Project description:In dinoflagellates, the most unique and divergent nuclear organization among the known diversity of eukaryotes has evolved. The list of highly unusual features of dinoflagellate nuclei and genomes is long -- permanently condensed liquid crystalline chromosomes, in which histones are not the main packaging component, genes organized as very long unidirectional gene arrays, general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. Most of these fascinating properties were originally identified in the 1970s and 1980s but have received very little attention in recent decades using modern genomic tools. In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, and also often coincides with the boundaries between gene arrays. It is generally anti-correlated with chromatin accessibility, the levels of which are lower in those regions. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.
Project description:To identify the target genes of Stat92E in adult Drosophila testis cyst cells, the testes of c587ts;UAS-Stat92E were dissected and cross-linked to conduct chromatin immunoprecipitation(ChIP) assay and ChIP-high throughput sequencing.
Project description:To identify the target genes of Stat92E in adult Drosophila testis cyst cells, the testes of control (c587ts) and c587ts;UAS-upd were dissected and cross-linked to conduct chromatin immunoprecipitation(ChIP) assay and ChIP-high throughput sequencing.
Project description:We report how unique RNA seq profiles of ribosomal RNA (18S, 28S) present in sperm indicate specific cleavage sites. Additionally, these sequencing results reveal how overall character of RNA (GC content) can significantly affect overall distribution of mapped reads.
Project description:Dinoflagellate chromosomes are extraordinary, as their organization is independent of architectural nucleosomes unlike typical eukaryotes and shows a cholesteric liquid crystal state. 5-hydroxymethyluridine (5hmU) is present at unusually high levels and its function remains an enigma in dinoflagellates chromosomal DNA for several decades. Here, we demonstrate that 5hmU contents vary among different dinoflagellates and are generated through thymidine hydroxylation. Importantly, we identified the enzyme, which is a putative dinoflagellate TET/JBP homologue, catalyzing 5hmU production using both in vivo and in vitro biochemical assays. Based on the near-chromosomal level genome assembly of dinoflagellate Amphidinium carterae, we depicted a comprehensive 5hmU landscape and found that 5hmU loci are significantly enriched in repeat elements. Moreover, inhibition of 5hmU via dioxygenase inhibitor leads to transcriptional activation of 5hmU-marked transposable elements (TEs), implying that 5hmU appears to serve as an epigenetic mark for silencing transposon. Together, our results revealed the biogenesis, genome-wide landscape and molecular function of dinoflagellate 5hmU, providing mechanistic insight into the function of this enigmatic DNA mark.
