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Series GSE193224 Query DataSets for GSE193224
Status Public on Sep 27, 2022
Title A giant virus genome is densely packaged by stable nucleosomes
Organisms Drosophila melanogaster; synthetic construct; Marseillevirus marseillevirus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The doublet histones of Marseillevirus are distantly related to the four eukaryotic core histones and wrap DNA to form remarkably similar nucleosomes. By releasing Marseillevirus chromatin from virions into solution and performing genome-wide nuclease digestion and chemical cleavage assays, we find that the higher-order organization of Marseillevirus chromatin differs greatly from that of eukaryotes. Marseillevirus nucleosomes fully protect DNA within virions, without linker DNA or phasing along genes. Likewise, we observe that most nucleosomes reconstituted onto 3-copy tandem repeats of a nucleosome positioning sequence are tightly packed and fully wrapped. We also document repeat generation and instability during viral passage in amoeboid culture. Dense promiscuous packing of fully wrapped nucleosomes rather than “beads-on-a-string” with genic punctuation suggests a viral genome protection function for doublet histones.
 
Overall design We used MNase-seq and MPE-seq, nucleosome mapping strategies in which either an endo/exonuclease or a small molecule DNA cleavage reagent removes accessible DNA, followed by end-polishing and ligation of sequencing adapters to produce libraries for paired-end DNA sequencing.
 
Contributor(s) Bryson TD, DeIoannes P, Valencia-Sanchez MI, Talbert PB, LaScola B, Armache K, Henikoff S
Citation(s) 36370708
Submission date Jan 07, 2022
Last update date Dec 27, 2022
Contact name Jorja Henikoff
E-mail(s) jorja@fhcrc.org
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
 
Platforms (7)
GPL17275 Illumina HiSeq 2500 (Drosophila melanogaster)
GPL19424 Illumina NextSeq 500 (synthetic construct)
GPL19604 Illumina HiSeq 2500 (synthetic construct)
Samples (117)
GSM5776934 601_12A_MPE_(20210810_TB_601_12A_MPE_210730)
GSM5776935 601_12B_MPE_(20210810_TB_601_12B_MPE_210730)
GSM5776936 601_300_MPE_1_(20210810_TB_601_3A_300_MPE_210730)
Relations
BioProject PRJNA795460

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE193224_G648_genome.fasta.gz 101.8 Kb (ftp)(http) FASTA
GSE193224_Genome_601x3.fasta.gz 199 b (ftp)(http) FASTA
GSE193224_Library_Preparation_TB2021.pdf 75.2 Kb (ftp)(http) PDF
GSE193224_MNase-extraction_TB2021.pdf 64.4 Kb (ftp)(http) PDF
GSE193224_MPE-extraction_TB2021.pdf 61.1 Kb (ftp)(http) PDF
GSE193224_RAW.tar 23.2 Gb (http)(custom) TAR (of BED, BEDGRAPH, BIGWIG)
GSE193224_T19_genome.fasta.gz 109.8 Kb (ftp)(http) FASTA
GSE193224_pUC19-601x7_KpnI.fasta.gz 1.1 Kb (ftp)(http) FASTA
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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