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…


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elife-67403-fixed.xml 1 month, 3 weeks ago 250.0KiB
01_library1_rho_qc.ipynb 1 month, 3 weeks ago 79.0KiB
02_library2_rho_qc.ipynb 1 month, 3 weeks ago 78.0KiB
03_polylinker_qc.ipynb 1 month, 3 weeks ago 128.1KiB
04_join_annotate_data.ipynb 1 month, 3 weeks ago 89.2KiB
05_compute_information_content.ipynb 1 month, 3 weeks ago 33.5KiB
06_fit_models.ipynb 1 month, 3 weeks ago 61.4KiB
07_figures.ipynb 1 month, 3 weeks ago 790.4KiB
08_revision_analyses.ipynb 1 month, 3 weeks ago 44.7KiB
Data 1 month, 3 weeks ago 35.6MiB
Dockerfile 1 month, 3 weeks ago 1.2KiB
Figures 1 month, 3 weeks ago 25.2MiB
LICENSE 1 month, 3 weeks ago 1.5KiB
README.md 1 month, 3 weeks ago 6.4KiB
Sequencing 1 month, 3 weeks ago 2.8MiB
bclab.yml 1 month, 3 weeks ago 350.0B
dataset_names.txt 1 month, 3 weeks ago 285.0B
elife-67403-fixed.ipynb 1 month, 3 weeks ago 285.1KiB
elife-67403-fixed.xml 1 month, 3 weeks ago 250.0KiB
elife-67403.xml 1 month, 3 weeks ago 250.1KiB
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era.ipynb Main 1 month, 3 weeks ago 1.2MiB
index.html 1 month, 3 weeks ago 986.9KiB
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png_to_tiff.py 1 month, 3 weeks ago 275.0B
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