Transcription and Beyond 

To define low oxygen sensing and response mechanisms that enable survival for a short period of oxygen deprivation in the model plant Arabidopsis, we have studied extensively the regulation of gene expression that occurs after a gene transcript is produced, as the modulation of mRNA translation and storage provides a means to conserve energy when cells are deprived of oxygen. 

Our group developed the method "Translating Ribosome Affinity Purification" (TRAP) that enables researchers to monitor the mRNAs undergoing translation by ribosomes (the Translatome). This method can be used to monitor gene activity in specific cells and developmentally defined regions of plants. We have promoted use of TRAP and INTACT for multi-scale and cell type specific gene regulation analysis in crops. 

In our recent work defines transcriptional gene regulatory networks  and post-transcriptional gene regulatory mechanisms across species and in response to abiotic and biotic stress. 

Recent Papers

Alek Thomas Kettenburg, Miguel Angel Lopez, Kalenahalli Yogendra, Matthew J Prior, Teresa Rose, Sabrina Bimson, Sigrid Heuer, Stuart John Roy, Julia Bailey-Serres. OsPSTOL1 is prevalent in upland rice and its expression in wheat enhances root growth and hastens low phosphate signaling, Plant Cell and Environment, 2023 https://onlinelibrary.wiley.com/doi/10.1111/pce.14588

Reynoso MA, Borowsky AT, Pauluzzi GC, Yeung E, Zhang J, Formentin E, Velasco J, Cabanlit S, Duvenjian C, Prior MJ, Akmakjian GZ, Deal RB, Sinha NR, Brady SM, Girke T, Bailey-Serres J. Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice. Dev Cell. 2022 May 9;57(9):1177-1192

Kajala, K., Goran, M., Shaar-Moshe L., Mason, G., Rodriguez-Medina, J., et al. Cell. 2021.  Innovation, conservation, and repurposing of gene function in root cell type development. Lead by our amazing collaborator Siobhan Brady, a translatome atlas for tomato root cell types, including comparisons with rice and Arabidopsis. 

• In the news from UC Davis

• Data at ePlant: Tomato and Rice

Bailey-Serres, J., Parker, J.E., Ainsworth, E.A. et al. Genetic strategies for improving crop yields. Nature 575, 109–118 (2019) doi:10.1038/s41586-019-1679-0  in the 150 years of Nature reviews collection.

Reynoso, Kajala, Bajic, West, Pauluzzi et al. Science. This is the NSF PGR funded "Plasticity Project" team's deep genomic study comparing root tip gene regulatory networks responding to submergence responses in rice, medicago, tomato and a wild tomato.  Resources on our Data page.

• In  the news from UC Riverside and in  Spanish, and Dutch.

Travis Lee and Julia Bailey-Serres;  The Plant  Cell.  A deep study of nuclear gene regulatory processes in response to hypoxia and re-aeration in Arabidopsis.  See chromtin, RNAPII, ATAC-seq, and four different popultions or mRNA for your favorite gene in a browser:  Data page.

• More about Travis Lee 

Traubenik S, et al.  Reprogramming of Root Cells during Nitrogen-Fixing Symbiosis Involves Dynamic Polysome Association of Coding and Noncoding RNAs Plant Cell 2020. 

• A demonstration of translated "non-coding" mRNAs during nodulation

• More about Soledad Traubenik from Maria Eugenia Zanetti's group at La Plata National University in Argentina. Sole visited us to produce her TRAP-seq and other libraries for this project.  

Chantarachot et al.  DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs associated with innate immunity and growth inhibition, Nature Plants.  Free Read Only Version https://rdcu.be/b5Msy

• Discoverd that the most short lived mRNAs in Arabidopsis are involved in stress responses including innate immunity

• Determined that the turnover of these short-lived mRNAs under non-stress conditions is mediated by a group of conserved RNA helicases that interact with the 5' decapping apparatus.  Mutation of these genes promotes innate immunity and supresses growth. 

• See the accopanying commentary by Rémy Merret and Cécile Bousquet-Antonelli.  

Alam, R., Hummel, M., Locke, A., Jia, Z., Ignaci, C.C.I., Baltazar, M.D., Ismail, A., Septiningsih, E.M. and Bailey-Serres, J. (2020) Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater. Plant Direct. https://onlinelibrary.wiley.com/doi/full/10.1002/pld3.240  

• Beachel lBorlaug International Scholar and PhD student, Rejbana Alam's, collaborative work with Endang Septiningshi and Abdel Ismail at International Rice Research Institute.  

• Rejbana asked, is there genetic interaction between the submergence tolerance regulator SUB1A-1 and the anaerobic germination booster Trehalose-6 Phosphate Phosphatase (OsTPP7)?

• She performed, growth, transcriptome and metabolite analyisis of four near-isogenic lines varying at SUB1A-1 and OsTPP7 and four time points in plants developed entirely underwater. 

• The study found that SUB1A promotes photoautotrophic development in seeds of seedlings sown underwater. 

• It also provides evidence that the boost of seedling elongation by OsTPP7 /AG1 and the submergene tolerance provided by SUB1A-1 clash if the seedlings of seeds sown underwater do not escape into air before SUB1A slows underwater elongation growth. This happens after the plants become dependent upon photosynthate for growth. These findings may be relevant to farmers. 

See our Publications page for more