Transcription, processing, and turnover of RNA from the Drosophila mobile genetic element copia

Abstract

We have investigated the transcription, processing, and size distribution of copia nuclear RNA in Drosophila cultured cells in order to characterize the steps which result in the high concentration of cytoplasmic copia RNA. Ninety-five percent of pulse-labeled (5 min) copia nuclear RNA is 5 kb or shorter. This is consistent with the previously determined absence of intervening sequence(s) in the copia gene and indicates that there is little transcription of contiguous regions 5′ or 3′ to the copia sequence. In pulse-chase experiments, we observed that only 10% or less of the labeled copia nuclear RNA could be chased into the cytoplasm. Continuous labeling experiments, analyzed by taking into account changing nucleotide precursor pool specific activities during labeling and fitting the data simultaneously to a series of differential equations, gave results consistent with the pulse-chase experiments. The data, whether analyzed according to a one-step or a two-step processing model, indicated that total copia nuclear RNA is processed to poly(A) + cytoplasmic RNA with an efficiency of only 7%. In the fit to the two-step processing model, only 7% of the poly(A) + copia nuclear RNA is exported to the cytoplasm; the remainder turns over in the nucleus. The poly(A) + copia nuclear RNA is discrete in size, in contrast to poly(A) − copia nuclear RNA, which is heterogeneous in size. We discuss the implications of these observations for the mechanism of intranuclear processing and decay of copia RNA.