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20 protocols using ab2621

1

ChIP-Seq for Histone Modifications

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ChIP was performed as described previously (Bernt et al., 2011 (link)). Briefly, crosslinking was performed with 1% formalin, and the cells were lysed in SDS buffer. Sonication was used to fragment DNA. ChIP for H3K79me1, H3K79me2, H3K79me3, and H3K27me3 was performed using the antibodies ab2886, ab3534, ab2621 (Abcam) and 07-449 (Millipore) specific to the respective modifications. Eluted DNA fragments were analyzed by qPCR, or subjected to sequencing using next-generation Ilumina sequencing. More details can be obtained in the supplemental methods section.
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2

Comprehensive Protein Detection and Histone Modification Analysis

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To identify histone modifications, acid extraction of histone was performed as previously reported [48 (link)]. To detect other proteins, cells were extracted with lysis buffer (50 mM Tris-HCl, 250 mM NaCl, 5 mM EDTA, 50 mM NaF, 1.5 mM PMSF and protease inhibitors cocktail). Equal amounts of protein were size fractionated on 6.0 to 15.0% SDS-PAGE gel. The antibodies used were anti-COX-2 (sc-19999, Santa Cruz), anti-c-Fos (ab7963, Abcam), anti-c-Jun (sc-44, Santa Cruz), anti-KMT3A (ab31358, Abcam), anti-KMT3B (17-10264, Merck Millipore), anti-KDM2A (ab31739, Abcam), anti-KDM2B (ab108276, Abcam), anti-KDM4A (ab70786, Abcam), anti-KDM4B (ab80473, Abcam), anti-NF-κB (sc-372G, Santa Cruz), anti-p300 (H-272, Santa Cruz), anti-CEBPβ (sc-150, Santa Cruz), anti-H3K4me1/2/3 (ab8895/ab7766/ab1012, Abcam), anti-H3K9me1/2/3 (ab9045/ab1220/ab8898, Abcam), anti-H3K27me1/2/3 (ab113671/ab24684/ab6002, Abcam), anti-H3K36me1/2/3 (ab9048/ab9049/ab9050, Abcam), anti-H3K79me1/2/3 (ab2886/ab3594/ab2621, Abcam), anti-H4K20me1/3 (ab9051/9053, Abcam), anti-histone H3 (ab131711, Abcam) and anti-β-actin (sc-1615, Santa Cruz).
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3

Comprehensive Western Blotting Antibody Panel

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The following antibodies used in Western blotting were purchased from Cell Signaling Technology (Danvers, MA, USA): anti-HA-tag (6E2) (1:1000, #2367, Cell Signaling Technology), anti-p53 (7F5) (1:1000, #2527, Cell Signaling Technology), anti-DDB-1 (D4C8) (1:1000, #6998, Cell Signaling Technology), anti-DDB-2 (D4C4) (1:1000, #5416, Cell Signaling Technology) anti-ERCC1 (1:1000, #3885, Cell Signaling Technology), and anti-XPC (D1M5Y) (1:1000, #14768, Cell Signaling Technology). The Polyclonal anti-KMT4/DOT1L (1:2000, ab72454, Abcam) antibody, anti-XPA (1:2000, ab85914, Abcam), polyclonal di-methylated H3K79 antibody (1:1000, ab3594, Abcam), polyclonal to mono-methylated H3K79 antibody (1:500, ab2886, Abcam), and polyclonal tri-methylated H3K79 antibody (1:1000, ab2621, Abcam) were purchased from Abcam. TFIIH p62 Antibody (1:500, Q-19) was purchased from Santa Cruz Biotechnologies, Inc. Other antibodies include monoclonal Anti-β-Actin-Peroxidase antibody (1:25000, AC-15, Sigma Aldrich), monoclonal ANTI-FLAG® M2 antibody (1:1000, Sigma Aldrich), and anti-H3 (1:500, 865R2, Thermo Fisher Scientific Inc.). Most important uncropped blot images are shown in Supplementary Fig. 11.
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4

Quantitative Western Blot Analysis

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Western blot was performed as previously described [40 (link)]. The antibodies used were listed as below: DOT1L (ab64077, Abcam), CDK2 (2546, CST), Cyclin A2 (4656, CST), PCNA (13110, CST), GAPDH (51332, CST), c-Myc (5605, CST), H3K79me1 (ab2886, Abcam, Cambridge, MA, USA), H3K79me2 (ab3594, Abcam), H3K79me3 (ab2621, Abcam), and H3 (17168-1-AP, Proteintech, Wuhan, China). Gray ratio of each blot was analyzed by using the Image J ver. 1.46 software and protein/GAPDH or protein/H3 ratio was shown.
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5

Western Blot Analysis of Knock-in Cell Lines

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For Western blot, whole cell lysate of knock-in cell lines were extracted as described elsewhere [26 ]. 30 μg or 150 μg total protein extract was loaded on SDS-PAGE gel (BIO-RAD, USA) to separate the proteins according to their sizes. The proteins from the gel were then transferred to a PVDF membranes and incubated with primary antibodies of Flag (1:1000, F3165, Sigma), DOT1L (1:4000, A300-953A, Bethyl), H3K79me2 (1:1000, Ab3594, Abcam), H3K79me3 (1:1000, Ab2621, Abcam) and β-actin (1:5000, A5441, Sigma) at 4 C overnight. After washing with 1 × TBST (BIO-RAD, USA), the membranes were incubated with horseradish peroxidase-labeled secondary antibodies (GE healthcare, UK and EPITOMICS, USA) and then detected with ECL western blotting detection reagent (GE healthcare, UK).
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6

