Information content differentiates enhancers from silencers in mouse photoreceptors

Abstract
Data availability
Article and author information
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Abstract

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 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.

Data availability

The pJK01 and pJK03 plasmids have been deposited with AddGene (IDs 173489, 173490). Raw sequencing data and barcode counts have been uploaded to the NCBI GEO database under accession GSE165812. All processed activity data, predicted occupancy, and information content values are available in the supplementary material. All code for data processing, analysis, and visualization is available on Github at https://github.com/barakcohenlab/CRX-Information-Content.

The following data sets were generated

1. Friedman RZ
2. Granas DM
3. Myers CA
4. Corbo JC
5. Cohen BA
6. White MA
(2021) Information Content Differentiates Enhancers From Silencers in Mouse Photoreceptors
NCBI Gene Expression Omnibus, GSE165812.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165812

The following previously published data sets were used

1. Langmann T
2. Corbo JC
(2010) Deciphering the cis-regulatory architecture of mammalian photoreceptors
NCBI Gene Expression Omnibus, GSE20012.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20012
1. Hughes AE
2. Enright JM
3. Myers CA
4. Shen SQ
5. Corbo JC
(2016) ATAC-seq and RNA-seq of adult mouse rods and cones
NCBI Gene Expression Omnibus, GSE83312.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83312
(2018) CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites
Additional file 1.

https://static-content.springer.com/esm/art%3A10.1186%2Fs13072-018-0212-2/MediaObjects/13072_2018_212_MOESM1_ESM.xlsx
1. Hao H
2. Kim DS
3. Klocke B
4. Johnson KR
5. Cui K
6. Gotoh N
7. Zang C
8. Gregorski J
9. Gieser L
10. Peng W
11. Fann Y
12. Seifert M
13. Zhao K
14. Swaroop A
(2012) Transcriptional Regulation of Rod Photoreceptor Homeostasis Revealed by In Vivo NRL Targetome Analysis
NEI Data Share, Hong PLoS-Genet-2012.

https://datashare.nei.nih.gov/nnrlMain.jsp
1. Andzelm MM
2. Cherry TJ
3. Harmin DA
4. Boeke AC
5. Lee C
6. Hemberg M
7. Pawlyk B
8. Malik AN
9. Flavell SW
10. Sandberg MA
11. Raviola E
12. Greenberg ME
(2015) MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers
NCBI Gene Expression Omnibus, GSE61392.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61392
1. Lee J
2. Myers CA
3. Williams N
4. Abdelaziz M
5. Corbo JC
(2010) Quantitative fine-tuning of photoreceptor cis-regulatory elements through affinity modulation of transcription factor binding sites
Supplementary Table S1.

https://static-content.springer.com/esm/art%3A10.1038%2Fgt.2010.77/MediaObjects/41434_2010_BFgt201077_MOESM3_ESM.doc
1. White MA
2. Myers CA
3. Corbo JC
4. Cohen BA
(2013) Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks
Dataset S1.

https://www.pnas.org/highwire/filestream/39288/field_highwire_adjunct_files/1/sd01.txt
1. White MA
2. Myers CA
3. Corbo JC
4. Cohen BA
(2013) Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks
Dataset S2.

https://www.pnas.org/highwire/filestream/39288/field_highwire_adjunct_files/2/sd02.txt

Article and author information

Author details

Ryan Z Friedman

Edison Family Center for Genome Sciences and Systems Biology, and Department of Genetics, Washington University School of Medicine, St. Louis, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-9013-8676
David M Granas

Edison Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, United States

Competing interests
The authors declare that no competing interests exist.
Connie A Myers

Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States

Competing interests
The authors declare that no competing interests exist.
Joseph C Corbo

Department of Pathology and Immunology, Washington University School of Medicine, St Louis, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-9323-7140
Barak A Cohen

Edison Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3350-2715
Michael A White

Edison Family Center for Genome Sciences and Systems Biology, and Department of Genetics, Washington University School of Medicine, St. Louis, United States

For correspondence
mawhite@wustl.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8511-6026

Funding

National Institutes of Health (F31HG011431)

Ryan Z Friedman

National Institutes of Health (R01GM121755)

Michael A White

National Institutes of Health (R01EY027784)

Barak A Cohen

National Institutes of Health (EY025196)

Joseph C Corbo

National Institutes of Health (EY03075)

Joseph C Corbo

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to protocol # A-3381-01 approved by the Institutional Animal Care and Use Committee of Washington University in St. Louis. Euthanasia of mice was performed according to the recommendations of the American Veterinary Medical Association Guidelines on Euthanasia. Appropriate measures are taken to minimize pain and discomfort to the animals during experimental procedures.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.