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

Nat Biotechnol. 2024 Apr;42(4):591-596. doi: 10.1038/s41587-023-01831-7. Epub 2023 Jun 22.

Authors

Yanjiao Li^#^{1

2}, Yunhao Wang^#^{3

4}, Maria Vera-Rodriguez^{1

5}, Leif Christopher Lindeman⁶, Linda Ellevog Skuggen¹, Erik M K Rasmussen⁶, Ingunn Jermstad⁷, Shaista Khan⁷, Madeleine Fosslie¹, Trine Skuland^{5

8}, Marie Indahl^{5

8}, Sherif Khodeer^{1

9}, Eva Kristine Klemsdal¹, Kang-Xuan Jin¹, Knut Tomas Dalen⁷, Peter Fedorcsak^{5

8}, Gareth D Greggains⁵, Mads Lerdrup¹⁰, Arne Klungland^{11

12}, Kin Fai Au^{13

14

15}, John Arne Dahl¹⁶

Affiliations

¹ Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
² Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
³ Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
⁴ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
⁵ Department of Reproductive Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
⁶ Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Aas, Norway.
⁷ Norwegian Transgenic Centre, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.
⁸ Division of Gynaecology and Obstetrics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
⁹ KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Institute for Single-Cell Omics (LISCO), Leuven Stem Cell Institute, Leuven, Belgium.
¹⁰ Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
¹¹ Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway. arne.klungland@medisin.uio.no.
¹² Department of Microbiology, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway. arne.klungland@medisin.uio.no.
¹³ Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA. kinfai@med.umich.edu.
¹⁴ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. kinfai@med.umich.edu.
¹⁵ Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA. kinfai@med.umich.edu.
¹⁶ Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway. j.a.dahl@medisin.uio.no.

^# Contributed equally.

Abstract

Current N⁶-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.

MeSH terms

Animals
Cells, Cultured
Embryonic Stem Cells
Mice
RNA* / genetics
RNA, Messenger / genetics
Zebrafish* / genetics
Zebrafish* / metabolism

Substances

RNA
RNA, Messenger

Abstract

MeSH terms

Substances

Grants and funding