Monoallelically-expressed Noncoding RNAs form nucleolar territories on NOR-containing chromosomes and regulate rRNA expression

Out of the several hundred copies of rRNA genes that are arranged in the nucleolar organizing regions (NOR) of the five human acrocentric chromosomes, ~50% remain transcriptionally inactive. NOR-associated sequences are speculated to influence the allele-specific expression of rRNAs in non-mammalian systems. However, the mechanism(s) that controls the dosage of active versus inactive rRNA genes in mammals is yet to be determined. Here, we have identified a family of human ncRNAs, SNULs (Single Nucleolus Localized), that form constrained sub-nucleolar territories on the NORs and contributes to differential rRNA expression. SNULs display a sequence similarity to pre-rRNA and shares share the same sub-nucleolar compartment. SNUL RNA territories associate with only one of the two alleles of each NOR-containing chromosomes. Finally, SNULs regulate the rRNA expression by regulatingvia pre-rRNA transcription and sorting. Our study unravels a novel class of ncRNAs that forms nucleolar territories on NORs to achieve differential expression of rRNA genes.