Architectural RNA in chromatin organization

Abstract

RNA plays a well-established architectural role in the formation of membraneless interchromatin nuclear bodies. However, a less well-known role of RNA is in organizing chromatin, whereby specific RNAs have been found to recruit chromatin modifier proteins. Whether or not RNA can act as an architectural molecule for chromatin remains unclear, partly because dissecting the architectural role of RNA from its regulatory role remains challenging. Studies that have addressed RNA's architectural role in chromatin organization rely on in situ RNA depletion using Ribonuclease A (RNase A) and suggest that RNA plays a major direct architectural role in chromatin organization. In this review, we will discuss these findings, candidate chromatin architectural long non-coding RNAs and possible mechanisms by which RNA, along with RNA binding proteins might be mediating chromatin organization.

Keywords: architectural RNA; chromatin; compaction; heterochromatin; nuclear bodies; phase separation.

Figure 1.. Schematic showing indirect regulatory and direct architectural role of RNA in chromatin organization.

RNA is known to recruit chromatin modifiers such as histone modifying enzymes, chromatin remodelers and chromatin compacting proteins (Left). RNA can also act as a tether to fold or compact chromatin by direct interactions (Right). In situ RNA depletion by RNase A treatment leads to loss of total nuclear RNA, while keeping the RNA-independent nuclear structures intact. The regions organized into specific chromatin configurations by architectural RNA will lose their structure upon RNA depletion while the regions maintained by chromatin modifiers proteins with not.

Figure 2.. In situ RNase A digestion approach to probe RNA's architectural role in chromatin/genome organization.

Cell permeabilization with detergents renders chromatin modifying enzymes inactivate. Upon in situ RNA depletion by RNase A treatment, histones remain stably bound to DNA in the nucleosomes suggesting that the primary chromatin structure remains unaffected by RNase A treatment [39]. However, the higher order chromatin structure may be affected by the loss of RNA. Whether or not architectural RNA maintains the higher order organization of nuclear structures including chromatin, can be investigated by in situ techniques such as cytological visualization, Cleavage Under Targets and Release Using Nuclease (CUT&RUN) [40] and Hi-C [41], in the control and RNase A treated cells.

Figure 3.. Architectural RNA and chromatin organization.

Architectural RNAs may contribute to heterochromatin organization by facilitating compaction and possibly LLPS and to chromatin loop formation by tethering CTCF to distant loci. Nucleosomal arrays are shown from two different chromosomes that are marked in two different colors. Large transparent purple bubbles represent LLPS of compact heterochromatin.