Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution

Dierks, David; Garcia-Campos, Miguel Angel; Uzonyi, Anna; Safra, Modi; Edelheit, Sarit; Rossi, Alice; Sideri, Theodora; Varier, Radhika A.; Brandis, Alexander; Stelzer, Yonatan; Werven, Folkert J. van; Scherz‐Shouval, Ruth; Schwartz, Schraga

doi:10.1038/s41592-021-01242-z

Cited by 79 publications

(82 citation statements)

References 70 publications

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“…In a manner similar with DNA and protein, RNAs can be modified by more than 170 chemically modifications 13 . Among them, N6-methyladenosine (m 6 A) is most abundant modification of messenger RNA (mRNAs) and non-coding RNA (ncRNAs) in mammals 14 , 15 . Although first discovered in the 1970s, the m 6 A modification began to revive in 2012, when a next-generation sequencing method, MeRIP-Seq was described and used 16 .…”

Section: Introductionmentioning

confidence: 99%

The role of Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) as m⁶A readers in cancer

Sun¹,

Cao²,

Du³

et al. 2022

Int. J. Biol. Sci.

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RNA can be modified by over 170 types of distinct chemical modifications, and the most abundant internal modification of mRNA in eukaryotes is N6-methyladenosine (m 6 A). The m 6 A modification accelerates mRNA process, including mRNA splicing, translation, transcript stability, export and decay. m 6 A RNA modification is installed by methyltransferase-like proteins (writers), and potentially removed by demethylases (erasers), and this process is recognized by m 6 A-binding proteins (readers). Notably, alterations of m 6 A-modified proteins (writers, erasers and readers) are involved in the tumorigenesis, progression and metastasis. Importantly, the fate of m 6 A-methylated mRNA is mediated mostly through m 6 A readers, and among these readers, insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) are unique RNA-binding proteins (RBPs) that stabilize their targets mRNA via m 6 A modification. In this review, we update the writers, erasers and readers, and their cross-talks in m 6 A modification, and briefly discuss the oncogenic role of IGF2BPs in cancer. Most importantly, we mainly review the up-to-date knowledges of IGF2BPs (IGF2BP1/2/3) as m 6 A readers in an m 6 A-modified manner in cancer progression.

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Section: Introductionmentioning

confidence: 99%

The role of Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) as m⁶A readers in cancer

Sun¹,

Cao²,

Du³

et al. 2022

Int. J. Biol. Sci.

View full text Add to dashboard Cite

show abstract

“…Experimental identification of RNA modifications can be achieved with three main approaches transcriptome-wide. Immunoprecipitation methods such as MeRIP-Seq 22 , m6A-Seq 23 , PA-m6A-Seq 24 , m6A-CLIP/IP 25 , miCLIP 26 , m6A-LAIC-Seq 27 , m6ACE-Seq 28 , and m6A-Seq2 29 use antibodies that specifically bind to the modified ribonucleotide. Chemical-based detection methods such as Pseudo-Seq 30 , AlkAniline-Seq 31 , utilise chemical compounds that selectively react with the modified ribonucleotide.…”

Section: Introductionmentioning

confidence: 99%

Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework

Hendra

Pratanwanich

Wan

et al. 2021

Preprint

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RNA modifications such as m6A methylation form an additional layer of complexity in the transcriptome. Nanopore direct RNA sequencing captures this information in the raw current signal for each RNA molecule, enabling the detection of RNA modifications using supervised machine learning. However, experimental approaches provide only site-level training data, whereas the modification status for each single RNA molecule is missing. Here we present m6Anet, a neural network-based method that leverages the Multiple Instance Learning framework to specifically handle missing read-level modification labels in site-level training data. m6Anet outperforms existing computational methods, shows similar accuracy as experimental approaches, and generalises to different cell lines with almost identical accuracy. We demonstrate that m6Anet captures the underlying read-level stoichiometry that can be used to approximate differences in modification rates. m6Anet achieves this without retraining model parameters, enabling the transcriptome-wide identification and quantification of m6A from a single run of direct RNA sequencing.

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“…m6A-MS and m6A-seq2 data were normalized to a control strain harbouring the TIR ligase. m6A-seq2 data were obtained from Dierks et al (2021). (F) Similar analysis as E, except that the signals for ime4 Δ and not3 Δ cells are shown (control, FW4911, FW6060 and FW6093).…”

Section: Resultsmentioning

confidence: 97%

“…Essential components were depleted using induction of the AID system at 4 hours in SPO and m6A levels were determined at 6 hours SPO (2 hours after depletion). We also compared the LC-MS data with m6A-seq2 data, a technique that relies on multiplexed m6A-immunoprecipitation of barcoded and pooled samples, of the same depletion alleles (Dierks et al , 2021). We found that not3 Δ displayed an increase in m6A levels detected by LC-MS and m6A-seq2 (Figure 5F).…”

Section: Resultsmentioning

confidence: 99%

m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast

Varier

Sideri

Capitanchik

et al. 2022

Preprint

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N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3 prime end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contingent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate correct translation and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.

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Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution

Cited by 79 publications

References 70 publications

The role of Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) as m⁶A readers in cancer

The role of Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) as m⁶A readers in cancer

Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework

m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast

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Multiplexed profiling facilitates robust m6A quantification at site, gene and sample resolution

Cited by 79 publications

References 70 publications

The role of Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) as m6A readers in cancer

The role of Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) as m6A readers in cancer

Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework

m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast

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The role of Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) as m⁶A readers in cancer

The role of Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) as m⁶A readers in cancer