The main steps of BioTAP-XL procedure: harvesting cells, formaldehyde cross-linking, chromatin preparation, affinity purification, input and IP protein recovery were performed as described (12, 36). Cross-linked chromatin for ChIP-seq experiments using antibodies against proteins and histone modifications was prepared from 5 × 10(8) 24335 (ZNF532-NUT) NMC cells as described (36). Nascent RNA was purified as described (3). Each RNA library was constructed from 50 ng of nascent RNA following the manufacturer’s instructions (NEBNext Ultra directional RNA library prep kit, New England BioLabs) ChIP-seq library preparation were performed as described (Alekseyenko et al. 2015). RNA library was constructed from 50 ng of nascent RNA following the manufacturer’s instructions (NEBNext Ultra directional RNA library prep kit, New England BioLabs)