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| Status |
Public on Aug 09, 2023 |
| Title |
Global mapping of RNA-chromatin contacts reveals a proximity-dominated connectivity model for ncRNA-gene interactions |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
|
| Summary |
Non-coding RNAs (ncRNAs) are transcribed throughout the genome and provide regulatory inputs to gene expression through their interaction with chromatin. Yet, the genomic targets and functions of most ncRNAs are unknown. Here we use chromatin-associated RNA sequencing (ChAR-seq) to map the global network of ncRNA interactions with chromatin in human embryonic stem cells, and the dynamic changes in interactions during differentiation into definitive endoderm. We uncover general principles governing the organization of the RNA-chromatin interactome, demonstrating that nearly all ncRNAs exclusively interact with genes in close three-dimensional proximity to their locus, and provide a model predicting the interactome. We uncover RNAs that interact with many loci across the genome, and unveil thousands of unannotated RNAs that dynamically interact with chromatin. By relating the dynamics of the interactome to changes in gene expression, we demonstrate that activation or repression of individual genes is unlikely to be controlled by a single ncRNA.
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| Overall design |
To map chromatin interacting RNAs during cell differentiation we performed ChAR-seq on human ES cells and after differentiation into definitive endoderm (DE). We generated two datasets for each cell state. We also performed RNA-seq in quadruplicate on these samples to characterize changes in transcriptional output.
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| Contributor(s) |
Limouse C, Smith OK, Jukam D, Fryer KA, Greenleaf WJ, Straight AF |
| Citation(s) |
37770513 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 HG009909 |
Genome wide identification and functional analysis of chromatin regulatory RNAs |
STANFORD UNIVERSITY |
Aaron F Straight |
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| |
| Submission date |
Aug 09, 2023 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Aaron F Straight |
| E-mail(s) |
astraigh@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Biochemistry
|
| Street address |
279 Campus Drive, B409A
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (2) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (22)
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| Relations |
| BioProject |
PRJNA1003796 |
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