Extended Data Fig. 2. Dynamic association between the active VSG gene and the spliced leader RNA (SL) array transcription compartments.

a, Immunofluorescence-based colocalization studies of tSNAP^myc (SL-RNA transcription compartment) and a nucleolar and active VSG transcription compartment marker (Pol I, largest subunit) using super resolution microscopy - a plot showing signal intensity across a defined area (cyan line) is presented. b-c, The violin plot shows ‘outside edge’ (b) or ‘inside edge’ distance (c) measurements between the SL-RNA and VSG transcription compartments in G1, S phase or G2 nuclei – n values correspond to number of nuclei except in G2 where the n value corresponds to the number of expression-site body (ESB) / tSNAP pairs detected (in a total of 68 and 61 nuclei). d, Immunofluorescence-based colocalization studies of tSNAP^myc and a nucleolar compartment marker (NOG1) using super resolution microscopy. e, The plot shows signal intensity measurements of the SL-RNA compartments, adjacent or non-adjacent to the expression-site-body (ESB). f, The plot shows ‘inside edge’ distance measurements between the SL-RNA compartments, adjacent or non-adjacent to the ESB and the nucleolus. ESB: Pol I extranucleolar reservoir and VSG transcription compartment. a, d, DNA was counter-stained with DAPI; the images correspond to maximal 3D projections of stacks of 0.1 μm slices and are representative of two biological replicates and three independent experiments; scale bars 2 μm. Violin plots (b, c, e, f): white circles show the medians; box limits indicate the 25th and 75th percentiles; whiskers extend 1.5 times the interquartile range from the 25th and 75th percentiles; polygons represent density estimates of data and extend to extreme values. P values were determined using a two-tailed unpaired (b-c) or paired (e-f) Student’s t-test. Detailed n and p values are provided in Source Data Extended Data Fig.2.