DHX9 suppresses spurious RNA processing defects originating from the Alu invasion of the human genome [XL8 DHX9 FLASH CLIP-seq]

Transposable elements increase genetic diversity thus making them an important part of evolution and gene regulation in all organisms that carry these sequences. Bulk of our nascent transcriptome is comprised of transposable elements that have the propensity to form strong secondary structures. It is essential to resolve such strong secondary structures to maintain normal cellular function. Here, we show that the major nuclear RNA helicase DHX9/RHA interacts and remodels embedded Alu retrotransposable elements in the human transcriptome and B1 retrotransposable elements in the mouse transcriptome. To understand the function of DHX9 we used FLASH (Fast cloning of RNA After some Sort of affinity purification for High-throughput sequencing) to identify the in-vivo targets of human DHX9. Overall design: FLASH (Fast cloning of RNA After some Sort of affinity purification for High-throughput sequencing) for mouse DHX9 and one control (IgG-Rb); two biological replicates each.