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Welcome to EMTRAC Project
Multiomics dissection of hierarchical translational control
in epitranscriptome-mediated translatome reprogramming
Mechanistic axis: genome → transcriptome → epitranscriptome → translatome → phenome
Interconnected metabolic–regulatory axis: Metabolome ↔ epigenome / epitranscriptome → methylome
Mechanistic axis: genome → transcriptome → epitranscriptome → translatome → phenome
Interconnected metabolic–regulatory axis: Metabolome ↔ epigenome / epitranscriptome → methylome
Table-1. RMTC & EMTRAC - mediated translational control hierarchy.
Table-1. RMTC & EMTRAC - mediated translational control hierarchy.
At the global level, translational output is governed by kinetic uORF-based cis-acting sensors decoded by ternary-complex availability and stress-activated trans-acting pathways, while EMTRAC contributes a universal m⁷G-cap–dependent competence layer controlled by dedicated capping machinery and mTOR-regulated cap accessibility.
At the intermediate level, translational regulons defined by shared cis-acting elements within 5′UTRs are decoded by functionally specialized ribosomes and a broad set of trans-acting initiation, remodeling, and 3′UTR-associated factors, while EMTRAC-driven rRNA and tRNA modifications program ribosomal capacity to selectively translate structurally complex regulon transcripts in response to signaling cues.
At the local level, transcript-specific cis-acting features integrate with EMTRAC-encoded, sequence- and structure-dependent RNA modifications that are written, erased, and interpreted by dedicated enzymatic machineries, enabling precise, context-dependent fine-tuning of translation efficiency and isoform-specific protein output.
Table Conceptual Description: Translational control (TCtrl) constitutes a hierarchical regulatory system that determines protein output independently of transcriptional changes. At its core, TCtrl integrates two interdependent decision layers: regulome-mediated translational control (RMTC), which decodes RNA-encoded regulatory logic, and epitranscriptome-mediated translational control (EMTRAC), which programs RNA modification states that shape translational competence.
At the global level, TCtrl operates as a system-wide decision gate. Translational initiation is primarily determined by ternary complex availability and stress-activated signaling pathways. Cis-acting kinetic sensors encoded within mRNAs, most prominently overlapping uORF architectures, are decoded by trans-acting stress kinases and initiation factors, enabling selective translation under conditions of globally reduced protein synthesis. In parallel, EMTRAC contributes a universal competence layer through m⁷G-cap formation and cap-dependent initiation machinery, establishing the baseline capacity for translation.
At the intermediate level, translational control is organized into translational regulons—cohorts of mRNAs sharing common cis-acting elements embedded within 5′UTRs. These elements encode structural and sequence features that define competitive translation under specific cellular states. Decoding of regulons is executed by functionally specialized ribosomes, initiation and elongation factors, RNA helicases, 3′UTR-associated complexes, and non-coding RNAs, while signaling pathways such as mTOR–S6K modulate translational capacity. At this level, EMTRAC-driven rRNA and tRNA modifications program ribosomal properties, enabling preferential translation of structurally complex regulon transcripts.
At the local level, translational output is fine-tuned in a transcript-specific manner. Unique RNA sequences, structures, and isoform-specific untranslated regions integrate with site-specific RNA modifications, including m⁶A, m¹A, m⁵C, m⁶Am, ac⁴C, and pseudouridylation. These modifications are dynamically written, erased, and interpreted by dedicated enzymatic machineries that recognize local sequence and structural context, allowing precise control of individual mRNA translation and protein isoform production.
Together, this hierarchical organization enables translational reprogramming, whereby cells selectively maintain or enhance translation of defined transcripts despite global translational repression. This decoupling of mRNA abundance from protein output underlies the translatomic paradox, a phenomenon particularly evident in stress responses, development, and cancer, where adaptive protein synthesis supports survival, plasticity, and therapy resistance.
This structural–functional stratification provides a conceptual and practical framework for disentangling information-encoding RNA features from the executive machineries that decode them. By explicitly separating cis-acting regulatory architectures from trans-acting effectors, the table enables systematic identification of regulatory bottlenecks, layer-specific vulnerabilities, and points of functional distortion across global, intermediate, and local levels of translational control. This distinction is critical for experimental design, as it allows targeted perturbation of either informational RNA elements or their decoding machineries, facilitating causal inference rather than correlative observation. In the context of discovery-driven research and grant planning, this framework supports rational prioritization of interventions, hypothesis-driven mapping of regulatory rewiring, and identification of novel biomarkers and therapeutic targets arising from layer-specific dysregulation within RMTC and EMTRAC.
For a detailed discussion of translational control mechanisms underlying this framework, see our related publications, inventions, and RESEARCH.
Selected databases
Selected databases
RNA Modification Base (RMBase) is a comprehensive database that integrates multidimensional epitranscriptome sequencing data from healthy human samples and multiple model species to map, mechanistically characterise and functionally annotate RNA modifications. RMBase provides analytical modules for modification landscape exploration, mechanistic inference, interactome analysis, co-localisation with histone marks and regulatory protein associations; no disease-specific models are included. Xuan JJ et al. RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications. Nucleic Acids Research (2023).
UTRdb is a curated database of eukaryotic 5′ and 3′ untranslated regions (UTRs) derived from experimentally supported transcript annotations. The resource integrates sequence features, regulatory motifs and functional elements involved in post-transcriptional and translational control, including binding sites for RNA-binding proteins and regulatory sequence patterns. UTRdb can be used as a starting point for identifying translational regulons within the regulome, while not providing direct disease-specific or functional perturbation models.
