TRACE-seq: A transgenic system for unbiased and non-invasive transcriptome profiling of living cells

iScience - Tập 25 - Trang 103806 - 2022
François Cherbonneau1,2, Guoping Li2, Priyanka Gokulnath2, Parul Sahu2, Aurore Prunevieille3,4, Robert Kitchen2, Gilles Benichou4, Jérôme Larghero1, Ibrahim Domian2, Saumya Das2
1Université de Paris, AP-HP, Hôpital Saint-Louis, Unité de Thérapie Cellulaire, U976, CICBT CBT501, INSERM, Paris, France
2Cardiovascular Research Center, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Simches 3(rd.) Floor, Boston, MA 02114, USA
3Université de Paris, AP-HP, Hôpital Saint-Louis, Human Immunology and Immunopathology, UMR976, INSERM, Paris, France
4Transplant Research Center, Department of Surgery, Center for Transplantation Sciences, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA

Tài liệu tham khảo

Bao, 2009, Fluorescent probes for live-cell RNA detection, Annu. Rev. Biomed. Eng., 11, 25, 10.1146/annurev-bioeng-061008-124920 Batagov, 2013, Exosomes secreted by human cells transport largely mRNA fragments that are enriched in the 3'-untranslated regions, Biol. Direct., 8, 12, 10.1186/1745-6150-8-12 Cao, 2017, Nondestructive nanostraw intracellular sampling for longitudinal cell monitoring, Proc. Natl. Acad. Sci. U S A., 114, E1866, 10.1073/pnas.1615375114 Corces, 2016, Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution, Nat. Genet., 48, 1193, 10.1038/ng.3646 Darr, 2020, iTAG-RNA isolates cell-specific transcriptional responses to environmental stimuli and identifies an RNA-based endocrine Axis, Cell Rep., 30, 3183, 10.1016/j.celrep.2020.02.020 Dobin, 2013, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635 Dominissini, 2012, Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq, Nature, 485, 201, 10.1038/nature11112 Du, 2016, YTHDF2 destabilizes m(6)A-containing RNA through direct recruitment of the CCR4-NOT deadenylase complex, Nat. Commun., 7, 12626, 10.1038/ncomms12626 Grün, 2015, Design and analysis of single-cell sequencing experiments, Cell, 163, 799, 10.1016/j.cell.2015.10.039 Heiman, 2014, Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP), Nat. Protoc., 9, 1282, 10.1038/nprot.2014.085 Hrdlickova, 2017, RNA-Seq methods for transcriptome analysis, Wiley Interdiscip. Rev. RNA, 8, wrna.1364, 10.1002/wrna.1364 Hu, 2017, POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins, Nucleic Acids Res., 45, D104, 10.1093/nar/gkw888 Kirchhofer, 2010, Modulation of protein properties in living cells using nanobodies, Nat. Struct. Mol. Biol., 17, 133, 10.1038/nsmb.1727 Koh, 2018, Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome, Nucleic Acids Res., 46, 11659, 10.1093/nar/gky1104 Kowal, 2016, Proteomic comparison defines novel markers to characterize heterogeneous populations of extracellular vesicle subtypes, Proc. Natl. Acad. Sci. U S A., 113, E968, 10.1073/pnas.1521230113 Liao, 2019, The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads, Nucleic Acids Res., 47, e47, 10.1093/nar/gkz114 Mateescu, 2017, Obstacles and opportunities in the functional analysis of extracellular vesicle RNA - an ISEV position paper, J. Extracell Vesicles, 6, 1286095, 10.1080/20013078.2017.1286095 Miller, 2012, Ccr4-Not complex: the control freak of eukaryotic cells, Crit. Rev. Biochem. Mol. Biol., 47, 315, 10.3109/10409238.2012.667214 Monaco, 2019, RNA-seq signatures normalized by mRNA abundance allow absolute deconvolution of human immune cell