Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq
Abstract
Deep sequencing of size-selected DNase I–treated chromatin (DNase-seq) allows high-resolution measurement of chromatin accessibility to DNase I cleavage, permitting identification of de novo active cis-regulatory modules (CRMs) and individual transcription factor (TF) binding sites. We adapted DNase-seq to nuclei isolated from C. elegans embryos and L1 arrest larvae to generate high-resolution maps of TF binding. Over half of embryonic DNase I hypersensitive sites (DHSs) were annotated as noncoding, with 24% in intergenic, 12% in promoters, and 28% in introns, with similar statistics observed in L1 arrest larvae. Noncoding DHSs are highly conserved and enriched in marks of enhancer activity and transcription. We validated noncoding DHSs against known enhancers from myo-2, myo-3, hlh-1, elt-2, and lin-26/lir-1 and recapitulated 15 of 17 known enhancers. We then mined DNase-seq data to identify putative active CRMs and TF footprints. Using DNase-seq data improved predictions of tissue-specific expression compared with motifs alone. In a pilot functional test, 10 of 15 DHSs from pha-4, icl-1, and ceh-13 drove reporter gene expression in transgenic C. elegans. Overall, we provide experimental annotation of 26,644 putative CRMs in the embryo containing 55,890 TF footprints, as well as 15,841 putative CRMs in the L1 arrest larvae containing 32,685 TF footprints.
Additional Information
© 2017 Ho et al.; Published by Cold Spring Harbor Laboratory Press This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. Received April 6, 2017; Accepted October 18, 2017; Published in Advance October 26, 2017. Data access: The DNase-seq data from this study have been submitted to the NCBI Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE97425. Additional analysis files, including DNase I signal data, all DHSs and nearest genes, putative TF footprints, novel motifs, motif-associated genes, and GO analysis, are available from WormBase (detailed list of files in Supplemental Table S3). We thank WormBase, especially Xiaodong Wang and James Done. This research was supported by NIH (National Institute of General Medical Sciences) grant GM084389 to P.W.S. and the Howard Hughes Medical Institute (047101), with which P.W.S. is an investigator. M.C.W.H. was supported by a National Science Foundation GRFP predoctoral fellowship. We would like to thank Ali Mortazavi, Igor Antoshechkin, John DeModena, Steven Kuntz, Erich Schwarz, Jim McGhee, and Erin Osborne Nishimura for assistance and advice on experimental design, sequence library construction, and analysis and interpretation of data. We thank David Angeles for help performing anatomy enrichment analysis. We thank Mark Wu, Mihoko Kato, and Hillel Schwartz for helpful suggestions on the manuscript.Attached Files
Published - Genome_Res.-2017-Ho-2108-19.pdf
Supplemental Material - Supplemental_Fig_S1.pdf
Supplemental Material - Supplemental_Fig_S10.pdf
Supplemental Material - Supplemental_Fig_S11.pdf
Supplemental Material - Supplemental_Fig_S2.pdf
Supplemental Material - Supplemental_Fig_S3.pdf
Supplemental Material - Supplemental_Fig_S4.pdf
Supplemental Material - Supplemental_Fig_S5.pdf
Supplemental Material - Supplemental_Fig_S6.pdf
Supplemental Material - Supplemental_Fig_S7.pdf
Supplemental Material - Supplemental_Fig_S8.pdf
Supplemental Material - Supplemental_Fig_S9.pdf
Supplemental Material - Supplemental_Table_S1.pdf
Supplemental Material - Supplemental_Table_S2.pdf
Supplemental Material - Supplemental_Table_S3.pdf
Supplemental Material - Supplemental_Table_S4.pdf
Supplemental Material - Supplemental_Table_S5.pdf
Supplemental Material - Supplemental_Table_S6.pdf
Supplemental Material - Supplemental_Table_S7.pdf
Supplemental Material - Supplemental_Table_S8.pdf
Supplemental Material - Supplemental_Table_S9.pdf
Supplemental Material - Supplementary_Text.docx
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Additional details
- PMCID
- PMC5741056
- Eprint ID
- 82769
- DOI
- 10.1101/gr.223735.117
- Resolver ID
- CaltechAUTHORS:20171030-102102638
- NIH
- GM084389
- Howard Hughes Medical Institute (HHMI)
- NSF Graduate Research Fellowship
- Created
-
2017-10-30Created from EPrint's datestamp field
- Updated
-
2022-03-21Created from EPrint's last_modified field
- Caltech groups
- WormBase