Fig. 1

Properties of the D. melanogaster 3′-seq atlas. a 3′-Seq is a quantitative measure of gene expression. Correlation of gene expression measurements derived using either RNA-seq or 3′-seq of matched female head samples. Pearson correlation coefficient is reported. Red line represents linear regression fit. b 3′-Seq-derived 3′ ends are aligned around the predicted cleavage site and the nucleotide distribution around putative cleavage site is plotted (centered at 0). Percentages of each of four nucleotides in a window of 200 bp centered at the cleavage site are shown. Location of A-rich PAS and U-rich downstream sequence element are shown as well as insect-specific A-rich sequence ~ 5 nucleotides upstream of the cleavage site. c Positional enrichment of the top three hexamers found in a ±100-nucleotide window around cleavage sites. d De novo derivation of most represented hexamers in a 50-nucleotide window upstream of 3′-seq-derived 3′ end positions in terminal 3′ UTRs. e, f Distribution of 3′-seq reads (e) and derived 3′ end sites (f) onto existing genomic features in the D. melanogaster annotation (r6.12). Statistical significance test of each region against intergenic space was performed by determining total number of reads (e) or 3′ ends (f) in each region relative to their proportion of base frequencies, which was assessed by binomial tests. *** p < 0.0005; n.s. p > 0.05. g Examples of 3′ end extensions of current FlyBase r6.12 gene models. RNA-seq and 3′-seq IGV tracks are shown in autoscale. A head-specific extension is evident for chb. An additional set of scaled tracks is shown for msi, to highlight the low, but discrete, expression of its extension which terminates with a defined 3′-seq cluster. h Barplot summarizing the numbers of 3′ UTR extensions of FlyBase r6.12 gene models that were made on the basis of downstream 3′-seq clusters connected by RNA-seq evidence. i Quality of PAS motifs associated with novel 3′ UTR extensions to FlyBase r6.12 gene models. A higher frequency of AAUAAA is observed at the most distal extensions