To determine if lincRNAs interact with additional chromatin proteins, we systematically analysed chromatin-modifying proteins that have been shown to play critical roles in ESCs18–21,42. Specifically, we screened antibodies against 28 chromatin complexes (see Methods, Supplemental Figure 14, Supplemental Table 18) and identified 11 additional chromatin complexes that are strongly and reproducibly associated with lincRNAs (see Methods, Supplemental Figure 15, 16). These chromatin complexes are involved in ‘reading’ (PRC1, Cbx1, and Cbx3), ‘writing’ (Tip60/P400, PRC2, Setd8, ESET, and Suv39h1), and ‘erasing’ (Jarid1b, Jarid1c, and HDAC1) histone modifications, as well as a chromatin-associated DNA binding protein (YY1) (Figure 5a). Altogether, we found that 74 (~30%) of the ESC lincRNAs are associated with at least one of these 12 chromatin complexes (Figure 5b, Supplemental Table 17). While most of the identified interactions are with repressive chromatin regulators, this is likely due to limitations of our selection criteria and available antibodies.
