ONE-seq: epitranscriptome and gene-specific profiling of NAD-capped RNA

Abstract The hub metabolite, nicotinamide adenine dinucleotide (NAD), can be used as an initiating nucleotide in RNA synthesis to result in NAD-capped RNAs (NAD-RNA). Since NAD has been heightened as one of the most essential modulators in aging and various age-related diseases, its attachment to RNA might indicate a yet-to-be discovered mechanism that impacts adult life-course. However, the unknown identity of NAD-linked RNAs in adult and aging tissues has hindered functional studies. Here, we introduce ONE-seq method to identify the RNA transcripts that contain NAD cap. ONE-seq has been optimized to use only one-step chemo-enzymatic biotinylation, followed by streptavidin capture and the nudix phosphohydrolase NudC-catalyzed elution, to specifically recover NAD-capped RNAs for epitranscriptome and gene-specific analyses. Using ONE-seq, we discover more than a thousand of previously unknown NAD-RNAs in the mouse liver and reveal epitranscriptome-wide dynamics of NAD-RNAs with age. ONE-seq empowers the identification of NAD-capped RNAs that are responsive to distinct physiological states, facilitating functional investigation into this modification.

[1]  Hailei Zhang,et al.  SPAAC-NAD-seq, a sensitive and accurate method to profile NAD+-capped transcripts , 2021, Proceedings of the National Academy of Sciences.

[2]  E. Verdin,et al.  NAD+ metabolism and its roles in cellular processes during ageing , 2020, Nature Reviews Molecular Cell Biology.

[3]  Anushya Muruganujan,et al.  The Gene Ontology resource: enriching a GOld mine , 2020, Nucleic Acids Res..

[4]  Hailei Zhang,et al.  NAD tagSeq for transcriptome-wide identification and characterization of NAD+-capped RNAs , 2020, Nature Protocols.

[5]  J. Vilo,et al.  gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler , 2020, F1000Research.

[6]  D. Frick,et al.  Fluorescent probe displacement assays reveal unique nucleic acid binding properties of human nudix enzymes. , 2020, Analytical biochemistry.

[7]  J. Auwerx,et al.  NAD+ homeostasis in health and disease , 2020, Nature Metabolism.

[8]  T. Lu,et al.  Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA , 2019, bioRxiv.

[9]  Y. Wang,et al.  NAD+-capped RNAs are widespread in the Arabidopsis transcriptome and can probably be translated , 2019, Proceedings of the National Academy of Sciences.

[10]  L. Tong,et al.  Structural and mechanistic basis of the mammalian Nudt12 RNA deNADding , 2019, Nature Chemical Biology.

[11]  V. Cowling,et al.  mRNA cap regulation in mammalian cell function and fate , 2019, Biochimica et biophysica acta. Gene regulatory mechanisms.

[12]  Gary D Bader,et al.  Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap , 2019, Nature Protocols.

[13]  R. Ebright,et al.  Highly efficient 5' capping of mitochondrial RNA with NAD+ and NADH by yeast and human mitochondrial RNA polymerase , 2018, eLife.

[14]  G. Freeman,et al.  LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade , 2018, Cell.

[15]  Matthew E. Ritchie,et al.  Covering all your bases: incorporating intron signal from RNA-seq data , 2018, bioRxiv.

[16]  Zhandong Liu,et al.  Epigenetic drift of H3K27me3 in aging links glycolysis to healthy longevity in Drosophila , 2018, eLife.

[17]  Deanne M. Taylor,et al.  “CapZyme-Seq” comprehensively defines promoter-sequence determinants for RNA 5’ capping with NAD+ , 2017, bioRxiv.

[18]  Frieda A. Sorgenfrei,et al.  Boronate affinity electrophoresis for the purification and analysis of cofactor-modified RNAs. , 2017, Methods.

[19]  L. Tong,et al.  5′ End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding , 2017, Cell.

[20]  R. Parker,et al.  Identification of NAD+ capped mRNAs in Saccharomyces cerevisiae , 2016, Proceedings of the National Academy of Sciences.

[21]  Hana Cahová,et al.  Capture and sequencing of NAD-capped RNA sequences with NAD captureSeq , 2016, Nature Protocols.

[22]  Carlos López-Otín,et al.  Metabolic Control of Longevity , 2016, Cell.

[23]  G. B. Robb,et al.  mRNA capping: biological functions and applications , 2016, Nucleic acids research.

[24]  R. Aebersold,et al.  NAD+ repletion improves mitochondrial and stem cell function and enhances life span in mice , 2016, Science.

[25]  Hana Cahová,et al.  NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs , 2014, Nature.

[26]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[27]  Henning Hermjakob,et al.  The Reactome pathway knowledgebase , 2013, Nucleic Acids Res..

[28]  D. Sinclair,et al.  Manipulation of a nuclear NAD+ salvage pathway delays aging without altering steady-state NAD+ levels. , 2013, The Journal of Biological Chemistry.

[29]  L. Guarente,et al.  The NAD+/Sirtuin Pathway Modulates Longevity through Activation of Mitochondrial UPR and FOXO Signaling , 2013, Cell.

[30]  Manuel Serrano,et al.  The Hallmarks of Aging , 2013, Cell.

[31]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[32]  Wei Li,et al.  RSeQC: quality control of RNA-seq experiments , 2012, Bioinform..

[33]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[34]  S. Imai,et al.  Nicotinamide mononucleotide, a key NAD(+) intermediate, treats the pathophysiology of diet- and age-induced diabetes in mice. , 2011, Cell metabolism.

[35]  Nahum Sonenberg,et al.  Cap and cap‐binding proteins in the control of gene expression , 2011, Wiley interdisciplinary reviews. RNA.

[36]  David R. Liu,et al.  LC/MS analysis of cellular RNA reveals NAD-linked RNA , 2009, Nature chemical biology.

[37]  K. Maiese,et al.  Life Span Extension and Neuronal Cell Protection by Drosophila Nicotinamidase* , 2008, Journal of Biological Chemistry.

[38]  P. Shannon,et al.  Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks , 2003 .

[39]  G. Igloi,et al.  Affinity electrophoresis for monitoring terminal phosphorylation and the presence of queuosine in RNA. Application of polyacrylamide containing a covalently bound boronic acid. , 1985, Nucleic acids research.

[40]  J. Vilo,et al.  gprofiler 2-- an R package for gene list functional enrichment analysis and namespace conversion toolset , 2021 .

[41]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..