Eukaryotes generally employ nucleosome array to organize their DNA in nucleus. After DNA replication, DNA condensation is the only mechanism that reduces the volume of interphase chromatins, and packs DNA into highly condensed form for chromosome segregation. Condensin is one of the SMC-related protein complexes, which is composed of SMC2/SMC4 proteins and other chromosome-associated proteins. Its significances are involved in transforming interphase chromatins into metaphase chromosomes and regulating chromosome segregation. Unlike most eukaryotes including the sister groups of apicomplexans and ciliates, dinoflagellates have their nuclesomeless chromosomes organized in quasi-permanently condensed state. Consequently, the architecture of dinoflagellate chromosomes remains elusive.

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Eukaryotes generally employ nucleosome array to organize their DNA in nucleus. After DNA replication, DNA condensation is the only mechanism that reduces the volume of interphase chromatins, and packs DNA into highly condensed form for chromosome segregation. Condensin is one of the SMC-related protein complexes, which is composed of SMC2/SMC4 proteins and other chromosome-associated proteins. Its significances are involved in transforming interphase chromatins into metaphase chromosomes and regulating chromosome segregation. Unlike most eukaryotes including the sister groups of apicomplexans and ciliates, dinoflagellates have their nuclesomeless chromosomes organized in quasi-permanently condensed state. Consequently, the architecture of dinoflagellate chromosomes remains elusive.

In this research, the roles of condensin concerning the function and morphology transition of dinoflagellate chromosomes were focused. Firstly, condensin subunits – SMC2/SMC4 of Crypthecodinium cohnii were cloned and the deduced protein sequences were aligned with other retrieved SMC2/SMC4 orthologs for phylogenetic analysis. Surprisingly, dinoflagellate SMC2/SMC4 proteins formed clades with those of plantae/stramenopiles rather than alveolates. Correspondingly, rescue assay by transforming ccSMC2/4 genes into fission yeast cut14/cut3-temperature-sensitive mutants showed that transformants were viable. In addition, the supercoiling induction assay reveals that anti-SMC4 co-immunoprecipitates (condensin) from dinoflagellates were able to induce positive supercoilings in plasmid DNA. These suggest that functions of condensins are conserved in dinoflagellates. However, cell-cycle Western analysis demonstrates that condensin SMC2/4 proteins were constitutively expressed, but upregulated at S phase and peaked in G₂/M phases. Surprisingly, the following immunofluorescence study shows that condensin was mostly localized and enriched at the surface of chromosomes. To reveal in vivo functions of dinoflagellate condensin, seminal experiment to knock down genes in Crypthecodinium cohnii proves that downregulation of SMC4 protein led to mutant phenotypes including loss of viability, decondensed chromosomes and fragmentized genomic DNA. Unexpectedly, qPCR analysis of cDNAs of the knocked-down cells illustrates that genes were selectively downregulated in various degrees.

This study is the first attempt to reveal what and how factors might be involved in dinoflagellate permanently-condensed and nucleosome-deficient chromosomes. The findings imply that dinoflagellate condensin has adapted its functions including maintenance of chromosome integrity and regulation of gene transcriptions, to chromosome environments of dinoflagellates.