Figure 1.
Alternative polyadenylation is apparent in AML patient samples, affecting genes that promote leukemia development. (A) Schematic of AML patient samples and healthy HSPCs used for 3'READS and/or RNA-sequencing. (B) Scatter plot showing the change in expression of the proximal poly(A) site (pPAS) isoform (x-axis) and distal poly(A) site (dPAS) isoform (y-axis), per gene, in t(8;21) AML patient blasts compared with healthy HSPCs. Significant APA events (Fisher’s exact test, P < .05) are classified and divided according to type: 3'UTR-APA (left) and CDS-APA (right). Each dot corresponds to a single gene. Blue dots indicate significantly more pPAS usage; red dots indicate significantly more dPAS usage. (C) Venn diagrams showing the overlap of genes with 3'UTR shortening and CDS lengthening in t(8;21) AML blasts and non-t(8;21) AML blasts compared with healthy HSPCs. (D) Genome browser tracks depicting normalized sequencing reads (reads per million [RPM]) in the BAALC gene obtained from 3'READS of HSPCs and AML patient blasts. The full BAALC genomic structure is shown (top) with the purple, boxed region expanded (below). The percent usage of each indicated PAS was calculated by using 3'READS and is shown in the bar graph to the right. n = 2, HSPCs; n = 4, t(8;21) and non-t(8;21) AML patient samples. (E) Relative ratio of Renilla to firefly luciferase activity in Kasumi-1 cells nucleofected with the indicated dual luciferase reporter. Red bars represent activity when the full 3'UTR of the indicated gene was subcloned downstream of Renilla luciferase; blue bars represent activity when the shortened 3'UTR was present. Data are mean ± standard deviation of 3 independent experiments. ***P < .001, Student t test. (F) Genome browser tracks depicting normalized sequencing reads (RPM) in the CUL4A gene obtained from 3'READS of HSPCs and AML patient blasts. The proximal, intronic PAS is boxed. The percent usage of each indicated PAS was calculated by using 3'READS and is shown in the bar graph to the right. n = 2, HSPCs; n = 4, t(8;21) and non-t(8;21) AML patient samples.

Alternative polyadenylation is apparent in AML patient samples, affecting genes that promote leukemia development. (A) Schematic of AML patient samples and healthy HSPCs used for 3'READS and/or RNA-sequencing. (B) Scatter plot showing the change in expression of the proximal poly(A) site (pPAS) isoform (x-axis) and distal poly(A) site (dPAS) isoform (y-axis), per gene, in t(8;21) AML patient blasts compared with healthy HSPCs. Significant APA events (Fisher’s exact test, P < .05) are classified and divided according to type: 3'UTR-APA (left) and CDS-APA (right). Each dot corresponds to a single gene. Blue dots indicate significantly more pPAS usage; red dots indicate significantly more dPAS usage. (C) Venn diagrams showing the overlap of genes with 3'UTR shortening and CDS lengthening in t(8;21) AML blasts and non-t(8;21) AML blasts compared with healthy HSPCs. (D) Genome browser tracks depicting normalized sequencing reads (reads per million [RPM]) in the BAALC gene obtained from 3'READS of HSPCs and AML patient blasts. The full BAALC genomic structure is shown (top) with the purple, boxed region expanded (below). The percent usage of each indicated PAS was calculated by using 3'READS and is shown in the bar graph to the right. n = 2, HSPCs; n = 4, t(8;21) and non-t(8;21) AML patient samples. (E) Relative ratio of Renilla to firefly luciferase activity in Kasumi-1 cells nucleofected with the indicated dual luciferase reporter. Red bars represent activity when the full 3'UTR of the indicated gene was subcloned downstream of Renilla luciferase; blue bars represent activity when the shortened 3'UTR was present. Data are mean ± standard deviation of 3 independent experiments. ***P < .001, Student t test. (F) Genome browser tracks depicting normalized sequencing reads (RPM) in the CUL4A gene obtained from 3'READS of HSPCs and AML patient blasts. The proximal, intronic PAS is boxed. The percent usage of each indicated PAS was calculated by using 3'READS and is shown in the bar graph to the right. n = 2, HSPCs; n = 4, t(8;21) and non-t(8;21) AML patient samples.

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