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| Status |
Public on Feb 23, 2022 |
| Title |
Integrating RNA-seq and assay for transposase-accessible chromatin by sequencing (ATAC-seq) predicts functionally-relevant chromatin regions |
| Organism |
Drosophila melanogaster |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Gene regulation is critical for proper cellular function. Next-generation sequencing technology has revealed the presence of regulatory networks that regulate gene expression and essential cellular functions. Studies investigating the epigenome have begun to uncover the complex mechanisms regulating transcription. Assay for transposase-accessible chromatin by sequencing (ATAC-seq) is quickly becoming the assay of choice for epigenomic investigations. Integrating epigenomic and transcriptomic data has the potential to reveal the chromatin-mediated mechanisms regulating transcription. However, integrating these two data types remains challenging. We used the insulin signaling pathway as a model to investigate chromatin regions and gene expression changes using ATAC- and RNA-seq in insulin-treated Drosophila S2 cells. We show that insulin causes widespread changes in chromatin accessibility and gene expression. Then, we attempted to integrate ATAC- and RNA-seq data to predict functionally-relevant chromatin regions that control the transcriptional response to insulin. We show that using differential chromatin accessibility can predict functionally-relevant genome regions, but that stratifying differentially-accessible chromatin regions by annotated feature type provides a better prediction of whether a chromatin region regulates gene expression. In particular, our data demonstrate a strong correlation between chromatin regions annotated to distal promoters (1-2 kb from the transcription start site). To test this prediction, we cloned candidate distal promoter regions upstream of luciferase and validated the functional relevance of these chromatin regions. Our data show that distal promoter regions selected by correlations with RNA-seq are more likely to control gene expression. Thus, correlating ATAC- and RNA-seq data can home in on functionally-relevant chromatin regions
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| Overall design |
ATAC-seq and mRNA profiles of insulin-treated Drosophila S2 cells
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| Contributor(s) |
Merrill CB, Montgomery AB, Pabon MA, Rodan AR, Rothenfluh A |
| Citation(s) |
35614386 |
| BioProject |
PRJNA730574 |
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| Submission date |
Feb 22, 2022 |
| Last update date |
Jun 14, 2022 |
| Contact name |
Adrian Rothenfluh |
| E-mail(s) |
adrian.rothenfluh@hsc.utah.edu
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| Organization name |
University of Utah
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| Department |
Psychiatry
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| Street address |
15 N 2030 E
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| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84132 |
| Country |
USA |
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| Platforms (1) |
| GPL17275 |
Illumina HiSeq 2500 (Drosophila melanogaster) |
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| Samples (12)
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| GSM5911302 |
S2 cells - Vehicle-treated, ATAC-seq, rep1 |
| GSM5911303 |
S2 cells - Vehicle-treated, ATAC-seq, rep2 |
| GSM5911304 |
S2 cells - Vehicle-treated, ATAC-seq, rep3 |
| GSM5911305 |
S2 cells - Insulin-treated, ATAC-seq, rep1 |
| GSM5911306 |
S2 cells - Insulin-treated, ATAC-seq, rep2 |
| GSM5911307 |
S2 cells - Insulin-treated, ATAC-seq, rep3 |
| GSM5911308 |
S2 cells - Vehicle-treated, RNA-seq, rep1 |
| GSM5911309 |
S2 cells - Vehicle-treated, RNA-seq, rep2 |
| GSM5911310 |
S2 cells - Vehicle-treated, RNA-seq, rep3 |
| GSM5911311 |
S2 cells - Insulin-treated, RNA-seq, rep1 |
| GSM5911312 |
S2 cells - Insulin-treated, RNA-seq, rep2 |
| GSM5911313 |
S2 cells - Insulin-treated, RNA-seq, rep3 |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE197224_14989R_RNA_metrics.html.gz |
396.1 Kb |
(ftp)(http) |
HTML |
| GSE197224_ATAC_GO_Pathways.csv.gz |
7.1 Kb |
(ftp)(http) |
CSV |
| GSE197224_ATAC_Insulin.narrowPeak.gz |
140.3 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE197224_ATAC_Insulin_vs_Vehicle.DESeq.txt.gz |
398.6 Kb |
(ftp)(http) |
TXT |
| GSE197224_ATAC_Peak_Annotation.xlsx |
1.5 Mb |
(ftp)(http) |
XLSX |
| GSE197224_ATAC_Vehicle.narrowPeak.gz |
138.8 Kb |
(ftp)(http) |
NARROWPEAK |
| GSE197224_RAW.tar |
395.0 Mb |
(http)(custom) |
TAR (of BW) |
| GSE197224_RNA_Insulin_vs_Vehicle.DESeq.xlsx |
4.5 Mb |
(ftp)(http) |
XLSX |
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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