The Arabidopsis thaliana AtCARP9 is a novel ELL ortholog and associates with AtEAF proteins.

Arabidopsis thaliana possesses hitherto unknown Occludin domain containing ELL ortholog identified as CARP9. The AtCARP9 protein similar to ELL orthologs across species, interacts with both the Arabidopsis EAF orthologs. Transcription is one of the early steps during which the expression of most protein-coding genes is controlled in cells. Accumulating evidence suggests that elongation of transcription is another dynamic step, which is regulated by 'transcription elongation factors'. ELL (eleven nineteen lysine rich leukemia) belongs to a family of conserved transcription elongation factors, which interacts with EAF proteins (ELL Associated Factors), and this interaction is conserved across organisms. However, orthologs of the ELL-EAF family were not identified in plants. Recently, we reported the identification of two EAF orthologs (AtEAF1 and AtEAF2) in Arabidopsis thaliana. In the present study, we employed a yeast two-hybrid library screening approach to identify potential interaction partners of AtEAF proteins. AtCARP9 (CONSTITUTIVE ALTERATIONS IN THE SMALL RNAS PATHWAYS9) was identified as a novel interaction partner of both the AtEAFs, and the interaction was also confirmed in planta. Deletion mapping experiments were used to map the domains of AtCARP9 and AtEAFs that are involved in their interaction. Bioinformatics analysis revealed that AtCARP9 exhibits many sequence and structural features similar to those of other ELL orthologs. Furthermore, it could also complement the absence of ell1+ in S. pombe. Confocal microscopy demonstrated that both AtCARP9 and AtEAFs co-localize in the nucleus and nuclear speckles of unknown nature. Furthermore, AtCARP9 displays both developmentally regulated and tissue-specific expression patterns. Taken together, this work identifies AtCARP9 as the putative, hitherto unidentified ELL ortholog in A. thaliana, underscoring the importance of this family of transcription factors across organisms, including plants.