The 5' region of RNA has the potential to associate with chromatin through the A-repeat.

X inactive-specific transcript () is a long noncoding RNA that plays an essential role in X chromosome inactivation. Although RNA, like common protein-coding mRNAs, is transcribed by RNA polymerase II, spliced and polyadenylated, it is retained in the nucleus and associates with the X chromosome it originates from. It has been assumed that RNA recruits proteins involved in epigenetic modifications and chromatin compaction to the X chromosome. One of the major proteins constituting the nuclear matrix, hnRNP U, has been shown to be required for the association of RNA with the inactive X chromosome (Xi). In this study, we found that the first 950-nt sequence of RNA had the potential to associate with chromatin in a manner independent of hnRNP U. Furthermore, its chromatin association is apparently dependent on the presence of an intact A-repeat sequence, which is one of the repeats in / RNA conserved among many mammalian species, and has been shown to be important for RNA-mediated silencing. Taking this unexpected finding and a previous study demonstrating the effect of RNA lacking the A-repeat on the formation of the silent heterochromatin domain together, we suggest that the A-repeat captures chromatin near the initial loading site of RNA and relocates it into the core of the heterochromatin domain.