The DOI matches its Crossref record; 66 of the 66 references it cites were found in a registry or an index.
Thiol-linked alkylation for the metabolic sequencing of RNA
Open accessPreprint — published as 10.1038/nmeth.4435 · Paper page
Abstract
Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes in RNA species at steady-state but obscures the intracellular dynamics of RNA transcription, processing and decay. We developed thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq), an orthogonal chemistry-based epitranscriptomics-sequencing technology that uncovers 4-thiouridine (s 4 U)-incorporation in RNA species at single-nucleotide resolution. In combination with well-established metabolic RNA labeling protocols and coupled to standard, low-input, high-throughput RNA sequencing methods, SLAM-seq enables rapid access to RNA polymerase II-dependent gene expression dynamics in the context of total RNA. When applied to mouse embryonic stem cells, SLAM-seq provides global and transcript-specific insights into pluripotency-associated gene expression. We validated the method by showing that the RNA-polymerase II-dependent transcriptional output scales with Oct4/Sox2/Nanog-defined enhancer activity; and we provide quantitative and mechanistic evidence for transcript-specific RNA turnover mediated by post-transcriptional gene regulatory pathways initiated by microRNAs and N 6 -methyladenosine. SLAM-seq facilitates the dissection of fundamental mechanisms that control gene expression in an accessible, cost-effective, and scalable manner. One Sentence Summary: Chemical nucleotide-analog derivatization provides global insights into transcriptional and post-transcriptional gene regulation
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Liao, Y., Smyth, G. K., & Shi, W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt656 · Cited by 27,219
MicroRNAs: Target Recognition and Regulatory Functions
Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.01.002 · Cited by 20,068
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
Mootha, V. K., Lindgren, C. M., Eriksson, K.-F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstråle, M., Laurila, E., et al. (2003) · Nature Genetics · doi:10.1038/ng1180 · Cited by 10,197
Most mammalian mRNAs are conserved targets of microRNAs
Friedman, R. C., Farh, K. K.-H., Burge, C. B., & Bartel, D. P. (2009) · Genome Research · doi:10.1101/gr.082701.108 · Cited by 8,462
deepTools2: a next generation web server for deep-sequencing data analysis
Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., Heyne, S., Dündar, F., & Manke, T. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw257 · Cited by 8,096
Global quantification of mammalian gene expression control
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · cited 3×
“Note, that the ability to determine de novo synthesized transcripts will depend on (1) the s(4)U uptake kinetics of the chosen cellular system, (2) the overall transcriptional activity of the cell type and (3) the library sequencing depth.”
BackgroundImproved vectors and genome-wide libraries for CRISPR screening
Sanjana, N. E., Shalem, O., & Zhang, F. (2014) · Nature Methods · doi:10.1038/nmeth.3047 · Cited by 5,239
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencingPreprint
Koboldt, D. C., Zhang, Q., Larson, D. E., Shen, D., McLellan, M. D., Lin, L., Miller, C. A., Mardis, E. R., Ding, L., & Wilson, R. K. (2012) · Genome Research · doi:10.1101/gr.129684.111 · Cited by 4,954
Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., Rahl, P. B., Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.03.035 · Cited by 4,143
PANTHER: A Library of Protein Families and Subfamilies Indexed by FunctionPreprint
Thomas, P. D., Campbell, M. J., Kejariwal, A., Mi, H., Karlak, B., Daverman, R., Diemer, K., Muruganujan, A., & Narechania, A. (2003) · Genome Research · doi:10.1101/gr.772403 · Cited by 2,979
Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP
Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M., Jungkamp, A.-C., Munschauer, M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.03.009 · Cited by 2,873
MicroRNA maturation: stepwise processing and subcellular localization
