PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants

Abstract

The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN.itps.ncku.edu.tw/) is an effective resource for predicting regulatory elements and reconstructing transcriptional regulatory networks for plant genes. In this release (PlantPAN 3.0), 17 230 TFs were collected from 78 plant species. To explore regulatory landscapes, genomic locations of TFBSs have been captured from 662 public ChIP-seq samples using standard data processing. A total of 1 233 999 regulatory linkages were identified from 99 regulatory factors (TFs, histones and other DNA-binding proteins) and their target genes across seven species. Additionally, this new version added 2449 matrices extracted from ChIP-seq peaks for cis-regulatory element prediction. In addition to integrated ChIP-seq data, four major improvements were provided for more comprehensive information of TF binding events, including (i) 1107 experimentally verified TF matrices from the literature, (ii) gene regulation network comparison between two species, (iii) 3D structures of TFs and TF-DNA complexes and (iv) condition-specific co-expression networks of TFs and their target genes extended to four species. The PlantPAN 3.0 can not only be efficiently used to investigate critical cis- and trans-regulatory elements in plant promoters, but also to reconstruct high-confidence relationships among TF–targets under specific conditions.

The Tomato Metallocarboxypeptidase Inhibitor I, which Interacts with a Heavy Metal-Associated Isoprenylated Protein, Is Implicated in Plant Response to Cadmium

“…A 2334 bp-long sequence upstream of the ATG translation initiation codon of TCMP-1 was chosen as putative promoter sequence (Figure 2a). By using the Plant Promoter Analysis Navigator (PlantPAN3.0; [31]), a cis element starting at position 795 of the plus DNA strand implicated in Cd responsiveness was found (Figure 2a), which corroborates the results on the TCMP-1 gene expression regulation by Cd ( Figure 1c). In addition, several cis elements related to wounding and abiotic stress as well as to plant defense were also predicted ( Figure 2a).…”

Basal leakage in oscillation: coupled transcriptional and translational control using feed-forward loops

“…Black and blue lines represent transcriptional regulations, and the red line represents the degradation control. Solid lines indicate that the data were derived from experimental results, whereas dashed lines indicate that the data were derived from TF binding prediction tools, PlantTFDB (67) and PlantPAN3 (68). …”

“…From our results, we hypothesized that the clock system could have the advantages that we mentioned above if CCA1 and LHY can directly (or indirectly) regulate COP1. Hence, we performed a quick analysis combining ChIP-seq data for CCA1 (17, 73) and LHY (74) with TF binding prediction tools, PlantTFDB (67) and PlantPAN3 (68), to predict the direct or indirect regulation of CCA1 / LHY to COP1 . Interestingly, our analysis suggests that a well-studied transcriptional factor, TCP21 (TCP21/CHE) , could bind to the COP1 promoter region and both CCA1 and LHY could also bind to the TCP21 promoter region.…”

Allele specific expression of Dof genes responding to hormones and abiotic stresses in sugarcane

“…We extracted the 1.5kb upstream sequence of SsDof genes promoter. With the PlantPAN program [27] (http://plantpan.itps.ncku.edu.tw/) and PlantCARE program [28] (http:// bioinformatics.psb.ugent.be/webtools/plantcare/html/), we investigated the cis-elements of SsDof genes and collected the cis-element about growth and development, abiotic stresses and hormones responses in plant. The heatmap of cis-elements of SsDof genes was performed by TBtools software [29].…”