Quantitative digital analysis of diffuse and concentrated nuclear distributions of nascent transcripts, SC35 and poly(A).

Digital imaging microscopy was used to analyze the spatial distribution and levels of newly synthesized RNA in relation to steady-state poly(A) RNA and to the splicing factor SC35. Transcription was monitored over time after microinjection of BrUTP and was detected using antibodies. Poly(A) RNA was detected with probes directly conjugated to fluorochromes, allowing direct detection of the hybrids. Objective methods were used to determine genuine signal. A defined threshold level to separate signal from noise was established for each nucleus. The nucleolus was used to determine poly(A) and SC35 background and the juxtanuclear cytoplasm was used for the BrUTP background. The remaining signal was segmented into high (concentrated) and low (diffuse) levels. Surprisingly, for all probes examined, most of the signal was not in concentrated areas, but rather was diffusely spread throughout the nucleoplasm. A minority (20-30%) of the SC35 signal was in concentrated areas ("speckles") and the rest was dispersed throughout the nucleoplasm. In addition, the concentrated areas had a mean intensity only twice the average. The amount and significance of the colocalization of the diffuse, or concentrated, areas of SC35 [or poly(A)] with BrUTP incorporation were analyzed. The image from one probe was translated with respect to the other in three dimensions to compare colocalization with random alignments. Both poly(A) and SC35 were found to have low colocalization with the total BrU signal. Sites of transcription were determined using an algorithm to find maxima of BrUTP signal within clusters. From 849 to as many as 3888 sites per nucleus were detected. A rim of hybridization to poly(A) coinciding with the nuclear envelope was eliminated by actinomycin treatment, suggesting that these transcripts were exiting from the nucleus. These results emphasize the importance of utilizing the full dynamic range of the image before drawing conclusions as to the distribution of nuclear components.