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[eboileau]

Aims/objectives.

We currently have BID-seq, eTAM-seq, and GLORI, amounting to a total of 65 dataset. We need to add more data from the public domain, esp. if we aim for a publication. We cannot rely on RMaP members to "fill" the database. I expect anyway that most users will not have data in the bedRMod format to start with.

A clear and concise description of todo items.

• [ ] Create a list of dataset @CDieterich
• [ ] Contact AB to generate bedRMod files, according to the Sci-ModoM specs (in particular check Attention boxes).
• [ ] Check the status of bedRMod-tools? Can RMaP members eventually use it to generate data for SCIMODOM?

[CDieterich]

1: Baek A, Lee GE, Golconda S, Rayhan A, Manganaris AA, Chen S, Tirumuru N, Yu H, Kim S, Kimmel C, Zablocki O, Sullivan MB, Addepalli B, Wu L, Kim S. Single- molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As. Nat Microbiol. 2024 Apr 11. doi: 10.1038/s41564-024-01638-5. Epub ahead of print. PMID: 38605174.

2: Dai Q, Ye C, Irkliyenko I, Wang Y, Sun HL, Gao Y, Liu Y, Beadell A, Perea J, Goel A, He C. Ultrafast bisulfite sequencing detection of 5-methylcytosine in DNA and RNA. Nat Biotechnol. 2024 Jan 2. doi: 10.1038/s41587-023-02034-w. Epub ahead of print. PMID: 38168991.

3: Hartstock K, Kueck NA, Spacek P, Ovcharenko A, Hüwel S, Cornelissen NV, Bollu A, Dieterich C, Rentmeister A. MePMe-seq: antibody-free simultaneous m6A and m5C mapping in mRNA by metabolic propargyl labeling and sequencing. Nat Commun. 2023 Nov 7;14(1):7154. doi: 10.1038/s41467-023-42832-z. PMID: 37935679; PMCID: PMC10630376.

4: Chen L, Zhang LS, Ye C, Zhou H, Liu B, Gao B, Deng Z, Zhao C, He C, Dickinson BC. Nm-Mut-seq: a base-resolution quantitative method for mapping transcriptome- wide 2'-O-methylation. Cell Res. 2023 Sep;33(9):727-730. doi: 10.1038/s41422-023-00836-w. Epub 2023 Jun 15. PMID: 37316584; PMCID: PMC10474006.

[CDieterich]

@eboileau - it is hard to find these data sets via PubMed. I wonder how we should search for them

[CDieterich]

I guess it would also make a lot of sense to walk through the latest review papers such as: https://pubs.acs.org/doi/10.1021/acs.accounts.3c00532

[CDieterich]

just in case we dont have that yet: https://pubmed.ncbi.nlm.nih.gov/35288668/

[eboileau]

Hu, L.; Liu, S.; Peng, Y.; Ge, R.; Su, R.; Senevirathne, C.; Harada, B. T.; Dai, Q.; Wei, J.; Zhang, L.-S.; Hao, Z.; Luo, L.; Wang, H.; Wang, Y.; Luo, M.; Chen, M.; Chen, J.; He, C. m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome. Nat. Biotechnol. 2022, 40, 1210–1219. (1) m6A-selective allyl chemical labeling and sequencing (m6A-SAC-seq) directly reads out m6A sites as mutation signatures and, for the first time, achieves the whole-transcriptome base-resolution quantification of m6A methylations at diverse motif contexts unbiasedly.

Dai, Q.; Ye, C.; Irkliyenko, I.; Wang, Y.; Sun, H.-L.; Gao, Y.; Liu, Y.; Beadell, A.; García, J. P.; Goel, A.; He, C. Ultrafast bisulfite sequencing for efficient and accurate 5-methylcytosine detection in DNA and RNA. Nat. Biotechnol. In Press. (3) Ultrafast BS sequencing (UBS-seq) employs the new chemistry with a high bisulfite concentration and a high reaction temperature, to improve C-to-U conversion efficiency and reduce RNA damage, outperforming all of the reported BS conditions in terms of lower background and higher sensitivity in quantitatively detecting RNA m5C sites transcriptome-wide.

Zhang, L.-S.; Xiong, Q.-P.; Peña Perez, S.; Liu, C.; Wei, J.; Le, C.; Zhang, L.; Harada, B. T.; Dai, Q.; Feng, X.; Hao, Z.; Wang, Y.; Dong, X.; Hu, L.; Wang, E.-D.; Pan, T.; Klungland, A.; Liu, R.-J.; He, C. ALKBH7-mediated demethylation regulates mitochondrial polycistronic RNA processing. Nat. Cell Biol. 2021, 23, 684–691. (4) Demethylation-assisted multiple methylation sequencing (DAMM-seq) simultaneously detects m1A, m1G, m3C, and m22G methylations as mutation signatures in one sequencing run, enabling the base-resolution quantitative mapping of these four methylations with low RNA input.

Zhang, L.-S.; Ju, C.-W.; Liu, C.; Wei, J.; Dai, Q.; Chen, L.; Ye, C.; He, C. m7G-quant-seq: Quantitative detection of RNA internal N7-methylguanosine and abasic sites. ACS Chem. Biol. 2022, 17, 3306– 3312, DOI: 10.1021/acschembio.2c00792

[eboileau]

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