Grillo G et al. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Research 38(Database issue):D75–D80 (2010).
AURA (Atlas of UTR Regulatory Activity) is a specialised database dedicated to the annotation and functional characterisation of cis-acting regulatory elements within the 5′ and 3′ untranslated regions (UTRs) and interacting with them trans-acting factors that may help in bilding the Atlas of Regulome Mediated Translational Control (RMTC).
REFERENCES
REFERENCES
Regulome and epitranscriptome mediated translational control
Regulome and epitranscriptome mediated translational control
Akirtava C, McManus CJ. Control of translation by eukaryotic mRNA transcript leaders-Insights from high-throughput assays and computational modeling. Wiley Interdiscip Rev RNA. 2021 May;12(3):e1623. doi: 10.1002/wrna.1623. Epub 2020 Aug 31. PMID: 32869519; PMCID: PMC7914273.
Ankit Sharma, Madankumar Ghatge, Vrushali Deshpande, Rajani Kanth Vangala. A systems biology approach to elucidate the post-translational regulome of coronary artery disease. bioRxiv 2022.02.09.479759; doi: https://doi.org/10.1101/2022.02.09.479759
Atrian F, Ramirez P, De Mange J, Marquez M, Gonzalez EM, Minaya M, Karch CM, Frost B. m6A-dependent circular RNA formation mediates tau-induced neurotoxicity. bioRxiv [Preprint]. 2024 Jan 26:2024.01.25.577211. doi: 10.1101/2024.01.25.577211. PMID: 38328044; PMCID: PMC10849734.
Bai Y, Li K, Peng J, Yi C. m6A modification: a new avenue for anti-cancer therapy. Life Med. 2023 Apr 8;2(1):lnad008. doi: 10.1093/lifemedi/lnad008. PMID: 39872957; PMCID: PMC11749794.
Baleriola J, Walker CA, Jean YY, Crary JF, Troy CM, Nagy PL, Hengst U. Axonally synthesized ATF4 transmits a neurodegenerative signal across brain regions. Cell. 2014 Aug 28;158(5):1159-1172. doi: 10.1016/j.cell.2014.07.001. PMID: 25171414; PMCID: PMC4149755.
Bassell GJ, Warren ST. Fragile X syndrome: loss of local mRNA regulation alters synaptic development and function. Neuron. 2008 Oct 23;60(2):201-14. doi: 10.1016/j.neuron.2008.10.004. PMID: 18957214; PMCID: PMC3691995.
Basu A, Yang JY, Tsirukis VE, Loiacono A, Koch G, Khwaja IA, Krishnamurthy M, Fazio N, White E, Jha A, Shah S, Takmil C, Bagdas D, Demirer A, Master A, Natke E, Honkanen R, Huang L, Rigas B. Phosphosulindac (OXT-328) prevents and reverses chemotherapy induced peripheral neuropathy in mice. Front Neurosci. 2024 Jan 29;17:1240372. doi: 10.3389/fnins.2023.1240372. PMID: 38347876; PMCID: PMC10860339.
Behrens A, Rodschinka G, Nedialkova DD. High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq. Mol Cell. 2021 Apr 15;81(8):1802-1815.e7. doi: 10.1016/j.molcel.2021.01.028. Epub 2021 Feb 12. PMID: 33581077; PMCID: PMC8062790.
Bisogno LS, Keene JD. RNA regulons in cancer and inflammation. Curr Opin Genet Dev. 2018 Feb;48:97-103. doi: 10.1016/j.gde.2017.11.004. Epub 2017 Nov 22. PMID: 29175729; PMCID: PMC6489128.
Borden KLB, Volpon L. The diversity, plasticity, and adaptability of cap-dependent translation initiation and the associated machinery. RNA Biol. 2020 Sep;17(9):1239-1251. doi: 10.1080/15476286.2020.1766179. Epub 2020 Jun 4. PMID: 32496897; PMCID: PMC7549709.
Bugaut A, Balasubramanian S. 5'-UTR RNA G-quadruplexes: translation regulation and targeting. Nucleic Acids Res. 2012 Jun;40(11):4727-41. doi: 10.1093/nar/gks068. Epub 2012 Feb 20. PMID: 22351747; PMCID: PMC3367173.
Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK, Chang HY. Structured elements drive extensive circular RNA translation. Mol Cell. 2021 Oct 21;81(20):4300-4318.e13. doi: 10.1016/j.molcel.2021.07.042. Epub 2021 Aug 25. PMID: 34437836; PMCID: PMC8567535.
Chen QM. The Odds of Protein Translation Control Under Stress. Antioxid Redox Signal. 2024 Jun;40(16-18):943-947. doi: 10.1089/ars.2023.0478. Epub 2024 Apr 24. PMID: 38573012; PMCID: PMC11538090.
Das S, Vera M, Gandin V, Singer RH, Tutucci E. Intracellular mRNA transport and localized translation. Nat Rev Mol Cell Biol. 2021 Jul;22(7):483-504. doi: 10.1038/s41580-021-00356-8. Epub 2021 Apr 9. Erratum in: Nat Rev Mol Cell Biol. 2021 Jul;22(7):505. doi: 10.1038/s41580-021-00374-6. PMID: 33837370; PMCID: PMC9346928.
Dassi E, Malossini A, Re A, et al. AURA: Atlas of UTR Regulatory Activity. Bioinformatics. 2012;28(1):142–143. Available from: http://aura.science.unitn.it
Dever TE, Ivanov IP, Hinnebusch AG. Translational regulation by uORFs and start codon selection stringency. Genes Dev. 2023 Jun 1;37(11-12):474-489. doi: 10.1101/gad.350752.123. Epub 2023 Jul 11. PMID: 37433636; PMCID: PMC10393191.
