Thiol-linked alkylation for the metabolic sequencing of RNA
Herzog, Veronika A., Reichholf, Brian, Neumann, Tobias, Rescheneder, Philipp, Bhat, Pooja, Burkard, Thomas R., Wlotzka, Wiebke, von Haeseler, Arndt +2 more·2017·Nature Methods
DOI 10.1101/177642
Cited by (627)
Items 201–300 of 627
- Adapting systems biology to address the complexity of human disease in the single-cell eraDavid S. Fischer, Martin Arreola Villanueva, Peter S. Winter, Alex K. Shalek · 2025 · Nature Reviews Genetics
- A genetically encoded device for transcriptome storage in mammalian cellsYu-Kai Chao, Michelle Wu, Qiyu Gong, Fei Chen · 2026 · Science
- A YTHDF–PABP interaction is required for m6A‐mediated organogenesis in plantsMathias Due Tankmar, Marlene Reichel, Laura Arribas‐Hernández, Peter Brodersen · 2023 · EMBO Reports
- Special function methods for bursty models of transcriptionGennady Gorin, Lior S. Pachter · 2020 · Physical review. E
- Chemical methods for measuring RNA expression with metabolic labelingMonika K. Singha, Leslie Spitalny, Kim Nguyen, Abigail Vandewalle, Robert C. Spitale · 2021 · Wiley Interdisciplinary Reviews - RNA
- NANOS2 is a sequence-specific mRNA-binding protein that promotes transcript degradation in spermatogonial stem cellsAzzurra Codino, Tomasz W. Turowski, Louie N. van de Lagemaat, Ivayla Ivanova, Andrea Tavosanis, Christian Much, Tania Auchynnikava, Lina Vasiliauskaitė, Marcos Morgan, Juri Rappsilber et al. · 2021 · iScience
- piRNA-Independent Transposon Silencing by The Drosophila THO ComplexGen Zhang, Tianxiong Yu, Swapnil S. Parhad, Samantha Ho, Zhiping Weng, William E. Theurkauf · 2021 · Developmental Cell
- Concatenation of Transgenic DNA: Random or Orchestrated?A. V. Smirnov, Нариман Рашитович Баттулин · 2021 · Genes
- Distinct transcription kinetics of pluripotent cell statesRui Shao, Banushree Kumar, Katja Lidschreiber, M. Lidschreiber, P. Cramer, S. Elsässer · 2022 · Molecular Systems Biology
- Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactionsTianxin Liu, Qian Zhu, Yan Kai, Trevor Bingham, Stacy Wang, Hye Ji Cha, Stuti Mehta, T. Schlaeger, Guo‐Cheng Yuan, Stuart H. Orkin · 2024 · Nature Communications
- Dyna-vivo-seq unveils cellular RNA dynamics during acute kidney injury via in vivo metabolic RNA labeling-based scRNA-seqKun Yin, Yiling Xu, Ye Guo, Zhong Zheng, Xinrui Lin, Meijuan Zhao, He Dong, Dianyi Liang, Zhi Zhu, Junhua Zheng et al. · 2024 · Nature Communications
- DNA methyltransferase 1 modulates mitochondrial function through bridging m5C RNA methylationJing Wang, Xiaoqian Deng, Tianshen Jian, Shanshan Yin, L.R. Chen, Laurent Vergnes, Zhehao Li, H.-C. Liu, Ryan C. Lee, Sin Yee Lim et al. · 2025 · Molecular Cell
- Analyzing RNA posttranscriptional modifications to decipher the epitranscriptomic codeLili Deng, Jyotsna Kumar, Rebecca E. Rose, William D. McIntyre, Daniele Fabris · 2022 · Mass Spectrometry Reviews
- Rapid nuclear deadenylation of mammalian messenger RNAJonathan Alles, Ivano Legnini, Maddalena Pacelli, Nikolaus Rajewsky · 2022 · iScience
- A tRNA modification in Mycobacterium tuberculosis facilitates optimal intracellular growthFrancesca G. Tomasi, 木村聡, Eric J. Rubin, Matthew K. Waldor · 2023 · eLife
