Figure 1: ARE-containing transcripts are frequently upregulated during neural differentiation.

(a) Empirical cumulative distribution function (ECDF) plots for 3′READS-deduced expression changes in P19 cells undergoing neural differentiation. Individual curves correspond to groups of transcripts with specified numbers of AUUUA motifs within the 3′ UTR. (b) Comparison of the transcript groups in a using two-sided KS test suggests that mRNAs containing one or several AUUUA motifs are more frequently upregulated than their AUUUA-less counterparts. (c) Changes in the expression levels of ARE-containing mRNAs in P19 cells after 3.5 days of EB/RA-induced neural differentiation. Top, 3′ UTR diagrams showing positions of pA sites, AREs and primers used for RT–qPCR analyses. Long black ticks, canonical AAUAAA and AUUAAA pA hexamers occurring within 10–30 nt upstream of the 3′ end in at least one cDNA or EST clone (UCSC Genome Browser) or one-nucleotide modifications of these hexamers used as pA sites in at least five cDNA/EST clones. Short black ticks, AAUAAA and AUUAAA pA hexamers not associated with available cDNA clones. Red ovals, UAUUUAU motifs occurring as a part of ⩾12 nt consecutive AU-nucleotide sequences with the number of individual UAUUUAU heptamers indicated inside the oval. Red ticks, UAUUUAU motifs present within <12 nt AU sequences. Bottom, RT–qPCR relative expression data obtained for undifferentiated (Undif) P19 cultures and cultures differentiated for 3.5 days using upstream (Fu/Ru) or downstream (Fd/Rd) primer pairs. Expression levels in the corresponding undifferentiated samples are set to 1. Data are averaged from three experiments±s.d. and compared by t-test.