Table 1.

Distinguishing transcription from downstream sites

Labeling conditions			Colocalization
	Clusters/μm2		% Br-clusters associated with bio-clusters (C)	% Bio-Clusters associated with Br-clusters (D)
	Br-clusters (A)	Bio-clusters (B)
1. 2.5 min, 5   mM Br-U; 15 min bio-CTP	1.1 ± 0.5	1.1 ± 0.5	85	85
2. 10 min, 2.5 mM Br-U; 15 min bio-CTP	2.0 ± 0.5	1.0 ± 0.4	58	85
3. 30 min, 2.5 mM Br-U; 15 min bio-CTP	4.6 ± 1.6	1.1 ± 0.3	28	84
4. 60 min, 2.5 mM Br-U; 15 min bio-CTP	7.1 ± 2.2	0.9 ± 0.6	18	85

Cells were grown in Br-U, permeabilized, and allowed to make RNA in the presence of bio-CTP, and clusters of gold particles marking nucleoplasmic sites containing Br- and bio-RNA were counted. Br- and bio-clusters had average diameters of 82 and 78 nm, respectively; neither size changed with labeling time. Clusters were considered to be colocalized if a gold particle in one lay within 40 nm of gold particle in another.