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.