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. 2015 Jun 23;25(7):864–876. doi: 10.1038/cr.2015.77

Figure 5.

Figure 5

HLP1 directs poly(A) site choice at the FCA transcripts. (A) The genomic structures of FCA transcripts are shown in the top panel. CDS regions are boxed in black. The 5′-UTR and 3′-UTR are boxed in green and grey, respectively. Introns are indicated as lines. Blue line above gene structure indicates RIP-qPCR amplified region. Wiggle plots of two HITS-CLIP/CLIP-seq (CLIP-1 and CLIP-2) and two PAS-seq (PAS-1 and PAS-2) replicates are shown below the gene structure. HLP1 binding peaks in the third intron and 3′-UTR of FCA transcripts are indicated by blue and purple wiggle plots. The x axis indicates genome site in chromosome. The y axis indicates normalized HITS-CLIP/CLIP-seq or PAS-seq abundance. HITS-CLIP/CLIP-seq or PAS-seq tag counts were normalized to tag per 10 million (TP10M) to adjust for differences of two libraries (wild-type and mutant) in sequencing depth. PAS-Seq analyses show decreased PAC numbers at the distal 3′-UTR poly(A) site in hlp1-1 mutant (red plots in PAS-1 and brown plots in PAS-2) compared with Col (light blue plots in PAS-1 and green plots in PAS-2). (B) RIP-qPCR validation of HLP1 binding to the third intron and 3′-UTR of FCA transcripts. (C) Quantitative PCR results show decreased APA at the distal poly(A) site of FCA in hlp1-1 mutant. (D) Working model for HLP1-directed APA of FCA in the regulation of flowering.