Validation and characterisation of a wheat GENIE3 network using an independent RNA-Seq dataset

Gene regulatory networks are powerful tools which facilitate hypothesis generation and candidate gene discovery. However, the extent to which the network predictions are biologically relevant is often unclear. Recently, as part of an analysis of the RefSeqv1.0 wheat transcriptome, a GENIE3 network which predicted targets of wheat transcription factors was produced. Here we have used an independent and publicly-available RNA-Seq dataset to validate the predictions of the wheat GENIE3 network for the senescence-regulating transcription factor NAM-A1 (TraesCS6A02G108300). We re-analysed the RNA-Seq data against the RefSeqv1.0 genome and identified a de novo set of differentially expressed genes (DEGs) between the wild-type and nam-a1 mutant which recapitulated the known role of NAM-A1 in senescence and nutrient remobilisation. We found that the GENIE3-predicted target genes of NAM-A1 overlap significantly with the de novo DEGs, more than would be expected for a random transcription factor. Based on high levels of overlap between GENIE3-predicted target genes and the de novo DEGs, we also identified a set of candidate senescence regulators. We then explored genome-wide trends in the network related to polyploidy and homoeolog expression levels and found that only homoeologous transcription factors are likely to share predicted targets in common. However, homoeologs in dynamic triads, i.e. with higher variation in homoeolog expression levels across tissues, are less likely to share predicted targets than stable triads. This suggests that homoeologs in dynamic triads are more likely to act on distinct pathways. This work demonstrates that the wheat GENIE3 network can provide biologically-relevant predictions of transcription factor targets, which can be used for candidate gene prediction and for global analyses of transcription factor function. The GENIE3 network has now been integrated into the KnetMiner web application, facilitating its use in future studies.

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Author Harrington, Sophie A.
Last Updated September 2, 2019, 13:22 (UTC)
Created September 2, 2019, 11:24 (UTC)
Article Host Type publisher
Article Is Open Access true
Article License Type cc-by-nc
Article Version Type publishedVersion
Citation Report https://scite.ai/reports/10.1101/684183
DFW Organisation JIC
DFW Work Package 2
DOI 10.1101/684183
Date Last Updated 2019-07-31T13:54:27.230791
Evidence open (via page says license)
Journal Is Open Access false
Open Access Status hybrid
PDF URL https://www.biorxiv.org/content/biorxiv/early/2019/06/27/684183.full.pdf
Publisher URL https://doi.org/10.1101/684183