- High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcriptionAnnkatrin Bressin, O. Jasnovidova, Mirjam Arnold, E. Altendorfer, Filip Trajkovski, Thomas A Kratz, Joanna E. Handzlik, Denes Hnisz, A. Mayer · 2023 · Nature Communications
- Nuclear export is a limiting factor in eukaryotic mRNA metabolismJason M. Müller, Katharina Moos, Till Baar, Kerstin C. Maier, Kristina Žumer, Achim Tresch · 2024 · PLoS Computational Biology
- A conserved coupling of transcriptional ON and OFF periods underlies bursting dynamicsPo-Ta Chen, Michal Levo, Benjamin Zoller, Thomas Gregor · 2025 · Nature Structural & Molecular Biology
- Measuring RNA polymerase activity genome-wide with high-resolution run-on-based methodsAntonio Jordán‐Pla, Maria E. Pérez-Martínez, José Enrique Pérez-Ortín · 2019 · Methods
- Chemoenzymatic strategies for RNA modification and labelingJohanna Mattay, Maria Dittmar, Andrea Rentmeister · 2021 · Current Opinion in Chemical Biology
- A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnoverEtienne Boileau, Janine Altmüller, Isabel S. Naarmann‐de Vries, Christoph Dieterich · 2021 · Briefings in Bioinformatics
- Reactivation of the G1 enhancer landscape underlies core circuitry addiction to SWI/SNFKateřina Čermáková, Ling Tao, Milan Dejmek, Michal Šála, Matthew D. Montierth, Yuen San Chan, Ivanshi Patel, Courtney Chambers, Mario Loeza Cabrera, Dane K. Hoffman et al. · 2023 · Nucleic Acids Research
- Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinomaChristina M. Fitzsimmons, Mariana D. Mandler, Judith C. Lunger, Dalen Chan, Siddhardha S. Maligireddy, Alexandra C Schmiechen, Supuni Thalalla Gamage, Courtney N. Link, Lisa M. Miller Jenkins, King C. Chan et al. · 2024 · NAR Cancer
- Bioorthogonal Metabolic Labeling of Nascent RNA in Neurons Improves the Sensitivity of Transcriptome-Wide ProfilingEsmi Lau Zajaczkowski, Qiongyi Zhao, Zong Hong Zhang, Xiang Li, Wei Wei, Paul Robert Marshall, Laura Jane Leighton, Sarah Nainar, Chao Feng, Robert C. Spitale et al. · 2018 · ACS Chemical Neuroscience
- Single-cell temporal dynamics reveals the relative contributions of transcription and degradation to cell-type specific gene expression in zebrafish embryosLior Fishman, Gal Nechooshtan, Florian Erhard, Aviv Regev, Jeffrey A. Farrell, Michal Rabani · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
- PRO‐seq: Precise Mapping of Engaged RNA Pol II at Single‐Nucleotide ResolutionClaudia A. Mimoso, Seth Raphael Goldman · 2023 · Current Protocols
- Selective RNA sequestration in biomolecular condensates directs cell fate transitionsPatrizia Pessina, Mika Nevo, Junchao Shi, Srikanth Kodali, Eduard Casas, Yingzhi Cui, Alicia Richards, Emily J. Park, Xi Chen, Florencia Levin-Ferreyra et al. · 2025 · Nature Biotechnology
- Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq dataKevin Berg, Manivel Lodha, Isabel Delazer, Karolina Bartosik, Yilliam Cruz Garcia, Thomas Hennig, Elmar Wolf, Lars Dölken, Alexandra Lusser, Bhupesh Kumar Prusty et al. · 2024 · Nucleic Acids Research
- Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&TagNadiya Khyzha, Kami Ahmad, Steven Henikoff · 2025 · Molecular Cell
