Cell were subfractionated using chromatin extraction protocol, and  RNA extracted using the RNeasy kit (QIAGEN, cat#74106), following the manufacturer instruction. RNA integrity was assessed with the Agilent 2100 Bioanalyzer System (Agilent Technologies). RNA library preparations were carried out using theNEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® # E7760, according to manufacturer's protocol. The libraries were size-selected using Ampure XP Beads (Beckman Coulter, cat# A63880) and quantified using the KAPA Library Quantification kit - Universal (KAPA Biosystems, cat# KK4828).