NSP2 INCREASES RNA BACKBONE FLEXIBILITY RELEVANT TO ROTAVIRUS GENOME PACKAGING, AND COMPARATIVE RNA STRUCTURE ANALYSIS AT SPLICEOSOME FOOTPRINTS

RNA is single-stranded and thus, readily basepairs into intricate structures known to regulate many cellular processes. Using SHAPE-MaP RNA structure probing data, I investigated how NSP2, an RNA chaperone, increases the RNA backbone flexibilities of rotaviral genome segments, particularly at nucleotides basepaired in stems. These results provide insight into the incompletely understood process by which all eleven genome segments are stoichiometrically packaged into virions. Next, I examined RNA structure within 87 spliceosome footprints, which span 43 nucleotides around the 5’ splice site and 42 nucleotides around the branchpoint nucleotide. Analysis of DMS-MaP RNA structure probing data revealed that GC-rich footprints form stronger and more persistent structures, particularly at and upstream of the branchpoint nucleotide, which may promote structural openness of polypyrimidine tracts. At GC-rich footprints near 5’ splice sites, stronger structures in exonic regions may stabilize the exon and preserve accessibility of the sequence that basepairs with the spliceosome.