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| Status |
Public on Nov 30, 2021 |
| Title |
Protein-RNA-Chromatin Interactions Reveal Nuclear RNA Architecture Functions in Transcriptional Condensation and Chromatin Folding |
| Organism |
Drosophila melanogaster |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
It has been proposed that nucleome organization and genome function involve interplays between protein, RNA and chromatin architectures. However, how chromatin interactions are cooperatively mediated by nuclear proteins and RNAs have not been fully explored. Here, we report the multivalent interplays in Drosophila cells involving RNA Polymerase II (RNAPII), nuclear RNAs and chromatin interactions. Using a novel genomic approach (pRChIA-PET) for protein-RNA-chromatin interactions, we discovered that extensive combination of nuclear RNAs cooperatively act in trans and co-localize with RNAPII and associated protein cofactors at chromatin interaction loci of active promoters and enhancers. Nuclear perturbation by aliphatic alcohol and RNase-A revealed that chromatin associated nuclear RNAs (canRNAs) are likely integral components in phase-separation for transcriptional condensation, and may act to maintain open chromatin accessibility and long-range chromatin interactions. These findings suggest a significant architectural role for combinatorial canRNAs as potential scaffolding elements in 3D genome organization and transcriptional regulation.
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| Overall design |
Investigation of protein-RNA-chromatin interactions by pRChIA-PET.
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| Contributor(s) |
Zheng M, Luo OJ, Tian SZ, Ruan Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Dec 06, 2018 |
| Last update date |
Dec 01, 2021 |
| Contact name |
Zhongyuan Tian |
| E-mail(s) |
[email protected]
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| Phone |
860-837-2358
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| Organization name |
The Jackson Laboratory for Genomic Medicine
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| Street address |
10 Discovery Drive
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| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06032 |
| Country |
USA |
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| Platforms (2) |
| GPL16479 |
Illumina MiSeq (Drosophila melanogaster) |
| GPL19132 |
Illumina NextSeq 500 (Drosophila melanogaster) |
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| Samples (22)
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| GSM3504350 |
pRChIA-PET, Rep2 |
| GSM3504351 |
roX2-ChIRP-Seq, Rep1 |
| GSM3504352 |
roX2-ChIRP-Seq, Rep2 |
| GSM3504353 |
Input ChIRP-Seq |
| GSM3504354 |
ATAC-Seq (RNaseA - control), Rep1 |
| GSM3504355 |
ATAC-Seq (RNaseA + 200μg/ml), Rep1 |
| GSM3504356 |
ATAC-Seq (RNaseA + 400μg/ml), Rep1 |
| GSM3504357 |
ATAC-Seq (RNaseA + 800μg/ml), Rep1 |
| GSM3504358 |
ATAC-Seq (RNaseA - control), Rep2 |
| GSM3504359 |
ATAC-Seq (RNaseA + 200μg/ml), Rep2 |
| GSM3504360 |
ATAC-Seq (RNaseA + 400μg/ml), Rep2 |
| GSM3504361 |
ATAC-Seq (RNaseA + 800μg/ml), Rep2 |
| GSM3504362 |
S2-RNAPII-ChIA-PET, Rep1 |
| GSM3504363 |
S2-RNAPII-ChIA-PET, Rep2 |
| GSM3504364 |
S2-RNAPII-ChIA-PET (RNaseA - control) |
| GSM3504365 |
S2-RNAPII-ChIA-PET (RNaseA + 400μg/ml) |
| GSM3955642 |
RNAPII-ChIA-PET_HD_Control |
| GSM3955643 |
RNAPII-ChIA-PET_HD_Treatment |
| GSM3955644 |
RNAPII-ChIA-PET_HD_Recovery |
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| Relations |
| BioProject |
PRJNA508781 |
| SRA |
SRP172771 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE123455_RAW.tar |
2.1 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, TXT) |
| GSE123455_RChIA-PET_Combined_DNA-RNA_PET.txt.gz |
13.0 Mb |
(ftp)(http) |
TXT |
| GSE123455_S2-RNAPII-ChIA-PET_Combined_PET_clusters.txt.gz |
3.7 Mb |
(ftp)(http) |
TXT |
| GSE123455_S2-RNAPII-ChIA-PET_Combined_coverage.bedgraph.gz |
179.4 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE123455_pRChIA-PET_Combined_DNA-RNA_PET.txt.gz |
76.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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