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. Author manuscript; available in PMC: 2021 Dec 1.
Published in final edited form as: Neurobiol Dis. 2020 Oct 13;146:105139. doi: 10.1016/j.nbd.2020.105139

Table 1. Compilation of RNA modifications mapped in various cell types.

The number of modified sites (peaks) and total number of unique transcripts that contain at least one modification varies greatly by tissue or cell type, detection method, and lab.

Mod. Tissue or Cell Type Detection Method # of modified sites (peaks) # of modified transcripts Comments Reference
m6A Mouse ESCs m6A RIP-seq 8,645 3,942 annotated 6,667 and 6,159 peaks in Mettl3 KD and Mettl14 KD cells. Wang et al., Nat Cell Biology 2015
m6A Mouse ESCs m6A RIP-seq 9,754 5,461 mRNAs, 117 ncRNAs Average 2 peaks per transcript, including on core pluripotency factors Batista et al., Cell Stem Cell 2015
m6A Mouse naïve ESCs m6A RIP-seq 10,431 6,412 Geula et al., Science 2015
m6A Mouse embryonic fibroblasts m6A RIP-seq 16,487 -- 10,609 peaks are WTAP-dependent (64.3%) Schwartz et al., Cell Reports 2017
m6A Total mouse brain m6A RIP-seq 13,471 4,654 coding 236 non-coding

10,483 mRNAs		 Meyer et al., Cell 2012
m6A Mouse cerebellum m6A RIP-seq with bioinformatic correction for m6Am 18,594 16,576 peaks shared with cortex, and 8,924 mRNAs shared with cortex Chang et al., Open Biology 2017
m6A Mouse cortex m6A RIP-seq with bioinformatic correction for m6Am 18,032 9,636 mRNAs 16,989 peaks shared with cerebellum, and 8,924 mRNAs shared with cerebellum Chang et al., Open Biology 2017
m6A E13.5 mouse cortex m6A RIP-seq 4,055 2,179 mRNAs Yoon et al., Cell 2017
m6A PCW11 human cortex m6A RIP-seq 10,980 5,960 mRNAs Yoon et al., Cell 2017
m6A Mouse P7 cerebellum m6A RIP-seq 19,459 10,449 total 9,879 mRNA

7,982		 Increases to 20,722 peaks on 11,215 RNAs upon hypobaric hypoxia exposure Ma et al., Genome Biology 2018
m6A/m Mouse cortex m6A RIP-seq 14,656 25 m6A/m peaks (in 20 genes) were significantly modified in response to 4 h stress Engel et al., Neuron 2018
m6A Human brainstem m6A RIP-seq 30,459 12,659 Donor ID 5 Liu et al., Mol Cell 2019
m6A Human cerebellum m6A RIP-seq 45,975 14,048 Donor ID 5 Liu et al., Mol Cell 2019
m6A Human cerebrum m6A RIP-seq 28,001 11,770 Donor ID 5 Liu et al., Mol Cell 2019
m6A Human hypothalamus m6A RIP-seq 26,993 11,751 Donor ID 5 Liu et al., Mol Cell 2019
m6A HEK293 CITS miCLIP, mutation calling 9,536 -- 12,051 residues identified by truncation calling, and 33,157 identified by RIP-seq Linder et al., Nature Methods 2016
m6A HEK293T m6A RIP-seq 18,756 5,768 43% conserved transcripts with mouse brain Meyer et al., Cell 2012
m6A HeLa cells m6A-CLIP 37,557 -- ~90% peaks are deposited at pre-mRNA stage, 99% are constant between nucleus and cytoplasm Ke et al., Genes Dev 2017
m6Am HEK293 CITS miCLIP 487 -- Linder et al., Nature Methods 2016
m6Am HEK293 miCLIP 2,350 -- Compared miCLIP in PCIF1 KO cells and WT cells to distinguish m6Am and m6A Boulias et al, Molecular Cell 2019
m6Am MEL624 m6Am-Exo-Seq -- 1,521 Compared PCIF1 WT and KO cells Sendinc et al., Molecular Cell 2019
m6Am Human brainstem m6A RIP-seq peaks at TSS 511 497 annotated Donor ID 5; one peak per transcript Liu et al., Mol Cell 2019
m6Am Human cerebellum m6A RIP-seq peaks at TSS 601 583 annotated Donor ID 5; one peak per transcript Liu et al., Mol Cell 2019
m6Am Human cerebrum m6A RIP-seq peaks at TSS 513 494 annotated Donor ID 5; one peak per transcript Liu et al., Mol Cell 2019
m6Am Human hypothalamus m6A RIP-seq peaks at TSS 472 455 annotated Donor ID 5; one peak per transcript Liu et al., Mol Cell 2019
m1A HeLa m1A RIP-seq 7,154 4,151 coding 63 non-coding

