ASAR RNAs control replication through interactions with dozens of RNA binding proteins

AbstractASARs are a family of very-long noncoding RNAs that control replication timing on individual human autosomes, and are essential for chromosome integrity. The eight known ASAR genes express RNAs that remain localized to their parent chromosomes. Analysis of eCLIP data revealed >30 nuclear matrix/RNA binding proteins (RBPs) that interact with multiple ASAR RNAs. An ∼7kb domain within the ASAR6-141 RNA shows a striking density of RBP interaction sites. Genetic deletion and ectopic integration assays indicate that the ∼7kb RNA binding protein domain contains functional sequences for controlling replication timing of entire chromosomes in cis. Depletion of 10 different ASAR-associated RBPs results in loss of the chromosome territory localization of ASAR RNAs, and alters the normal synchronous replication timing program on all human autosomes, recapitulating the effect of individual ASAR gene knockouts on a genome-wide scale. Our results indicate that ASAR RNAs serve as an essential RNA scaffold for the assembly of RBP complexes that function in normal chromosome replication and help maintain the structural integrity of each mammalian chromosome.