Our data suggest a model whereby a distinct set of lincRNAs is transcribed in a given cell type and interacts with ubiquitous regulatory protein complexes to form cell-type-specific RNA-protein complexes that coordinate cell-type specific gene expression programs (Figure 6). Because many of the lincRNAs studied here interact with multiple different protein complexes, they may act as cell-type specific ‘flexible scaffolds’44 to bring together protein complexes into larger functional units (Figure 6). This model has been previously demonstrated for the yeast telomerase RNA44 and suggested for the XIST45 and HOTAIR46 lincRNAs. The hypothesis that lincRNAs serve as flexible scaffolds could explain the uneven patterns of evolutionary conservation seen across the length of lincRNA genes3: the more highly conserved patches could correspond to regions of interaction with protein complexes.
