Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis

Author Profile

Xiang Yu and Matthew R. Willmann

Highlighted Paper: Yu, X., Willmann, M.R., Anderson, S.J., and Gregory, B.D. (2016). Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Co-translational RNA Decay in Arabidopsis. Plant Cell. Advance Publication October 7, 2016; doi:10.1105/tpc.16.00456.

Xiang Yu

Current Position: Postdoctoral researcher in Bioinformatics, Department of Biology, University of Pennsylvania.

Education: Ph.D. in Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences.

Non-scientific Interests: Coding, writing poetry, running, and playing badminton.

When I was a graduate student, I studied micro RNA-directed post-transcriptional regulation in the lab of Yuke He, stimulating my interest in RNA biology. As a post-doc in the Brian Gregory Lab, I am learning many new cutting-edge scientific concepts, ideas, and tools from a variety of my research projects. Our research focuses on many aspects of RNA biology including RNA degradation, RNA secondary structure, RNA-binding protein-RNA interactions, and RNA modifications. As a post-doc, Brian developed a very important technique known as genome-wide mapping of uncapped and cleaved tran-scripts (GMUCT), and this technique was updated recently by my collaborator Dr. Matthew R. Willmann. Inspired by recent work in yeast, we decided to survey whether co-translational RNA decay also occurs in a plant transcriptome, using numerous GMUCT datasets for Arabidopsis thaliana. To do this, we developed customized analysis pipelines, and observed clear evidence for co-translational RNA decay. First, we found that free 5' RNA ends, representing truncated RNA molecules, accumulate at the ribosome boundary site at the stop codon of mRNA open reading frames. We also showed a 3-nucleotide periodicity throughout these open reading frames. Next, we found that the exoribonuclease XRN4 and the mRNA cap-binding protein ABH1, which function in RNA decay, also function in this process. In cells, recent evidence has demonstrated that many linked molecular events are coupled with each other. A well known example is co-transcriptional splicing, in which gene transcription and pre-mRNA processing are closely coupled. Therefore, it is not unexpected that RNA decay is coupled with translation. As compared to canonical RNA decay, which involves ribosome-free RNAs, mRNA turnover by co-translational RNA decay seems to be more efficient and faster, and this is likely important for plants to rapidly respond to changing environmental stimuli.

Matthew R. Willmann

Current Position: Director, Plant Transformation Facility, School of Integrative Plant Science, Cornell University.

Education: Ph.D. at Harvard University.

Non-scientific Interests: Reading, gardening, growing orchids, baking, and singing.

I have been interested in and have studied the regulation of gene expression since I was a graduate student in Jen Sheen's lab. At that time, my research focused on transcriptional control of responses to flagellin in Arabidopsis. When I moved to Scott Poethig's lab at the University of Pennsylvania as a postdoctoral fellow, his lab was studying trans-acting silencing RNAs and micro RNAs and their ability to control developmental transitions. As a result, my focus switched from transcriptional to post-transcriptional regulation of gene expression. During my time in Scott's lab, I performed a microarray study in collaboration with another postdoc. I became fascinated because some of the most highly up-regulated genes at the RNA level showed no change in expression at the protein level. This finding suggested regulation at the level of translation or protein stability or degradation. Although we did not pursue the question further, I was left with a great interest in studying translational control of gene ex-pression. When I joined Brian Gregory's lab as a research associate, in addition to my other projects, he allowed me to follow this passion. I began by developing a protocol for ribosome profiling in plants, and then, when another group showed co-translational decapping and 5'-to-3' exonucleolytic decay in yeast, we decided to try using genome-wide mapping of uncapped and cleaved transcripts as an alternative method for studying translation in plants, leading to the current study. Although I do not study translational control in my current position, my time investigating it in Brian's lab was a highlight of my research career I will always be grateful for.