Embedded Files
Multiomics dissection
of hierarchical translatome reprogramming
via regulome- and epitranscriptome-mediated
translational control
Mechanistic axis: genome → transcriptome → epitranscriptome + regulome → translatome → phenome
Interconnected metabolic–regulatory axis: Metabolome ↔ epigenome / epitranscriptome → methylome
Mechanistic axis: genome → transcriptome → epitranscriptome + regulome → translatome → phenome
Interconnected metabolic–regulatory axis: Metabolome ↔ epigenome / epitranscriptome → methylome
GRAPHICAL ABSTRACT
GRAPHICAL ABSTRACT
illustrating the state of the art in translational control, a three -level hierarchical regulatory system governing protein synthesis through two interdependent frameworks: I) regulome -mediated translational control (RMTC), in which the translational regulome is defined as the system of shared cis-acting RNA structures that enable coordinated translation of mRNA cohorts (regulons), and II) epitranscriptome -mediated translational control (EMTRAC), where the epitranscriptome comprises chemical RNA modifications that program translational competence across mRNA, rRNA, tRNA, and regulatory non-coding RNAs. Both frameworks operate via 1) structural (cis-acting) and 2) functional (trans-acting) subsystems organized across a) global, b) intermediate, and c) local levels.
At the global RMTC level, translation is gated by ternary complex availability, with overlapping uORF architectures enabling selective translation of low–TC-activated mRNAs such as ATF4 and DDIT3, while global EMTRAC establishes translational competence through m⁷G-cap–dependent initiation, modulated by mTOR–4E-BP–eIF4E signaling.
At the intermediate level, RMTC defines translational regulons via shared 5′UTR cis-elements, including secondary structures, IRESs, TOP/TISU motifs, RNA G-quadruplexes, and m⁶A sites, decoded by specialized ribosomes and trans-acting factors, whereas EMTRAC programs ribosome function through snoRNA-guided rRNA and tRNA 2′-O-methylation, enabling preferential translation of structurally complex regulon transcripts such as MYC, VEGFA, TP53, TGFB1, CCND1.
At the local level, transcript-specific RMTC integrates with sequence- and context-dependent EMTRAC modifications (m⁶A, m¹A, m⁶Am, m⁵C) to fine-tune translation efficiency and isoform-specific protein output, exemplified by DNMT3. Other RNA modifications—including pseudouridylation (Ψ), acetylation (ac⁴C), and RNA editing (A-to-I, C-to-U)—operate within this framework in a structure- and sequence-dependent manner.
SELECTED GENES BY HIERARCHICAL LEVEL: GLOBAL – ATF4, ATF3, DDIT3, GADD34, GCN4, GLOBAL EMTRAC, INTERMEDIATE TRANSLATIONAL REGULONS – MYC, MDM2, VEGFA, FGF2, EGFR, HIF1A, JUN, SOX2, TP53, RB1, NF1, STK11, BRCA1, CHEK1, CHEK2, APC, CCND1, CCNB1, CDK1, CDK4, CDK6, E2F1, BCL2, MCL1, BIRC5, TGFB1, PDGFA, RPS6, EIF3B, EEF2, LOCAL: DNMT3, DNMT3, TET3, SLC2A1, PDP1, ADAR1, METTL3, YTHDF2, NF1, RB1, APC.
Together, these layered regulatory mechanisms enable translational reprogramming and the translatomic paradox, whereby selective protein synthesis is maintained or enhanced despite global translational repression in stress, differentiation, mitosis, or cancer. Although this project focuses on EMTRAC, the presented hierarchical structural–functional stratification enables rational experimental design to dissect causal mechanisms of civilization-related disease–associated translatome reprogramming through a multiomics dissection of hierarchical translational control in epitranscriptome-mediated translatome reprogramming, while supporting RMTC- and EMTRAC-wide association studies and atlas generation, thereby facilitating the discovery of clinically relevant biomarkers and therapeutic targets.
Hypothesis: TC is executed via RMTC and EMTRAC interaction, wherein RNA modifications modulate RNA secondary structure formation and thereby influence protein translation. In this framework, RNA modifications can be viewed as covalently attached and dynamically reversible regulatory marks that behave analogously to trans-acting factors in regulating RNA structural states, thereby modulating the functional output of RNA cis-acting elements in controlling translation efficacy.
