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Series GSE241969 Query DataSets for GSE241969
Status Public on Oct 19, 2023
Title Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome
Organisms Saccharomyces cerevisiae; Candida albicans; Homo sapiens; Bigelowiella natans; Breviolum minutum
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary 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.
Overall design ATAC-seq in B. minutum; mapping of 5-hmU in B. minutum using MeDIP-seq and chemical mapping; SMF and ATAC-seq on yeast cells exogenously expressing various dinoflagellate DVNP proteins
Contributor(s) Marinov GK, Chen X, Swaffer MP, He C, Xiang T, Kundaje A, Grossman AR, Greenleaf WJ
Citation(s) 37781619
Submission date Aug 30, 2023
Last update date Oct 20, 2023
Contact name Georgi Kolev Marinov
Department Genetics
Street address 279 Campus Drive West, Beckman Center, B-257A/259
City Stanford
State/province California
ZIP/Postal code 94305-5101
Country USA
Platforms (4)
GPL30494 NextSeq 550 (Bigelowiella natans)
GPL33721 NextSeq 550 (Breviolum minutum)
GPL33722 NextSeq 550 (Breviolum minutum; Homo sapiens)
Samples (34)
GSM7746898 L08_Symbiodinium_minutum_SSb01_omniATAC
GSM7746899 L503-27C-ATAC-rep1
GSM7746900 L504-27C-ATAC-rep2
BioProject PRJNA1010827

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GSE241969_RAW.tar 3.6 Gb (http)(custom) TAR (of BEDGRAPH, BIGWIG)
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Raw data are available in SRA

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