Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome
Navrátilová, Pavla; Pavlů, Šimon; Zhu, Zihao; Tulpová, Zuzana; Kopecký, Ondřej; Novák, Petr; Stein, Nils; Šimková, Hana
- Publisher
- Zenodo
- Language
- en
Abstract
Regulation of transcription initiation is the ground level of modulating gene expression during plant development. This process relies on interactions between transcription factors and cis-regulatory elements (CREs), which become promising targets for crop bioengineering. To annotate CREs in the barley genome and understand mechanisms of distal regulation, we profiled several epigenetic features across three stages of barley embryo and leaves, and performed HiChIP to identify activating and repressive genomic interactions. Using machine learning, we integrated the data into seven chromatin states, predicting over 70,000 CRE candidates, collectively representing ~1% of the barley genome. Identified genomic interactions, often spanning multiple genes, linked thousands CREs with their targets and revealed notably frequent promoter-promoter contacts. Using the LEA gene family as an example, we discuss possible roles of these interactions in transcription regulation. Finally, we demonstrate the potential of our datasets to predict CREs for other developmental stages and conditions. We also made visualization of all data available to the community throught an interactive genome browser (see the link below in Related works).
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2193 (5.48%) 2069 (5.17%) 6942 (17.4%) 381 (0.952%) 2634 (6.58%) 14760 (36.9%) 1424 (3.56%) 2268 (5.67%) 2183 (5.46%) 1305 (3.26%) 1874 (4.68%) 71 (0.177%) 46 (0.115%) 1581 (3.95%) 277 (0.692%) 8DAP leaf 24DAP 4DAG 27112 6621 3284 2171 1796 1710 619 538 0 10000 20000 30000 Number of Regions ATACseq E7 H3K9ac UMRs 0 1e42e4 3e4 4e4 Count 18762 8330 2726 2276 1733 930 733 40 0 5000 10000 15000 20000 Number of Regions ATACseq E7 UMRs H3K9ac 0 2e43e4 Count 12638 10003 4205 2960 1609 1406 116 18 0 5000 10000 Number of Regions ATACseq E7 UMRs H3K9ac 02e4 3e4 Count 1e4 1e4 8DAP 4DAG leaf
-10.0 peak center 10.0Kb 0 5 10 15 Coverage HiChIP Signal Enrichment at ChIP Peaks HiChIP morex24DAP H3K4me3_1 -10.0 peak center 10.0Kb HiChIPmorex24DAP_H3K4me3_1 0 5 10 15 20 25
AA H3K4me3 - 10kb A:E7 H3K4me3 - 10kb AA H3K4me3 - 20kb A:E7 H3K4me3 - 20kb SS H3K27me3 - 10kb S:E4/E7 H3K27me3 - 10kb SS H3K27me3 - 20kb S:E4/E7 H3K27me3 - 20kb H3K4me3 - 10kb H3K27me3 - 10kb H3K4me3 - 20kb H3K27me3 - 20kb
47.1 % 5.15 % 5.2 % 5.84 % 5.89 % 6.93 % 8.69 % 15.2 % 25.1 % 6.47 % 9.03 % 11 % 22.6 % 25.8 % v
category count Intron-Intron 45 Intron-Silent_promoter 59 Intron-Silent_terminator 21 Intron-E4 68 Intron-E7 77 Intron-Active_promoter 41 Intron-TE 30 Intron-Active_terminator 17 Intron-Distal 0 Silent_promoter-Silent_promoter 195 Silent_promoter-Silent_terminator 117 Silent_promoter-E4 326 Silent_promoter-E7 170 Silent_promoter-Active_promoter 108 Silent_promoter-TE 100 Silent_promoter-Active_terminator 33 Silent_promoter-Distal 0 Silent_terminator-Silent_terminator 3 Silent_terminator-E4 69 Silent_terminator-E7 28 Silent_terminator-Active_promoter 12 Silent_terminator-TE 13 Silent_terminator-Active_terminator 5 Silent_terminator-Distal 0 E4-E4 571 E4-E7 260 E4-Active_promoter 115 E4-TE 184 E4-Active_terminator 33 E4-Distal 3 E7-E7 219 E7-Active_promoter 221 E7-TE 193 E7-Active_terminator 78 E7-Distal 4 Active_promoter-Active_promoter 68 Active_promoter-TE 75 Active_promoter-Active_terminator 68 Active_promoter-Distal 1 TE-TE 86 TE-Active_terminator 23 TE-Distal 3 Active_terminator-Active_terminator 8 Active_terminator-Distal 1 Distal-Distal 0 Table S6. Quantification of various types of interactions in the HiChIP significant-interaction set (related to Figure 5 and Figure S9) (B) 24DAP_H3K27me3_Q0.1 interaction set at 5 kb resolution
