The insulating activity of theDrosophilaBX-C chromatin boundaryFub-1is parasegmentally regulated by lncRNA read-through

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)Fub-1boundary is segmentally regulated by its own lncRNA. TheFub-1boundary is located between theUltrabithorax(Ubx) gene and thebxd/pbxregulatory domain, which is responsible for regulatingUbxexpression in parasegment PS6/segment A1.Fub-1consists of two hypersensitive sites,HS1andHS2. HS1is an insulator whileHS2functions primarily as a lncRNA promoter. To activateUbxexpression in PS6/A1 enhancers in thebxd/pbxdomain must be able to bypassFub-1blocking activity. We show that expression of theFub-1lncRNAs in PS6/A1 from theHS2promoter inactivatesFub-1insulating activity. Inactivation is due to readthrough as theHS2promoter must be directed towardsHS1to disrupt blocking.