ABBREVIATIONS: TCtrl – Translational Control, PS – Protein Synthesis, RMTC – Regulome Mediated Translational Control, EMTRAC – Epitranscriptome Mediated Translational Control, TR – Translational Regulon, TC – Ternary Complex eIF2 GTP Met tRNAi, CAE – Cis Acting Element - a functional structure within RNA 5'UTR, CDS or 3'UTR that can interact with TAFs, TAF - Trans acting factor - a molecule that can interact with CAE (usually nucleic acids, proteins), pTAF – Protein based Trans Acting Factor, naTAF – Nucleic Acid based Trans Acting Factor, RBP – RNA Binding Protein, RMP – RNA-modifying proteins, ncRNA – Non coding RNA, lncRNA – Long Non coding RNA, sncRNA – Small Non coding RNA, snoRNA – Small Nucleolar RNA, miRNA – microRNA, 5UTR – 5 prime Untranslated Region, uORF – Upstream Open Reading Frame, uAUG – Upstream AUG codon, IRES – Internal Ribosome Entry Site, TOP – Terminal Oligopyrimidine motif, TISU – Translation Initiator of Short 5UTR, rG4 – RNA G quadruplex, Kozak – Translation initiation consensus sequence, m7G – N7 methylguanosine cap, m⁶A – N6 methyladenosine, m¹A – N1 methyladenosine, m⁶Am – N6 2 prime O dimethyladenosine, m⁵C – 5 methylcytidine, Ψ – Pseudouridine, ac⁴C – N4 acetylcytidine, A/I – Adenosine to Inosine RNA editing, C/U – Cytidine to Uridine RNA editing, 2'-O-Me – 2 prime O methylation, eIF – Eukaryotic Initiation Factor, eIF2α – Alpha subunit of eIF2, eIF4E – Cap binding initiation factor, 4E-BP – eIF4E Binding Protein, mTOR – Mechanistic Target of Rapamycin, S6K – Ribosomal Protein S6 Kinase, RPS6 – Ribosomal Protein S6, EEF2 – Eukaryotic Elongation Factor 2, EEF2K – EEF2 kinase.
PROJECT OVERVIEW
PROJECT OVERVIEW
Project in brief: TRANSREP dissects EMTRAC–RMTC control of the translatome for biomedical applications.
Models: Cancer and other non-communicable diseases.
Pathways: ISR, EMT, cellular plasticity, metabolism, tumor-educated cells, exosome signaling.
Technologies: Ribo-seq, RNA-seq, single-cell multiomics, RNA modification profiling, proteomics, dGoligo/eRNA.
BASIC INFORMATION:
TRANSREP is a basic research project aimed at advancing fundamental mechanistic understanding of the interplay between reactome-mediated translational control (RMTC) and epitranscriptome-mediated translational control (EMTRAC) in driving translatome reprogramming, with direct relevance to biomedical innovation.
KEYWORDS: Transcriptome, epitranscriptome, epitranscriptomics, RNA methylation, regulome, translational control, translatome, translatome reprogramming, translatomic paradox, proteome, metabolome, cancer translatome, cis-acting elements, trans-acting factors, cap-dependent, cap-independent translation, 5’UTR, integrated stress response (ISR), 2′-O-methylation, m6A, m6Am, m1A, m5C, m7G, snoRNA, ribosome profiling, single-cell multi-omics, tumor microenvironment, metabolic reprogramming, EMT, tumor-educated cells, TEPs, biomarkers, molecular targets, systems biology, precision medicine, molecular diagnostics, pharmacogenomics, gene therapy, medical biotechnology, FBL, METTL3, FTO, THRB, SAM/SAH.
Disease models: cancer and other non-communicable diseases within the human diseasome.
Key Biological Pathways: and programs critically dependent on translational control include: integrated stress response (ISR)–driven epithelial–mesenchymal transition (EMT) programs, cellular plasticity and stemness programs, vascular remodeling, thyroid hormone–mediated metabolic differentiation, Warburg-like metabolic reprogramming, translation-dependent tumor-educated cells (TECs), including tumor-educated platelets (TEPs), as well as exosome-mediated intercellular communication.