Lee, Y., Jeon, K., Lee, J., Kim, S., & Kim, V. N. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf476 · Cited by 2,572
Gene silencing by microRNAs: contributions of translational repression and mRNA decay
Huntzinger, E., & Izaurralde, E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2936 · Cited by 2,339
BEDTools: The Swiss‐Army Tool for Genome Feature Analysis
Quinlan, A. R. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1112s47 · Cited by 2,286
Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
Core, L. J., Waterfall, J. J., & Lis, J. T. (2008) · Science · doi:10.1126/science.1162228 · Cited by 1,986
Gene expression regulation mediated through reversible m6A RNA methylation
Fu, Y., Dominissini, D., Rechavi, G., & He, C. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3724 · Cited by 1,961
AmiGO: online access to ontology and annotation data
Carbon, S., Ireland, A., Mungall, C., Shu, S., Marshall, B., Lewis, S., Hub, T. A., & the Web Presence Working Group (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn615 · Cited by 1,918
m 6 A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation
Geula, S., Moshitch-Moshkovitz, S., Dominissini, D., Mansour, A. A., Kol, N., Salmon‐Divon, M., Hershkovitz, V., Peer, E., Mor, N., Manor, Y. S., et al. (2015) · Science · doi:10.1126/science.1261417 · Cited by 1,583
Relief of microRNA-Mediated Translational Repression in Human Cells Subjected to Stress
Bhattacharyya, S. N., Habermacher, R., Martiné, U., Closs, E. I., & Filipowicz, W. (2006) · Cell · doi:10.1016/j.cell.2006.04.031 · Cited by 1,384
m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells
Batista, P. J., Molinié, B., Wang, J., Qu, K., Zhang, J., Li, L., Bouley, D. M., Lujan, E., Haddad, B., Daneshvar, K., et al. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.09.019 · Cited by 1,276
Control of the Embryonic Stem Cell State
Young, R. A. (2011) · Cell · doi:10.1016/j.cell.2011.01.032 · Cited by 1,246
Structural basis of N6-adenosine methylation by the METTL3–METTL14 complex
Wang, X., Feng, J. Q., Xue, Y. C., Guan, Z., Zhang, D., Liu, Z., Gong, Z., Wang, Q., Huang, J. B., Tang, C., et al. (2016) · Nature · doi:10.1038/nature18298 · Cited by 1,226
Diversifying microRNA sequence and function
Ameres, S. L., & Zamore, P. D. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3611 · Cited by 1,175
Self-citationBrennan, C. M., & Steitz*, J. A. (2001) · Cellular and Molecular Life Sciences · doi:10.1007/pl00000854 · Cited by 1,095
The dynamic epitranscriptome: N6-methyladenosine and gene expression control
Meyer, K. D., & Jaffrey, S. R. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3785 · Cited by 1,073
RNA N 6 -methyladenosine methylation in post-transcriptional gene expression regulationPreprint
Yue, Y., Liu, J., & He, C. (2015) · Genes & Development · doi:10.1101/gad.262766.115 · Cited by 937
Enhancer function: new insights into the regulation of tissue-specific gene expression
Ong, C.-T., & Corces, V. G. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2957 · Cited by 929
Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing
Kwak, H., Fuda, N. J., Core, L. J., & Lis, J. T. (2013) · Science · doi:10.1126/science.1229386 · Cited by 849
Nascent transcript sequencing visualizes transcription at nucleotide resolution
Churchman, L. S., & Weissman, J. S. (2011) · Nature · doi:10.1038/nature09652 · Cited by 823
Pott, S., & Lieb, J. D. (2014) · Nature Genetics · doi:10.1038/ng.3167 · Cited by 786
Rabani, M., Levin, J. Z., Fan, L., Adiconis, X., Raychowdhury, R., Garber, M., Gnirke, A., Nusbaum, C., Hacohen, N., Friedman, N., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1861 · Cited by 583
TT-seq maps the human transient transcriptome
Schwalb, B., Michel, M., Zacher, B., Frühauf, K., Demel, C., Tresch, A., Gagneur, J., & Cramer, P. (2016) · Science · doi:10.1126/science.aad9841 · Cited by 570
Ke, S., Pandya‐Jones, A., Saito, Y., Fak, J. J., Vågbø, C. B., Geula, S., Hanna, J. H., Black, D. L., Darnell, J. E., Jr., & Darnell, R. B. (2017) · Genes & Development · doi:10.1101/gad.301036.117 · Cited by 537
Summary: the modified nucleosides of RNA
Limbach, P. A., Crain, P. F., & McCloskey, J. A. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.12.2183 · Cited by 523