types, Cell Rep., 26, 1627, 10.1016/j.celrep.2019.01.041 Morales-Kastresana, 2019, High-fidelity detection and sorting of nanoscale vesicles in viral disease and cancer, J. Extracell Vesicles, 8, 1597603, 10.1080/20013078.2019.1597603 Morales-Kastresana, 2017, Labeling extracellular vesicles for nanoscale flow cytometry, Sci. Rep., 7, 1878, 10.1038/s41598-017-01731-2 O'Brien, 2020, RNA delivery by extracellular vesicles in mammalian cells and its applications, Nat. Rev. Mol. Cell Biol., 21, 585, 10.1038/s41580-020-0251-y Ozsolak, 2011, RNA sequencing: advances, challenges and opportunities, Nat. Rev. Genet., 12, 87, 10.1038/nrg2934 Patil, 2018, Reading m6A in the transcriptome:m6A-binding proteins, Trends Cell Biol., 28, 113, 10.1016/j.tcb.2017.10.001 Peter, 2015, Molecular architecture of 4E-BP translational inhibitors bound to eIF4E, Mol. Cell, 57, 1074, 10.1016/j.molcel.2015.01.017 Picelli, 2013, Smart-seq2 for sensitive full-length transcriptome profiling in single cells, Nat. Methods, 10, 1096, 10.1038/nmeth.2639 Picelli, 2014, Full-length RNA-seq from single cells using Smart-seq2, Nat. Protoc., 9, 171, 10.1038/nprot.2014.006 Pérez-Boza, 2018, Exploring the RNA landscape of endothelial exosomes, RNA, 24, 423, 10.1261/rna.064352.117 Ritchie, 2015, Limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Res., 43, e47, 10.1093/nar/gkv007 Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616 Rodrigues, 2021, Quantification of mRNA ribosomal engagement in human neurons using parallel translating ribosome affinity purification (TRAP) and RNA sequencing, STAR Protoc., 2, 100229, 10.1016/j.xpro.2020.100229 Saadatpour, 2015, Single-cell analysis in cancer genomics, Trends Genet., 31, 576, 10.1016/j.tig.2015.07.003 Saliba, 2014, Single-cell RNA-seq: advances and future challenges, Nucleic Acids Res., 42, 8845, 10.1093/nar/gku555 Sandberg, 2014, Entering the era of single-cell transcriptomics in biology and medicine, Nat. Methods, 11, 22, 10.1038/nmeth.2764 Shi, 2017, YTHDF3 facilitates translation and decay of N6-methyladenosine-modified RNA, Cell Res., 27, 315, 10.1038/cr.2017.15 Tang, 2011, Development and applications of single-cell transcriptome analysis, Nat. Methods, 8, S6, 10.1038/nmeth.1557 Tang, 2013, A nanobody-based system using fluorescent proteins as scaffolds for cell-specific gene manipulation, Cell, 154, 928, 10.1016/j.cell.2013.07.021 Valadi, 2007, Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells, Nat. Cell Biol., 9, 654, 10.1038/ncb1596 van Balkom, 2015, Quantitative and qualitative analysis of small RNAs in human endothelial cells and exosomes provides insights into localized RNA processing, degradation and sorting, J. Extracell Vesicles, 4, 26760, 10.3402/jev.v4.26760 Wang, 2014, N6-methyladenosine-dependent regulation of messenger RNA stability, Nature, 505, 117, 10.1038/nature12730 Wang, 2015, N(6)-methyladenosine modulates messenger RNA translation efficiency, Cell, 161, 1388, 10.1016/j.cell.2015.05.014 Wei, 2017, Coding and noncoding landscape of extracellular RNA released by human glioma stem cells, Nat. Commun., 8, 1145, 10.1038/s41467-017-01196-x Yim, 2016, Exosome engineering for efficient intracellular delivery of soluble proteins using optically reversible protein-protein interaction module, Nat. Commun., 7, 12277, 10.1038/ncomms12277 Zhu, 2019, POSTAR2: deciphering the post-transcriptional regulatory logics, Nucleic Acids Res., 47, D203, 10.1093/nar/gky830