Extended Data Fig. 2. Cer interacts with various loop extrusion impediments across the Vκ locus but not substantially with sequences downstream of Sis. Related to Fig. 2.

a, 3C-HTGTS profiles in the Igκ downstream region from Cer to the downstream Rpia gene from RAG-deficient v-Abl cells, baiting from iEκ (red), Sis CBE2 (green) and Cer CBE1 (blue) and from RAG-deficient primary pre-B cells baiting from Cer CBE1 (pink). Black asterisks indicate the location of baits. b, 3C-HTGTS interaction profiles across the Vκ locus when baiting from Cer CBE1 in RAG-deficient primary pre-B (pink) and v-Abl (blue) cells. Cer interaction peaks and their underlying features in the Vκ locus are shown. A total of 110 peaks were called to be significantly above background in either primary pre-B cells or v-Abl cells. Peaks are indicated with black lines and numbered according to their locations from distal to proximal. For each peak, underlying features within ± 1 kb are indicated, including rightward CBE (“C” in red), leftward CBE (“C” in blue), E2A-binding sequence (“E”) and transcription (“T”). Peaks without any obvious underlying features are labeled as unknown (“U”). CBE annotation and transcription were determined based on published CTCF ChIP-seq and GRO-seq data in RAG-deficient v-Abl cells⁶. E2A binding was determined based on published E2A ChIP-seq data in RAG-deficient primary pro-B cells⁴⁶. See Methods for more details. 3C-HTGTS data are presented as mean value from 2 biological repeats.