Extended Data Fig. 7: Malat1 interacts directly with DNA sequences near subsets of differentially expressed genes.

a, RNA retrieval displayed as percentage of Gapdh (negative control) and Malat1 in Odd, Even, and LacZ pulldown samples (n = 3 independent experiments). Probe sequences are listed in Supplementary Table 6. b, GREAT MSigDB pathway analysis of genes identified by Malat1 ChIRP. c, Venn diagram showing the substantial overlap between genes identified by Malat1- ChIRP and genes differentially expressed genes upon Malat1 KO. d, RT-qPCR analysis of the expression of Serpins in 4T1 cells (n = 3 independent experiments). e, RT-qPCR analysis of ChIRP DNA shows retrieval of Serpinb6b DNA with a Malat1-specific probe, but not the LacZ probe. Gapdh served as a negative control (n = 3 independent experiments). f, The expression of Wnts and Serpins was analyzed RT-qPCR in WT or Malat1 KO 4T1 cells (n = 3 independent experiments). g, Malat1 ChIRP-seq peaks in WT 4T1 cells were mapped to the genome tracks of Serpinb6b, Wnt3, Wnt6, and Wnt9b by using the UCSC genome browser. h, An enrichment map of proteins identified by Malat1 ChIRP-MS was generated by using g:Profiler. Clusters of nodes were automatically labeled by using the AutoAnnotate application. i, Immunofluorescence staining of YAP under the indicated conditions. Nuclei were counter stained with DAPI. Images are the representative of three independent experiments. j and k, Western blot (j) and RT-qPCR (k) analysis of YAP signaling-associated proteins and mRNAs (n = 3 independent experiments). P values in a and k were calculated using a two-way ANOVA with multiple comparisons, in d using a two-tailed, unpaired Student’s t-test and in e and f using a one-way ANOVA with multiple comparisons. Data are presented as mean values +s.e.m.