- Toward a Comprehensive View of MicroRNA BiologyYao Xiao, Ian J. MacRae · 2019 · Molecular Cell
- Roadblock-qPCR: a simple and inexpensive strategy for targeted measurements of mRNA stabilityMaegan J. Watson, Yeonwoo Park, Carson C. Thoreen · 2020 · RNA
- Pervasive compartment‐specific regulation of gene expression during homeostatic synaptic scalingDavid Colameo, Marek Rajman, Michael Soutschek, S. Bicker, Lukas M. von Ziegler, J. Bohacek, Jochen Winterer, P. Germain, C. Dieterich, G. Schratt · 2020 · bioRxiv
- Non-coding antisense transcripts: fine regulation of gene expression in cancerFrancisco dos Santos, Ana Maria Capela, Francisca Cazaux Mateus, Sandrina Nóbrega Pereira, Bruno Bernardes de Jesus · 2022 · Computational and Structural Biotechnology Journal
- Transcriptional bursting: from fundamentals to novel insightsDaniel Hebenstreit, Pradip Karmakar · 2024 · Biochemical Society Transactions
- Measuring mRNA Decay with Roadblock‐qPCRMaegan J. Watson, Carson C. Thoreen · 2022 · Current Protocols
- m6Am sequesters PCF11 to suppress premature termination and drive neuroblastoma differentiationHuihui An, Yifan Hong, Yeek Teck Goh, Casslynn W.Q. Koh, Shahzina Kanwal, Yi Zhang, Zhaoqi Lu, Phoebe M. L. Yap, Suat Peng Neo, Chun‐Ming Wong et al. · 2024 · Molecular Cell
- Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencingMichael B. Wolfe, Aaron C. Goldstrohm, Lydia Freddolino · 2018 · Methods
- Interrogating the Transcriptome with Metabolically Incorporated RibonucleosidesR. Kleiner · 2021 · Molecular Omics
- Capture of the newly transcribed RNA interactome using click chemistryXiangpeng Guo, Muqddas Tariq, Yiwei Lai, Shahzina Kanwal, Yuan Lv, Xiwei Wang, Na Li, Mengling Jiang, Jin Meng, Jieyi Hu et al. · 2021 · Nature Protocols
- Sister chromatid–sensitive Hi-C to map the conformation of replicated genomesMichael Mitter, Zsuzsanna Takács, Thomas Köcher, Ronald Micura, Christoph C. H. Langer, Daniel W. Gerlich · 2022 · Nature Protocols
- Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liverHurni, Clémence, Weger, Benjamin D., Gobet, Cédric, Naef, Felix · 2022 · PLOS Genetics
- Interphase chromosome conformation is specified by distinct folding programmes inherited through mitotic chromosomes or the cytoplasmAllana Schooley, Sergey V. Venev, Vasilisa Aksenova, Jesse W. Lehman, Emily Navarrete, Athma A. Pai, Mary Dasso, Job Dekker · 2025 · Nature Cell Biology
- Acute NIPBL depletion reveals in vivo dynamics of loop extrusion and its role in transcription activationTessa M. Popay, Ami Pant, Femke W. Munting, Melodi Tastemel, Morgan E Black, Nicholas K. Haghani, Jesse R. Dixon · 2026 · Nature Genetics
- Inhibition of Nonsense-Mediated Decay Induces Nociceptive Sensitization through Activation of the Integrated Stress ResponseJune Bryan de la Peña, Rebecca Chase, Nikesh Kunder, Patrick R. Smith, Tzu‐Fang Lou, Alexander D. Stanowick, Prarthana Suresh, Tarjani N. Shukla, Samuel E. Butcher, Theodore John Price et al. · 2023 · Journal of Neuroscience
- The tissue-specific transcriptional landscape underlines the involvement of endothelial cells in health and diseaseSushant Parab, Elisa Setten, Elena Astanina, Federico Bussolino, Gabriella Doronzo · 2023 · Pharmacology & Therapeutics
- Coinhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcriptionDonald P. Cameron, Jan Grosser, Swetlana Ladigan, Vladislav Kuzin, Evanthia Iliopoulou, Anika Wiegard, Hajar Benredjem, Kathryn Jackson, Sven Thorsten Liffers, Smiths Lueong et al. · 2023 · Science Advances
- Metabolic RNA labeling in non-engineered cells following spontaneous uptake of fluorescent nucleoside phosphate analoguesPauline Pfeiffer, Jesper R. Nilsson, Audrey Gallud, Tom Baladi, Hoang‐Ngoan Le, Mattias Bood, Malin Lemurell, Anders Dahlén, Morten Grøtli, Elin K. Esbjörner et al. · 2024 · Nucleic Acids Research
- Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complexGe, Tiffany, Brickner, Donna Garvey, Zehr, Kara, VanBelzen, D. Jake, Zhang, Wenzhu, Caffalette, Christopher, Moeller, Gavin C., Ungerleider, Sara, Marcou, Nikita, Jacob, Alexis et al. · 2025 · Molecular Cell
- Tagger—A Swiss army knife for multiomics to dissect cell type–specific mechanisms of gene expression in miceLech Kaczmarczyk, Vikas Bansal, Ashish Rajput, Raza‐Ur Rahman, Wiesław Krzyżak, Joachim Degen, Stefanie Poll, Martin Fuhrmann, Stefan Bonn, Walker S. Jackson · 2019 · PLoS Biology
- The Temporal Profile of Circulating miRNAs during Gestation in Overweight and Obese Women with or without Gestational Diabetes MellitusAnja E. Sørensen, Mireille N. M. van Poppel, Gernot Desoyé, David S Simmons, Peter Damm, Dorte Møller Jensen, Louise T. Dalgaard, The DALI Core Investigator Group · 2022 · Biomedicines
- Metabolic labeling of cardiomyocyte‐derived small extracellular‐vesicle (sEV) miRNAs identifies miR‐208a in cardiac regulation of lung gene expressionChaoshan Han, Junjie Yang, Eric Zhang, Ying Yan Jiang, Aijun Qiao, Yipeng Du, Qinkun Zhang, Junqing An, Jiacheng Sun, Meimei Wang et al. · 2022 · Journal of Extracellular Vesicles
- Synthesis and Metabolic Fate of 4‐Methylthiouridine in Bacterial tRNAChristoph Borek, Valentin F. Reichle, Stefanie M. Kellner · 2020 · ChemBioChem
- Imprinted X chromosome inactivation at the gamete-to-embryo transitionChunyao Wei, Barry Kesner, Hao Yin, Jeannie T. Lee · 2024 · Molecular Cell
- Subcellular mRNA kinetic modeling reveals nuclear retention as rate-limiting2024
- SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomesVanessa Luzak, Esteban Osses, Anna Danese, Christoff Odendaal, Raúl O. Cosentino, Stefan H. Stricker, Jurgen R. Haanstra, Florian Erhard, T. Nicolai Siegel · 2024 · Nucleic Acids Research
- mRNA stability fine-tunes gene expression in the developing cortex to control neurogenesisSerdar, Lucas D., Egol, Jacob R., Lackford, Brad, Bennett, Brian D., Hu, Guang, Silver, Debra L. · 2025 · PLOS Biology
- Adventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic AcidsJustine Cheval, Erika Muth, Gaëlle Gonzalez, Muriel Coulpier, Pascale Beurdeley, Stéphane Cruveiller, Marc Éloit · 2019 · mSphere
- Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified TranscriptsMattia Furlan, Iris Tanaka, Tommaso Leonardi, Stefano de Pretis, Mattia Pelizzola · 2020 · Frontiers in Genetics
