Fig. 1

Unstable intergenic transcripts captured by GRO-seq and pNET-seq and eRNA characterization. a GRO-seq and pNET-seq reads aligned to different genomic regions. TSS1K indicates the 1 kb upstream region of the gene transcription start site. TES1K indicates the 1 kb downstream region of the transcription end site/polyadenylation site. b Browser shot of a protein-coding transcript and an intergenic transcript, the number of reads aligned to forward (+) and reverse (−) genomic strands are separately displayed. c Expression levels of nascent/steady-state transcripts from protein-coding and intergenic regions. d Read densities of pNET-seq, DHS and ChIP-seq of Pol II, H3K9ac, H3K4me3, H3K36me3, H3K27ac, and H3K4me1 around the intergenic and genic TCs (± 3 kb). All intergenic and genic TCs were ranked in a descending order of pNET-seq signals (±250 bp around the 5′ end), and chromatin features were plotted around the 5′ end of each intergenic TC. e pNET-seq signals around the intergenic TCs. Intergenic TCs were divided into ten equal parts based on the decreasing level of pNET-seq signals (± 250 bp). f Read densities of DHS and ChIP-seq of H3K9ac, H3K4me3, H3K36me3, H3K27ac, and H3K4me1 around each of the ten parts of intergenic TCs. g Intergenic TCs counts within different chromatin states defined in wheat genome [1]. h Chromatin signatures of transcribed and untranscribed enhancer examples. i Boxplots showing the expression levels of unidirectional and bidirectional enhancers determined by pNET-seq. j A heatmap displays the expression levels of unidirectional and bidirectional enhancers in primary (sense) and/or secondary (antisense) orientations (± 3 kb)