A protein complex regulates RNA processing of intronic heterochromatin-containing genes in <i>Arabidopsis</i>

Significance How heterochromatin affects RNA processing is unclear. The chromatin regulators ASI1 and EDM2 function in regulating alternative polyadenylation at genes with intronic heterochromatin. We found that ASI1 and EDM2 are associated in planta through interactions with a putative RNA-binding protein, AIPP1. Protein interaction assays suggest that the RNA Pol II C-terminal domain phosphatase CPL2 and two other proteins (AIPP2 and AIPP3) are associated with the ASI1-AIPP1-EDM2 complex. Like ASI1 and EDM2, AIPP1 also functions in promoting the expression of heterochromatin-containing genes. However, the function of CPL2, AIPP2, and AIPP3 is antagonistic to that of ASI1, EDM2, and AIPP1. Our discovery of the ASI1-AIPP1-EDM2 complex and associated proteins is important for understanding how heterochromatin regulates RNA processing.