Identifying Regulatory Networks That Control Seed Development Using DNA-Protein Interaction Profiling with Chromatin Immunoprecipitation (ChIP) Assays and Sequencing

We have generated a regulatory atlas of soybean seeds by identifying transcription factor (TF) mRNAs that are specific for every seed region and subregion throughout development (see project outlined above). A series of ChIP-Seq experiments are being carried out to determine (1) what downstream genes these TFs regulate, (2) what DNA regulatory motifs they interact with, and (3) how region- and subregion-specific TFs are organized into regulatory networks that program developmental events that give rise to a soybean seed.

Experiments carried out at UC Davis with our collaborator, John Harada, investigated target genes that interact with one, or more, soybean TFs that program major developmental and physiological events during different periods of seed development. These include LEC1, AREB3, bZIP67, and ABI3 seed-specific TFs. They determined that LEC1 regulates gene sets at different developmental stages and generates distinct biological processes by interacting with AREB3, bZIP67, and ABI3 TFs in specific combinations. DNA binding sites of target genes bound by these TFs are organized into cis-regulatory modules (CRMs) that are in close proximity to their target genes, and are enriched for DNA motifs known to bind to LEC1, AREB3, bZIP67, and ABI3 TFs. Early maturation stage embryo protoplast transcriptional assays validated that the CRMs are functional.

ChIP-Seq experiments carried out in our laboratory at UCLA identified target genes for TFs that are specific for different regions and subregions of soybean post-fertilization stage globular seeds. These include AGL62, YAB1, and WOX9 TFs that are specific for the endosperm, embryo proper, and suspensor, respectively. In addition, comparative genomic approaches are being used to identify embryo-proper- and suspensor-specific TFs present in seeds across the plant kingdom to uncover major regulatory pathways that program region-specific events during early seed development.

To date, we have generated 126 ChIP-Seq Datasets and submitted all to GEO. Click here to download the ChIP-Seq datasets.


Pelletier, J.M., Kwong, R. Park, S., Le, B.H., Baden, R., Cagliari, A., Hashimoto, M., Munoz, M., Fischer, R.L., Goldberg, R.B., Harada J.J. (2017) LEC1 sequentially regulates the transcription of genes involved in diverse developmental processes during seed development. Proc. Natl. Acad. Sci. USA, 114:32, E6710–E6719. [DOWNLOAD PDF]

Jo, L., Pelletier, J.M., Hsu, S., Baden, R., Goldberg, R.B., Harada, J.J. (2020) Combinatorial interactions of the LEC1 transcription factor specify diverse developmental programs during soybean seed development Proc. Natl. Acad. Sci. USA, 117:2, 1223-1232.[DOWNLOAD PDF]