Diatom centromeres suggest a mechanism for nuclear DNA acquisition

Abstract

Centromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. We observed 25 unique centromere sequences typically occurring once per chromosome, a finding that helps to resolve nuclear genome organization and indicates monocentric regional centromeres. Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved sequence features. Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain episomes and recruit the diatom centromeric histone protein CENH3, suggesting nonnative sequences can also function as diatom centromeres. Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition.diatom | Phaeodactylum tricornutum | episome | centromere | CENH3

Long transposon-rich centromeres in an oomycete reveal divergence of centromere features in Stramenopila-Alveolata-Rhizaria lineages

“…Information on centromeres is limited in other eukaryotic lineages. The malaria pathogen Plasmodium falciparum and the diatom Phaeodactylum tricornutum CENP-A binding regions are characterized by short simple AT-rich sequences (16, 17), while the parasite Toxoplasma gondii has a simple centromere without nucleotide bias (18).…”

Systematic and functional analysis of horizontal gene transfer events in diatoms

“…To gain insight in the functional repertoire of HGT genes, a gene ontology (GO) and functional domain 77 (Interpro) enrichment was performed. Out of the 7,461 diatom HGT genes, 6,024 (81%) were 78 annotated with an Interpro domain and 3,893 (52%) with a GO term. The only GO term which was 79 enriched for HGT genes in all nine diatom species is pseudouridine synthesis (GO:0001522), while 80 enriched protein domains covered pseudouridine synthase (IPR006145), S-adenosyl-L-methionine-81 dependent methyltransferase (IPR029063) and nitroreductase (IPR029479).…”

“…and vertically transferred genes among several age categories. Also the distance for every gene in P. 73 tricornutum to the closest transposable element as defined by 27 , centromeric and telomeric regions 74 elucidated by 78 was calculated and compared among the different origins. Statistical significance was 75 calculated by the Wilcoxon rank sum test.…”

Cellular Dynamics and Genomic Identity of Centromeres in the Cereal Blast Fungus

“…Furthermore, centromeres in many organisms are heterochromatic in nature and harbor the heterochromatic marks like H3K9di/trimethylation and DNA methylation [8, 13, 29]. A preference for AT-rich DNA sequence is evident for centromere formation in some organisms [13, 30-32]. It is important to note that none of these features exclusively define centromeres and, in most cases, the importance of an individual factor in defining centromere loci is not well understood.…”