The plant Cleavage Factor I complex is essential for precise cleavage and polyadenylation site determination

Cleavage factor I (CFI) is a four-subunit protein complex of the pre-mRNA 3' end processing machinery in eukaryotes. In Arabidopsis (Arabidopsis thaliana), AtCFI25a, AtCFI25b, AtCFI59, and AtCFI68 have been identified as potential components of AtCFI, in silico. Here, we showed that AtCFI25a, AtCFI59, and AtCFI68 are each able to pull down each other as components of CFI, revealing the plant CFI complex composition. Furthermore, either AtCFI59 or AtCFI68 was essential for nuclear localization of the smallest subunit, AtCFI25a. Mutants with single loss-of-function for AtCFI59 or AtCFI68 showed no visible differences compared to wild-type plants, while the double mutant displayed pleiotropic morphological defects, identical to those previously reported for AtCFI25a loss-of-function plants. Moreover, these morphological defects correlated with alterations in the usage of 3' UTR cleavage and polyadenylation sites. atcfi25a, the atcfi25a atcfi25b double mutant, and the atcfi59 atcfi68 double mutant showed widespread changes in the selection of cleavage and polyadenylation sites. In addition to the loss of diversity for 3' UTR usages in these mutants, proximal cleavage and polyadenylation sites were favored in most cases, leading to shorter 3' UTRs. In particular, genes involved in light intensity, light harvesting, photosynthesis, and cold responses showed significant dependence on AtCFI function. Interestingly, transcripts coding for AtCFI subunits showed altered 3' end processing in these mutants, suggesting a self-regulation function of AtCFI.