Examples

The following examples PEGS used in different analyses:

Mouse glucocorticoidal dataset

Thanks to Louise Hunter for providing this example.

Note

The input files and the resulting outputs can be obtained by downloading and unpacking the tar.gz archive at glucocorticoid_example.tar.gz

Background

An example application of PEGS is the analysis of up- and down-regulated glucocorticoidal targets from an RNA-seq study of liver samples from mice treated acutely with dexamethasone or vehicle (Caratti et al. 2018), combined with corresponding GR ChIP-seq and chromatin accessibility data (DNase I hypersensitive (DHS) regions) (Grontved et al. 2013 and Sobel et al. 2017 respectively), and mouse liver TAD boundary data (Kim et al. 2018).

The files for these datasets are:

  • RNA-seq data: 1_zt6up.txt and 2_zt6down.txt (placed in a clusters dirctory)

  • ChIP-seq and chromatin accessibility data: Grontved_GR_ChIP.bed and ZT6_DNase.bed (placed in a peaks directory)

  • TAD boundary data: mESC-TADs_mm10.txt

PEGS analysis

PEGS can be run on these data using the command:

pegs mm10 \
  --peaks data/peaks/*.bed --genes data/clusters/*.txt \
  -d 1000 5000 10000 50000 100000 200000 500000 1000000 5000000 \
  --tads data/mESC-TADs_mm10.txt \
  --name glucocorticoid \
  -o results/

This outputs a PNG heatmap glucocorticoid_heatmap.png:

Heatmap from PEGS for mouse glucocorticoid data

along with an XLSX file that contains the raw data glucocorticoid_results.xlsx.

Conclusions

The analyses indicate a strong association of dexamethasone up-regulated genes with dexamethasone-induced GR peaks at distances up to 500kbp from these peaks, but no evidence of down-regulated genes - indicating distinct mechanisms of gene activation and repression by glucocorticoids. At the same time, there is promoter proximal enrichment for both up-and down-regulated genes in the DHSs.

References

  • Caratti, G. et al. (2018) REVERBa couples the clock to hepatic glucocorticoid action. J Clin Invest 128(10):4454-4471

  • Grontved, L. et al. (2013) C/EBP maintains chromatin accessibility in liver and facilitates glucocorticoid receptor recruitment to steroid response elements. EMBO J 32(11), 1568-83

  • Kim, Y.H. et al. (2018) Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription. Science 359(6381):1274-1277

  • Sobel, J.A. et al. (2017) Transcriptional regulatory logic of the diurnal cycle in the mouse liver. PLoS Biol 15(4): e2001069