Selected technologies: Illumina miCLIP-m6A, Merk Magna MeRIP m6A kit, EpiNext CUT&RUN RNA m6A-Seq Kit, The EpiPlex assay from AlidaBio, GLORI, CHEUI (CH3 (methylation) Estimation Using Ionic current), as well as Ribosome profiling (Ribo-seq), RNA-seq, single-cell multiomics, quantitative proteomics, RNA modification profiling (m⁶A-seq / MeRIP-seq or direct RNA sequencing), polysome profiling / TRAP-seq, site-directed mutagenesis (SDM) and proprietary author-developed technology dGoligo/eRNA for regulome-level interrogation of translational control.
EXTENDED ABSTRACT
I. BACKROUND
In brief:
1. Translational control (TC) enables rapid, selective protein synthesis and is linked to major diseases.
2. TC operates hierarchically via EMTRAC (RNA methylation) and RMTC (cis-regulatory logic) across global, intermediate, and local layers.
Translational control (TC) is a post-transcriptional regulatory mechanism of gene expression that enables the fastest cellular and subcellular responses to environmental cues. Its dysregulation is linked to major civilization diseases, including cancer, neurodegenerative and cardiovascular diseases, as well as aging. Accumulating evidence demonstrates that transcriptomic changes alone fail to explain disease-associated proteomic states, particularly in stress-adapted cells, thereby identifying translation as a critical yet underexplored regulatory layer. Acting downstream of transcription, TC directly shapes the set of actively translated proteins (the translatome), enabling rapid and selective protein synthesis independently of mRNA abundance. This gives rise to a translatomic paradox, whereby global protein synthesis can be suppressed while selected transcripts or transcript cohorts remain efficiently translated, leading to profound changes in cellular proteome composition. Carcinogenesis represents a paradigmatic pathological process characterized by extensive translatome reprogramming that favors oncogenic drivers over tumour suppressors.
TC is executed through multiple mechanistically distinct but interacting layers, including RNA methylation–dependent mechanisms that define Epitranscriptome-Mediated Translational Control (EMTRAC), as well as cis-regulatory logic decoded by dedicated trans-acting machineries, collectively referred to here as Regulome-Mediated Translational Control (RMTC). Increasing evidence indicates that translational control is hierarchically organized across three interconnected levels—global, intermediate, and local—at which EMTRAC and RMTC operate in complementary but non-redundant roles.
Three interacting levels of CT across the EMTRAC and RMTC layers
In Brief:
1. Global level: EMTRAC sets overall translation initiation logic (m⁷G-cap–dependent and cap-independent), while RMTC imposes kinetic constraints via eIF2α phospho-rylation, selectively allowing stress-responsive transcripts.
2. Intermediate level: EMTRAC programs ribosomes via rRNA modifications to favor transcripts with defined 5′UTR features; RMTC groups mRNAs into translational regulons to coordinate pathway-level protein output.
3. Local level: EMTRAC RNA modifications (m⁶A, m⁶Am, m¹A, m⁵C) fine-tune translation of individual transcripts, while RMTC decodes cis-elements via RNA-binding proteins, microRNAs, and lncRNAs for precise, context-dependent protein control.
1. At the global level, EMTRAC defines the dominant mode of translation initiation across the translatome through m⁷G-cap–dependent and cap-independent mechanisms, thereby setting overall initiation logic and translational permissiveness. This layer is regulated by trans-acting signaling pathways, including the mTORC1–4E-BP–eIF4E axis, and does not confer sequence-based selectivity. Superimposed on this regime, RMTC introduces a global kinetic constraint through regulation of ternary complex availability via stress-induced phosphorylation of eIF2α, selectively permitting translation of transcripts encoding intrinsic uORF-based initiation sensors without invoking regulon logic.