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, et. al. Landscape of transcription in human cells. Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233. PMID: 22955620; PMCID: PMC3684276.
Dolatshahi M, Salehipour A, Saghazadeh A, Sanjeari Moghaddam H, Aghamollaii V, Fotouhi A, Tafakhori A. Thyroid hormone levels in Alzheimer disease: a systematic review and meta-analysis. Endocrine. 2023 Feb;79(2):252-272. doi: 10.1007/s12020-022-03190-w. Epub 2022 Sep 27. PMID: 36166162.
Eleftheriou M, Russell J, Tzelepis K. Epitranscriptomic advances in normal and malignant hematopoiesis. Leukemia. 2025 Dec;39(12):2848-2857. doi: 10.1038/s41375-025-02765-6. Epub 2025 Sep 19. PMID: 40973767; PMCID: PMC12634440.
Enríquez JA, Fernández-Silva P, Garrido-Pérez N, López-Pérez MJ, Pérez-Martos A, Montoya J. Direct regulation of mitochondrial RNA synthesis by thyroid hormone. Mol Cell Biol. 1999 Jan;19(1):657-70. doi: 10.1128/MCB.19.1.657. PMID: 9858589; PMCID: PMC83923.
Fernandopulle MS, Lippincott-Schwartz J, Ward ME. RNA transport and local translation in neurodevelopmental and neurodegenerative disease. Nat Neurosci. 2021 May;24(5):622-632. doi: 10.1038/s41593-020-00785-2. Epub 2021 Jan 28. PMID: 33510479; PMCID: PMC8860725.
Gadekar VP, Munk AW, Miladi M, Junge A, Backofen R, Seemann SE, Gorodkin J. Clusters of mammalian conserved RNA structures in UTRs associate with RBP binding sites. NAR Genom Bioinform. 2024 Aug 9;6(3):lqae089. doi: 10.1093/nargab/lqae089. PMID: 39131818; PMCID: PMC11310781.
Gay DM, Lund AH, Jansson MD. Translational control through ribosome heterogeneity and functional specialization. Trends Biochem Sci. 2022 Jan;47(1):66-81. doi: 10.1016/j.tibs.2021.07.001. Epub 2021 Jul 23. PMID: 34312084.
Gebert LFR, MacRae IJ. Regulation of microRNA function in animals. Nat Rev Mol Cell Biol. 2019 Jan;20(1):21-37. doi: 10.1038/s41580-018-0045-7. PMID: 30108335; PMCID: PMC6546304.
Girón-Pïllado M, Cruz-Bautista I, Saavedra-González V, Atisha-Fregoso Y, Barraza G, Aguilar-Salinas CA, Hernández-Molina G. Autoimmune Thyroid Disease in Primary Sjögren's Syndrome: Real-life Screening Practice and Clinical Outcomes. Curr Rheumatol Rev. 2022;18(3):272-277. doi: 10.2174/1573397118666220127105546. PMID: 35086454.
Girón-Pïllado M, Cruz-Bautista I, Saavedra-González V, Atisha-Fregoso Y, Barraza G, Aguilar-Salinas CA, Hernández-Molina G. Autoimmune Thyroid Disease in Primary Sjögren's Syndrome: Real-life Screening Practice and Clinical Outcomes. Curr Rheumatol Rev. 2022;18(3):272-277. doi: 10.2174/1573397118666220127105546. PMID: 35086454.
Grillo G et al. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Research 38(Database issue):D75–D80 (2010).
Harvey RF, Smith TS, Mulroney T, Queiroz RML, Pizzinga M, Dezi V, Villenueva E, Ramakrishna M, Lilley KS, Willis AE. Trans-acting translational regulatory RNA binding proteins. Wiley Interdiscip Rev RNA. 2018 May;9(3):e1465. doi: 10.1002/wrna.1465. Epub 2018 Jan 17. PMID: 29341429; PMCID: PMC5947564.
Heneka MT, Gauthier S, Chandekar SA, Hviid Hahn-Pedersen J, Bentsen MA, Zetterberg H. Neuroinflammatory fluid biomarkers in patients with Alzheimer's disease: a systematic literature review. Mol Psychiatry. 2025 Jun;30(6):2783-2798. doi: 10.1038/s41380-025-02939-9. Epub 2025 Mar 6. PMID: 40050444; PMCID: PMC12092255.
Ho JJD, Man JHS, Schatz JH, Marsden PA. Translational remodeling by RNA-binding proteins and noncoding RNAs. Wiley Interdiscip Rev RNA. 2021 Sep;12(5):e1647. doi: 10.1002/wrna.1647. Epub 2021 Mar 10. PMID: 33694288.
Hu H, Song H, Han B, Zhao H, He J. Tumor-Educated Platelet RNA and Circulating Free RNA: Emerging Liquid Biopsy Markers for Different Tumor Types. Front Biosci (Landmark Ed). 2024 Feb 22;29(2):80. doi: 10.31083/j.fbl2902080. PMID: 38420812.
Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJ, Jackson SE, Wills MR, Weissman JS. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep. 2014 Sep 11;8(5):1365-79. doi: 10.1016/j.celrep.2014.07.045. Epub 2014 Aug 21. PMID: 25159147; PMCID: PMC4216110.
Iwata M, Kosai K, Ono Y, Oki S, Mimori K, Yamanishi Y. Regulome-based characterization of drug activity across the human diseasome. NPJ Syst Biol Appl. 2022 Nov 7;8(1):44. doi: 10.1038/s41540-022-00255-4. PMID: 36344521; PMCID: PMC9640590.
Jia X, He X, Huang C, Li J, Dong Z, Liu K. Protein translation: biological processes and therapeutic strategies for human diseases. Signal Transduct Target Ther. 2024 Feb 23;9(1):44. doi: 10.1038/s41392-024-01749-9. PMID: 38388452; PMCID: PMC10884018.
Jiang X, Liu B, Nie Z, Duan L, Xiong Q, Jin Z, Yang C, Chen Y. The role of m6A modification in the biological functions and diseases. Signal Transduct Target Ther. 2021 Feb 21;6(1):74. doi: 10.1038/s41392-020-00450-x. PMID: 33611339; PMCID: PMC7897327.
Karsh J, Pavlidis N, Weintraub BD, Moutsopoulos HM. Thyroid disease in Sjögren's syndrome. Arthritis Rheum. 1980 Nov;23(11):1326-9. doi: 10.1002/art.1780231118. PMID: 7447970.
Karsh J, Pavlidis N, Weintraub BD, Moutsopoulos HM. Thyroid disease in Sjögren's syndrome. Arthritis Rheum. 1980 Nov;23(11):1326-9. doi: 10.1002/art.1780231118. PMID: 7447970.
Keene JD. RNA regulons: coordination of post-transcriptional events. Nat Rev Genet. 2007 Jul;8(7):533-43. doi: 10.1038/nrg2111. PMID: 17572691
Kenessey A, Ojamaa K. Thyroid hormone stimulates protein synthesis in the cardiomyocyte by activating the Akt-mTOR and p70S6K pathways. J Biol Chem. 2006 Jul 28;281(30):20666-20672. doi: 10.1074/jbc.M512671200. Epub 2006 May 22. PMID: 16717100.
Khan MA, Mohammad T, Alalami ZS, Hassan MI. Iron activates Alzheimer's amyloid precursor protein synthesis through an iron responsive element (IRE) mRNA binding to translation initiation factor. Int J Biol Macromol. 2025 Sep;321(Pt 3):146231. doi: 10.1016/j.ijbiomac.2025.146231. Epub 2025 Jul 22. PMID: 40706937.
Kwantwi LB. Exosome-mediated crosstalk between tumor cells and innate immune cells: implications for cancer progression and therapeutic strategies. J Cancer Res Clin Oncol. 2023 Sep;149(11):9487-9503. doi: 10.1007/s00432-023-04833-9. Epub 2023 May 8. PMID: 37154928; PMCID: PMC11796874.
Lamping JP, Krebber H. The hidden power of antisense long non-coding RNAs: a dive into a novel regulatory layer mediated by double-stranded RNA formation. RNA Biol. 2025 Dec;22(1):1-16. doi: 10.1080/15476286.2025.2530797. Epub 2025 Jul 9. PMID: 40629869; PMCID: PMC12247107.
Leppek K, Das R, Barna M. Functional 5' UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat Rev Mol Cell Biol. 2018 Mar;19(3):158-174. doi: 10.1038/nrm.2017.103. Epub 2017 Nov 22. Erratum in: Nat Rev Mol Cell Biol. 2018 Oct;19(10):673. doi: 10.1038/s41580-018-0055-5. PMID: 29165424; PMCID: PMC5820134.
Li C, Chen K, Li X, Xiong X. Epitranscriptome-epigenome interactions in development and disease mechanisms. Trends Genet. 2025 Aug;41(8):691-705. doi: 10.1016/j.tig.2025.04.009. Epub 2025 May 15. PMID: 40374434.
Li J, Singh U, Arendsee Z, Wurtele ES. Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data. Front Genet. 2021 Aug 16;12:722981. doi: 10.3389/fgene.2021.722981. PMID: 34484307; PMCID: PMC8415361.
Li W, Deng X, Chen J. RNA-binding proteins in regulating mRNA stability and translation: roles and mechanisms in cancer. Semin Cancer Biol. 2022 Nov;86(Pt 2):664-677. doi: 10.1016/j.semcancer.2022.03.025. Epub 2022 Apr 2. PMID: 35381329; PMCID: PMC9526761.
Li X, Gui Z, Han Y, Yang X, Wang Z, Zheng L, Zhang L, Wang D, Fan X, Su L. Comprehensive analysis of dysregulated exosomal long non-coding RNA networks associated with arteriovenous malformations. Gene. 2020 May 15;738:144482. doi: 10.1016/j.gene.2020.144482. Epub 2020 Feb 19. PMID: 32087271.
Li Y, Dou X, Liu J, Xiao Y, Zhang Z, Hayes L, Wu R, Fu X, Ye Y, Yang B, Ostrow LW, He C, Sun S. Globally reduced N6-methyladenosine (m6A) in C9ORF72-ALS/FTD dysregulates RNA metabolism and contributes to neurodegeneration. Nat Neurosci. 2023 Aug;26(8):1328-1338. doi: 10.1038/s41593-023-01374-9. Epub 2023 Jun 26. PMID: 37365312; PMCID: PMC11361766.