- The influence of 4-thiouridine labeling on pre-mRNA splicing outcomesJessie A. C. Altieri, Klemens J. Hertel · 2021 · PLoS ONE
- Decoding murine cytomegalovirusManivel Lodha, Ihsan Muchsin, Christopher Jürges, Vanda Juranić Lisnić, Anne L’Hernault, Andrzej J. Rutkowski, Bhupesh Kumar Prusty, Arnhild Grothey, Andrea Milić, Thomas Hennig et al. · 2023 · PLoS Pathogens
- A dynamical perspective: moving towards mechanism in single-cell transcriptomicsRory J. Maizels · 2024 · Philosophical Transactions of the Royal Society B Biological Sciences
- A transient transcriptional activation governs unpolarized-to-polarized morphogenesis during embryo implantationXuehui Lyu, Yingzi Cui, Yinfei Kong, Min Yang, Hui Shen, Shuyun Liao, Shiyu Li, Chenrui An, Haoyi Wang, Zhe Zhang et al. · 2024 · Molecular Cell
- Epstein-Barr virus induces host shutoff extensively via BGLF5-independent mechanismsAlejandro Casco, Makoto Ohashi, Eric Johannsen · 2024 · Cell Reports
- Non-canonical transcriptional consequences of BET inhibition in cancerChristopher T. Letson, Eric Padron · 2019 · Pharmacological Research
- Real-Time Detection of Thiols Using CoPc Modified Black-Phosphorus Based SensorsPrashant K. Sarswat, Michael L. Free · 2019 · Journal of The Electrochemical Society
- Selective and sensitive fluorescence “turn-on” detection of 4-thiouridine in nucleic acids via oxidative aminationJingyi Wang, Jiachen Shang, Zichen Qin, Aijun Tong, Yu Xiang · 2019 · Chemical Communications
- Probing Nascent RNA with Metabolic Incorporation of Modified NucleosidesMrityunjay Gupta, Samantha R. Levine, Robert C. Spitale · 2022 · Accounts of Chemical Research
- CircaKB: a comprehensive knowledgebase of circadian genes across multiple speciesXingchen Zhu, Xiao Han, Zhijin Li, Xiaobo Zhou, Seung Hee Yoo, Zheng Chen, Zhiwei Ji · 2024 · Nucleic Acids Research
- Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12Selina Troester, Thomas Eder, Nadja Wukowits, Martin Piontek, Pablo Fernández‐Pernas, Johannes Schmoellerl, Ben Haladik, Gabriele Manhart, Melanie Allram, Margarita Maurer‐Granofszky et al. · 2025 · Nature Communications
- A Protocol for Transcriptome-Wide Inference of RNA Metabolic Rates in Mouse Embryonic Stem CellsAdriano Biasini, Ana Claudia Marques · 2020 · Frontiers in Cell and Developmental Biology
- Protein expression/secretion boost by a novel unique 21-mer cis-regulatory motif (Exin21) via mRNA stabilizationYuanjun Zhu, A. Sami Sarıbaş, Jinbiao Liu, Yuan Lin, Brittany H. Bodnar, Ruotong Zhao, Qian Guo, Julia Ting, Zhengyu Wei, Aidan Ellis et al. · 2023 · Molecular Therapy
- Regulation of cytoplasmic RNA stability: Lessons from DrosophilaBenjamin P. Towler, Sarah Faith Newbury · 2018 · Wiley Interdisciplinary Reviews - RNA
- A CDK11-dependent RNA polymerase II pause-checkpoint precedes CDK9-mediated transition to transcriptional elongation.J. Devlin, B. Martin, Nenad Bartonicek, Keziah E. Ting, Zheng Fan, Izabela Todorovski, Filip Bjelosevic, Sandra Verschoor, A. Ciccone, Joseph A. Trapani et al. · 2025 · Molecules and Cells
- Site-Specific Profiling of 4-Thiouridine Across Transfer RNA Genes in Escherichia coliPraneeth Bommisetti, Vahe Bandarian · 2022 · ACS Omega