2. At the intermediate level, EMTRAC operates through ribosome programming driven by small nucleolar RNA (snoRNA)–guided ribosomal RNA (rRNA) modifications, including 2′-O-methylation (2′-O-Me) and pseudouridylation (Ψ), which generate functionally specialized ribosomes. These programmed ribosomes do not alter global protein synthesis rates but bias translational competence toward transcripts with defined architectural features, such as long, highly structured 5′ untranslated regions (5′UTRs). At the same depth, RMTC organizes translation into translational regulons (TRs)—cohorts of mRNAs sharing common cis-acting elements that are coordinately decoded by compatible ribosomes and shared protein trans-acting factors. Together, EMTRAC-driven ribosome specialization and RMTC-defined regulons reshape pathway-level protein output independently of transcript abundance.
3. At the local level, translational regulation becomes transcript-specific and sequence-encoded. Local EMTRAC is mediated by position- and context-dependent RNA modifications, including N6-methyladenosine (m⁶A), N6,2′-O-dimethyladenosine (m⁶Am), N1-methyladenosine (m¹A), and 5-methylcytosine (m⁵C), which fine-tune translation efficiency, elongation dynamics, and isoform-specific protein output. In parallel, local RMTC decodes cis-acting RNA elements through recruitment of dedicated trans-acting factors, including RNA-binding proteins, microRNAs, and regulatory long non-coding RNAs. This level integrates EMTRAC-imposed RNA modification states with regulon-encoded cis logic to achieve precise, context-dependent control of individual proteins.
II. MAJOR KNOWLEDGE GAPS
In Brief:
1. Gap: No integrated resource exists for cell state– or disease-driven EMTRAC- and RMTC-mediated translatome reprogramming, limiting identification of translational vulnerabilities.
2. Regulation: Cis-elements and non-coding RNAs form a multilayered network decoded by RMTC and modulated by EMTRAC, with long, structured mRNAs remaining poorly understood.
Major knowledge gaps: Although comprehensive epitranscriptome databases for model organisms and reference physiological conditions exist—such as RMBase v3.0, which catalogs RNA modification sites across species and healthy reference models—there is currently no integrated resource capturing cell state– or disease-driven EMTRAC- and RMTC-mediated translatome reprogramming. This gap precludes systematic identification of functional, targetable translational vulnerabilities.
Most mRNAs harbor regulatory sequences within their 5′UTRs, coding sequences (CDSs), and 3′UTRs, collectively referred to as cis-acting elements. These elements encode translational logic that is decoded by RMTC through shared trans-acting factors, while RNA methylation within these regions modulates ribosome engagement and translational efficiency via EMTRAC. In parallel, a large diversity of non-coding RNAs—including long non-coding RNAs, pseudogene-derived transcripts, snoRNAs, small non-coding RNAs, and microRNAs—actively participate in translational regulation, forming a multilayered regulatory architecture that governs protein synthesis in a context-dependent manner.
It is well established that transcripts characterized by short, m⁷G-capped, weakly structured, and AT-rich 5′UTRs are efficiently translated under basal conditions and are preferentially suppressed during mitosis or cellular stress. In contrast, the expression dynamics, regulatory mechanisms, and functional relevance of long, GC-rich, highly structured mRNA isoforms that are inefficiently translated under basal conditions remain poorly understood. This knowledge gap underscores the need for systematic, multi-omics approaches to dissect how epitranscriptome-mediated (EMTRAC) and reactome-mediated translational control (RMTC) hierarchically cooperate to reprogram the translatome in health and disease.
III. HYPOTHESIS
III. HYPOTHESIS
In Brief:
1. Long, GC-rich, highly structured 5′UTRs with uORFs and IRESs form a pool of weakly translated mRNAs that can be rapidly mobilized under mitosis or stress.
2. EMTRAC-driven RNA modifications modulate these RMTC-defined architectures, enabling context-dependent recruitment of trans-acting factors and revealing functional roles for complex mRNAs in oncogenes and tumor suppressors.
