Supplementary Figure 5: HDAC3 deacetylase-null mutant induces H3K27ac change at pluripotency loci in OSKM reprogramming.

(a) Radial plots indicating the genomic distribution of H3K27ac peaks in relation to the TSS. Each radial plot indicates the locations of H3K27ac on the indicated days, the left set of plots are MEFs transduced with OSKM and empty vector in serum+Vc, whereas the right set are MEFs with OSKM and HDAC3-YF. (b) Genome views of H3K27ac tag density at Nanog and Zic2 (note that the 2610035F20Rik gene beside Zic2 is an antisense long intergenic non-coding RNA that shares the TSS with Zic2) in cells transduced with OSKM and HDAC3-YF or empty vector in serum+Vc. (c) ChIP-qPCR analysis of H3K27ac at the Nanog and Zic2 promoters on days 5, 9, and 13 of MEFs tranduced with OSKM and HDAC3-YF or empty vector in serum+Vc. Data are the mean ± s.e.m. (n=3 biological replicates with 3 technical replicates each), P value was calculated using two-tailed unpaired Student’s t-test, ** indicates P value <0.01. (d) ChIP-qPCR for HDAC3-YF binding at Nanog and Zic2 promoters in MEFs transduced with OSKM and HDAC3-YF-FLAG or empty vector on day 9 in serum+Vc. Data are the mean ± s.e.m. (n=3 biological replicates with 3 technical replicates), P value was calculated using two-tailed unpaired Student’s t-test, * indicates P value <0.05. (e) RT-qPCR detection of the expression of Nanog and Zic2 on days 5, 9, and 13 of OSKM reprogramming in serum+Vc. Data are the mean ± s.e.m. (n=3 biological replicates with 3 technical replicates each). (f) Genome views of the level of H3K27ac at the indicated somatic loci (S100a4, Col6a1, and Acta2) in MEFs, OG2 ESCs, and MEFs transduced with OSKM and HDAC3-YF or empty vector in serum+Vc.