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| Status |
Public on Nov 29, 2021 |
| Title |
Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton (RNA-Seq) |
| Organism |
Gossypium hirsutum |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Cotton is an excellent model for studying heterosis, crop domestication and bioengineering improvement. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenome in allotetraploid cotton. However, the detailed profiling and functional characterization of H3K27me3 and H3K4me3/H3K27me3 bivalent mark are still understudied in cotton. In this study, we conducted H3K4me3 and H3K27me3-related ChIP-seq followed by comprehensively characterizing their roles in regulating gene transcription in cotton. We found that H3K4me3 and H3K27me3 exhibited active and repressive roles in regulating expression of genes between A and D subgenome, respectively. Expression of H3K4me3-H3K27me3 bivalent genes was regulated by combinatorial actions of both marks and may be dominantly controlled by H3K4me3. More importantly, H3K4me3 exhibited enrichment levels, positioning and distance-related effects on expression levels of related genes. In addition, H3K4me3, H3K27me3 and bivalent mark can indirectly influence gene expression through TF-mediated regulatory networks. Thus, our study provides insights in functions of H3K4me3 and H3K27me3 in regulating differential gene expression between A and D subgenome in cotton.
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| Overall design |
RNA-seq,ChIP-seq
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| Contributor(s) |
Zhang A, Wei Y, Gao J, Deng X, Shi Y, Feng Y, Zheng D, Cheng X, Liu F, Peng R, Zhang W |
| Citation(s) |
34975944 |
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| Submission date |
Jan 21, 2021 |
| Last update date |
Jan 10, 2022 |
| Contact name |
Li Wen Zhang |
| E-mail(s) |
wzhang25@njau.edu.cn
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| Organization name |
Nanjing Agricultural University
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| Street address |
No.1 Weigang
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| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platforms (1) |
| GPL29633 |
HiSeq X Ten (Gossypium hirsutum) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE165245 |
Profiling of H3K4me3 and H3K27me3 and their roles in regulating gene transcription in allotetraploid cotton |
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| Relations |
| BioProject |
PRJNA693816 |
| SRA |
SRP302697 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE165244_RAW.tar |
1.3 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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