Chromatin-associated lncRNA-splicing factor condensates regulate hypoxia responsive RNA processing of genes pre-positioned near nuclear speckles [RAP-seq]

The underlying mechanism specifying hypoxia-responsive AS needs to be determined. We demonstrate the role of nuclear speckle (speckle) nuclear domain (ND) and the long noncoding RNA, MALAT1, in hypoxia-responsive AS.

Hypoxia-responsive genes position near speckles, the NDs that enhance splicing efficiency, and their differentially spliced exons harbor features that are characteristic of inefficiently spliced transcripts. Speckle-resident MALAT1, induced in response to hypoxia, boosts hypoxia-responsive AS by regulating the binding of SR-family splicing factor1 (SRSF1) to pre-mRNAs of speckle-associated genes. Mechanistically, MALAT1 facilitates the recruitment of SRSF1 to elongating RNA pol II (RNAP II) by promoting the formation of phase-separated SRSF1 condensates that are preferentially recognized and recruited to pre-mRNA by RNAP II.