TY - JOUR T1 - Neighborhood regulation by lncRNA promoters, transcription, and splicing JF - bioRxiv DO - 10.1101/050948 SP - 050948 AU - Jesse M. Engreitz AU - Jenna E. Haines AU - Glen Munson AU - Jenny Chen AU - Elizabeth M. Perez AU - Michael Kane AU - Patrick E. McDonel AU - Mitchell Guttman AU - Eric S. Lander Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/04/28/050948.abstract N2 - Mammalian genomes are pervasively transcribed to produce thousands of spliced long noncoding RNAs (lncRNAs), whose functions remain poorly understood. Because recent evidence has implicated several specific lncRNA loci in the local regulation of gene expression, we sought to determine whether such local regulation is a property of many lncRNA loci. We used genetic manipulations to dissect 12 genomic loci that produce lncRNAs and found that 5 of these loci influence the expression of a neighboring gene in cis. Surprisingly, however, none of these effects required the specific lncRNA transcripts themselves and instead involved general processes associated with their production, including enhancer-like activity of gene promoters, the process of transcription, and the splicing of the transcript. Interestingly, such effects are not limited to lncRNA loci: we found similar effects on local gene expression at 4 of 6 protein-coding loci. These results demonstrate that ‘crosstalk’ among neighboring genes is a prevalent phenomenon that can involve multiple mechanisms and cis regulatory signals, including a novel role for RNA splicing. These mechanisms may explain the function and evolution of some genomic loci that produce lncRNAs. ER -