RNA-seq of Wild type Arabidopisis and nups mutants

Lines of evidence indicate that nuclear pore complex profoundly affects the timing of plant flowering, but the underlying mechanisms remain poorly elucidated. In Nup107-160 sub-complex, Nup85, Nup96, Nup107, Nup160, and HOS1 genes displayed association with flowering control, and their mutants were all earlier flowering. The nup96-1, hos1-3, and nup160-3 mutants had similar flowering times in long-day conditions and flowered earlier than the nup107-3 and nup85-1 mutants. To analyze the relationship of these nucleoporins with flowering regulation, we carried out transcriptome assays of these gene mutants. As for flowering time, transcriptomes of the nup96-1, hos1-3, and nup160-3 were in the same group, while those of nup107-3 and nup85-1 were clustered in another one. Interestingly, all these mutants shared high similarity in expression patterns and had 219 common genes (100 up-regulated genes and 119 down-regulated genes). Gene Ontology analysis according to biological process and molecular function revealed that the significantly upregulated DEGs in Nup107-160 sub-complex mutants were highly enriched in gene expression processes, including DNA binding, transcription regulator activity, and RNA biosynthetic process. Among these common genes, key flowering activators were enhanced, whereas flowering inhibitors were repressed compared to wild-type plants.