Based on previous findings (see References), it can be hypothesized that, at the RMTC-defined cis-regulatory layer, transcripts characterized by long, GC-rich, and highly structured 5′UTRs containing upstream open reading frames (uORFs), internal ribosome entry sites (IRESs), and other inhibitory motifs constitute a pool of translationally inactive or weakly translated mRNAs that can be selectively mobilized for rapid protein synthesis under defined physiological or pathological conditions such as mitosis or ISR. Furthermore, it can be hypothesized that this selective recruitment can be enabled by EMTRAC-driven RNA modification states that could affect RNA secondary structure formation, modulate RMTC-defined cis-regulatory architectures by increasing or decreasing the extent of RNA modifications, thereby promoting context-dependent recruitment of sequence- and modification-specific trans-acting factors. This framework assigns a previously unrecognized functional role to structurally complex mRNA variants, frequently observed in oncogenes and tumor suppressor genes, whose translational potential has remained largely unexplored.
IV. AIMS
IV. AIMS
In Brief:
1. EMTRAC + RMTC enable selective translation of complex mRNAs with long 5′UTRs.
2. Global, intermediate, and local layers—ribosome programming, regulons, RNA methylation-coordinate translatome reprogramming.
The primary aim of this project is to define the mechanistic principles by which EMTRAC and RMTC cooperatively enable selective recruitment and activation of transcripts, particularly structurally complex mRNA variants with long, regulatory-rich 5′UTRs. Specifically, the project aims to dissect how global, intermediate, and local layers of translational regulation—including ribosome programming driven by snoRNA-guided rRNA modifications, translational regulon logic, and transcript-specific RNA methylation—cooperate to reprogram the translatome independently of transcript abundance in health and disease.
V. METHODS
V. METHODS
In Brief:
1. Framework: Multi-omics + targeted pertur-bations to dissect hierarchical EMTRAC- and RMTC-mediated translational control.
2. Analyses: Ribo-seq, TRAP-seq, polysome profiling, RNA-seq, single-cell multiomics, RNA modification profiling, metabolomics, proteomics.
3. Mechanistic Validation: Modulation of translation initiation, rRNA and RNA methylation, and 5′UTR-targeted oligonucleotides (dGoligo/ eRNA) in vitro and in vivo.
The proposed hypothesis will be tested using an integrated multi-omics framework combined with targeted functional perturbations to dissect hierarchical translational control mediated by EMTRAC and RMTC. Transcriptome- and translatome-wide analyses, including alternative transcript isoforms, will integrate ribosome profiling (Ribo-seq), polysome profiling and TRAP-seq with bulk RNA-seq and single-cell multiomics to quantify global, intermediate, and transcript-specific translational outputs. Epitranscriptomic regulation will be interrogated using RNA modification profiling (GLORI, m⁶A-seq / MeRIP-seq or direct RNA sequencing), complemented by metabolomic analyses as determinants of RNA methylation capacity and quantitative proteomics to validate functional protein output. Mechanistic interrogation will involve modulation of cap-dependent and cap-independent translation initiation, targeted perturbation of rRNA-specific modifications (e.g. 2′-O-methylation), and transcript- and isoform-specific modulation of RNA methylation states.
Functional mechanistic validation will be performed in vitro and in vivo. Regulome-driven translational control will be causally tested using a proprietary author-developed 5′UTR-targeted oligonucleotide-based platform (dGoligo/eRNA) enabling gene-specific modulation of translation.
VI. DELIVERABLES
VI. DELIVERABLES
In Brief:
1. Libraries: Health-, disease-, and cell-type–specific EMTRAC and RMTC datasets.
2. Atlas & Impact: Integrated into the TRANSREP Atlas to identify biomarkers, therapeutic targets, and enable selective protein synthesis.
The project will generate health-, disease-, and cell-type–specific libraries of (a) epitranscriptomic states, (b) cis-element–resolved transcript architectures, and (c) associated trans-acting regulatory factors, integrated into a comprehensive open-access database of EMTRAC- and RMTC-mediated translatome reprogramming across the human diseasome. Ultimately, this work will produce a unified TRANSREP Atlas enabling the identification of novel biomarkers and therapeutic targets and providing a foundation for the selective enhancement of native protein synthesis from endogenous transcripts.
VII. IMPACT
VII. IMPACT
In Brief:
1. Framework: Establish a unified, hierarchical, and targetable EMTRAC–RMTC model of translational regulation.
2. Impact: Integrate multi-omics into an atlas to reveal disease-associated translational vulnerabi-lities and support diagnostics, precision medicine and oligonucleotide therapeutics.
