VARIATION IN THE SIZE OF NASCENT RNA CLEAVAGE PRODUCTS AS A FUNCTION OF TRANSCRIPT LENGTH AND ELONGATION COMPETENCE

RNA polymerase II arrested at specific template locations can be rescu ed by elongation factor SII via RNA cleavage, The size of the products removed from the S'-end of the RNA varies, The release of single nucl eotides, dinucleotides, and larger oligonucleotides has been detected by different workers, Dinucleotides tend to originate from SII-indepen dent complexes and 7-14 base products from SII-dependent complexes (Iz ban, M, G., and Luse, D. S. (1993) J. Biol. Chem. 268, 12874-12885), D ifferent modes of cleavage have also been recognized for bacterial tra nscription complexes and are thought to represent important structural differences between functionally distinct transcription intermediates . Using an elongation complex ''walking'' technique, we have observed factor-independent complexes as they approach and become arrested at a n arrest site. Dinucleotides or 7-9-base (large) oligonucleotides were released from SII-independent or dependent complexes, respectively. T he abrupt shift between the release of dinucleotide versus large produ cts accompanied the change from factor-dependent to factor-independent elongation, as described by others. However, not all factor-independe nt complexes showed cleavage in dinucleotide intervals since oligonucl eotides 2-6 bases long were also liberated from elongation-competent c omplexes, These were all 5'-coterminal oligonucleotides indicating tha t a preferred phosphodiester bond is targeted for cleavage in a series of related complexes, This is consistent with recent models postulati ng a large product binding site that can hold RNA chains whose size in creases as a function of chain polymerization, A specific transitional complex was identified that acquired the ability to cleave in a large increment one base insertion event prior to attaining the arrested co nfiguration.