Lin J, Chen Y, Zhang Y, Lin H, Ouyang Z. Deciphering the role of RNA structure in translation efficiency. BMC Bioinformatics. 2022 Dec 23;23(Suppl 3):559. doi: 10.1186/s12859-022-05037-7. PMID: 36564729; PMCID: PMC9783404
Liu S, Zhao M, Yang X, Liu Y, Xu H, Yan H, Xu Y. Exosomal microRNA biomarkers in Alzheimer's disease: Systematic review and meta-analysis. Clin Chim Acta. 2026 Jan 1;578:120542. doi: 10.1016/j.cca.2025.120542. Epub 2025 Aug 7. PMID: 40783152.
Marro S, Chiabrando D, Messana E, Stolte J, Turco E, Tolosano E, Muckenthaler MU. Heme controls ferroportin1 (FPN1) transcription involving Bach1, Nrf2 and a MARE/ARE sequence motif at position -7007 of the FPN1 promoter. Haematologica. 2010 Aug;95(8):1261-8. doi: 10.3324/haematol.2009.020123. Epub 2010 Feb 23. PMID: 20179090; PMCID: PMC2913073.
Martinez De La Cruz B, Markus R, Malla S, Haig MI, Gell C, Sang F, Bellows E, Sherif MA, McLean D, Lourdusamy A, Self T, Bodi Z, Smith S, Fay M, Macdonald IA, Fray R, Knight HM. Modifying the m6A brain methylome by ALKBH5-mediated demethylation: a new contender for synaptic tagging. Mol Psychiatry. 2021 Dec;26(12):7141-7153. doi: 10.1038/s41380-021-01282-z. Epub 2021 Oct 19. PMID: 34663904; PMCID: PMC8872986.
Master A, Huang L, Tsirukis VE, Loiacono A, Khawja A, Takmil C, Tsioulias A, Honkanen R, Rigas B . Transcriptomic landscape of the Dorsal Root Ganglia (DRG) and the Sciatic Nerve (SN) in a mouse model of Paclitaxel-Induced Peripheral Neuropathy (PIPN). PLoS One in preparation (2026). Transcriptome datasets published on Dec 08 2023, NCBI GEO acc. no.: GSE249643
Master A, Huang L, Tsirukis VE, Loiacono A, Khawja A, Takmil C, Tsioulias A, Honkanen R, Rigas B . Transcriptomic landscape of the Dorsal Root Ganglia (DRG) and the Sciatic Nerve (SN) in a mouse model of Paclitaxel-Induced Peripheral Neuropathy (PIPN). PLoS One in preparation. Abstract published on Dec 08 2023, NCBI GEO acc. no.: GSE249643
Master A, Huang W, Huang L, Honkanen R, Rigas B. An Improved Ocular Impression Cytology Method: Quantitative Cell Transfer to Microscope Slides Using a Novel Polymer. Curr Eye Res. 2022 Jan;47(1):41-50. doi: 10.1080/02713683.2021.1951300. Epub 2021 Nov 27. PMID: 34841993; PMCID: PMC8792174.
Master A, Huang W, Huang L, Honkanen R, Rigas B. An Improved Ocular Impression Cytology Method: Quantitative Cell Transfer to Microscope Slides Using a Novel Polymer. Curr Eye Res. 2022 Jan;47(1):41-50. doi: 10.1080/02713683.2021.1951300. Epub 2021 Nov 27. PMID: 34841993; PMCID: PMC8792174.
Master A, Huang W, Huang L, Li W, Saglam S, Honkanen R, Rigas B. Simplified ex-vivo drug evaluation in ocular surface cells: Culture on cellulose filters of cells obtained by impression cytology. Exp Eye Res. 2021 Dec;213:108827. doi: 10.1016/j.exer.2021.108827. Epub 2021 Nov 3. PMID: 34742691.
Master A, Huang W, Huang L, Li W, Saglam S, Honkanen R, Rigas B. Simplified ex-vivo drug evaluation in ocular surface cells: Culture on cellulose filters of cells obtained by impression cytology. Exp Eye Res. 2021 Dec;213:108827. doi: 10.1016/j.exer.2021.108827. Epub 2021 Nov 3. PMID: 34742691.
Master A, Kontzias A, Huang L, Huang W, Tsioulias A, Zarabi S, Wolek M, Wollocko BM, Honkanen R, Rigas B. The transcriptome of rabbit conjunctiva in dry eye disease: Large-scale changes and similarity to the human dry eye. PLoS One. 2021 Jul 29;16(7):e0254036. doi: 10.1371/journal.pone.0254036. PMID: 34324523; PMCID: PMC8321226.
Master A, Kontzias A, Huang L, Huang W, Tsioulias A, Zarabi S, Wolek M, Wollocko BM, Honkanen R, Rigas B. The transcriptome of rabbit conjunctiva in dry eye disease: Large-scale changes and similarity to the human dry eye. PLoS One. 2021 Jul 29;16(7):e0254036. doi: 10.1371/journal.pone.0254036. PMID: 34324523; PMCID: PMC8321226.
Master A, Nauman A. Gene expression regulation by long naturally occurring antisense transcripts [Regulacja ekspresji genów przez długie naturalnie występujące antysensowne transkrypty]. Post. Biol. Kom. (PBK) 2014;41(1):3-28. Review.
Master A, Nauman A. Genomic context and expression regulation of nuclear thyroid hormone receptors by long naturally occurring antisense transcripts [Genomowy kontekst i regulacja ekspresji receptorów hormonu tarczycy przez długie naturalnie występujące antysensowne transkrypty]. Post. Biol. Kom. (PBK) 2014; 41(1):29-58. Review.
