BID-seq for transcriptome-wide quantitative sequencing of mRNA pseudouridine at base resolution – Nature Protocols

  • Frye, M., Harada, B. T., Behm, M. & He, C. RNA modifications modulate gene expression during development. Science 361, 1346–1349 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roundtree, I. A., Evans, M. E., Pan, T. & He, C. Dynamic RNA modifications in gene expression regulation. Cell 169, 1187–1200 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao, B. S., Roundtree, I. A. & He, C. Post-transcriptional gene regulation by mRNA modifications. Nat. Rev. Mol. Cell Biol. 18, 31–42 (2017).

    Article  CAS  PubMed  Google Scholar 

  • Carlile, T. M. et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515, 143–146 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schwartz, S. et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159, 148–162 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lovejoy, A. F., Riordan, D. P. & Brown, P. O. Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS One 9, e110799 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  • Li, X. et al. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nat. Chem. Biol. 11, 592–597 (2015).

    Article  CAS  PubMed  Google Scholar 

  • Marchand, V. et al. HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA. Nucleic Acids Res. 48, e110 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dai, Q. et al. Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution. Nat. Biotechnol. 41, 344–354 (2023).

    Article  CAS  PubMed  Google Scholar 

  • Chen, L. et al. Nm-Mut-seq: a base-resolution quantitative method for mapping transcriptome-wide 2′-O-methylation. Cell Res. 33, 727–730 (2023).

    Article  CAS  PubMed  Google Scholar 

  • Yang, X. et al. 5-methylcytosine promotes mRNA export—NSUN2 as the methyltransferase and ALYREF as an m5C reader. Cell Res. 27, 606–625 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang, T. et al. Genome-wide identification of mRNA 5-methylcytosine in mammals. Nat. Struct. Mol. Biol. 26, 380–388 (2019).

    Article  CAS  PubMed  Google Scholar 

  • Liu, J. et al. Developmental mRNA m5C landscape and regulatory innovations of massive m5C modification of maternal mRNAs in animals. Nat. Commun. 13, 2484 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dominissini, D. et al. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature 530, 441–446 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Safra, M. et al. The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution. Nature 551, 251–255 (2017).

    Article  CAS  PubMed  Google Scholar 

  • Li, X. et al. Base-resolution mapping reveals distinct m1A methylome in nuclear- and mitochondrial-encoded transcripts. Mol. Cell 68, 993–1005 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou, H. et al. Evolution of a reverse transcriptase to map N1-methyladenosine in human messenger RNA. Nat. Methods 16, 1281–1288 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, L.-S. et al. Transcriptome-wide mapping of internal N7-methylguanosine methylome in mammalian mRNA. Mol. Cell 74, 1304–1316 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Malbec, L. et al. Dynamic methylome of internal mRNA N7-methylguanosine and its regulatory role in translation. Cell Res. 29, 927–941 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arango, D. et al. Acetylation of cytidine in mRNA promotes translation efficiency. Cell 175, 1872–1886 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sas-Chen, A. et al. Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping. Nature 583, 638–643 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).

    Article  CAS  PubMed  Google Scholar 

  • Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635–1646 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khoddami, V. et al. Transcriptome-wide profiling of multiple RNA modifications simultaneously at single-base resolution. Proc. Natl Acad. Sci. USA 116, 6784–6789 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fleming, A. M. et al. Structural elucidation of bisulfite adducts to pseudouridine that result in deletion signatures during reverse transcription of RNA. J. Am. Chem. Soc. 141, 16450–16460 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fleming, A. M. et al. Pseudouridine and N1-methylpseudouridine display pH-independent reaction rates with bisulfite yielding ribose adducts. Org. Lett. 24, 6182–6185 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zaringhalam, M. & Papavasiliou, F. N. Pseudouridylation meets next-generation sequencing. Methods 107, 63–72 (2016).

    Article  CAS  PubMed  Google Scholar 

  • Begik, O. et al. Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing. Nat. Biotechnol. 39, 1278–1291 (2021).

    Article  CAS  PubMed  Google Scholar 

  • Tavakoli, S. et al. Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing. Nat. Commun. 14, 334 (2023).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Safra, M., Nir, R., Farouq, D., Vainberg Slutskin, I. & Schwartz, S. TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code. Genome Res. 27, 393–406 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar