Figure 2

Nucleosome repositioning at 3ʹ ends of long genes precedes transcription by pioneering (elongating) polymerases. Browser views show (log₂ fold) changes in nucleosome occupancy 10 or 30 min post-stimulation calculated using 5-kbp non-overlapping windows and a running-means average along up-regulated long genes ALCAM and SAMD4A. Changes (read enrichment - grey; read depletion - orange) are shown normalized to those in transcriptionally inert genomic regions. Total RNA-seq tracks (magenta) show elongating polymerases generating intronic signal close to the 5′ ends of genes after 10 and 30 min, as they have not yet reached termini (dotted lines - positions of pioneering RNAPs after 10 and 30 min). The long, constitutively expressed HUWE1 locus (bottom) serves as a control. Kbp, kilobase pair; RNAP, RNA polymerase; RNA-seq, sequencing of total RNA.