Fig. 4

Dynamics of chromatin architecture-related proteins involved in the formation of Nanog chromatin loop during cell differentiation. a Scheme of the engineered chromatin immunoprecipitation (enChIP) 3× FLAG-dCas9 technique. b Chromatin immunoprecipitation (ChIP) for FLAG binding to the Nanog x45s and x14s Alus were done in NTERA2-wt cells left untreated (UT) or treated with 1 µM of RA for 48 h. ChIP was quantified by qPCR using specific oligonucleotides (see Additional file 3: Table S2). Input DNAs and immunoprecipitation without specifics antibodies were also preformed. c Table of main NANOG chromatin loop interacting proteins obtained with enChIP-dCas9 proteomic analysis (complete information enclosed in Additional file 3: Table S2). d Chromatin immunoprecipitation (ChIP) for CHAF1B, DDX5, KSRP, LAMIN A/C and PRMT1 binding to the Nanog x45s and x14s Alus were done in NTERA2-wt cells left untreated (UT) or treated with 1 µM of RA for 48 h. ChIP was quantified by qPCR using specific oligonucleotides (see Additional file 3: Table S2). Input DNAs and immunoprecipitation without specifics antibodies were also preformed for normalization and negative controls, respectively. Three biological replicates and three experimental replicates were done for panels B and D. *P < 0.05, **P < 0.01 and ***P < 0,001. Data are shown as mean ± SD