Master A, Nauman A. Molecular mechanisms of protein biosynthesis initiation - biochemical and biomedical implications of a new model of translation enhanced by the RNA hypoxia response element (rHRE) [Molekularne mechanizmy inicjacji biosyntezy białek - biochemiczne i biomedyczne implikacje nowego modelu translacji wzmacnianej przez element RNA odpowiedzi na hipoksję (rHRE)]. Postepy Biochem. 2014;60(1):39-54. Review. The Polish Biochemical Society has granted this work with Boleslaw Skarzynski Award for the best article published in a quarterly journal “Postepy Biochemii” published in year 2014
Master A, Nauman A. THRB (Thyroid Hormone Receptor, Beta). Atlas Genet Cytogenet Oncol Haematol (AGCOH). 2014; 18(6). https://atlasgeneticsoncology.org/gene/42554/thrb-(thyroid-hormone-receptor-beta)
Master A, Wójcicka A, Giżewska K, Popławski P, Williams GR, Nauman A. A Novel Method for Gene-Specific Enhancement of Protein Translation by Targeting 5’UTRs of Selected Tumor Suppressors. PLoS ONE. 2016 May 12; 11(5): e0155359.
Master A. Nucleic acid molecule designed for selective enhancement of protein synthesis. Polish patent PL237080B1 (P.393170). Filed 12 Apr 2010; published 21 Oct 2020. Developed within Adam Master’s grant project Dz.3.4/ML/2/05 (ZPORR). Patent Office of the Republic of Poland.
Master A. Opinion on novelty of concept of invention PL237080B1: document submitted to Polish Patent Office (available as internal file and referenced by patent attorney). (Patent Office of the Republic of Poland, Opinion on novelty of concept of invention PL237080B1. 2024). (Direct link not indexed in PubMed / DOI — use as grey literature citation).
Mateusz Garbulowski, Riccardo Mosca, Carlos J. Gallardo-Dodd, Claudia Kutter, Erik L. L. Sonnhammer. Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer. bioRxiv 2024.09.04.611258 doi: https://doi.org/10.1101/2024.09.04.611258
Meyer KD, Patil DP, Zhou J, Zinoviev A, Skabkin MA, Elemento O, Pestova TV, Qian SB, Jaffrey SR. 5' UTR m(6)A Promotes Cap-Independent Translation. Cell. 2015 Nov 5;163(4):999-1010. doi: 10.1016/j.cell.2015.10.012. Epub 2015 Oct 22. PMID: 26593424; PMCID: PMC4695625.
Mikesell AR, Meyer AR, García G, Frietze LR, Stucky CL, Pan T, Campbell ZT. GCN2 regulates paclitaxel-induced neuropathic pain. Br J Pharmacol. 2025 Dec;182(23):5913-5930. doi: 10.1111/bph.70154. Epub 2025 Aug 13. PMID: 40803344.
Milenkovic I, Cruciani S, Llovera L, Lucas MC, Medina R, Pauli C, Heid D, Muley T, Schneider MA, Klotz LV, Allgäuer M, Lattuca R, Lafontaine DLJ, Müller-Tidow C, Novoa EM. Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures. Mol Cell. 2025 Jan 2;85(1):177-190.e7. doi: 10.1016/j.molcel.2024.11.014. Epub 2024 Dec 10. PMID: 39662470.
Milenkovic I, Novoa EM. Dynamic rRNA modifications as a source of ribosome heterogeneity. Trends Cell Biol. 2025 Jul;35(7):604-614. doi: 10.1016/j.tcb.2024.10.001. Epub 2024 Nov 4. PMID: 39500673.
Mir DA, Ma Z, Horrocks J, Rogers A. Stress-Induced Eukaryotic Translational Regulatory Mechanisms. J Clin Med Sci. 2024;8(2):1000277. Epub 2024 Jun 24. PMID: 39364184; PMCID: PMC11448810.
Nagaraj S, Zoltowska KM, Laskowska-Kaszub K, Wojda U. microRNA diagnostic panel for Alzheimer's disease and epigenetic trade-off between neurodegeneration and cancer. Ageing Res Rev. 2019 Jan;49:125-143. doi: 10.1016/j.arr.2018.10.008. Epub 2018 Nov 2. PMID: 30391753.
Nappi A, Moriello C, Morgante M, Fusco F, Crocetto F, Miro C. Effects of thyroid hormones in skeletal muscle protein turnover. J Basic Clin Physiol Pharmacol. 2024 Sep 20;35(4-5):253-264. doi: 10.1515/jbcpp-2024-0139. PMID: 39297559.
Park SM, Kang TI, So JS. Roles of XBP1s in Transcriptional Regulation of Target Genes. Biomedicines. 2021 Jul 8;9(7):791. doi: 10.3390/biomedicines9070791. PMID: 34356855; PMCID: PMC8301375.
Patent: EP3313989B1 Modified CRISPR RNA and modified single CRISPR RNA and uses thereof. European patent EP3313989B1, publication 25 Dec 2024; priority and family data listed under EP3313989C0. Inventor and assignee: Ionis Pharmaceuticals, Inc.
Patent: WO2023111337A1 Antisense oligonucleotide. World Intellectual Property Organization (WIPO) patent application WO2023111337A1, filed 16 Dec 2022, published 22 Jun 2023. F. Hoffmann-La Roche AG, Hoffmann La Roche Inc.
Peer E, Moshitch-Moshkovitz S, Rechavi G, Dominissini D. The Epitranscriptome in Translation Regulation. Cold Spring Harb Perspect Biol. 2019 Aug 1;11(8):a032623. doi: 10.1101/cshperspect.a032623. PMID: 30037968; PMCID: PMC6671940.
