lncRNA read-through regulates the BX-C insulator .

Though long non-coding RNAs (lncRNAs) represent a substantial fraction of the Pol II transcripts in multicellular animals, only a few have known functions. Here we report that the blocking activity of the Bithorax complex (BX-C) boundary is segmentally regulated by its own lncRNA. The boundary is located between the () gene and the regulatory domain, which is responsible for regulating expression in parasegment PS6/segment A1. consists of two hypersensitive sites, and is an insulator while functions primarily as an lncRNA promoter. To activate expression in PS6/A1, enhancers in the domain must be able to bypass blocking activity. We show that the expression of the lncRNAs in PS6/A1 from the promoter inactivates insulating activity. Inactivation is due to read-through as the promoter must be directed toward to disrupt blocking.