TNRC18 recognizes H3K9me3 to mediate transposable elements silencing at ERV regions [RNA-seq]

Trimethylation of histone H3 lysine 9 (H3K9me3) is critical for regulation of gene repression and heterochromatin formation, cell-fate determination, and organismal development. In particular, H3K9me3 provides an essential mechanism for silencing various transposon elements (TEs). However, previous studies showed that the canonical H3K9me3 readers (e.g. HP1 and MPP8) play rather limited roles in silencing endogenous retroviruses (ERVs), one of major TE classes in the mammalian genome. Here, we report that Trinucleotide Repeat Containing 18 (TNRC18), a previously under-studied chromatin regulator, recognizes H3K9me3 and directly binds ERVs, mediating ERV silencing. Our biochemical, biophysical and structural studies identified the C-terminal Bromo Adjacent Homology (BAH) domain of TNRC18 (TNRC18BAH) as a H3K9me3-specific reader, and its N-terminal segment as a platform for direct recruitment of co-repressors such as TRIM28 and HDAC-Sin3-NCoR complexes, thereby enforcing optimal repression of the H3K9me3-demarcated ERVs. Point mutagenesis that disrupts the TNRC18BAH-mediated H3K9me3 engagement caused neonatal lethality in mice and, in multiple mammalian cell models, led to de-repressed expression of ERVs, affecting the landscape of cis-regulatory elements and thus gene-expression programs. Collectively, this study describes a previously-unknown TNRC18BAH-directed H3K9me3-sensing pathway, which operates to epigenetically silence the evolutionarily young ERVs, thereby exerting profound impacts on host genome integrity, transcriptomic regulation, immunity, and development. We used RNA-seq to assess transcriptomic profiles of HEK293 cells, either mock treated (shCtl), with the knock-down (KD) of endogenous TNRC18 (shTNRC18), or with rescued re-expression of TNRC18 in cells with TNRC18 KD (TNRC18_KD_rescue). RNA-seq analysis was also conducted with the HEK293 cells or mouse embryonic fibroblast (MEF) cells carrying the H3K9me3-binding-defective mutation at TNRC18?s BAH domain, relative to wildtype (WT) controls. The processing of transcriptomic profiles used two different methods for analysis of either regular genes or transposable elements (TEs).