RNA in situ conformation sequencing reveals novel long-range RNA structures with impact on splicing

RNA contacts. (A) Digestion and religation of RNA strands adjacent to a PCCR result in RNA contacts (in the form of split reads) supporting the PCCR from the inner (2–3) or the outer (1–4) side. (B) The inner (I) and the outer (O) contacts correspond to the inner and outer arcs with respect to the RNA structure. The outer and the inner contacts are represented by neo-junctions and chimeric split reads, respectively.