2016 November 17 | Jesse M. Engreitz, Jenna E. Haines, Elizabeth M. Perez, Glen Munson, Jenny Chen, Michael Kane, Patrick E. McDonel, Mitchell Guttman, Eric S. Lander
The study investigates the local regulation of gene expression by long noncoding RNAs (lncRNAs) through their promoters, transcription, and splicing. Using genetic manipulations, the researchers analyzed 12 genomic loci that produce lncRNAs and found that 5 of these loci influence the expression of a neighboring gene in cis, without requiring the specific lncRNA transcripts themselves. These effects were mediated by general processes associated with lncRNA production, such as enhancer-like activity of gene promoters, transcription, and splicing. Additionally, 4 out of 6 protein-coding loci also influenced the expression of a neighbor, demonstrating that 'crosstalk' among neighboring genes is a prevalent phenomenon. The mechanisms underlying these effects include DNA regulatory elements in promoters, transcription-related processes, and RNA splicing. The study suggests that lncRNA loci can encode multiple independent categories of functions, and that the evolutionary origins of some lncRNAs may involve non-functional byproducts or co-transcriptional processes. These findings highlight the importance of *cis* regulatory connections in mammalian gene regulatory networks.The study investigates the local regulation of gene expression by long noncoding RNAs (lncRNAs) through their promoters, transcription, and splicing. Using genetic manipulations, the researchers analyzed 12 genomic loci that produce lncRNAs and found that 5 of these loci influence the expression of a neighboring gene in cis, without requiring the specific lncRNA transcripts themselves. These effects were mediated by general processes associated with lncRNA production, such as enhancer-like activity of gene promoters, transcription, and splicing. Additionally, 4 out of 6 protein-coding loci also influenced the expression of a neighbor, demonstrating that 'crosstalk' among neighboring genes is a prevalent phenomenon. The mechanisms underlying these effects include DNA regulatory elements in promoters, transcription-related processes, and RNA splicing. The study suggests that lncRNA loci can encode multiple independent categories of functions, and that the evolutionary origins of some lncRNAs may involve non-functional byproducts or co-transcriptional processes. These findings highlight the importance of *cis* regulatory connections in mammalian gene regulatory networks.