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| Status |
Public on Dec 01, 2022 |
| Title |
Transcription elongator SPT6L regulates the occupancies of the SWI2/SNF2 chromatin remodelers SYD/BRM and nucleosomes at transcription start sites in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with the Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). The association of SYD and BRM to chromatin is dramatically reduced in spt6l and can be Chromatin remodelers have been thought to be crucial in creating an accessible chromatin environment before transcription activation. However, it is still unclear how chromatin remodelers recognize and bind to the active regions. In this study, we found that chromatin remodelers SPLAYED (SYD) and BRAHMA (BRM) interact and co-occupy with Suppressor of Ty6-like (SPT6L), a core subunit of the transcription machinery, at thousands of the transcription start sites (TSS). The association of SYD and BRM to chromatin is dramatically reduced in spt6l and can be restored mainly by SPT6LΔtSH2, which binds to TSS in a RNA polymerase II (Pol II)-independent manner. Furthermore, SPT6L and SYD/BRM are involved in regulating the nucleosome and Pol II occupancy around TSS. The presence of SPT6L is sufficient to restore the association of the chromatin remodeler SYD to chromatin and maintain normal nucleosome occupancy. Our findings suggest that the two chromatin remodelers can form protein complexes with the core subunit of the transcription machinery and regulate nucleosome occupancy in the early transcription stage.
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| Overall design |
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Pol II, SPT6L, SYD, and BRM in Arabidposis.MNase-seq for WT, SPT6L, and SPT6LdetlaSH2
10-day old seedlings were used for ChIP-seq and Mnase-seq assays.
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| Contributor(s) |
Shu J, Ding N, Liu J, Cui Y, Chen C |
| Citation(s) |
36453990 |
| Submission date |
Jul 02, 2022 |
| Last update date |
Dec 04, 2022 |
| Contact name |
Chen Chen |
| E-mail(s) |
chenchen101@scbg.ac.cn
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| Organization name |
South China Botanical Garden, Chinese Academy of Science
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| Lab |
Dr. Chen Chen
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| Street address |
723 Xinke Rd.
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510650 |
| Country |
China |
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| Platforms (1) |
| GPL26208 |
Illumina NovaSeq 6000 (Arabidopsis thaliana) |
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| Samples (40)
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| Relations |
| BioProject |
PRJNA855120 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE207391_RAW.tar |
1023.5 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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