Single-cell m6A mapping in vivo using picoMeRIP–seq

Yanjiao Li; Yunhao Wang; Maria Vera-Rodriguez; Leif Christopher Lindeman; Linda Ellevog Skuggen; Erik M.K. Rasmussen; Ingunn Jermstad; Shaista Khan; Madeleine Fosslie; Trine Skuland; Marie Indahl; Sherif Khodeer; Eva Kristine Klemsdal; Kang Xuan Jin; Knut Tomas Dalen; Peter Fedorcsak; Gareth D. Greggains; Mads Lerdrup; Arne Klungland; Kin Fai Au; John Arne Dahl

doi:10.1038/s41587-023-01831-7

Single-cell m⁶A mapping in vivo using picoMeRIP–seq

Yanjiao Li, Yunhao Wang, Maria Vera-Rodriguez, Leif Christopher Lindeman, Linda Ellevog Skuggen, Erik M.K. Rasmussen, Ingunn Jermstad, Shaista Khan, Madeleine Fosslie, Trine Skuland, Marie Indahl, Sherif Khodeer, Eva Kristine Klemsdal, Kang Xuan Jin, Knut Tomas Dalen, Peter Fedorcsak, Gareth D. Greggains, Mads Lerdrup, Arne Klungland^*, Kin Fai AuJohn Arne Dahl

^*Corresponding author af dette arbejde

Molecular Aging Program

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

11 Citationer (Scopus)

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Abstract

Current N ⁶-methyladenosine (m⁶A) mapping methods need large amounts of RNA or are limited to cultured cells. Through optimized sample recovery and signal-to-noise ratio, we developed picogram-scale m⁶A RNA immunoprecipitation and sequencing (picoMeRIP–seq) for studying m⁶A in vivo in single cells and scarce cell types using standard laboratory equipment. We benchmark m⁶A mapping on titrations of poly(A) RNA and embryonic stem cells and in single zebrafish zygotes, mouse oocytes and embryos.

Originalsprog	Engelsk
Tidsskrift	Nature Biotechnology
Vol/bind	42
Sider (fra-til)	591-596
Antal sider	6
ISSN	1087-0156
DOI	https://doi.org/10.1038/s41587-023-01831-7
Status	Udgivet - 2024

Bibliografisk note

Funding Information:
We thank P. Aleström for planning and supervising the collection of zebrafish zygotes. We thank G. Luo for discussions. We thank J. H. Hanna for Mettl3 and WT control mES cell lines. We thank the Norwegian Transgenic Center for help with animal housing and oocyte collection. We thank the Norwegian Sequencing Centre (Oslo University Hospital and University of Oslo; www.sequencing.uio.no ) and the Genomics Core Facility (Oslo University Hospital; https://oslo.genomics.no ) for high-throughput sequencing. K.F.A. and Y.W. acknowledge an institutional fund from the Department of Biomedical Informatics, The Ohio State University; an institutional fund from the Department of Computational Medicine and Bioinformatics, University of Michigan; and the National Institutes of Health (R01HG008759, R01HG011469 and R01GM136886). M.L. was supported by the Danish National Research Foundation (grant DNRF115). This work was supported by the South‐Eastern Norway Regional Health Authority, Early Career Grant 2016058 and Grant 2018063, and by the Research Council of Norway, FRIPRO grant 289467 (to J.A.D.). Y.L. was supported by a UiO:Life Science convergence environment grant (to A.K., G.D.G., P.F. and J.A.D.). –/–

Publisher Copyright:
© 2023, The Author(s).

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Citationsformater

Li, Y., Wang, Y., Vera-Rodriguez, M., Lindeman, L. C., Skuggen, L. E., Rasmussen, E. M. K., Jermstad, I., Khan, S., Fosslie, M., Skuland, T., Indahl, M., Khodeer, S., Klemsdal, E. K., Jin, K. X., Dalen, K. T., Fedorcsak, P., Greggains, G. D., Lerdrup, M., Klungland, A., ... Dahl, J. A. (2024). Single-cell m⁶A mapping in vivo using picoMeRIP–seq. Nature Biotechnology, 42, 591-596. https://doi.org/10.1038/s41587-023-01831-7

Single-cell m⁶A mapping in vivo using picoMeRIP–seq. / Li, Yanjiao; Wang, Yunhao; Vera-Rodriguez, Maria; Lindeman, Leif Christopher; Skuggen, Linda Ellevog; Rasmussen, Erik M.K.; Jermstad, Ingunn; Khan, Shaista; Fosslie, Madeleine; Skuland, Trine; Indahl, Marie; Khodeer, Sherif; Klemsdal, Eva Kristine; Jin, Kang Xuan; Dalen, Knut Tomas; Fedorcsak, Peter; Greggains, Gareth D.; Lerdrup, Mads; Klungland, Arne; Au, Kin Fai; Dahl, John Arne.

I: Nature Biotechnology, Bind 42, 2024, s. 591-596.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Li, Y, Wang, Y, Vera-Rodriguez, M, Lindeman, LC, Skuggen, LE, Rasmussen, EMK, Jermstad, I, Khan, S, Fosslie, M, Skuland, T, Indahl, M, Khodeer, S, Klemsdal, EK, Jin, KX, Dalen, KT, Fedorcsak, P, Greggains, GD, Lerdrup, M, Klungland, A, Au, KF & Dahl, JA 2024, 'Single-cell m⁶A mapping in vivo using picoMeRIP–seq', Nature Biotechnology, bind 42, s. 591-596. https://doi.org/10.1038/s41587-023-01831-7

Li, Yanjiao ; Wang, Yunhao ; Vera-Rodriguez, Maria ; Lindeman, Leif Christopher ; Skuggen, Linda Ellevog ; Rasmussen, Erik M.K. ; Jermstad, Ingunn ; Khan, Shaista ; Fosslie, Madeleine ; Skuland, Trine ; Indahl, Marie ; Khodeer, Sherif ; Klemsdal, Eva Kristine ; Jin, Kang Xuan ; Dalen, Knut Tomas ; Fedorcsak, Peter ; Greggains, Gareth D. ; Lerdrup, Mads ; Klungland, Arne ; Au, Kin Fai ; Dahl, John Arne. / Single-cell m⁶A mapping in vivo using picoMeRIP–seq. I: Nature Biotechnology. 2024 ; Bind 42. s. 591-596.

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abstract = "Current N 6-methyladenosine (m6A) mapping methods need large amounts of RNA or are limited to cultured cells. Through optimized sample recovery and signal-to-noise ratio, we developed picogram-scale m6A RNA immunoprecipitation and sequencing (picoMeRIP–seq) for studying m6A in vivo in single cells and scarce cell types using standard laboratory equipment. We benchmark m6A mapping on titrations of poly(A) RNA and embryonic stem cells and in single zebrafish zygotes, mouse oocytes and embryos.",

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AU - Li, Yanjiao

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AU - Vera-Rodriguez, Maria

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AU - Skuggen, Linda Ellevog

AU - Rasmussen, Erik M.K.

AU - Jermstad, Ingunn

AU - Khan, Shaista

AU - Fosslie, Madeleine

AU - Skuland, Trine

AU - Indahl, Marie

AU - Khodeer, Sherif

AU - Klemsdal, Eva Kristine

AU - Jin, Kang Xuan

AU - Dalen, Knut Tomas

AU - Fedorcsak, Peter

AU - Greggains, Gareth D.

AU - Lerdrup, Mads

AU - Klungland, Arne

AU - Au, Kin Fai

AU - Dahl, John Arne

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