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Series GSE104347 Query DataSets for GSE104347
Status Public on Mar 01, 2018
Title Genome-wide localisation of histone variants in Toxoplasma gondii implicates variant exchange in transcriptional control by demarcation of functional chromatin regions (ChIP-seq)
Organism Toxoplasma gondii RH
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin is composed of DNA wrapped around nucleosomes, complexes consisting of highly basic proteins called histones. Histone variants are non-canonical variants of histones that have specific functions. The Apicomplexan parasite Toxoplasma gondii possesses conserved histone variants CenH3, H3.3, H2A.Z, H2A.X, as well as the parasite-specific H2B variant, H2BV (or H2B.Z). We surveyed the genome-wide distribution of T. gondii histone variants by chromatin immunoprecipitation coupled with microarray (ChIP-chip) and next generation sequencing (ChIP-seq). Histone variants have specific localisations in chromosomes and in relation to genomic features. Histones H2BV and H2AZ localise to promoter regions with the transcriptional activation mark H3K4me3. Sites where H2BV, H2AZ and H3K4me3 colocalise are enriched in motifs recognised by AP2 transcription factors, particularly in the nucleosome-free region just upstream of the transcription start site. In contrast, histone variants H3.3 and H2AX are largely absent from promoters but enriched in gene bodies. Consistent with previous biochemical work, the majority of H2AX and H2AZ loci do not overlap, suggesting that they are present in different nucleosomes. In addition, the T. gondii homologue of the centromeric histone CenH3 demarcates centromeric chromatin and appears to be part of a unique centromeric histone complex including H3.3 that localises to centromeric chromatin as detected in proteomic analysis of co-immunoprecipitated CenH3 complexes. Together, these data suggest that the position of variant histones demarcates specific functional regions of chromatin and that exchange of histone variants is an important transcriptional regulatory mechanism in T. gondii.
 
Overall design Localization of histone variants in Toxoplasma gondii by ChIP-chip and ChIP-seq
 
Contributor(s) Nardelli SC, Silmon de Monerri NC, Wang X, Dalmasso MC, Brown L, Ting L, Sullivan WJ, Angel S, Kim K
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Submission date Sep 27, 2017
Last update date Jul 25, 2021
Contact name Kami Kim
E-mail(s) kami.kim@einstein.yu.edu
Phone 7184302611
Organization name Albert Einstein College of Medicine
Department Medicine
Lab Ullmann 1223
Street address 1300 Morris Park Avenue
City Bronx
State/province New York
ZIP/Postal code 10461
Country USA
 
Platforms (1)
GPL24058 Illumina HiSeq 2500 (Toxoplasma gondii RH)
Samples (23)
GSM2795864 H3.3 replicate 1
GSM2795865 H3.3 replicate 2
GSM2795866 H2AX replicate 2
Relations
BioProject PRJNA416926
SRA SRP123510

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Supplementary file Size Download File type/resource
GSE104347_RAW.tar 3.3 Gb (http)(custom) TAR (of BED, BROADPEAK, BW, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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