Extended Data Fig. 7: Repeats are de-repressed in absence of DNA methylation but not MBD proteins in neurons. | Nature Genetics

Extended Data Fig. 7: Repeats are de-repressed in absence of DNA methylation but not MBD proteins in neurons.

From: Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation

Extended Data Fig. 7

a, Volcano plot showing differentially expressed repeat subfamilies in MBD-QKO neurons using random assignment of multi mapping reads. Dashed lines indicate two-fold expression change. Repeat subfamilies belonging to ERVK or simple repeats that are differentially expressed (FDR = < 0.01 and |log2FC| >= 1) are colored. b, Same as in a but for DNMT-TKO neurons. c, Reproducibility of IAP expression changes in DNMT-TKO versus WT neurons in all IAP elements annotated by RepeatMasker. Only uniquely mapping RNA-seq reads and elements with more than 8 counts in at least one condition are considered. d, RNA expression of the top six most significant differentially expressed internal sequence of class-2 endogenous retroviruses from b. Only uniquely mapping RNA-seq reads were used. Internal IAP elements selected to have more than 8 counts in at least one condition. Boxplots as in Fig. 2d.

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