Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction

Nuclear chromosomes transcribe far more RNA than required to code for protein. Here we investigate whether non-coding RNA broadly contributes to cytological-scale chromosome territory architecture. We develop a procedure that depletes soluble proteins, chromatin and most nuclear RNA from the nucleus, but does not delocalize XIST, a known architectural RNA, from an insoluble chromosome “scaffold.” RNA-seq analysis reveals most RNA in the nuclear scaffold is repeat-rich, non-coding, and predominantly derived from introns of nascent transcripts. This repeat-rich (C0T-1) RNA inversely correlates with chromatin compaction in normal and experimentally manipulated nuclei, demonstrating RNA physically antagonizes a propensity for chromatin to condense. C0T-1 hnRNA co-distributes on euchromatin with several known scaffold proteins including scaffold attachment factor A (SAF-A). We further show that RNA is required for SAF-A to interact with chromatin and to form structurally embedded scaffold-attachment regions (SARs) in the nuclear genome. Collectively, results indicate nascent transcripts serve a dynamic structural role in the open architecture of active chromosome territories RNA-sequencing and DNA-sequencing of TIG-1 cells after subnuclear fractionation