Investigating Epigenetic Regulation by DOT1L

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The following antibodies were used for immunoprecipitation and Western blot analyses: C-terminal anti-ERα (F-10 sc-8002, Santa Cruz Biotechnology, Dallas, Texas), rabbit anti-estrogen Receptor Alpha (ab32063, Abcam, Cambridge, UK), rabbit polyclonal anti-DOT1L (A300-953A, Bethyl Laboratories, Montgomery, Alabama), β-actin (A1978, Sigma Aldrich, Milan, Italy), Rabbit anti-KMT4/DOT1L (ab72454), anti-Histone H3, total, (ab1791), anti-H3K79me1 (ab2886), anti-H3k79me2 (ab3594), anti-H3K79me3 (ab2621), anti-H3K4me3 (ab7766), anti-H3K27me3 (ab24684) from Abcam, anti-Rabbit IgG Isotype Control (31235, Thermo-Fisher), and the anti-Mouse IgG antibody (RM104, Aurogene, Rome, Italy).
Cells were treated with the following compounds: DOT1L inhibitors EPZ004777 (S7353), Pinometostat (EPZ5676)(S7062), SGC0946 (S7079), all from Selleckchem, and with 4-hydroxytamoxifen (4-OHT) (H7904, Sigma-Aldrich), Fulvestrant (ICI 182,780) (I4409, Sigma-Aldrich), and β-estradiol (E887-5G, Sigma-Aldrich) or vehicles (DMSO and/or EtOH), according to different experimental settings.
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7

Cps60/Bre2 Isolation and Protein Analysis

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Whole-cell extracts were prepared and subjected to Western blotting. IgG Sepharose was used to isolate Cps60/Bre2 from nuclear extracts. Immunoprecipitations were assayed by Western blotting with antibodies to Set1, the Flag epitope on Set1, or the TAP tag on Cps60/Bre2. TAP purification of Cps60 was performed as previously described (Miller et al. 2001 (link); Takahashi et al. 2011 (link)).
For LEO1 complementation, cells containing the pRS315 vector bearing LEO1 under the control of the GAL1 promoter were cultured in SD medium deficient of leucine overnight at 30°C, transferred to synthetic medium containing dextrose and galactose, respectively, and incubated for 6 h at 30°C. Cell extracts were prepared and analyzed by Western blotting. Antibodies were generated by our laboratory except for anti-H3K79me3 (Abcam, ab2621), anti-monoubiquitinated histone H2B (Cell Signaling Technology, #5546), anti-TAP (Thermo Scientific, CAB1001), and the M2 anti-Flag antibody (Sigma, F3165).
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8

Chromatin Modification Antibody Validation

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Antibodies against H3K79me1 (ab2886), H3K79me2 (ab3594), H3K79me3 (Abcam; ab2621), H3K27me2 (07-452), caspase3 (04-439), H2BK120ub (17-650), H3K4me2 (07-030), H3K9me2 (Millipore ;07-441), NSD2/MMSET (EpicypherTM ;13-0002), GAL4 (sc-577), β-actin (sc-47778), c-myc (sc-40), MEIS1/2 (sc-10599), GFP (sc-9996), H3 (sc-8654), His (sc-53073), and HA (Santa Cruz Biotechnology; sc-805) were employed.
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9

Colorectal Tissue Profiling with IHC

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Colorectal tissues (45) and normal colon tissues (N = 46) in a tissue microarray (CO1002b) were provided by US Biomax Inc. (Rockville, MD, USA) through the agency, the Alenabio Inc. (Xi’an, Shaanxi). Hematoxylin-eosin (H&E) and immunocytochemistry (IHC) were performed as previously described [41 (link)]. Antibodies used were the following: DOT1L (ab64077, Abcam), c-Myc (ab32072, Abcam), Ki67 (ab15580), H3K79me1 (ab2886, Abcam), H3K79me2 (ab3594, Abcam), and H3K79me3 (ab2621, Abcam). Signal-positive rate was calculated by using the IHC profiler in the Image J ver.1.46 software.
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10

Histone Methylation Analysis in Leukemia

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1×106 NUP98-NSD1 and HM-2 cells in required medium with 10% FBS and 1% Pen Strep were collected, washed, and whole cell lysate was prepared using RIPA lysis buffer supplemented with 1X proteinase inhibitor cocktail. For compound-treated samples, 1×105 NUP98-NSD1 cells or 1×104 HM-2 cells in required medium with 10% FBS and 1% Pen Strep were seeded in 24-well culture plates in 1 ml medium and treated with indicated doses of BT5 for 4 days. Cells were collected, counted and re-plated at initial cell density with fresh medium and compound for another 4 days. On day 8, cells were collected, washed, and whole cell lysate was prepared using RIPA lysis buffer supplemented with 1X proteinase inhibitor cocktail. Western blot detection of histone H3K36me2 (Cell signaling technology #2901S, clone CZ5H12, dilution 1:2,000), histone H3K36me3 (Cell signaling technology, #4909S, clone D5A7, dilution 1:2,000), histone H3K27me3 (Cell signaling technology, #9733S, clone C36B11, dilution 1:2,000), H3K79me3 (abcam, #ab2621, dilution 1:2,000) was performed using 12% SDS-PAGE gel. Total H3 (abcam, #ab1791, dilution 1:50,000) and Actin (Santa Cruz, #sc-47778, dilution 1:10,000 or Genescript, #A00702, dilution 1:10,000) were used as loading controls.
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