- Improving the RNA velocity approach with single-cell RNA lifecycle (nascent, mature and degrading RNAs) sequencing technologiesChen Zhang, Yitong Fang, Weitian Chen, Zhichao Chen, Ying Zhang, Yeming Xie, Wenfang Chen, Zhe Xie, Mei Li Guo, Juan Wang et al. · 2023 · Nucleic Acids Research
- SRSF2 safeguards efficient transcription of DNA damage and repair genesRebecca E. Wagner, Leonie Arnetzl, Thiago Britto‐Borges, Anke Heit-Mondrzyk, Ali Bakr, Etienne Sollier, Nikoletta A. Gkatza, Jasper Panten, Sylvain Delaunay, Daniela Sohn et al. · 2024 · Cell Reports
- m6A and the NEXT complex direct Xist RNA turnover and X-inactivation dynamicsGuifeng Wei, Heather A. Coker, Lisa Rodermund, Mafalda R. Almeida, Holly L. Roach, Tatyana B. Nesterova, Neil Brockdorff · 2025 · Nature Structural & Molecular Biology
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methodsCarlos Alfonso-Gonzalez, Valérie Hilgers · 2025 · Nature Reviews Molecular Cell Biology
- Toxicity effects of size fractions of incinerated sewage sludge bottom ash on human cell linesAnbu Mozhi, Arun Kumar Prabhakar, Babu Cadiam Mohan, Vishnu Sunil, Jia Heng Teoh, Chi‐Hwa Wang · 2021 · Environment International
- KSHV transactivator-derived small peptide traps coactivators to attenuate MYC and inhibits leukemia and lymphoma cell growthMichiko Shimoda, Yuanzhi Lyu, Kang-Hsin Wang, Ashish Kumar, Hiroki Miura, Joshua F. Meckler, Ryan R. Davis, Chanikarn Chantarasrivong, Chie Izumiya, Clifford G. Tepper et al. · 2021 · Communications Biology
- Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptationBingnan Li, Patrice Zeis, Yujie Zhang, Alisa Alekseenko, Eliška Fürst, Yerma Pareja Sanchez, Gen Lin, Manu M. Tekkedil, Ilaria Piazza, Lars Michael Steinmetz et al. · 2023 · Nature Communications
- Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genomeGeorgi K. Marinov, Xinyi Chen, Matthew P. Swaffer, Tingting Xiang, Arthur Robert Grossman, William James Greenleaf · 2024 · Genome biology
- Poised PABP–RNA hubs implement signal-dependent mRNA decay in developmentMiha Modic, Klara Kuret, Sebastian Steinhauser, Rupert Faraway, Emiel van Genderen, Igor Ruiz de los Mozos, Jona Novljan, Žiga Vičič, Flora C. Y. Lee, Derk ten Berge et al. · 2024 · Nature Structural & Molecular Biology
- iTAG-RNA Isolates Cell-Specific Transcriptional Responses to Environmental Stimuli and Identifies an RNA-Based Endocrine AxisJonatan Darr, Archana Tomar, Maximilian Lassi, Raffaele Gerlini, Lucia Berti, Annette Hering, Fabienne Scheid, Martin Hrabě de Angelis, Michael A. Witting, Raffaele Teperino · 2020 · Cell Reports
- A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3XZiad Mohamoud Jowhar, Albert Xu, Srivats Venkataramanan, Francesco Dossena, Mariah L. Hoye, Debra L. Silver, Stephen N. Floor, Lorenzo Calviello · 2024 · Molecular Systems Biology
- CDK9 inhibition activates innate immune response through viral mimicryShivani Yalala, Aishwarya Gondane, Ninu Poulose, Jing Liang, Ian Geoffrey Mills, Harri M. Itkonen · 2024 · The FASEB Journal
- Translation elongation inhibitors stabilize select short-lived transcriptsNicolle A. Rosa-Mercado, Allen R. Buskirk, Rachel Green · 2024 · RNA
