Figure 1.

SFPQ Regulated Genes Containing Long Introns

(A) Relationships between pre-mRNA lengths and log₂ FC in Sfpq-KD and control (Cont-si) Neuro2a cells. The red dots show 176 genes that were significantly downregulated (FC of Sfpq-KD/Cont ratio <1/3) with significant SFPQ binding peaks. The green dots show 432 genes meeting the same SFPQ binding criteria, but without changes in FC values (0.83 < FC < 1.20).

(B) Higher magnification of the graph in A from the range of 20 kb to 1 Mb, showing similar distributions of 120 gene pairs with pre-mRNA lengths (length difference <10 kb).

(C and D) Heatmaps showing pre-mRNA expression profiles for the 120 downregulated genes, captioned as target genes (C) and 120 non-downregulated genes, captioned as non-target genes. (D). Each block shows a 5-kb window for the gene bodies. Down- or upregulation of pre-mRNA expression levels is shown with color according to the Log₂ FC of Sfpq-KD/Cont.

(E) Genomic view for Samd4, which was shown to be an SFPQ target gene in a previous study. Smoothed Ribo(−) RNA-seq profiles of Sfpq-KD/si-Cont (orange), Sfpq-KD Ribo(−) RNA-seq profiles (pink), and si-Cont (blue) positions of high-S (red) and low-S peaks (green) are shown.

(F) Genomic view of Ralgapa1, a size-matched gene pair partner of Samd4, among non-target genes.

See also Figures S1, S2, and S7.