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4 protocols using αh3k27ac

1

Investigating Histone Modifications and DNA-binding Proteins

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The following antibodies were used: α-H3 (Cell Signaling; #4499), α-H3K27Ac (Active Motif; #39685), α-H3K27Ac (Cell Signaling; 8173), α-H4K16Ac (Active Motif; #61529), α-H4K16Ac (Cell Signaling; #13534), anti-G-quadruplex DNA 1H6 (Millipore; #MABE1126), α-MeCP2 (AbCam; #ab2828), α-Pan-Methyl-H3K9 (Cell Signaling; #4473), α-methyl-histone H3K9 (Cell Signaling; #5327), α-RNA Pol II (Santa Cruz Biotechnology; #sc-899), α-APE1 (Novus Biologicals; #NB100-116). The α-NEIL1 antibody was as in (28 (link)); the α-AcNEIL1 antibody was custom-generated through EZBiolab using a chemically synthesized NEIL1 peptide (288APKGRKSRK*K*K*SKA301) with acetylated Lys (*) as hapten to induce IgG antibody in rabbit, as previously described (17 (link)).
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2

Immunostaining of Dechorionated Drosophila Embryos

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Dechorionated embryos were transferred into a 1.5 ml tube with 500 μl heptane, and then 500 μl of freshly prepared 4% formaldehyde in PBS was added. The tube was vigorously shaken for 20 min at room temperature. After removing the lower aqueous layer carefully and as much as possible, 500 μl methanol was added, and the mixture was shaken for 1–2 min. Devitellinized embryos which sank to the bottom were kept and washed with methanol for three times. Fixed embryos were stored at −20 °C in methanol until use. To perform immunostaining, fixed embryos were rehydrated with 500 μl PBST (0.3% Tween-20) for 5 min at room temperature four times. Embryos were blocked in PBST with 3% donkey serum (Sigma-Aldrich) for 30 min. 1:500 rabbit α-H3K27ac (Active Motif, #39133) was then added and incubated at 4 °C overnight. Next, embryos were washed with PBST for 15 min three times, incubated with 1:500 anti-rabbit Alexa Fluor 488 (Thermo Fisher, #A11008) at room temperature for 1 h, washed with PBST for 15 min three times, and mounted on a glass slide in Fluoromount (Sigma-Aldrich, #F4680). Hoechst 33258 (Thermo Fisher, #H3569) was added at 1:2000 during the second wash after secondary antibody incubation.
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3

Chromatin Immunoprecipitation Antibodies

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ChIP-grade antibodies were αH3.3K27me3 (custom antibody made by Proteintech), αH3.3 (Invitrogen RM190), αH3K27me3 (Active Motif 39155), αH3 (Abcam 1791), rabbit IgG (Abcam 171870) (Fig. S5). Additional antibodies used for western blotting (WB) included αH3K27me3 (Abcam 6002), αREST (EMD Millipore 07–579), αH3K4me3 (Abcam 8580), αH3K27ac (Active Motif 39133), and αH3K9me3 (Abcam 8898).
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4

Chromatin Profiling using CUT&RUN and Immunoblotting

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Antibodies used for CUT&RUN are αH2A (Abcam, 15653), αFLAG (Sigma, F1804), αmouse rb IgG (Jackson ImmunoResearch, 315-005-003). Primary antibodies used for immunoblotting include: αγH2Ax (Milipore, ab26350), αFLAG (Sigma, F7425), αH2B (CST, D2H6), αH4 (CST, D2X4V), αH3 (Immunoway, YM3038), αNAP1L1 (Abcam, ab33076), αNAP1L2 (Abnova, H00004674-D01), αSPT16 (Santa Cruz, sc-377028), αSSRP1 (Santa Cruz, sc-74536), αHSC70 (Santa Cruz, sc-7298), αC23 (Santa Cruz, sc-55486), αH2BK120ub (CST, D11), αH2AK119ub (CST, D11), αH3K4me3 (Active Motif, 61379), αH3K36me3 (Immunoway), αH3K36me2 (CST, 29015), αH3K9me3 (Abcam, ab8898), αH3K27me3 (CST, 9733), αH4K16ac (Immunoway, YK0014), αH4K20me3 (Active Motif, 39671), αH3K27ac (Active Motif, 39685), αH3K79me3 (Immunoway, YM3091), αH3K9ac (Immunoway, YK0006), αHA (Santa Cruz, SC7392), αβ-Actin (Immunoway, YM3028). αFLAG M2 Affinity Gel (Sigma), αH2A (Abcam, 15653), and αRpb1 (CST, 14958) were used for ChIP.
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