Messenger RNA 5′ NAD+ Capping Is a Dynamic Regulatory Epitranscriptome Mark That Is Required for Proper Response to Abscisic Acid in Arabidopsis

Yu, Xiang; Willmann, Matthew R.; Vandivier, Lee E.; Trefely, Sophie; Kramer, Marianne C.; Shapiro, Jeffrey; Guo, Ruiyun; Lyons, Eric; Snyder, Nathaniel W.

doi:10.1016/j.devcel.2020.11.009

Cited by 40 publications

(39 citation statements)

References 62 publications

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“…Notably, "response to water deprivation" and "response to ABA" are GO terms identified by SPAAC-NAD-seq (Datasets S7 and S9). This is consistent with a recent study showing that the hormone ABA remodels the NAD-RNA transcriptome (32).…”

Section: Discussionsupporting

confidence: 93%

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SPAAC-NAD-seq, a sensitive and accurate method to profile NAD ⁺ -capped transcripts

Flynn

Zhang

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Nicotinamide adenine diphosphate (NAD+) is a novel messenger RNA 5′ cap in Escherichia coli, yeast, mammals, and Arabidopsis. Transcriptome-wide identification of NAD+-capped RNAs (NAD-RNAs) was accomplished through NAD captureSeq, which combines chemoenzymatic RNA enrichment with high-throughput sequencing. NAD-RNAs are enzymatically converted to alkyne-RNAs that are then biotinylated using a copper-catalyzed azide–alkyne cycloaddition (CuAAC) reaction. Originally applied to E. coli RNA, which lacks the m7G cap, NAD captureSeq was then applied to eukaryotes without extensive verification of its specificity for NAD-RNAs vs. m7G-capped RNAs (m7G-RNAs). In addition, the Cu2+ ion in the CuAAC reaction causes RNA fragmentation, leading to greatly reduced yield and loss of full-length sequence information. We developed an NAD-RNA capture scheme utilizing the copper-free, strain-promoted azide–alkyne cycloaddition reaction (SPAAC). We examined the specificity of CuAAC and SPAAC reactions toward NAD-RNAs and m7G-RNAs and found that both prefer the former, but also act on the latter. We demonstrated that SPAAC-NAD sequencing (SPAAC-NAD-seq), when combined with immunodepletion of m7G-RNAs, enables NAD-RNA identification with accuracy and sensitivity, leading to the discovery of new NAD-RNA profiles in Arabidopsis. Furthermore, SPAAC-NAD-seq retained full-length sequence information. Therefore, SPAAC-NAD-seq would enable specific and efficient discovery of NAD-RNAs in prokaryotes and, when combined with m7G-RNA depletion, in eukaryotes.

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Section: Discussionsupporting

confidence: 93%

“…NAD-RNAs transfected into human cells and Arabidopsis protoplasts undergo DXO-dependent degradation (9,37). In an Arabidopsis dxo mutant, NAD + -capped transcripts are channeled to RNA silencing for degradation (32,36). NAD captureSeq was performed in yeast, human, and Arabidopsis dxo mutants to identify the in vivo targets of DXO (9,13,32).…”

Section: Discussionmentioning

confidence: 99%

SPAAC-NAD-seq, a sensitive and accurate method to profile NAD ⁺ -capped transcripts

Flynn

Zhang

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…We propose that NAD-capped RNAs serve as a reservoir for this critical nucleotide metabolite in mitochondria and Xrn1-mediated turnover of NAD-capped RNA is vital for mitochondrial NAD homeostasis and cellular growth during respiration in budding yeast. A recent report in Arabidopsis thaliana reinforces the equilibrium between NAD caps and free NAD where stabilization of NAD caps leads to a decrease in free NAD and compensatory increase in NAD production following stress 13 . Whether NAD molecules stored in the 5′ end of RNA are used in adverse scenarios like nutrient starvation or quiescence in mammalian cells and the contribution of Xrn1 in NAD homeostasis will be an important area of future exploration.…”

Section: Discussionmentioning

confidence: 63%

“…Functional analyses of the NAD-capped RNAs have revealed disparate roles in bacterial and mammalian cells. In bacteria, the NAD cap is considered to protect the RNA from 5′-end degradation 2 , whereas in mammals 3 and plants 13 NAD caps have been shown to promote RNA decay. In bacteria, NAD caps are found on certain regulatory RNAs 2 , while in budding yeast Saccharomyces cerevisiae, they are on a subset of mitochondrial genes and genes encoding the translational machinery 4 .…”

