Quantitative 3C (3C-qPCR) analysis confirmed decreased frequencies of chromatin looping.

(A) q4C profile of Tax⁻cells of clone 11.63. The technical peak seen in the q4C viewpoint (VP) and two of the main peaks (Peak 1) and (Peak 2) identified in the output of the Tax⁻fraction of clone 11.63. (B) As control, the frequency of chromatin interactions was quantified by 3C-qPCR on sorted Tax⁻and Tax⁺ cells, using a primer pair and Taqman probe to detect the contacts between two regions: VP and another region in the provirus (S1 Table). There was no significant difference between Tax⁺ and Tax⁻cells (combined p value = 0.932, Fisher’s method of combining p values). (C and D) Primer pairs and probe were used to detect long-range chromatin contacts between the provirus and host genome region at Peak 1 (C) or Peak 2 (D). Results of 3C-qPCR of two biological replicates (rep) are shown. Peak1 contact frequency was significantly higher in Tax⁻cells than in Tax⁺ cells (combined p value 0.012, Fisher’s method). Peak2 contact frequency was significantly higher in Tax- cells than in Tax⁺ cells (combined p value 0.000607, Fisher’s method).

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