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

Zafar SA and Bailey-Serres J. Decoding the evolution of C4 photosynthesis. Trends in Plant Science. 2025:S1360138525000421. https://doi.org/10.1016/j.tplants.2025.02.008

Ashikari M, Nagai K, and Bailey-Serres J. Surviving floods: Escape and quiescence strategies of rice coping with submergence. Plant Physiology. 2025:197(2):kiaf029. https://doi.org/10.1093/plphys/kiaf029

Manzano C, Morimoto KW, Shaar-Moshe L, Mason GA, Cantó-Pastor A, Gouran M, De Bellis D, Ursache R, Kajala K, Sinha N, et al. Regulation and function of a polarly localized lignin barrier in the exodermis. Nat Plants. 2024:11(1):118–130. https://doi.org/10.1038/s41477-024-01864-z

Bailey-Serres J, Geigenberger P, Perata P, Sasidharan R, and Schwarzländer M. Hypoxia as challenge and opportunity: From cells to crops, to synthetic biology. Plant Physiology. 2024:197(1):kiae640. https://doi.org/10.1093/plphys/kiae640

Gibbs DJ, Theodoulou FL, and Bailey-Serres J. Primed to persevere: Hypoxia regulation from epigenome to protein accumulation in plants. Plant Physiology. 2024:197(1):kiae584. https://doi.org/10.1093/plphys/kiae584

Borowsky AT and Bailey-Serres J. Rewiring gene circuitry for plant improvement. Nat Genet. 2024:56(8):1574–1582. https://doi.org/10.1038/s41588-024-01806-7

Cantó-Pastor A, Kajala K, Shaar-Moshe L, Manzano C, Timilsena P, De Bellis D, Gray S, Holbein J, Yang H, Mohammad S, et al. A suberized exodermis is required for tomato drought tolerance. Nat Plants. 2024:10(1):118–130. https://doi.org/10.1038/s41477-023-01567-x

Kettenburg AT, Lopez MA, Yogendra K, Prior MJ, Rose T, Bimson S, Heuer S, Roy SJ, and Bailey‐Serres J. PHOSPHORUS‐STARVATION TOLERANCE 1 (OsPSTOL1) is prevalent in upland rice and enhances root growth and hastens low phosphate signaling in wheat. Plant Cell & Environment. 2023:46(7):2187–2205. https://doi.org/10.1111/pce.14588

Reynoso MA, Borowsky AT, Pauluzzi GC, Yeung E, Zhang J, Formentin E, Velasco J, Cabanlit S, Duvenjian C, Prior MJ, et al. Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice. Developmental Cell. 2022:57(9):1177-1192.e6. https://doi.org/10.1016/j.devcel.2022.04.013

Kajala K, Gouran M, Shaar-Moshe L, Mason GA, Rodriguez-Medina J, Kawa D, Pauluzzi G, Reynoso M, Canto-Pastor A, Manzano C, et al. Innovation, conservation, and repurposing of gene function in root cell type development. Cell. 2021:184(12):3333-3348.e19. https://doi.org/10.1016/j.cell.2021.04.024

• Led 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 JE, Ainsworth EA, Oldroyd GED, and Schroeder JI. Genetic strategies for improving crop yields. Nature. 2019:575(7781):109–118. https://doi.org/10.1038/s41586-019-1679-0

• In the 150 years of Nature reviews collection.

Reynoso MA, Kajala K, Bajic M, West DA, Pauluzzi G, Yao AI, Hatch K, Zumstein K, Woodhouse M, Rodriguez-Medina J, et al. Evolutionary flexibility in flooding response circuitry in angiosperms. Science. 2019:365(6459):1291–1295. https://doi.org/10.1126/science.aax8862

• 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.

Lee TA and Bailey-Serres J. Integrative analysis from the epigenome to translatome uncovers patterns of dominant nuclear regulation during transient stress. Plant Cell. 2019:tpc.00463.2019. https://doi.org/10.1105/tpc.19.00463

• 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, Reynoso MA, Hobecker K, Lancia M, Hummel M, Rosen B, Town C, Bailey-Serres J, Blanco F, and Zanetti ME. Reprogramming of Root Cells during Nitrogen-Fixing Symbiosis Involves Dynamic Polysome Association of Coding and Noncoding RNAs. Plant Cell. 2020:32(2):352–373. https://doi.org/10.1105/tpc.19.00647

• 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 T, Sorenson RS, Hummel M, Ke H, Kettenburg AT, Chen D, Aiyetiwa K, Dehesh K, Eulgem T, Sieburth LE, et al. DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs. Nat Plants. 2020:6(6):675–685. https://doi.org/10.1038/s41477-020-0681-8

• 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, Yeung E, Locke AM, Ignacio JCI, Baltazar MD, Jia Z, Ismail AM, Septiningsih EM, and Bailey‐Serres J. Flood resilience loci SUBMERGENCE 1 and ANAEROBIC GERMINATION 1 interact in seedlings established underwater. Plant Direct. 2020:4(7):e00240. https://doi.org/10.1002/pld3.240

• Beachell-Borlaug International Scholar and PhD student, Rejbana Alam's, collaborative work with Endang Septiningshi and Abdel Ismail at the 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