Figure 1.

snoRNAs associate with CPSF in vivo and its potential role in gene regulation. (A) Schematic drawing of the assembly of four multi-subunit protein complexes (CPSF, CstF, CF Im, CF IIm) and PAP on PAS RNA sequence (upper panel), the lower panel shows the composition of CPSF complex and the association of SNORD50A with CPSF via Fip1. (B) Schematic representation of the SVL and L3 RNA substrates used in the biotin–streptavidin pull-down assays (upper panel). The AAUAAA hexamer in wild-type RNA substrate and AACAAA in mutant substrate (boxes) are shown. The asterisk is used to highlight the single nucleotide change. Venn diagram showing the number of snoRNAs in three datasets (lower panel). Cutoff values of snoRNA reads were set as below. SVL and L3 RNA pull-down assays: fold enrichment >1.5 and average RPM>100; Fip1 iCLIP-seq: RPM>10. (C) Venn diagram showing the number of snoRNAs detected by CLIP-seq experiments of several CPSF factors (reference 13). RPM cutoff value was set as 5. (D) Fip1 binding frequency profile across snoRNA regions based on our Fip1 iCLIP-seq data described in reference 11. Mature snoRNA regions were defined according to reference 14, The regions upstream and downstream of mature snoRNAs were defined accordingly. For reads mapped to mature snoRNA regions, the RPM values were aligned based on the middle position of each snoRNA, the y axis value represents the average RPM at each position for all Fip1 iCLIP-seq+ snoRNAs. For reads mapped to upstream and downstream of mature snoRNAs, RPM values were averaged and plotted at each position for all Fip1 iCLIP-seq+ snoRNAs. (E) Schematic representation of potential regulatory role of snoRNA in gene expression at mRNA 3′ processing level. If a gene has two (gene A) or multiple PASes, snoRNA could affect the level of each transcript and also the APA profile. Moreover, aberrant mRNA 3′ processing for gene A might also lead to transcription of downstream gene B, which might also be regulated by snoRNAs.