Pino LK, Canzani D, Gutierrez A, Robbins J, McEllin B, Hubbard E, Broderick E, Prymolenna A, Tatka L, Paez JS, Mercenne G, Siebenthall K, Fondrie WE, Federation AJ. Native, Spatiotemporal Profiling of the Global Human Regulome. bioRxiv [Preprint]. 2025 Jun 25:2025.06.14.659727. doi: 10.1101/2025.06.14.659727. PMID: 40667134; PMCID: PMC12262435.
Pupak A, Rodríguez-Navarro I, Sathasivam K, Singh A, Essmann A, Del Toro D, Ginés S, Mouro Pinto R, Bates GP, Vang Ørom UA, Martí E, Brito V. m6A modification of mutant huntingtin RNA promotes the biogenesis of pathogenic huntingtin transcripts. EMBO Rep. 2024 Nov;25(11):5026-5052. doi: 10.1038/s44319-024-00283-7. Epub 2024 Oct 11. PMID: 39394467; PMCID: PMC11549361.
Razumova E, Makariuk A, Dontsova O, Shepelev N, Rubtsova M. Structural Features of 5' Untranslated Region in Translational Control of Eukaryotes. Int J Mol Sci. 2025 Feb 25;26(5):1979. doi: 10.3390/ijms26051979. PMID: 40076602; PMCID: PMC11900008.
Roy B. Effects of mRNA Modifications on Translation: An Overview. Methods Mol Biol. 2021;2298:327-356. doi: 10.1007/978-1-0716-1374-0_20. PMID: 34085254.
Ruden DM. Uncovering the Epitranscriptome: A Review on mRNA Modifications and Emerging Frontiers. Genes (Basel). 2025 Aug 12;16(8):951. doi: 10.3390/genes16080951. PMID: 40870000; PMCID: PMC12385769.
Shi Z, Fujii K, Kovary KM, Genuth NR, Röst HL, Teruel MN, Barna M. Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide. Mol Cell. 2017 Jul 6;67(1):71-83.e7. doi: 10.1016/j.molcel.2017.05.021. Epub 2017 Jun 15. PMID: 28625553; PMCID: PMC5548184.
Sloan KE, Warda AS, Sharma S, Entian KD, Lafontaine DLJ, Bohnsack MT. Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function. RNA Biol. 2017 Sep 2;14(9):1138-1152. doi: 10.1080/15476286.2016.1259781. Epub 2016 Dec 2. PMID: 27911188; PMCID: PMC5699541.
Sokoloff L, Roberts PA, Januska MM, Kline JE. Mechanisms of stimulation of protein synthesis by thyroid hormones in vivo. Proc Natl Acad Sci U S A. 1968 Jun;60(2):652-9. doi: 10.1073/pnas.60.2.652. PMID: 5248822; PMCID: PMC225096.
Sol N, Wurdinger T. Platelet RNA signatures for the detection of cancer. Cancer Metastasis Rev. 2017 Jun;36(2):263-272. doi: 10.1007/s10555-017-9674-0. PMID: 28681241; PMCID: PMC5557864.
Tata JR, Widnell CC. Ribonucleic acid synthesis during the early action of thyroid hormones. Biochem J. 1966 Feb;98(2):604-20. doi: 10.1042/bj0980604. PMID: 5941352; PMCID: PMC1264884.
Thomas-Jardin S, Suresh S, Arce A, Novaresi N, Deng Q, Stein E, Thomas L, Lewis C, Ahn C, Evers BM, Akbay EA, Salvatierra ME, Lu W, Khan K, Solis Soto LM, Wistuba II, Minna JD, O'Donnell KA. The Integrated Stress Response Pathway Coordinates Translational Control of Multiple Immune Checkpoints in Lung Cancer. Cancer Res. 2025 Jul 15;85(14):2574-2590. doi: 10.1158/0008-5472.CAN-24-3844. PMID: 40327600; PMCID: PMC12260515.
Tidu A, Martin F. The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes. Biochimie. 2024 Feb;217:20-30. doi: 10.1016/j.biochi.2023.09.017. Epub 2023 Sep 21. PMID: 37741547.
Tidu A, Martin F. The interplay between cis- and trans-acting factors drives selective mRNA translation initiation in eukaryotes. Biochimie. 2024 Feb;217:20-30. doi: 10.1016/j.biochi.2023.09.017. Epub 2023 Sep 21. PMID: 37741547.
Wang J, Wang W, Ma F, Qian H. A hidden translatome in tumors-the coding lncRNAs. Sci China Life Sci. 2023 Dec;66(12):2755-2772. doi: 10.1007/s11427-022-2289-6. Epub 2023 May 5. PMID: 37154857.
Wang S, Sun S. Translation dysregulation in neurodegenerative diseases: a focus on ALS. Mol Neurodegener. 2023 Aug 25;18(1):58. doi: 10.1186/s13024-023-00642-3. PMID: 37626421; PMCID: PMC10464328.
Wang SF, Chen MS, Chou YC, Ueng YF, Yin PH, Yeh TS, Lee HC. Mitochondrial dysfunction enhances cisplatin resistance in human gastric cancer cells via the ROS-activated GCN2-eIF2α-ATF4-xCT pathway. Oncotarget. 2016 Nov 8;7(45):74132-74151. doi: 10.18632/oncotarget.12356. PMID: 27708226; PMCID: PMC5342041.