Epitranscriptome sequencing technologies: decoding RNA modifications
Li, X., Xiong, X., & Yi, C. (2017) · Nature Methods · doi:10.1038/nmeth.4110 · Cited by 447
NextGenMap: fast and accurate read mapping in highly polymorphic genomes
Sedlazeck, F. J., Rescheneder, P., & von Haeseler, A. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt468 · Cited by 429
Self-citationMohn, F., Sienski, G., Handler, D., & Brennecke, J. (2014) · Cell · doi:10.1016/j.cell.2014.04.031 · Cited by 417
Dölken, L., Ruzsics, Z., Rädle, B., Friedel, C. C., Zimmer, R., Mages, J., Hoffmann, R. F. G., Dickinson, P., Forster, T., Ghazal, P., et al. (2008) · RNA · doi:10.1261/rna.1136108 · Cited by 407
Mullokandov, G., Baccarini, A., Ruzo, A., Jayaprakash, A. D., Tung, N., Israelow, B., Evans, M. J., Sachidanandam, R., & Brown, B. D. (2012) · Nature Methods · doi:10.1038/nmeth.2078 · Cited by 394
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast
Miller, C., Schwalb, B., Maier, K. C., Schulz, D., Dümcke, S., Zacher, B., Mayer, A., Sydow, J. F., Marcinowski, L., Dölken, L., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2010.112 · Cited by 393
Regulating RNA polymerase pausing and transcription elongation in embryonic stem cellsPreprint
Min, I. M., Waterfall, J. J., Core, L. J., Munroe, R. J., Schimenti, J. C., & Lis, J. T. (2011) · Genes & Development · doi:10.1101/gad.2005511 · Cited by 310
Sun, M., Schwalb, B., Schulz, D., Pirkl, N., Etzold, S., Larivière, L., Maier, K. C., Seizl, M., Tresch, A., & Cramer, P. (2012) · Genome Research · doi:10.1101/gr.130161.111 · Cited by 305
QuantSeq 3′ mRNA sequencing for RNA quantification
Moll, P. R., Ante, M., Seitz, A., & Reda, T. (2014) · Nature Methods · doi:10.1038/nmeth.f.376 · Cited by 296
Forward and Reverse Genetics through Derivation of Haploid Mouse Embryonic Stem Cells
Elling, U., Taubenschmid, J., Wirnsberger, G., O’Malley, R. C., Demers, S.-P., Vanhaelen, Q., Иванович, Ш. А., Schmauss, G., Schramek, D., Schnütgen, F., et al. (2011) · Cell stem cell · doi:10.1016/j.stem.2011.10.012 · Cited by 231
Self-citationHigh-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies
Rabani, M., Raychowdhury, R., Jovanovic, M., Rooney, M., Stumpo, D. J., Pauli, A., Hacohen, N., Schier, A. F., Blackshear, P. J., Friedman, N., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.015 · Cited by 226
WGE: a CRISPR database for genome engineering
Hodgkins, A., Farne, A., Perera, S., Grego, T., Parry-Smith, D., Skarnes, W., & Iyer, V. (2015) · Bioinform. · doi:10.1093/bioinformatics/btv308 · Cited by 202
Cleary, M. D., Meiering, C. D., Jan, E., Guymon, R., & Boothroyd, J. C. (2005) · Nature Biotechnology · doi:10.1038/nbt1061 · Cited by 198
Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry
Duffy, E. E., Rutenberg-Schoenberg, M., Stark, C., Kitchen, R. R., Gerstein, M., & Simon, M. D. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.07.023 · Cited by 193
TU-tagging: cell type–specific RNA isolation from intact complex tissues
Miller, M. R., Robinson, K. J., Cleary, M. D., & Doe, C. Q. (2009) · Nature Methods · doi:10.1038/nmeth.1329 · Cited by 176
The 3′-to-5′ Exoribonuclease Nibbler Shapes the 3′ Ends of MicroRNAs Bound to Drosophila Argonaute1
Han, B., Hung, J., Weng, Z., Zamore, P. D., & Ameres, S. L. (2011) · Current Biology · doi:10.1016/j.cub.2011.09.034 · Cited by 164
Self-citation4-thiouridine inhibits rRNA synthesis and causes a nucleolar stress response
Burger, K., Mühl, B., Kellner, M., Michaela, R., Anita, G.-E., Windhager, L., Friedel, C. C., Dölken, L., & Eick, D. (2013) · RNA Biology · doi:10.4161/rna.26214 · Cited by 133
Nucleobase Transport by Human Equilibrative Nucleoside Transporter 1 (hENT1)
Yao, S. Y. M., Ng, A. M. L., Cass, C. E., Baldwin, S. A., & Young, J. D. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.236117 · Cited by 128
Genome-wide technology for determining RNA stability in mammalian cells
Tani, H., & Akimitsu, N. (2012) · RNA Biology · doi:10.4161/rna.22036 · Cited by 120
Gay, L. S., Miller, M. R., Ventura, P. B., Devasthali, V., Vue, Z., Thompson, H. L., Temple, S., Zong, H., Cleary, M. D., Stankunas, K., et al. (2013) · Genes & Development · doi:10.1101/gad.205278.112 · Cited by 117
PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation)
Spitzer, J., Hafner, M., Landthaler, M., Ascano, M., Farazi, T. A., Wardle, G. S., Nusbaum, J. D., Khorshid, M., Burger, L., Zavolan, M., et al. (2014) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-420120-0.00008-6 · Cited by 111
UV-Induced Stabilization of c-fos and Other Short-Lived mRNAs
Blattner, C., Kannouche, P. L., Litfin, M., Bender, K., Rahmsdorf, H. J., Angulo, J. F., & Herrlich, P. A. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.10.3616-3625.2000 · Cited by 108
Gorospe, M., Wang, X., & Holbrook, N. J. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.3.1400 · Cited by 104
Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila
Reimão-Pinto, M. M., Ignatova, V. V., Burkard, T. R., Hung, J., Manzenreither, R. A., Sowemimo, I., Herzog, V. A., Reichholf, B., Fariña-Lopez, S., & Ameres, S. L. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.05.033 · Cited by 79
Self-citationDetection of nucleic acid modifications by chemical reagents
Heiß, M., & Kellner, S. M. (2016) · RNA Biology · doi:10.1080/15476286.2016.1261788 · Cited by 26
Shugart, L. R. (1972) · Archives of Biochemistry and Biophysics · doi:10.1016/0003-9861(72)90167-1 · Cited by 14
Thiol-linked alkylation for the metabolic sequencing of RNA (SLAMseq)
Ameres, S. L., Herzog, V. A., Reichholf, B., & Ameres, S. L. (2017) · Protocol Exchange · doi:10.1038/protex.2017.105 · Cited by 9
Self-citationRNA Sequencing by Primer ExtensionPreprint
Nilsen, T. W. (2013) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot079400 · Cited by 3
Flagged first, then by citations
Cited by
Sorted by citations
RNA sequencing: the teenage years
Stark, R., Grzelak, M., & Hadfield, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0150-2 · Cited by 2,041
mRNAs, proteins and the emerging principles of gene expression control
Buccitelli, C., & Selbach, M. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0258-4 · Cited by 1,243
Paris, J., Morgan, M., Campos, J., Spencer, G. J., Shmakova, A., Ivanova, I., Mapperley, C., Lawson, H., Wotherspoon, D., Sepúlveda, C., et al. (2019) · Cell stem cell · doi:10.1016/j.stem.2019.03.021 · Cited by 509
Deciphering the “m6A Code” via Antibody-Independent Quantitative Profiling
García-Campos, M. A., Edelheit, S., Toth, U., Safra, M., Shachar, R., Viukov, S. V., Winkler, R., Nir, R., Lasman, L., Brandis, A. S., et al. (2019) · Cell · doi:10.1016/j.cell.2019.06.013 · Cited by 479
Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm
Sharma, U., Sun, F., Conine, C. C., Reichholf, B., Kukreja, S., Herzog, V. A., Ameres, S. L., & Rando, O. J. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.06.023 · Cited by 446
Self-citation
Metadata
- Authors
- Herzog, V. A., Reichholf, B., Neumann, T., Rescheneder, P., Bhat, P., Burkard, T. R., Wlotzka, W., von Haeseler, A., Zuber, J., & Ameres, S. L.
- Affiliations
- Institute of Molecular Biotechnology (AT)
- Research Institute of Molecular Pathology (AT)
- Max Perutz Labs (AT)
- Corresponding author
- Ameres, Stefan L.
- ORCID
- Venue
- Nature Methods
- Publisher
- openRxiv
- Published
- 2017-08-17
- Volume
- 14
- Issue
- 12
- Pages
- 1198-1204
- ISSN
- 1548-7091 (ISSN-L)
- PMC
- PMC5712218
- OpenAlex
- W2759506905
- Cited by
- 622
- References
- 66
- Citations by year
- 2026: 80 · 2025: 79 · 2024: 117 · 2023: 84 · 2022: 71 · 2021: 73 · 2020: 52 · 2019: 44 · 2018: 21 · 2017: 1
- FWCI
- 13.19
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Nature Methods (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Österreichischen Akademie der Wissenschaften
- Austrian Science Fund (W12-7-B09, Y-733-B22 START, F4322)
- Wirtschaftsagentur Wien
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- SLAM-seq, RNA turnover, RNA metabolism, RNA polymerase II transcription, gene expression dynamics, microRNA, N6-methyladenosine, post-transcriptional regulation, mouse embryonic stem cells, enhancer activity
- MeSH terms
- Alkylation, RNA, RNA Polymerase II, RNA Processing, Post-Transcriptional, Sulfhydryl Compounds, Thiouridine, Gene Expression Profiling, Gene Regulatory Networks, Embryonic Stem Cells, High-Throughput Screening Assays, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