Section: Introductionmentioning

confidence: 99%

Xrn1 is a deNADding Enzyme Modulating Mitochondrial NAD Levels

Sharma

Yang

et al. 2021

Preprint

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The existence of non-canonical nicotinamide adenine diphosphate (NAD) 5′-end capped RNAs is now well established. Nevertheless, the biological function of this nucleotide metabolite cap remains elusive. Here, we show that the yeast Saccharomyces cerevisiae cytoplasmic 5′-end exoribonuclease Xrn1 is also a NAD cap decapping (deNADding) enzyme that releases intact NAD and subsequently degrades the RNA. The significance of Xrn1 deNADding is evident in a deNADding deficient Xrn1 mutant that still retains its 5′-monophosphate exonuclease activity. This mutant reveals Xrn1 deNADding is necessary for normal growth on non-fermenting sugar and is involved in modulating mitochondrial NAD-capped RNA levels and in turn intramitochondrial NAD levels. Our findings uncover a functional role for mitochondrial NAD-capped RNAs as a reservoir to maintain overall NAD homeostasis. We propose NAD-capped RNAs function as a cistern for mitochondrial NAD with Xrn1 serving as a rheostat for NAD-capped RNAs.

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“…Then, the cap-binding complex heterodimer (CBC20/CBC80) binds with m7G. This binding supports mRNA export to the cytoplasm and protects the RNA from decapping [10]. A second alteration that pre-mRNA undergoes is 3' cleavage and polyadenylation.…”

Section: A Transcriptionmentioning

confidence: 99%

A Novel Approach of Transcriptomic microRNA Analysis Using Text Mining Methods: An Early Detection of Multiple Sclerosis Disease

Ali¹,

Shaheen

Mabrouk

et al. 2021

IEEE Access

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Multiple sclerosis is an autoimmune disease that causes psychological impacts and severe physical disabilities, including motor disabilities and partial blindness. This work introduces an early detection method for multiple sclerosis disease by analyzing transcriptomic microRNA data. By transforming this phenotype classification problem into a text mining problem, multiple sclerosis disease biomarkers can be obtained. To our knowledge, text mining methods have not been introduced previously in transcriptomic data analysis of multiple sclerosis disease. Hence, this work presents a complete predictive model by combining consecutive transcriptomic data preprocessing procedures, followed by the proposed KmerFIDF method as a feature extraction method and linear discriminant analysis for dimensionality reduction. Predictive machine learning methods can then be obtained accordingly. This study describes experimental work on a transcriptomic dataset of noncoding microRNA sequences denoted from relapsingremitting multiple sclerosis patients before fingolimod treatment and after six consecutive months of treatment. The experimental results of the predictive methods with the proposed model report sensitivity, specificity, F1-score, and average accuracy scores of 96.4, 96.47, 95.6, and 97% with random forest, 92.89, 92.78, 93.2, and 94% with support vector machine and 91.95, 92.2, 93.1, and 94% with logistic regression, respectively. These promising results support the introduced model and the proposed KmerFIDF method in transcriptomic data analysis. Moreover, comparative experiments are conducted with two referenced studies. The obtained results show that the average reported accuracy scores of the proposed model outperform the referenced literature work.

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Messenger RNA 5′ NAD+ Capping Is a Dynamic Regulatory Epitranscriptome Mark That Is Required for Proper Response to Abscisic Acid in Arabidopsis

Cited by 40 publications

References 62 publications

SPAAC-NAD-seq, a sensitive and accurate method to profile NAD ⁺ -capped transcripts

SPAAC-NAD-seq, a sensitive and accurate method to profile NAD ⁺ -capped transcripts

Xrn1 is a deNADding Enzyme Modulating Mitochondrial NAD Levels

A Novel Approach of Transcriptomic microRNA Analysis Using Text Mining Methods: An Early Detection of Multiple Sclerosis Disease

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Messenger RNA 5′ NAD+ Capping Is a Dynamic Regulatory Epitranscriptome Mark That Is Required for Proper Response to Abscisic Acid in Arabidopsis

Cited by 40 publications

References 62 publications

SPAAC-NAD-seq, a sensitive and accurate method to profile NAD + -capped transcripts

SPAAC-NAD-seq, a sensitive and accurate method to profile NAD + -capped transcripts

Xrn1 is a deNADding Enzyme Modulating Mitochondrial NAD Levels

A Novel Approach of Transcriptomic microRNA Analysis Using Text Mining Methods: An Early Detection of Multiple Sclerosis Disease

Contact Info

Product

Resources

About

SPAAC-NAD-seq, a sensitive and accurate method to profile NAD ⁺ -capped transcripts

SPAAC-NAD-seq, a sensitive and accurate method to profile NAD ⁺ -capped transcripts