Ribonucleoprotein structure in nascent hnRNA is nonrandom and sequence-dependent

Abstract

We have studied the ribonucleoprotein morphology of nascent hnRNA using chromatin spreading methods. This approach allows visualization of multiple transcripts of the same DNA sequence. Thus the RNP structure of hnRNA molecules with the same nucleotide sequence can be compared. We find that RNP particles averaging 240 Å in diameter occur on the majority of hnRNA transcription units, but that RNA fibrils are generally not completely covered with particles. Furthermore, the RNP particle location is nonrandom for the transcripts of a given gene. Particle number and arrangement on RNP fibrils vary from one transcription unit to the next, and are not obviously related to transcription unit size or activity. Analysis of particle location with respect to the 5′ RNA terminus allows RNP particle localization to homologous sequences of less than 500 ribonucleotides on the different fibrils of a single transcription unit. RNP particles assemble very soon after synthesis of the particular sequence. Sites of particle formation are distinct from sites of double-stranded hairpin loops on the RNA fibrils. A differential, or differentially stable, RNP structure with respect to RNA sequence may bear on mechanisms of specific hnRNA processing.