ChIP-Seq for Chromatin Interactions

ChIP was performed as previously described (34 (link)). Immunoprecipitated DNA was quantified by polymerase chain reaction (PCR) using the Syber Green mix (Kapa) and all precipitations, except for those performed on histones and histone modifications, were compared to signals at the H27 site in the 45S rDNA (35 (link)) or to the actin promoter. The primer pairs used are given in the Supplementary Information (Supplementary Tables S2 and S3). Antibodies used were WSTF (Abcam), SNF2h (Abcam), RNA pol III (kind gift from Dr. Henry and from Abcam), TFIIIA (Abcam), TFIIIC220C (Santa Cruz and Abcam), Brf1 (Abnova and Abcam), GCN5 (Abcam), PCAF (Abcam), p300 (Abnova), TRRAP (Santa Cruz), c-Myc (Santa Cruz and Abcam), Max (Santa Cruz and Abcam), RNA pol II CTD (Abcam), H3-Ac, H3K9-Ac, H3K14-Ac, H3K27-Ac, H3K4-me3, H3K9-me3, H3K27-me3, H4, H4K8-Ac and H4K16-Ac (Abcam).

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Sadeghifar F., Böhm S., Vintermist A, & Östlund Farrants A.K. (2015). The B-WICH chromatin-remodelling complex regulates RNA polymerase III transcription by promoting Max-dependent c-Myc binding. Nucleic Acids Research, 43(9), 4477-4490.

Publication 2015

Syber Green mix SNF2h RNA pol III TFIIIA c-Myc RNA pol II CTD H3K9-Ac H3K14-Ac H3K27-Ac H3K4-me3 H3K9-me3 H3K27-me3 H4K8-Ac H4K16-Ac

Actin Antibodies C myc Chip Histone modifications Histones P300 Polymerase chain reaction Primer Rdna Rna pol ii Snf2h Tfiiia Trrap

Corresponding Organization : Stockholm University

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Variable analysis

independent variables

Antibodies used for ChIP: WSTF (Abcam), SNF2h (Abcam), RNA pol III (kind gift from Dr. Henry and from Abcam), TFIIIA (Abcam), TFIIIC220C (Santa Cruz and Abcam), Brf1 (Abnova and Abcam), GCN5 (Abcam), PCAF (Abcam), p300 (Abnova), TRRAP (Santa Cruz), c-Myc (Santa Cruz and Abcam), Max (Santa Cruz and Abcam), RNA pol II CTD (Abcam), H3-Ac, H3K9-Ac, H3K14-Ac, H3K27-Ac, H3K4-me3, H3K9-me3, H3K27-me3, H4, H4K8-Ac and H4K16-Ac (Abcam)

dependent variables

Immunoprecipitated DNA quantified by polymerase chain reaction (PCR) using the Syber Green mix (Kapa)

control variables

Precipitations, except for those performed on histones and histone modifications, were compared to signals at the H27 site in the 45S rDNA (35 (link)) or to the actin promoter
Primer pairs used are given in the Supplementary Information (Supplementary Tables S2 and S3)

controls

Positive control: H27 site in the 45S rDNA and actin promoter
Negative control: Not explicitly mentioned

Annotations

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