Cell Biology. Apr2016, Vol. 145 Issue 4, p447-461. 15p. DOI: 10.1007/s00418-015-1402-7. , Database: Academic Search Complete
MPP8   M-phase phosphoprotein 8 (MPP8) harbors an N-terminal chromodomain and a C-terminal ankyrin repeat domain. MPP8, via its chromodomain, binds histone H3 peptide tri- or di-methylated at lysine 9 (H3K9me3/H3K9me2) in submicromolar affinity. Chang, YQ; Horton, JR; Bedford, MT; Zhang, X; Cheng, XD. JOURNAL OF MOLECULAR BIOLOGY; MAY 20, 2011; 408; 5; p807-p814, Database: Science Citation Index
CBX1-8  CBX2 antibody

CBX4 antibody

CBX6 antibody

CBX8 antibody

The eight mammalian Cbx proteins are chromodomain-containing proteins involved in regulation of heterochromatin, gene expression, and developmental programs. They are evolutionarily related to the Drosophila HP1 (dHP1) and Pc (dPc) proteins that are key components of chromatin-associated complexes capable of recognizing repressive marks such as trim-ethylated Lys-9 and Lys-27, respectively, on histone H3. However, the binding specificity and function of the human homologs, Cbx1–8, remain unclear. To this end we employed structural, biophysical, and mutagenic approaches to characterize the molecular determinants of sequence contextual methyl-lysine binding to human Cbx1–8 proteins. Although all three human HP1 homologs (Cbx1, -3, -5) replicate the structural and binding features of their dHP counterparts, the five Pc homologs (Cbx2, -4, -6, -7, -8) bind with lower affinity to H3K9me3 or H3K27me3 peptides and are unable to distinguish between these two marks. Additionally, peptide permutation arrays revealed a greater sequence tolerance within the Pc family and suggest alternative non-histone sequences as potential binding targets for this class of chromo domains. Liu, Xing-Yong; Zhang, Xian-Bo; Li, Ming-Hui; Zheng, Shu-Qing; Liu, Zhi-Long; Cheng, Yun-Ying; Wang, De-Shou. In Comparative Biochemistry and Physiology, Part B. January 2017 203:25-34 Language: English. DOI: 10.1016/j.cbpb.2016.09.001, Database: ScienceDirect
Np95  Np 95 (UHRF1) antibody-ChIP Grade Np95 (also known as UHRF1 or ICBP90) has been found to interact with Dnmt1 and to bind hemimethylated DNA, indicating together with genetic studies a central role in the maintenance of DNA methylation. Rottach, A; Frauer, C; Pichler, G; Bonapace, IM; Spada, F; Leonhardt, H. NUCLEIC ACIDS RESEARCH; APR, 2010; 38; 6; p1796-p1804, Database: Science Citation Index
JARID1C  KDM5C/Jarid1C/SMCX antibody histone demethylase JARID1C is frequently inactivated in patients with clear cell renal cell carcinoma (ccRCC) Rondinelli, Beatrice; Rosano, Dalia; Antonini, Elena; Frenquelli, Michela; Montanini, Laura; Huang, DaChuan; Segalla, Simona; Yoshihara, Kosuke; Amin, Samir B.; Lazarevic, Dejan; The, Bin Tean; Verhaak, Roel G.W.; Futreal, P. Andrew; Croce, Luciano Di; Chin, Lynda; Cittaro, Davide; Tonon, Giovanni. In: Journal of Clinical Investigation. Dec 2015, Vol. 125 Issue 12, p4625, 13 p.; American Society for Clinical Investigation Language: English, Database: General OneFile
ATRX  ATRX antibody Loss of ATRX/H3.3 leads to loss of H3K9me3 modification at imprinted DMRs Voon, Hsiao P.J; Hughes, Jim R.; Rode, Christina; De La Rosa-Velázquez, Inti A.; Jenuwein, Thomas; Feil, Robert; Higgs, Douglas R.; Gibbons, Richard J.. In Cell Reports. Aug 2014 Language: English. DOI: 10.1016/j.celrep.2015.03.036, Database: ScienceDirect

 

Reference

(1)Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I., and Zhao, K. (2007). High-resolution profiling of histone methylations in the human genome. Cell 129, 823-837.
(2)Kallestad L, Christensen K, Woods E, Milavetz B. Transcriptional repression is epigenetically marked by H3K9 methylation during SV40 replication. Clinical Epigenetics. 2014;6(1):21. doi:10.1186/1868-7083-6-21.
(3)Pinheiro I, Margueron R, Shukeir N, Eisold M, Fritzsch C, Richter FM, Mittler G, Genoud C, Goyama S, Kurokawa M, et al. Prdm3 and Prdm16 are H3K9me1 methyltransferases required for mammalian heterochromatin integrity. Cell. 2012;150:948–960.