ABSTRACT The central mystery that drives our research is how thousands of genes are coordinately regulated during development to provide orchestrated expression programs that define specific cell-types. We hypothesize that this involves establishing stable patterns of heterochromatin and euchromatin which are, in part, controlled at the level of chromosomal domain and nuclear organization. For this MIRA application, we have worked to conceptually integrate research projects which address complementary aspects of our overall vision, focusing on a theme around the role of non-coding RNAs in chromatin regulation. We continue to contribute to the fascinating biology of XIST RNA, which controls inactivation of one X-chromosome in female cells. However, findings over several years motivate our increasing emphasis on the role of repeat-rich “junk” of the genome, the main component of chromosomes. In our view, this part of our genomes is dramatically understudied relative to its potential contribution to the biology and regulation of chromosomes. Based on strong preliminary results, we hypothesize that repeat-rich elements play a role at the DNA level in chromosome architecture, and at the RNA level in regulation of that architecture. Rather than RNA as an occasional modifier of chromatin, our results support that RNA with chromosome structure is more the rule than the exception. In fact, we will investigate whether ubiquitous RNAs are essential to maintaining decondensed and condensed chromatin structure in nuclei. Our preliminary RNAseq analysis supports that long-lived “junk” RNAs are structurally embedded in nuclear structure. In fact, our work is likely to show that, rather than RNA being tethered to chromatin by a scaffold protein, as currently believed, many architectural and regulatory proteins are actually tethered by RNA. This work is supported by a team of collaborators who are leaders in different aspects of RNA, chromatin and computational biology, and who are enthused to work with us on these compelling, potentially paradigm shifting ideas. Although this work is largely of a fundamental nature, aspects of our studies have direct relevance to the translation of this knowledge to the common problem of chromosomal trisomy.