Fig 2: Chd1 may play a role in establishing the Cga NDR.(a) MNase-qPCR and ChIP for (b) Chd1 and (c) Pol2 was carried out in αT3-1 wild-type (WT) cells that express Cga and in αT3-1 cells stably expressing shRNA against eRNA. MNase-qPCR data are analysed and presented as in Fig. 1b, and for ChIP data are as in Fig. 1d. Data are shown as mean±s.e.m., n=2–3.

Fig 3: Promoter-proximal DSBs occur independent of transcription initiation but are dependent on topoisomerase activity.a Gene promoter DSB levels in control and Chd1 KO cells with or without treatment of etoposide. N = 4 biologically independent experiments. Graphs show mean and standard deviation. Statistical tests performed are two-way ANOVA with Sidak’s correction. Values above bars indicate p-values. b Gene promoter DSB levels in control and Chd1 KO cells with or without treatment of triptolide. N = 4 biologically independent experiments. Graphs show mean and standard deviation. Statistical tests performed are two-way ANOVA with Sidak’s correction. Values above bars indicate p-values. c Proposed model for how Chd1 may protect genome integrity at transcribed promoters by preventing DNA break accumulation during hypertranscription in ES cells. See text for details.

Fig 4: Chd1 interacts with double-stranded DNA repair proteins in ES cells.a Putative Chd1 interactors, identified by IP-mass spectrometry using a Chd1-Flag knock-in ES cell line. IgG IP was performed as negative control. Each dot denotes an identified protein. Green dots indicate proteins that are significantly enriched in Chd1 IP vs IgG IP. Gray dots indicate detected, but not significantly enriched, proteins. Previously documented interactors of Chd1 are indicated in blue boxes. Key proteins involved in DNA repair are indicated in cream boxes. Trim28, an interactor identified in the 250 mM salt IP (Supplementary Fig. 1) is indicated in the gray box. The posterior error probability (PEP) score denotes the probability that the identified peptide is correct. False discovery rate was set to 1%. (Full list is available in Supplementary Data 1. b Gene ontology analysis of co-immunoprecipitated proteins. Selected pathways are shown. The color scale shows the adjusted p value of the enriched pathways. Full list is available in Supplementary Data 2. c Protein interaction network of factors co-immunoprecipitated with Chd1 and belonging to the gene ontology term “DNA repair”. Colors are randomly assigned to genes. d Co-IP validation of the interaction of Chd1 with selected DNA repair proteins. Figure is representative of two biologically independent experiments.

Fig 5: The function of miR-212-3p is associated with the regulation of hepatic FGF21. (A and B) miR-212-3p mimics the effects of exercise on MAFLD by regulating the FGF21 pathway, but not CHD1. (C) The inhibition of miR-212-3p suppresses lipogenesis, whereas the overexpression of miR-212-3p promotes lipogenesis. (D-I) Protein quantification of FGF21, EGR1, CHD1, p-ERK1/2, FASN and CPT1α. (J) Relative mRNA levels of FASN, CPT1α and EGR1. (K) Serum ELISA levels of FGF21. (L) Immunohistochemistry of FGF21. The positive areas are marked by triangles. The data are presented as the mean ± SEM. *P<0.05, **P<0.01 and ***P<0.001. NS, not significant; FGF21, fibroblast growth factor 21; CHD1, chromodomain helicase DNA binding protein 1; EGR1, early growth response 1; FASN, fatty acid synthase; CPT1α, carnitine palmitoyltransferase 1α; HFD, high-fat diet; HE, high-fat diet and exercise; SP, serotype (mice that received the tail vein injection of recombinant adeno-associated virus serotype 8 gene vectors).