- RNA degradation triggered by decapping is largely independent of initial deadenylationLéna Audebert, Frank Feuerbach, Mostafa Zedan, Alexandra P Schürch, Laurence Decourty, Abdelkader Namane, Emmanuelle Permal, Karsten Weis, Gwenaël Badis, Cosmin Saveanu · 2024 · The EMBO Journal
- Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suiteIsaac W. Vock, Justin W. Mabin, Martin Machyna, Alexandra Zhang, J. Robert Hogg, Matthew D. Simon · 2025 · PLoS Computational Biology
- Recent advances in single‐cell multimodal analysis to study immune cellsRaymond H. Y. Louie, Fabio Luciani · 2020 · Immunology and Cell Biology
- RNA-binding protein LIN28A upregulates transcription factor HIF1α by posttranscriptional regulation via direct binding to UGAU motifsHiroto Yamamoto, Yutaro Uchida, Ryota Kurimoto, Tomoki Chiba, Takahide Matsushima, Yoshiaki Ito, Maiko Inotsume, Kohei Miyata, Kenta Watanabe, Masaki Inada et al. · 2022 · Journal of Biological Chemistry
- ADAR RNA editing on antisense RNAs results in apparent U-to-C base changes on overlapping sense transcriptsRiccardo Pecori, Isabel Chillón, Claudio Lo Giudice, Annette Arnold, Sandra Wüst, Marco Binder, Marco Marcia, Ernesto Picardi, Fotini Nina Papavasiliou · 2023 · Frontiers in Cell and Developmental Biology
- KSHV vIL-6 enhances inflammatory responses by epigenetic reprogrammingTomoki Inagaki, Kang-Hsin Wang, Ashish Kumar, Chie Izumiya, Hiroki Miura, Somayeh Komaki, Ryan R. Davis, Clifford G. Tepper, Harutaka Katano, Michiko Shimoda et al. · 2023 · PLoS Pathogens
- Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside ConversionVeronika A. Herzog, Nina Fasching, Stefan Ludwig Ameres · 2019 · Methods in molecular biology
- The NEXT complex regulates H3K27me3 levels to affect cancer progression by degrading G4/U-rich lncRNAsQianqian Yang, Zihan Zhou, Lian Li, Runhui Lu, Guofang Hou, Caihu Huang, Jiayi Huang, Hongyan Li, Yafan Zhang, Jiayong Li et al. · 2025 · Nucleic Acids Research
- Ribosomes modulate transcriptome abundance via generalized frameshift and out-of-frame mRNA decayYujie Zhang, Lilit Nersisyan, Eliška Fürst, Ioannis Alexopoulos, Carlos Santolaria, Susanne Huch, Claudio Bassot, Elena Garré, Per Sunnerhagen, Ilaria Piazza et al. · 2025 · Molecular Cell
- Regulation of both transcription and RNA turnover contribute to germline specificationKun Tan, Miles Wilkinson · 2022 · Nucleic Acids Research
- Simultaneous measurement of nascent transcriptome and translatome using 4-thiouridine metabolic RNA labeling and translating ribosome affinity purificationImai, Hirotatsu, Utsumi, Daisuke, Torihara, Hidetsugu, Takahashi, Kenzo, Kuroyanagi, Hidehito, Yamashita, Akio · 2023 · Nucleic Acids Research
- VIRMA facilitates intrahepatic cholangiocarcinoma progression through epigenetic augmentation of TMED2 and PARD3B mRNA stabilizationHongfa Xu, Xiaowen Lin, Zhongliang Li, Xu He, Yong Li, Lige Qiu, Ligong Lu, Bing Liu, Meixiao Zhan, Ke He · 2023 · Journal of Gastroenterology
- MicroRNA biogenesis is broadly disrupted by inhibition of the splicing factor SF3B1Angela Downie Ruiz Velasco, Aimee Parsons, Matthew C. Heatley, Athena R G Martin, Alfredo D Smart, Niraj Shah, Catherine L. Jopling · 2024 · Nucleic Acids Research