Many lincRNAs are strongly associated with multiple chromatin complexes (Figure 5b). For example, we identified 8 lincRNAs that bind to the PRC2 H3K27 and ESET H3K9 methyltransferase complexes (‘writers’ of repressive marks) and the Jarid1c H3K4 demethylase complex (an ‘eraser’ of activating marks). Consistent with this, the PRC2 and ESET complexes have been reported to bind at many of the same ‘bivalent’ domains21 and to functionally associate with the Jarid1c complex43. Similarly, we identified a distinct set of 17 lincRNAs that bind to the PRC2 complex (‘writer’ of K27 repressive marks), PRC1 complex (‘reader’ of K27 repressive marks), and Jarid1b complex (‘eraser’ of K4 activating marks) (Figure 5b), as well as other functionally consistent ‘reader’, ‘writer’, and ‘eraser’ combinations (Supplemental Figure 17). One of several potential models consistent with this data is that lincRNAs may bind to multiple distinct protein complexes, perhaps serving as ‘flexible scaffolds’ to bridge functionally related complexes as previously described for telomerase RNA44.
