Alu repeat-containing RNA organizes actively transcribed genomic regions around nuclear speckle for co-transcriptional RNA processing

Accumulating evidences have shown that the genomic regions of highly transcribed genes and their corresponding nascent pre­mRNAs are organized around nuclear speckles to achieve co-transcriptional RNA processing. But, how the actively transcribed genes are organized around nuclear speckle is unknown.

Here, we identified RNAs localized in nuclear speckles and found that a class of Alu-repeat RNAs were highly enriched around the nuclear speckle. These RNAs tend to directly bind to the genomic regions of actively transcribed genes via its Alu element and form R-loops. Meanwhile, they can interact with nuclear speckle protein components and promote their aggregation and phase separation, synchronously mediating the formation of nuclear speckle and organization of the actively transcribed genes around them.