Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity

Authors: NIYIKIZA, DANIEL - University Of Tennessee; PIYA, SARBOTTAM - University Of Tennessee; ROUTRAY, PRATYUSH - University Of Tennessee; MIAO, LONG - University Of Tennessee; KIM, WON-SEOK - University Of Missouri; BURCH-SMITH, TESSA - University Of Tennessee; GILL, TOM - University Of Tennessee; SAMS, CARL - University Of Tennessee; Arelli, Prakash; PANTALONE, VINCE - University Of Tennessee; Krishnan, Hari; HEWEZI, TAREK - University Of Tennessee

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/20/2020
Publication Date: 6/3/2020
Citation: Niyikiza, D., Piya, S., Routray, P., Miao, L., Kim, W., Burch-Smith, T., Gill, T., Sams, C., Arelli, P.R., Pantalone, V., Krishnan, H.B., Hewezi, T. 2020. Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity. Plant Journal. 103(5):1744-1766. https://doi.org/10.1111/tpj.14861.
DOI: https://doi.org/10.1111/tpj.14861

Interpretive Summary: Soybean plants uniquely produce their own nitrogen by having nitrogen-fixing nodules on the roots through a symbiotic (mutually beneficial) interaction with specialized soil bacteria collectively known as rhizobia. Nitrogen fixation is a process by which nitrogen in the air is incorporated into a form that the plant can utilize, and this process involves both the plant and rhizobia. Thus, application of nitrogen fertilizer is not required for soybean fields. Symbiotic-interaction is a complex genetic process, and the objective of the current study was to identify the key genes and determine when they are turned on and off during the process. Understanding how the genes function together as nodules form, develop, and degrade, may help identify genetic engineering methods to increase the level of nitrogen fixation activity. In this research, more than 10,000 genes were identified as having a role in nodule development and function. Some of the complex processes for increased formation of nodules on the soybean roots are better understood because of this research. The implications are far reaching. Ultimately growers may have potential benefits for increased yields and higher profits.

Technical Abstract: Soybean nodulation is a highly controlled process that involves complex gene regulation at both transcriptional and post-transcriptional levels. In the present study, we pro'led gene expression changes, alternative splicing events, and DNA methylation patterns during nodule formation, development, and senescence. The transcriptome data uncovered key transcription patterns of nodule development that included 9669 core genes and 7302 stage-speci'c genes. Alternative splicing analysis uncovered a total of 2323 genes that undergo alternative splicing events in at least one nodule developmental stage, with activation of exon skipping and repression of intron retention being the most common splicing events in nodules compared to roots. Approximately 40% of the differentially spliced genes were also differentially expressed at the same nodule developmental stage, implying a substantial association between gene expression and alternative splicing. Genome-wide-DNA methylation analysis revealed dynamic changes in nodule methylomes that were speci'c to each nodule stage, occurred in a sequence-speci'c manner, and impacted the expression of 1864 genes. An attractive hypothesis raised by our data is that increased DNA methylation may contribute to the ef'ciency of alternative splicing. Together, our results provide intriguing insights into the associations between gene expression, alternative splicing, and DNA methylation that may shape transcriptome complexity and proteome speci'city in developing soybean nodules.