Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq

Yusheng Liu, Yiwei Zhang, Jiaqiang Wang, Falong Lu

Published: 2022-07-12 DOI: 10.1038/s41596-022-00704-8

PAIso-seq

poly(A) tails

PacBio sequencing

RNA isoform

single-oocyte sensitivity

AI 解读

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Poly(A) tails are added to the 3′ ends of most mRNAs in a non-templated manner and play essential roles in post-transcriptional regulation, including mRNA export, stability and translation. Measuring poly(A) tails is critical for understanding the
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ACKNOWLEDGMENTS

Subtelny, A. O., Eichhorn, S. W., Chen, G. R., Sive, H. & Bartel, D. P. Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508, 66–71 (2014).
Lim, J. et al. Uridylation by TUT4 and TUT7 marks mRNA for degradation. Cell 159, 1365–1376 (2014).
Lim, J. et al. Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadenylation. Science 361, 701–704 (2018).
Lim, J., Lee, M., Son, A., Chang, H. & Kim, V. N. mTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development. Genes Dev. 30, 1671–1682 (2016).
Ma, J., Fukuda, Y. & Schultz, R. M. Mobilization of dormant Cnot7 mRNA promotes deadenylation of maternal transcripts during mouse oocyte maturation. Biol. Reprod. 93, 48 (2015).
Kumar, A., Clerici, M., Muckenfuss, L. M., Passmore, L. A. & Jinek, M. Mechanistic insights into mRNA 3′-end processing. Curr. Opin. Struct. Biol. 59, 143–150 (2019).
Eckmann, C. R., Rammelt, C. & Wahle, E. Control of poly(A) tail length. Wiley Interdiscip. Rev. RNA 2, 348–361 (2011).
Charlesworth, A., Meijer, H. A. & de Moor, C. H. Specificity factors in cytoplasmic polyadenylation. Wiley Interdiscip. Rev. RNA 4, 437–461 (2013).
Sha, Q. Q. et al. CNOT6L couples the selective degradation of maternal transcripts to meiotic cell cycle progression in mouse oocyte. EMBO J. 37, e99333 (2018).
Yu, C. et al. BTG4 is a meiotic cell cycle-coupled maternal-zygotic-transition licensing factor in oocytes. Nat. Struct. Mol. Biol. 23, 387–394 (2016).
Pasternak, M., Pfender, S., Santhanam, B. & Schuh, M. The BTG4 and CAF1 complex prevents the spontaneous activation of eggs by deadenylating maternal mRNAs. Open Biol. 6, 160184 (2016).
Liu, Y. et al. BTG4 is a key regulator for maternal mRNA clearance during mouse early embryogenesis. J. Mol. Cell Biol. 8, 366–368 (2016).
Costa-Mattioli, M., Sossin, W. S., Klann, E. & Sonenberg, N. Translational control of long-lasting synaptic plasticity and memory. Neuron 61, 10–26 (2009).
Huang, Y. S., Jung, M. Y., Sarkissian, M. & Richter, J. D. N-methyl-D-aspartate receptor signaling results in Aurora kinase-catalyzed CPEB phosphorylation and alpha CaMKII mRNA polyadenylation at synapses. EMBO J. 21, 2139–2148 (2002).
Wu, L. et al. CPEB-mediated cytoplasmic polyadenylation and the regulation of experience-dependent translation of alpha-CaMKII mRNA at synapses. Neuron 21, 1129–1139 (1998).
Alarcon, J. M. et al. Selective modulation of some forms of schaffer collateral-CA1 synaptic plasticity in mice with a disruption of the CPEB-1 gene. Learn. Mem. 11, 318–327 (2004).
Chang, H., Lim, J., Ha, M. & Kim, V. N. TAIL-seq: genome-wide determination of poly(A) tail length and 3′ end modifications. Mol. Cell 53, 1044–1052 (2014).
Liu, Y., Nie, H., Liu, H. & Lu, F. Poly(A) inclusive RNA isoform sequencing (PAIso-seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails. Nat. Commun. 10, 5292 (2019).
Legnini, I., Alles, J., Karaiskos, N., Ayoub, S. & Rajewsky, N. FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control. Nat. Methods 16, 879–886 (2019).
Zhao, T. et al. Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency. Genome Biol. 20, 189 (2019).
Eisen, T. J. et al. The dynamics of cytoplasmic mRNA metabolism. Mol. Cell 77, 786–799.e10 (2020).
Eisen, T. J., Eichhorn, S. W., Subtelny, A. O. & Bartel, D. P. MicroRNAs cause accelerated decay of short-tailed target mRNAs. Mol. Cell 77, 775–785.e8 (2020).
