A new tool for discovering transcriptional regulators of co-expressed genes predicts gene regulatory networks that mediate ethylene-controlled root development

Abstract

Gene regulatory networks (GRNs) are defined by a cascade of transcriptional events by which signals, such as hormones or environmental cues, change development. To understand these networks, it is necessary to link specific transcription factors (TFs) to the downstream gene targets whose expression they regulate. Although multiple methods provide information on the targets of a single TF, moving from groups of co-expressed genes to the TF that controls them is more difficult. To facilitate this bottom-up approach, we have developed a web application named TF DEACoN. This application uses a publicly available Arabidopsis thaliana DNA Affinity Purification (DAP-Seq) dataset to search for TFs that show enriched binding to groups of co-regulated genes. We used TF DEACoN to examine groups of transcripts regulated by treatment with the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC), using a transcriptional dataset performed with high temporal resolution. We demonstrate the utility of this application when co-regulated genes are divided by timing of response or cell-type specific information, which provides more information on TF/target relationships than when less defined and larger groups of co-regulated genes are used. This approach predicted TFs that may participate in ethylene-modulated root development including the TF NAM (NO APICAL MERISTEM). We used a genetic approach to show that a mutation in NAM reduces the negative regulation of lateral root development by ACC. The combination of filtering and TF DEACoN used here can be applied to any group of co-regulated genes to predict GRNs that control coordinated transcriptional responses.

Partitioned Local Depth analysis of time course transcriptomic data reveals elaborate community structure

“…Using AgriGo v2.0, we looked for enriched function in these groups, finding that six out of seven PaLD groups were enriched in gene ontology annotations. We used TF DEACoN [23], which looks for significant enrichment in genes that have been shown to be targets of TFs defined by a publicly available DNA Affinity Purification (DAP)-Seq data set [24]. This analysis revealed that 5 out of 7 groups were enriched in targets of known TFs.…”

The Diverse Salt-Stress Response of Arabidopsis ctr1-1 and ein2-1 Ethylene Signaling Mutants Is Linked to Altered Root Auxin Homeostasis

“…The performed AthaMap analysis [38] of the promoter regions of the genes encoding TAA1, TAR1, and TAR2 identified the consistent presence of motifs for APETALA2/Ethyleneresponsive element binding proteins (AP2/ERBP), among which were Ethylene Response Factor 1 (ERF1), Ethylene Response Factor 2 (ERF2), Ethylene-Insensitive3-Like (TEIL), Target of Early Activation Tagged 1 /2 (TOE1/2), and EIN3 (Figure S1). The ethylene regulatory link to local auxin biosynthesis was also assessed by the TF DEACoN (Transcription Factor Discovery by Enrichment Analysis of Co-expression Networks) tool [47] which uses Arabidopsis DNA affinity purification sequencing (DAP-Seq) data to make predictions about which TFs may be involved in transcriptional responses of co-regulated genes.…”

“…were Ethylene Response Factor 1 (ERF1), Ethylene Response Factor 2 (ERF2), Ethylene-Insensitive3-Like (TEIL), Target of Early Activation Tagged 1 /2 (TOE1/2), and EIN3 (Figure S1). The ethylene regulatory link to local auxin biosynthesis was also assessed by the TF DEACoN (Transcription Factor Discovery by Enrichment Analysis of Co-expression Networks) tool [47] which uses Arabidopsis DNA affinity purification sequencing (DAP-Seq) data to make predictions about which TFs may be involved in transcriptional responses of co-regulated genes. TF DEACoN analysis of the genes encoding enzymes from the Tryptophan-dependent auxin biosynthesis (TAA1, TAR1, TAR2, YUC1-11) identified three AP2-EREBP transcription factors (RAP2.1, RAP2.9, and TINY or also known as ERF040) with fourfold enrichment of targets (Table S1).…”

“…AthaMap [38] (Figure S2) and TF DEACoN analyses [47] (Table S2) of the auxin transport genes were initially performed to check for ethylene-related regulatory elements. AthaMap analysis of the promoter regions of the auxin transporter genes AUX1, LAX3, PIN1, PIN2 and PIN3 outlined the presence of a number of AP2/ERBP transcription factors binding sites, including AtERF1 binding sequences in ProLAX3 and ProPIN1 as well as indications for the involvement of other AP2-EREBP transcription factors (RAP2.6 also known as ERF113, TEIL, DEAR3, ERF2, TOE1, TOE3, RAV2) (Figure S2).…”

“…The TF DEACoN tool (Transcription Factor Discovery by Enrichment Analysis of Coexpression Networks) [47] was used to characterize the TFs which may be involved in the transcriptional response of genes encoding enzymes from the Trp-dependent auxin biosynthesis (TAA1 -At1g70560; TAR1 -At1g23320; TAR2 -At4g24670, and YUC1/2/3/4/5/6/7/8/9/10/11: At4g32540, At4g13260, At1g04610, At5g11320, At5g43890, At5g25620, At2g33230, At4g28720, At1g04180, At1g48910, At1g21430) and transporter coding genes (PIN1/2/3/4/5/6/7/8: At1g73590, At5g57090, At1g70940, At2g01420, At5g16530, At1g77110, At1g23080, At5g15100; AUX1/LAX1/2/3: At2g38120, At5g01240, At2g21050, At1g77690; ABCB1/4/19: At2g36910, At2g47000, At3g28860). The displayed TF DEACoN results were narrowed down by setting the maximum p-value of 0.05 and logFC filter set on 2, corresponding to more than a fourfold enrichment.…”