The native cistrome and sequence motif families of the maize ear.
Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define the complete set of transcription factor (TF) binding sites. Although TF-binding sites are known to be generally located within accessible chromatin regions (ACRs), pinpointing the...
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2021
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oai:doaj.org-article:dfb1b2d7383146d09957a58381b2dbe12021-12-02T20:03:23ZThe native cistrome and sequence motif families of the maize ear.1553-73901553-740410.1371/journal.pgen.1009689https://doaj.org/article/dfb1b2d7383146d09957a58381b2dbe12021-08-01T00:00:00Zhttps://doi.org/10.1371/journal.pgen.1009689https://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define the complete set of transcription factor (TF) binding sites. Although TF-binding sites are known to be generally located within accessible chromatin regions (ACRs), pinpointing these DNA regulatory elements globally remains challenging. Current approaches primarily identify binding sites for a single TF (e.g. ChIP-seq), or globally detect ACRs but lack the resolution to consistently define TF-binding sites (e.g. DNAse-seq, ATAC-seq). To address this challenge, we developed MNase-defined cistrome-Occupancy Analysis (MOA-seq), a high-resolution (< 30 bp), high-throughput, and genome-wide strategy to globally identify putative TF-binding sites within ACRs. We used MOA-seq on developing maize ears as a proof of concept, able to define a cistrome of 145,000 MOA footprints (MFs). While a substantial majority (76%) of the known ATAC-seq ACRs intersected with the MFs, only a minority of MFs overlapped with the ATAC peaks, indicating that the majority of MFs were novel and not detected by ATAC-seq. MFs were associated with promoters and significantly enriched for TF-binding and long-range chromatin interaction sites, including for the well-characterized FASCIATED EAR4, KNOTTED1, and TEOSINTE BRANCHED1. Importantly, the MOA-seq strategy improved the spatial resolution of TF-binding prediction and allowed us to identify 215 motif families collectively distributed over more than 100,000 non-overlapping, putatively-occupied binding sites across the genome. Our study presents a simple, efficient, and high-resolution approach to identify putative TF footprints and binding motifs genome-wide, to ultimately define a native cistrome atlas.Savannah D SavadelThomas HartwigZachary M TurpinDaniel L VeraPei-Yau LungXin SuiMax BlankWolf B FrommerJonathan H DennisJinfeng ZhangHank W BassPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 8, p e1009689 (2021) |
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DOAJ |
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DOAJ |
| language |
EN |
| topic |
Genetics QH426-470 |
| spellingShingle |
Genetics QH426-470 Savannah D Savadel Thomas Hartwig Zachary M Turpin Daniel L Vera Pei-Yau Lung Xin Sui Max Blank Wolf B Frommer Jonathan H Dennis Jinfeng Zhang Hank W Bass The native cistrome and sequence motif families of the maize ear. |
| description |
Elucidating the transcriptional regulatory networks that underlie growth and development requires robust ways to define the complete set of transcription factor (TF) binding sites. Although TF-binding sites are known to be generally located within accessible chromatin regions (ACRs), pinpointing these DNA regulatory elements globally remains challenging. Current approaches primarily identify binding sites for a single TF (e.g. ChIP-seq), or globally detect ACRs but lack the resolution to consistently define TF-binding sites (e.g. DNAse-seq, ATAC-seq). To address this challenge, we developed MNase-defined cistrome-Occupancy Analysis (MOA-seq), a high-resolution (< 30 bp), high-throughput, and genome-wide strategy to globally identify putative TF-binding sites within ACRs. We used MOA-seq on developing maize ears as a proof of concept, able to define a cistrome of 145,000 MOA footprints (MFs). While a substantial majority (76%) of the known ATAC-seq ACRs intersected with the MFs, only a minority of MFs overlapped with the ATAC peaks, indicating that the majority of MFs were novel and not detected by ATAC-seq. MFs were associated with promoters and significantly enriched for TF-binding and long-range chromatin interaction sites, including for the well-characterized FASCIATED EAR4, KNOTTED1, and TEOSINTE BRANCHED1. Importantly, the MOA-seq strategy improved the spatial resolution of TF-binding prediction and allowed us to identify 215 motif families collectively distributed over more than 100,000 non-overlapping, putatively-occupied binding sites across the genome. Our study presents a simple, efficient, and high-resolution approach to identify putative TF footprints and binding motifs genome-wide, to ultimately define a native cistrome atlas. |
| format |
article |
| author |
Savannah D Savadel Thomas Hartwig Zachary M Turpin Daniel L Vera Pei-Yau Lung Xin Sui Max Blank Wolf B Frommer Jonathan H Dennis Jinfeng Zhang Hank W Bass |
| author_facet |
Savannah D Savadel Thomas Hartwig Zachary M Turpin Daniel L Vera Pei-Yau Lung Xin Sui Max Blank Wolf B Frommer Jonathan H Dennis Jinfeng Zhang Hank W Bass |
| author_sort |
Savannah D Savadel |
| title |
The native cistrome and sequence motif families of the maize ear. |
| title_short |
The native cistrome and sequence motif families of the maize ear. |
| title_full |
The native cistrome and sequence motif families of the maize ear. |
| title_fullStr |
The native cistrome and sequence motif families of the maize ear. |
| title_full_unstemmed |
The native cistrome and sequence motif families of the maize ear. |
| title_sort |
native cistrome and sequence motif families of the maize ear. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2021 |
| url |
https://doaj.org/article/dfb1b2d7383146d09957a58381b2dbe1 |
| work_keys_str_mv |
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