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 6 days, 5 hours ago 250.0KiB
01_library1_rho_qc.ipynb 5 days, 7 hours ago 79.0KiB
02_library2_rho_qc.ipynb 5 days, 7 hours ago 78.0KiB
03_polylinker_qc.ipynb 5 days, 7 hours ago 128.1KiB
04_join_annotate_data.ipynb 5 days, 7 hours ago 89.2KiB
05_compute_information_content.ipynb 5 days, 7 hours ago 33.5KiB
06_fit_models.ipynb 5 days, 7 hours ago 61.4KiB
07_figures.ipynb 5 days, 7 hours ago 790.4KiB
08_revision_analyses.ipynb 5 days, 7 hours ago 44.7KiB
Data 5 days, 7 hours ago 35.6MiB
Dockerfile 5 days, 7 hours ago 1.2KiB
Figures 5 days, 7 hours ago 25.2MiB
LICENSE 5 days, 7 hours ago 1.5KiB
README.md 5 days, 7 hours ago 6.4KiB
Sequencing 5 days, 7 hours ago 2.8MiB
bclab.yml 5 days, 7 hours ago 350.0B
dataset_names.txt 5 days, 7 hours ago 285.0B
elife-67403-fixed.ipynb 6 days, 5 hours ago 285.1KiB
elife-67403-fixed.xml 6 days, 5 hours ago 250.0KiB
elife-67403.xml 6 days, 5 hours ago 250.1KiB
elife-67403.xml.media 6 days, 5 hours ago 4.4MiB
era.ipynb Main 6 days, 5 hours ago 1.2MiB
index.html 6 days, 5 hours ago 986.9KiB
index.html.media 6 days, 5 hours ago 1.4MiB
png_to_tiff.py 5 days, 7 hours ago 275.0B
utils 5 days, 7 hours ago 126.3KiB