This project will establish a unified conceptual and mechanistic framework positioning EMTRAC and RMTC as hierarchically organized and experimentally targetable layers of gene expression regulation. By integrating multi-omics datasets into a mechanism-aware architecture, it will address critical gaps in understanding how epitranscriptomic modifications and regulon-encoded cis-regulatory logic cooperate to reprogram the translatome independently of transcript abundance. The resulting atlas will complement existing resources, such as RMBase v3.0, and enable the discovery of disease-associated translational vulnerabilities, thereby supporting the development of precision medicine strategies targeting translational control and next-generation oligonucleotide therapeutics.
SUPPORTING INFORMATION
SUPPORTING INFORMATION
Research Interests, Focus Areas and Future Directions:
Research Interests, Focus Areas and Future Directions:
Translational control is an underexplored yet highly actionable layer of gene expression regulation with direct relevance to human disease. By defining how reactome-mediated (RMTC) and epitranscriptome-mediated translational control (EMTRAC) cooperate to reprogram disease-specific translatomes, this project will generate a unified atlas of translational regulation across the human diseasome. This atlas will enable the identification of disease-associated translational vulnerabilities and provide a mechanistic foundation for selective, oligonucleotide-based therapeutic strategies that modulate endogenous protein synthesis with improved precision and reduced systemic toxicity.
For a detailed discussion of translational control mechanisms underlying this framework, see the general principles of translational control in RESEARCH, as well as related PUBLICATIONS and INVENTIONS.
NUMIEP is a related research project entitled “Multiomics-guided mechanistic understanding of gut microbiome-mediated epigenome reprogramming in response to functional food-based dietary intervention” (NCN OPUS-LAP). My role includes co-development of the scientific concept (microbiome–epigenome–transcriptome axis), participation as a U.S. consortium partner (in-kind contribution), and scientific advisory support
MSB-TBSN is an international initiative advancing translational systems biology and nutriomics to support precision nutrition in health promotion and prevention of non-communicable diseases. It integrates multi-omics data within the diet–microbiome–epigenome axis using AI-driven approaches to translate complex biological insights into actionable strategies. The network fosters international collaboration and training, contributing to a systems-level understanding of diet–host interactions and healthy longevity. My role includes co-development of the scientific concept and serving as a strategic and supporting partner.
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 J, Chen L, Chen Z, Pang J, Huang J, Lin J, Zheng L, Li B, Qu L, Yang J. RMBase v3.0: decode the landscape, mechanisms and functions of RNA modifications. Nucleic Acids Res. 2024 Jan 5;52(D1):D273-D284. doi: 10.1093/nar/gkad1070. PMID: 37956310
Sci-ModoM is a quantitative database of RNA modifications dedicated to novel assays that provide transcriptome-wide information at single-base resolution. A learnable user–interface allows to Search and Compare modifications site-wise across datasets, and to Browse through or download datasets and retrieve metadata.
Boileau E, Wilhelmi H, Busch A, Cappannini A, Hildebrand A, Bujnicki JM, Dieterich C. Sci-ModoM: a quantitative database of transcriptome-wide high-throughput RNA modification sites. Nucleic Acids Res. 2025 Jan 6;53(D1):D310-D317. doi: 10.1093/nar/gkae972. PMID: 39498498
This is a database of RNA modifications that provides comprehensive information concerning the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA modifying enzymes.
Sordyl D, Boileau E, Bernat A, Maiti S, Mukherjee S, Moafinejad SN, Farsani MA, Shavina A, Cappannini A, Agostini G, Conticello SG, Stefaniak F, Dieterich C, Purta E, Bujnicki JM. MODOMICS: a database of RNA modifications and related information. 2025 update and 20th anniversary. Nucleic Acids Res. 2026 Jan 6;54(D1):D219-D225. doi: 10.1093/nar/gkaf1284. PMID: 41277531
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).
