Fig. 1

ATAC-seq, PRO-seq and Pol II ChIP-seq are used for the identification of TREs. A Experimental outlines of the 3 genomic profiles used. B IGV browser snapshot of replicate genomic profiles at the H2A.Z locus, a highly expressed gene [36], left, which also includes a gene expressed at lower levels, right side. Number of 3′ end reads per million of PRO-seq run-on transcripts are shown for the plus and minus strands. PRO-seq peaks mark transcriptional pause sites. MACS peak and dREG TRE predictions for the combined data sets are shown underscoring each genomic profile. The CRM panel underscores a genomic region with enhancer activity tested by deletion in large reporter constructs [25]. PRO-seq and ATAC-seq profiles are set to the same scale between 12 and 20 h stages, with the range indicated between brackets at the beginning of each track