RNA modifications are ubiquitous in biology and present in all classes of cellular RNAs including eukaryotic messenger and long non-coding RNA. A large fraction of mammalian mRNA/lncRNA modifications are also known to be reversible, highly dynamic, and occur in cell type and cell state dependent manner. The dynamic RNA epitranscriptomes, those involving N6-methyladenosine (m6A) in particular, are known to regulate many cellular activities including mRNA splicing, export, cytoplasmic localization, stability, translation activity, microRNA processing, immune tolerance, and to impact cellular processes including proliferation, development, circadian rhythm, and embryonic stem cell differentiation. Consider m6A in mRNA/lncRNA as an example, dedicated writers, erasers, and readers exist in human cells to orchestrate an additional layer of complex post-transcriptional gene expression regulation. Emerging new functions of RNA modifications are expected to follow, with significant implications on many aspects of human health and disease. Despite high potentials and promises, current epitranscriptome studies are significantly hampered by the lack of technologies that enable quantitative mapping of any type of mRNA/lncRNA modifications at high resolution and high sensitivity. This proposal will develop new methods that target five abundant mRNA/lncRNA modifications, namely m6A, 5-methylcytosine (m5C), N1-methyladenosine (m1A), pseudo uridine (?), and 2'O- methyls (Nm) for high-throughput sequencing at single-base resolution and suitable for low input RNA isolated from just hundreds to thousands of cells. New bioinformatics tools will be developed in order to facilitate data analysis. The general approaches proposed can be broadly applied to sequence RNA modifications in other RNA species including more abundant ribosomal RNA, transfer RNA, snRNA, and snoRNA as well as miRNA and piRNA. We will apply the newly developed methods to obtain base-resolution maps of RNA modifications in order to associate with human diseases, and to proof-of-principle studies in neuro-biology. Our proposed research will establish high-throughput, high-resolution, and high-sensitivity methods for epitranscriptome research in all biological areas.

Public Health Relevance

Dynamic RNA modifications (epitranscriptomes) have emerged as a new mechanism of post-transcriptional gene expression regulation. The proposed research will develop high-throughput, high-resolution, and high- sensitivity technologies for functional investigations of epitranscriptomes.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project with Complex Structure (RM1)
Project #
5RM1HG008935-05
Application #
9973226
Study Section
National Human Genome Research Institute Initial Review Group (GNOM)
Program Officer
Smith, Michael
Project Start
2016-09-27
Project End
2021-06-30
Budget Start
2020-07-01
Budget End
2021-06-30
Support Year
5
Fiscal Year
2020
Total Cost
Indirect Cost
Name
University of Chicago
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
005421136
City
Chicago
State
IL
Country
United States
Zip Code
60637
Li, Miaomiao; Zhao, Xu; Wang, Wei et al. (2018) Ythdf2-mediated m6A mRNA clearance modulates neural development in mice. Genome Biol 19:69
Su, Rui; Dong, Lei; Li, Chenying et al. (2018) R-2HG Exhibits Anti-tumor Activity by Targeting FTO/m6A/MYC/CEBPA Signaling. Cell 172:90-105.e23
Liu, Jun; Eckert, Mark A; Harada, Bryan T et al. (2018) m6A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer. Nat Cell Biol 20:1074-1083
Shi, Hailing; Zhang, Xuliang; Weng, Yi-Lan et al. (2018) m6A facilitates hippocampus-dependent learning and memory through YTHDF1. Nature 563:249-253
Zhou, Katherine I; Clark, Wesley C; Pan, David W et al. (2018) Pseudouridines have context-dependent mutation and stop rates in high-throughput sequencing. RNA Biol 15:892-900
Richter, Uwe; Evans, Molly E; Clark, Wesley C et al. (2018) RNA modification landscape of the human mitochondrial tRNALys regulates protein synthesis. Nat Commun 9:3966
Koranda, Jessica L; Dore, Lou; Shi, Hailing et al. (2018) Mettl14 Is Essential for Epitranscriptomic Regulation of Striatal Function and Learning. Neuron 99:283-292.e5
Shi, Hailing; He, Chuan (2018) Phasing Gene Expression: mRNA N6-Methyladenosine Regulates Temporal Progression of Mammalian Cortical Neurogenesis. Biochemistry 57:1055-1056
Weng, Yi-Lan; Wang, Xu; An, Ran et al. (2018) Epitranscriptomic m6A Regulation of Axon Regeneration in the Adult Mammalian Nervous System. Neuron 97:313-325.e6
Frye, Michaela; Harada, Bryan T; Behm, Mikaela et al. (2018) RNA modifications modulate gene expression during development. Science 361:1346-1349

Showing the most recent 10 out of 30 publications