Information content differentiates enhancers from silencers in mouse photoreceptors

Enhancers and silencers often depend on the same transcription factors (TFs) and are conflated in genomic assays of TF binding or chromatin state. To identify sequence features that distinguish enhancers and silencers, we assayed massively parallel reporter libraries of genomic sequences targeted by the photoreceptor TF cone-rod homeobox (CRX) in mouse retinas. Both enhancers and silencers contain more TF motifs than inactive sequences, but relative to silencers, enhancers contain motifs from a more diverse collection of TFs. We developed a measure of information content that describes the number and diversity of motifs in a sequence and found that, while both enhancers and silencers depend on CRX motifs, enhancers have higher information content. The ability of information content to distinguish enhancers and silencers targeted by the same TF illustrates how motif context determines the activity of cis-regulatory sequences.Read more…

Enhancers and silencers often depend on the same transcription factors (TFs) and are conflated in genomic assays of TF binding or chromatin state. To identify sequence features that distinguish enhancers and silencers, we assayed massively parallel reporter libraries of genomic sequences targeted by the photoreceptor TF cone-rod homeobox (CRX) in mouse retinas. Both enhancers and silencers contain more TF motifs than inactive sequences, but relative to silencers, enhancers contain motifs from a more diverse collection of TFs. We developed a measure of information content that describes the number and diversity of motifs in a sequence and found that, while both enhancers and silencers depend on CRX motifs, enhancers have higher information content. The ability of information content to distinguish enhancers and silencers targeted by the same TF illustrates how motif context determines the activity of cis-regulatory sequences.Read more…


Type Path Last modified Size Actions
elife-67403-fixed.xml 2 years, 4 months ago 250.0KiB
01_library1_rho_qc.ipynb 2 years, 4 months ago 79.0KiB
02_library2_rho_qc.ipynb 2 years, 4 months ago 78.0KiB
03_polylinker_qc.ipynb 2 years, 4 months ago 128.1KiB
04_join_annotate_data.ipynb 2 years, 4 months ago 89.2KiB
05_compute_information_content.ipynb 2 years, 4 months ago 33.5KiB
06_fit_models.ipynb 2 years, 4 months ago 61.4KiB
07_figures.ipynb 2 years, 4 months ago 790.4KiB
08_revision_analyses.ipynb 2 years, 4 months ago 44.7KiB
Data 2 years, 4 months ago 35.6MiB
Dockerfile 2 years, 4 months ago 1.2KiB
Figures 2 years, 4 months ago 25.2MiB
LICENSE 2 years, 4 months ago 1.5KiB
README.md 2 years, 4 months ago 6.4KiB
Sequencing 2 years, 4 months ago 2.8MiB
bclab.yml 2 years, 4 months ago 350.0B
dataset_names.txt 2 years, 4 months ago 285.0B
elife-67403-fixed.ipynb 2 years, 4 months ago 285.1KiB
elife-67403-fixed.xml 2 years, 4 months ago 250.0KiB
elife-67403.xml 2 years, 4 months ago 250.1KiB
elife-67403.xml.media 2 years, 4 months ago 4.4MiB
era.ipynb Main 2 years, 4 months ago 1.2MiB
index.html 2 years, 4 months ago 986.9KiB
index.html.media 2 years, 4 months ago 1.4MiB
png_to_tiff.py 2 years, 4 months ago 275.0B
utils 2 years, 4 months ago 126.3KiB