Figure 2.
The image contains multiple graphs analyzing the contribution of inverted repeat A l u elements to human intron structure. Panel A shows scatter plots depicting the relationship between observed minimum free energy (Observed M F E) and the mean M F E of shuffled intron sequences (Mean M F E of shuffled ensemble) for human introns. The top plots compare all human introns and introns with no A l u, with r squared values of 0.84 and 0.94, respectively. The lower plots categorize introns by A l u content: 1 A l u (r squared equals 0.94), more than 1 A l u in the same orientation (r squared equals 0.93), and inverted repeat A l u (r squared equals 0.54). Each scatter plot includes a diagonal reference line (y equals x). The inverted repeat A l u group shows a noticeably weaker correlation compared to other groups. Panel B presents a stacked bar graph showing the A l u content across transcript regions (5 prime U T R, Exons, Introns, and 3 prime U T R). The legend indicates three categories: 1 A l u, more than 1 A l u in the same orientation, and inverted repeat A l u. Introns show the highest proportion of A l u elements, particularly inverted repeat A l u, compared to other regions. Panel C features a bar graph comparing I R A l u intron lariat levels in wild type and D B R 1 knockout samples. The y-axis is labeled I R A l u intron lariat level. The D B R 1 knockout shows a marked increase compared to wild type, with statistical significance indicated by a double asterisk. Together, the graphs show that inverted repeat A l u elements are enriched in introns, are associated with altered M F E correlation patterns, and lead to increased lariat accumulation in the D B R 1 knockout condition.
IR Alu elements contribute to human intron structure. (A) The relationship between observed MFE and the mean MFE of an ensemble of shuffled intron sequences for human introns is partitioned into distinct categories based on each intron’s Alu content (no Alu, 1 Alu, >1 Alu in the same orientation, and IR Alu). (B) The proportion of 5′ UTR, exons, introns and 3′ UTRs that contain 1 Alu, >1 Alu in the same orientation, and IR Alu. (C) The lariat levels of introns with IR Alu in WT and DBR1 KO samples. P value was from t test. **P < 0.01.