Fractionation of heterogeneous nuclear RNA: rates of hybridization and chromosomal distribution of reiterated sequences.
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A substantial portion of the hnRNA of mouse L cells contains internal residues of N6-methyl adenylate and blocked 5' terminal sequences which are apparently of the type m7G5' ppp5' YmpZp..., in which 7-methyl guanosine is joined by a 5'-5' pyrophosphate linkage to a 2'-0-methylated residue, Ym. These sequences are indistinguishable from those comprising one of the two classes of blocked 5' sequences found in mRNA, and are quite distinct from those comprising the other class. The remarkable similarity in 5' terminal methylated sequences of hnRNA and a major fraction of mRNA appears to extend even to the relative occurrence of each of the four 2'-0-methylated species in position Ym.
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Ultraviolet irradiation of cultured murine cells damages chromosomal DNA, thus causing premature termination of synthesis of hnRNA chains. We have utilized this effect for measuring the sizes of transcription units for the various classes of hnRNA. Target size analyses of the loss of synthesis of hnRNA species suggest that hnRNA, through its entire size range, constitutes mostly primary transcripts-that is, the shorter RNA molecules are not processed from longer precursors. Polyadenylated hnRNA appears to be a primary transcript as well. Our data, however, are also consistent with processing of precursors to poly(A)+ hnRNA from the 5'termini of larger hnRNA molecules. They are not consistent with models which postulate that poly(A)+ hnRNA sequences originate at the 3' termini of precursors which are considerably larger (greater than 30%) than the polyadenylated hnRNA molecules themselves. Finally, we have found that the process of polyadenylation is not measurably affected by ultraviolet irradiation of cells.
Rapidly sedimenting hnRNA complexes contain regions of stable intermolecular duplex. Disruption of such complexes, as judged by a reduction in sedimentation rate, requires conditions sufficient to denature the duplex regions. Rapidly sedimenting molecules reappear only when the complementary sequences reanneal-that is, the formation of such complexes is dependent upon time and the concentration of homologous RNA. These experiments lead us to the conclusion that rapidly sedimenting hnRNA complexes consist of two or more largely single-stranded RNA molecules held together by short duplex regions. Precisely such structures have been visualized in the electron microscope. Rapidly sedimenting fractions of native nuclear RNA from preparative sucrose gradients consist primarily of large, multi-molecular complexes interconnected by duplex regions averaging 300 base pairs in length. Exposure of the RNA to severely denaturing conditions eliminates such complexes. Reannealing of the RNA reconstitutes complexes which are indistinguishable from those observed in preparations before denaturation.
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