Fig. 6: The effect of TDP-43 binding on gene expression in L2C and the interaction between TDP-43 and Cyclin T1.
From: Maternal TDP-43 interacts with RNA Pol II and regulates zygotic genome activation
a The enrichment of TDP-43 at the promoter of DEGs identified in control and Tdp43oKO late two-cell embryos. All tests were run with two-sided Wilcoxon rank-sum. P-value were shown. DEGs, different expression genes; RPKM, reads per kilobase million; Up, Down, and Other, up-, down-regulated and other genes; TSS, transcription start site. b The box plots showing the mRNA fold-changes (log 2 ratio) for all genes at the promoters in control and Tdp43oKO (oKO) L2C. The promoters were characterized as Supplementary Fig. 7f (Unbound, 15325 genes; Q1, 1843 genes; Q2, 1847 genes, Q3, 1850 genes; Q4, 1848 genes). Upper and lower line of the box representing the 25th and 75th percentiles. Whiskers showing 1.5X interquartile range. Central line, the median. The tests were run with the two-sided Wilcoxon rank-sum. c The box plots showing the mRNA fold-changes (log 2 ratio) for major ZGA genes at the promoters in control and Tdp43oKO (oKO) L2C. The promoters of major ZGA genes were characterized by unbound or bound TDP-43. Upper and lower line of the box represent the 25th and 75th percentiles. Whiskers show 1.5X interquartile range. Central lines represent the median. The test was run with the two-sided Wilcoxon rank-sum. d, e Western blotting of the Co-IP products with Flag (d) or Myc (e) antibody. 293t cells were transfected with different vectors for Co-IP experiments. Flag-TDP-43, TDP-43 labeled with Flag; Myc-Ccnt1, Ccnt1 labeled with Myc and EGFP. f The PLA for the interaction between TDP-43 and Ccnt1 detected with the specific antibodies in control and Tdp43oKO L2C (n ≥ 22). Scale bar, 10 μm. g The PLA for the interaction between TDP-43 and Ccnt1 in control and oKO (Tdp43 oKO) E2C embryos (n ≥ 15) at different time points. pHCG post HCG, h hours. Scale bar, 10 μm.