Wang X, Zhao BS, Roundtree IA, Lu Z, Han D, Ma H, Weng X, Chen K, Shi H, He C. N(6)-methyladenosine Modulates Messenger RNA Translation Efficiency. Cell. 2015 Jun 4;161(6):1388-99. doi: 10.1016/j.cell.2015.05.014. PMID: 26046440; PMCID: PMC4825696.
Wang YH, Chen X, Bai YZ, Gao P, Yang Z, Guo Q, Lu YY, Zheng J, Liu D, Yang J, Tu PF, Zeng KW. Palmitoylation of PKCδ by ZDHHC5 in hypothalamic microglia presents as a therapeutic target for fatty liver disease. Theranostics. 2024 Jan 1;14(3):988-1009. doi: 10.7150/thno.89602. PMID: 38250049; PMCID: PMC10797291.
Wojda U. Alzheimer's disease lymphocytes: potential for biomarkers? Biomark Med. 2016;10(1):1-4. doi: 10.2217/bmm.15.79. Epub 2015 Dec 7. PMID: 26640978.
Wojsiat J, Laskowska-Kaszub K, Mietelska-Porowska A, Wojda U. Search for Alzheimer's disease biomarkers in blood cells: hypotheses-driven approach. Biomark Med. 2017 Oct;11(10):917-931. doi: 10.2217/bmm-2017-0041. Epub 2017 Oct 4. PMID: 28976776.
Wojsiat J, Zoltowska KM, Laskowska-Kaszub K, Wojda U. Oxidant/Antioxidant Imbalance in Alzheimer's Disease: Therapeutic and Diagnostic Prospects. Oxid Med Cell Longev. 2018 Jan 31;2018:6435861. doi: 10.1155/2018/6435861. PMID: 29636850; PMCID: PMC5831771.
Wolozin B, Ivanov P. Stress granules and neurodegeneration. Nat Rev Neurosci. 2019 Nov;20(11):649-666. doi: 10.1038/s41583-019-0222-5. Epub 2019 Oct 3. PMID: 31582840; PMCID: PMC6986315.
Wu CH, Yeh CT, Lin KH. Thyroid hormones suppress FOXM1 expression to reduce liver cancer progression. Oncol Rep. 2020 Oct;44(4):1686-1698. doi: 10.3892/or.2020.7716. Epub 2020 Aug 5. PMID: 32945493.
Xia X, Lei L, Qin W, Wang L, Zhang G, Hu J. GCN2 controls the cellular checkpoint: potential target for regulating inflammation. Cell Death Discov. 2018 Feb 14;4:20. doi: 10.1038/s41420-017-0022-5. PMID: 29531817; PMCID: PMC5841328.
Xuan JJ, et al. RMBase v3.0: Decode the landscape, mechanisms and functions of RNA modifications. Nucleic Acids Research. 2023 Nov 13. Available at http://bioinformaticsscience.cn/rmbase/
Xue S, Tian S, Fujii K, Kladwang W, Das R, Barna M. RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation. Nature. 2015 Jan 1;517(7532):33-8. doi: 10.1038/nature14010. Epub 2014 Nov 19. PMID: 25409156; PMCID: PMC4353651.
Yang J, Kim KS, Iyirhiaro GO, Marcogliese PC, Callaghan SM, Qu D, Kim WJ, Slack RS, Park DS. DJ-1 modulates the unfolded protein response and cell death via upregulation of ATF4 following ER stress. Cell Death Dis. 2019 Feb 12;10(2):135. doi: 10.1038/s41419-019-1354-2. PMID: 30755590; PMCID: PMC6372623.
Yang Y, Wang Q. Three genes expressed in relation to lipid metabolism considered as potential biomarkers for the diagnosis and treatment of diabetic peripheral neuropathy. Sci Rep. 2023 May 29;13(1):8679. doi: 10.1038/s41598-023-35908-9. PMID: 37248406; PMCID: PMC10227002.
Ye C, Yu X, Yan J, Ye G, Shao Y. Biological roles and potential clinical values of snoRNAs in Cancer. Int J Biol Macromol. 2025 Sep 12;328(Pt 2):147654. doi: 10.1016/j.ijbiomac.2025.147654. Epub ahead of print. PMID: 40946988.
Yu D, Dai N, Wolf EJ, Corrêa IR Jr, Zhou J, Wu T, Blumenthal RM, Zhang X, Cheng X. Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs. J Biol Chem. 2022 Apr;298(4):101751. doi: 10.1016/j.jbc.2022.101751. Epub 2022 Feb 19. PMID: 35189146; PMCID: PMC8931429.
Yuan S, Zhou G, Xu G. Translation machinery: the basis of translational control. J Genet Genomics. 2024 Apr;51(4):367-378. doi: 10.1016/j.jgg.2023.07.009. Epub 2023 Aug 1. PMID: 37536497.
Zambrano A, García-Carpizo V, Villamuera R, Aranda A. Thyroid hormone increases bulk histones expression by enhancing translational efficiency. Mol Endocrinol. 2015 Jan;29(1):68-75. doi: 10.1210/me.2014-1235. PMID: 25422881; PMCID: PMC5414774.
Zhou ZD, Tan EK. Iron regulatory protein (IRP)-iron responsive element (IRE) signaling pathway in human neurodegenerative diseases. Mol Neurodegener. 2017 Oct 23;12(1):75. doi: 10.1186/s13024-017-0218-4. PMID: 29061112; PMCID: PMC5654065.
29 refereed publications, 30 > abstracts, 4 patents
H-Index range: 11–16 (11/22/2024), depending on bibliographic databases, as some papers or journals may not be indexed. Citation counts can vary across different databases due to their unique indexing criteria. See Bibliographic Databases
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