--		 Average of 1.4 peaks per methylated gene Dominissini et al., Nature 2016
m1A HEK293T m1A RIP-seq 2,129 Dominissini et al., Nature 2016
m1A HEK293T m1A-ID-seq 901 841 mRNAs 46 ncRNAs

226 tRNA 28 mitochondrial 8 rRNA 15 mRNA/other

473 mRNA and lncRNAs

88 tRNA 2 rRNA 1 snoRNA		 1,989 peaks identified in ALKBH3 KO cells Li et al., Nature Chemical Biology 2016
m1A HEK293T m1A RIP-seq 277 Safa et al., Nature 2017
m1A HEK293T m1A-MAP 740 Subset of 53 sites is strongly enriched fro GUUCRA motif Li et al., Molecular Cell 2018
m1A HeLa RBS-Seq 91 mRNA peaks identified only if less stringent fdters used Khoddami et al., PNAS 2019
m5C HeLa RNA-BisSeq 5,399 1,995 mRNAs 336 ncRNAs

3,722 annotated		 45% in CDS Yang et al., Cell Research 2017
m5C Mouse small intestine RNA-BisSeq 12,201 Peaks counted that are modified in at least 10% of m1A sites in rep 1 Yang et al., Cell Research 2017
m5C Mouse heart RNA-BisSeq 12,397 3,915 annotated ‘’ Yang et al., Cell Research 2017
m5C Mouse muscle RNA-BisSeq 11,721 3,624 annotated ‘’ Yang et al., Cell Research 2017
m5C Mouse brain RNA-BisSeq 12,032 3,635 annotated ‘’ Yang et al., Cell Research 2017
m5C Mouse kidney RNA-BisSeq 12,149 3,800 annotated ‘’ Yang et al., Cell Research 2017
m5C Mouse liver RNA-BisSeq 11,414 3,751 ‘’ Yang et al., Cell Research 2017
m5C Mouse testis 3W RNA-BisSeq 11,853 2,727 ‘’ Yang et al., Cell Research 2017
m5C HeLa RBS-Seq 487 340 annotated High-threshold cutoff Khoddami et al., PNAS 2019
5hmC Drosophila S2 cells hMeRIP-seq 3,058 1,597 coding Confirmed via dTet KD Delatte et al. Science 2016
Ψ HeLa RBS-Seq 754 322 mRNA 44 pseudogenes 55 rRNA 246 tRNA 24 snRNA 41 snoRNA 22 ncRNA 88 mRNAs 9ncRNA

238 mRNA 40 ncRNA

168 mRNA 24 ncRNA 46 tRNA

322 mRNA 28 ncRNA		 HeLa cells collected with rRNA depleted total RNA, PolyA selected mRNAs & size selected small RNAs Khoddami et al., PNAS 2019
Ψ HeLa Pseudo-seq 96 mRNA 12 ncRNA

260 mRNA 74 ncRNA

328		 Carlile et al., Nature 2014
Ψ S. Cerevisiae (budding Pseudo-seq Lower threshold filter shows 466 Ψ on mRNAs. Carlile et al., Nature 2014
Ψ S. Cerevisiae (midlog) Ψ-seq Change under heat shock Schwartz et al., Cell 2014
Ψ HEK293 and fibroblasts Ψ-seq 396 All human sites were combined into one dataset Schwartz et al., Cell 2014
m7G mESCs m7G MeRIP 184 184 tRNa Functionally confirmed in Mettl1 KO mESCs Lin et al., Mol Cell 2019
m7G HeLa and HepG2 m7G meRIP, m7G-seq 801 681 mRNA present in two replicates in both HeLa and HepG2 cells Zhang et al., Mol Cell 2019