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Series GSE71418 Query DataSets for GSE71418
Status Public on Sep 30, 2016
Title Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton
Organism Gossypium hirsutum
Experiment type Expression profiling by high throughput sequencing
Summary Histone modifications regulate gene expression in eukaryotes, but their roles in gene expression changes in interspecific hybrids or allotetraploids are poorly understood. Histone modifications can be mapped by immunostaining of metaphase chromosomes at the single cell level and/or by chromatin immunoprecipitation-sequencing (ChIP-seq) for individual genes. Here we examined H3K4me3 density and transcriptome maps in root-tip cells of allotetraploid cotton (Gossypium hirsutum L.). The overall H3K4me3 levels were relatively equal between A and D chromosomes, which were consistent with equal numbers of expressed genes between the two subgenomes. However, intensities per chromosomal area were nearly twice as high in the D homoeologs as in the A homoeologs. Consistent with the cytological observation, ChIP-seq analysis showed more D-homoeologs with biased H3K4me3 levels than A-homoeologs with biased modifications, which correlated with the greater number of genes with D-biased expression than that with A-biased expression in most homoeologous chromosome pairs. Two chromosomes displayed different expression levels compared with other chromosomes probably because of translocations, which may affect the local chromatin structure (hence expression levels) for the genes involved. This example of genome-wide histone modifications that determine expression bias of homoeologous genes in allopolyploids provides a molecular basis for the evolution and domestication of polyploid species including important crops.
Overall design RNA-seq analysis using sequence libraries prepared from the root tip, which was the same tissue used to prepare for metaphase chromosome immune-staining assays. Three independent mRNA-seq libraries were constructed and sequenced by Illumina paired-end reads.
Contributor(s) Zheng D, Ye W, Song Q
Citation(s) 27637746
Submission date Jul 28, 2015
Last update date May 15, 2019
Contact name Dewei Zheng
Phone 15005160205
Organization name Nanjing Agricultural University
Department State Key Laboratory of Crop Genetics and Germplasm Enhancement
Lab Polyploid and Epigenetics Lab
Street address 1 Weigang Road
City Nanjing
State/province Jiangsu Province
ZIP/Postal code 210095
Country China
Platforms (1)
GPL19231 Illumina HiSeq 2500 (Gossypium hirsutum)
Samples (3)
GSM1833991 TM-1_root_tip_rep1
GSM1833992 TM-1_root_tip_rep2
GSM1833993 TM-1_root_tip_rep3
This SubSeries is part of SuperSeries:
GSE83372 Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton
BioProject PRJNA291194
SRA SRP061688

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Supplementary file Size Download File type/resource
GSE71418_TM-1_root_tip_genes.fpkm_tracking.gz 3.9 Mb (ftp)(http) FPKM_TRACKING
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