Hidden features of NAD-RNA epitranscriptome in Drosophila life cycle
Shuwen Ge,
Xueting Wang,
Yingqin Wang,
Minghui Dong,
Dean Li,
Kongyan Niu,
Tongyao Wang,
Rui Liu,
Chao Zhao,
Nan Liu,
Ming Zhong
Affiliations
Shuwen Ge
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
Xueting Wang
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
Yingqin Wang
Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Key Laboratory of Lung Inflammation and Injury, 180 Fenglin Road, Shanghai, China; Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
Minghui Dong
Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Key Laboratory of Lung Inflammation and Injury, 180 Fenglin Road, Shanghai, China; Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
Dean Li
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
Kongyan Niu
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
Tongyao Wang
National Clinical Research Center for Aging and Medicine, Huashan Hospital, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 131 Dong An Road, Shanghai 200032, China
Rui Liu
Singlera Genomics, 500 Fu Rong Hua Road, Shanghai 201204, China
Chao Zhao
National Clinical Research Center for Aging and Medicine, Huashan Hospital, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 131 Dong An Road, Shanghai 200032, China; Corresponding author
Nan Liu
Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Hai Ke Road, Shanghai 201210, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, 131 Dong An Road, Shanghai 200032, China; Shanghai Key Laboratory of Aging Studies, 100 Hai Ke Road, Shanghai 201210, China; Corresponding author
Ming Zhong
Department of Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China; Shanghai Key Laboratory of Lung Inflammation and Injury, 180 Fenglin Road, Shanghai, China; Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China; Corresponding author
Summary: Nicotinamide adenine dinucleotide (NAD), a nucleotide-containing metabolite, can be incorporated into the RNA 5′-terminus to result in NAD-capped RNA (NAD-RNA). Since NAD has been heightened as one of the most essential metabolites in cells, its linkage to RNA represents a critical but poorly studied modification at the epitranscriptomic level. Here, we design a highly sensitive method, DO-seq, to capture NAD-RNAs. Using Drosophila, we identify thousands of previously unexplored NAD-RNAs and their dynamics in the fly life cycle, from embryo to adult. We show the evidence that chromosomal clustering might be the structural basis by which co-expression can couple with NAD capping on physically and functionally linked genes. Furthermore, we note that NAD capping of cuticle genes inversely correlates with their gene expression. Combined, we propose NAD-RNA epitranscriptome as a hidden layer of regulation that underlies biological processes. DO-seq empowers the identification of NAD-capped RNAs, facilitating functional investigation into this modification.
