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. 2021 Aug 20;12:5056. doi: 10.1038/s41467-021-25326-8

Fig. 5. SALL4 and HDAC2 interact and have a set of common target genes in melanoma cells.

Fig. 5

a Western blot for SALL4 and HDAC2 after Co-Immunoprecipitation (Co-IP) with a SALL4 antibody in the human melanoma cells M010817. Experiment has been repeated independently with similar results two times. b CUT&RUN (C&R) in M010817 cells with two antibodies against SALL4 (SALL4_Ab#1 (S_Ab#1) and SALL4_Ab#2 (S_Ab#2)) and two antibodies against HDAC2 (HDAC2_Ab#1 (H_Ab#1) and HDAC2_Ab#2 (H_Ab#2)) and Ctrl (anti-FLAG) visualized as read density heatmaps of the centered peaks (within 10 kb) for all loci showing peaks with at least 3 of the 4 (2x SALL4, 2x HDAC2) antibodies. c C&R peak numbers called with SEACR for single antibodies, shared between antibodies and shared between at least 3 of the 4 SALL4-HDAC2 antibodies. In total 3319 loci contained peaks for at least 3 of 4 antibodies tested and were found in total 2301 different genes. Those peaks were used for further analyses correlating the direct targets with either expression (Fig. 6a, b) or acetylation status (Fig. 7h). d Annotation of C&R peaks to genetic regions. Green: the 5019 SALL4_Ab#1 and SALL4_Ab#2 shared peaks; yellow: the 1925 HDAC2_Ab#1 and HDAC2_Ab#2 shared peaks; grey: the 3319 peaks shared between at least 3 of the 4 SALL4_Ab#1, SALL4_Ab#2, HDAC2_Ab#1, and HDAC2_Ab#2 antibodies. TTS: transcription termination site, TSS: transcription start site, UTR: untranslated region. e–i Specific gene tracks visualized with IGV. Green: SALL4_Ab#1 and SALL4_Ab#2; yellow; HDAC2_Ab#1, and HDAC2_Ab#2. Red dashed lines highlight significantly called peaks (with at least 3 of 4 antibodies). j Selected de novo DNA binding motifs of SALL4-HDAC2 (at least 3 of 4 antibodies) shared peaks analyzed by HOMER. Source data for a and d are provided as a Source Data file.