Harrison, P. F. et al. PAT-seq: a method to study the integration of 3′-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA 21, 1502–1510 (2015).
Woo, Y. M. et al. TED-seq identifies the dynamics of poly(A) length during ER stress. Cell Rep. 24, 3630–3641.e7 (2018).
Yu, F. et al. Poly(A)-seq: a method for direct sequencing and analysis of the transcriptomic poly(A)-tails. PLoS One 15, e0234696 (2020).
Parker, M. T. et al. Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification. eLife 9, e49658 (2020).
Workman, R. E. et al. Nanopore native RNA sequencing of a human poly(A) transcriptome. Nat. Methods 16, 1297–1305 (2019).
Roach, N. P. et al. The full-length transcriptome of C. elegans using direct RNA sequencing. Genome Res. 30, 299–312 (2020).
Kim, D. et al. The architecture of SARS-CoV-2 transcriptome. Cell 181, 914–921.e10 (2020).
Long, Y., Jia, J., Mo, W., Jin, X. & Zhai, J. FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing. Nat. Protoc. 16, 4355–4381 (2021).
Jia, J. et al. Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants. Nat. Plants 6, 780–788 (2020).
Laehnemann, D., Borkhardt, A. & McHardy, A. C. Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction. Brief. Bioinform. 17, 154–179 (2016).
Ross, M. G. et al. Characterizing and measuring bias in sequence data. Genome Biol. 14, R51 (2013).
Minoche, A. E., Dohm, J. C. & Himmelbauer, H. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol. 12, R112 (2011).
Hebert, P. D. N. et al. A Sequel to Sanger: amplicon sequencing that scales. BMC Genomics 19, 219 (2018).
Zhang, Y. et al. Alternative polyadenylation: methods, mechanism, function, and role in cancer. J. Exp. Clin. Cancer Res. 40, 51 (2021).
Morgan, M., Kumar, L., Li, Y. & Baptissart, M. Post-transcriptional regulation in spermatogenesis: all RNA pathways lead to healthy sperm. Cell. Mol. Life Sci. 78, 8049–8071 (2021).
Liudkovska, V. & Dziembowski, A. Functions and mechanisms of RNA tailing by metazoan terminal nucleotidyltransferases. Wiley Interdiscip. Rev. RNA 12, e1622 (2021).
Kandhari, N., Kraupner-Taylor, C. A., Harrison, P. F., Powell, D. R. & Beilharz, T. H. The detection and bioinformatic analysis of alternative 3′ UTR isoforms as potential cancer biomarkers. Int. J. Mol. Sci. 22, 5322 (2021).
Yu, S. & Kim, V. N. A tale of non-canonical tails: gene regulation by post-transcriptional RNA tailing. Nat. Rev. Mol. Cell Biol. 21, 542–556 (2020).
Hu, S. B. et al. Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus. Genes Dev. 29, 630–645 (2015).
Wang, Y. et al. Genome-wide screening of NEAT1 regulators reveals cross-regulation between paraspeckles and mitochondria. Nat. Cell Biol. 20, 1145–1158 (2018).
Matz, M. et al. Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucleic Acids Res. 27, 1558–1560 (1999).
Ramskold, D. et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat. Biotechnol. 30, 777–782 (2012).
Picelli, S. et al. Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat. Methods 10, 1096–1098 (2013).
Zhu, Y. Y., Machleder, E. M., Chenchik, A., Li, R. & Siebert, P. D. Reverse transcriptase template switching: a SMART approach for full-length cDNA library construction. Biotechniques 30, 892–897 (2001).
Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171–181 (2014).
Kapteyn, J., He, R., McDowell, E. T. & Gang, D. R. Incorporation of non-natural nucleotides into template-switching oligonucleotides reduces background and improves cDNA synthesis from very small RNA samples. BMC Genomics 11, 413 (2010).
Wenger, A. M. et al. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat. Biotechnol. 37, 1155–1162 (2019).
van Dijk, E. L., Jaszczyszyn, Y., Naquin, D. & Thermes, C. The third revolution in sequencing technology. Trends Genet. 34, 666–681 (2018).
Luo, C. et al. Superovulation strategies for 6 commonly used mouse strains. J. Am. Assoc. Lab. Anim. Sci. 50, 471–478 (2011).

Transcriptome-wide measurement of poly(A) tail length and composition at subnanogram total RNA sensitivity by PAIso-seq

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