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

Chang Ye, Qing Dai, Chuan He, Fan Yang, Li-Sheng Zhang, Cheng-Wei Ju, Boyang Gao, Xinran Feng, Hui-Lung Sun, Jiangbo Wei

Published: 2023-11-15 DOI: 10.1038/s41596-023-00917-5

single-base resolution

RNA modification

BID-seq

pseudouridine

transcriptome-wide

AI 解读

Generation of mouse–human chimeric embryos

Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting

Generation of CRISPR–Cas9-mediated genetic knockout human intestinal tissue–derived enteroid lines by lentivirus transduction and single-cell cloning

A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues

Decoding personal biotic and abiotic airborne exposome

A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys

Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds

Biomimetic tail-to-head terpene cyclizations using the resorcin[4]arene capsule catalyst

Neuroscience robotics for controlled induction and real-time assessment of hallucinations

Scanorama: integrating large and diverse single-cell transcriptomic datasets

Single-cell RNA sequencing (scRNA-seq)（单细胞RNA测序）

Data integration（数据集成）

Heterogeneity（异质性）

查看全部

Sections

Figures

References

Frye, M., Harada, B. T., Behm, M. & He, C. RNA modifications modulate gene expression during development. Science 361, 1346–1349 (2018).
Roundtree, I. A., Evans, M. E., Pan, T. & He, C. Dynamic RNA modifications in gene expression regulation. Cell 169, 1187–1200 (2017).
Zhao, B. S., Roundtree, I. A. & He, C. Post-transcriptional gene regulation by mRNA modifications. Nat. Rev. Mol. Cell Biol. 18, 31–42 (2017).
Carlile, T. M. et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515, 143–146 (2014).
Schwartz, S. et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159, 148–162 (2014).
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).
Li, X. et al. Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nat. Chem. Biol. 11, 592–597 (2015).
Marchand, V. et al. HydraPsiSeq: a method for systematic and quantitative mapping of pseudouridines in RNA. Nucleic Acids Res. 48, e110 (2020).
Dai, Q. et al. Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution. Nat. Biotechnol. 41, 344–354 (2023).
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).
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).
Huang, T. et al. Genome-wide identification of mRNA 5-methylcytosine in mammals. Nat. Struct. Mol. Biol. 26, 380–388 (2019).
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).
Dominissini, D. et al. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature 530, 441–446 (2016).
Safra, M. et al. The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution. Nature 551, 251–255 (2017).
Li, X. et al. Base-resolution mapping reveals distinct m1A methylome in nuclear- and mitochondrial-encoded transcripts. Mol. Cell 68, 993–1005 (2017).
Zhou, H. et al. Evolution of a reverse transcriptase to map N1-methyladenosine in human messenger RNA. Nat. Methods 16, 1281–1288 (2019).
Zhang, L.-S. et al. Transcriptome-wide mapping of internal N7-methylguanosine methylome in mammalian mRNA. Mol. Cell 74, 1304–1316 (2019).
Malbec, L. et al. Dynamic methylome of internal mRNA N7-methylguanosine and its regulatory role in translation. Cell Res. 29, 927–941 (2019).
Arango, D. et al. Acetylation of cytidine in mRNA promotes translation efficiency. Cell 175, 1872–1886 (2018).
Sas-Chen, A. et al. Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping. Nature 583, 638–643 (2020).
Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).
Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635–1646 (2012).
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).
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).
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).
Zaringhalam, M. & Papavasiliou, F. N. Pseudouridylation meets next-generation sequencing. Methods 107, 63–72 (2016).
Begik, O. et al. Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing. Nat. Biotechnol. 39, 1278–1291 (2021).
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).
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).

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

Supplementary information

Supplementary Information

Reporting Summary

Supplementary Table 1 and 2

推荐阅读