Dassi E, Malossini A, Re A, et al. AURA: Atlas of UTR Regulatory Activity. Bioinformatics. 2012;28(1):142–143.
popular-science materials
popular-science materials
Omics in precision medicine
Omics in precision medicine
Proteogenomics Research: On the Frontier of Precision Medicine. By integrating genetic alterations with protein expression, translatome dynamics, regulome activity, and epitranscriptomic modifications, this approach reveals the functional consequences of mutations, identifies clinically relevant pathways, and enables more precise patient stratification. Such insights enhance biomarker discovery and support the development of targeted therapeutic strategies in oncology.
Protein neoantigens and cancer vaccines
Protein neoantigens and cancer vaccines
Neoantigens: promising targets for cancer therapy. Epitranscriptomic modifications can influence which tumor-specific protein neoantigens are produced and presented by cancer cells. These neoantigens can be selected as targets for personalized cancer vaccines designed to stimulate the immune system to recognize and eliminate tumor cells. Using protein-printing technology, these proteins can be "printed" to teach immune cells how to identify cancer-specific molecular signatures and mount a targeted immune response.
Epitranscriptomic biomarkers
Epitranscriptomic biomarkers
New Discoveries in m6A Epitranscriptomics – From Cancer and Cardiovascular Disease to COVID‑19
m6A epitranscriptomic modification is a key layer of translatome reprogramming and translational control, with aberrant m6A linked many diseases. Advances in profiling technologies now allow detection of m6A across mRNA and lncRNA, at single-base resolution. These tools are driving new discoveries and highlight the importance of m6A in both biological research and clinical applications, providing a roadmap for designing focused m6A studies for epitranscriptomic biomarkers, biomarker development and targeted therapies
Targeting epitranscriptomic machinery in cancer
Targeting epitranscriptomic machinery in cancer
METTL3 is a key gene involved in sequence-specific (local) epitranscriptomic modifications (m6A) of mRNA. Upregulation of the RNA methyltransferase METTL3 was found to drive several cancers, including aggressive chronic lymphocytic leukemia (CLL), by increasing m6A RNA methylation, which alters gene expression and promotes malignant cell survival and proliferation. Targeting METTL3‑mediated RNA methylation pathways represents a promising epitranscriptome-dependent strategy for controlling translation of hematologic malignancies, as supported by several clinical trials testing small-molecule inhibitors of epitranscriptomic machinery, including METTL3 (NCT06762925, NCT07163325, NCT06975293)
Visualization of m6A residues in individual mRNAs
Visualization of m6A residues in individual mRNAs
Techniques for visualizing m6A residues in individual mRNAs allow researchers to map epitranscriptomic modifications at high resolution, providing insight into how RNA methylation controls gene expression in contexts such as inflamation. In human cells, excess double-stranded RNA (dsRNA), arising during viral infections or from endogenous noncoding RNAs overlaping cellular transcripts, can activate innate immune pathways that inhibit cell growth and trigger inflammation. While many RNA modifications do not broadly affect dsRNA immunogenicity, m6A was found to suppresses the OAS/RNase L pathway, revealing a specific mechanism by which epitranscriptomic marks modulate inflammation. Dysregulation of these pathways may also contribute to autoimmune diseases, which can now be studied at the resolution of individual mRNAs.
The EpiPlex assay from AlidaBio
The EpiPlex assay from AlidaBio
A novel sensitive tool (EpiPlex) that enables simultaneous high-throughput detection of RNA modifications and gene expression within a single workflow. Using an enrichment-based approach with non-antibody binders, it allows quantitative profiling of m6A and inosine from low-input RNA samples, delivering integrated transcriptome-wide epitranscriptomic data in a rapid and scalable format compatible with Illumina sequencing. Abstract.
Targeting hypoxia stress–mediated translational control in cancer
Targeting hypoxia stress–mediated translational control in cancer
In tumors, regions of low oxygen (hypoxia) activate the Integrated Stress Response (ISR), which reprograms protein synthesis to promote cancer cell survival, angiogenesis, and metastasis. Hypoxia modulates translational control through eIF2α phosphorylation, selective mRNA translation via internal ribosome entry sites (IRESs) of some transcripts (eg. VEGF, MYC), and regulation by microRNAs and RNA-binding proteins. Targeting these pathways with translation inhibitors incluging inhibitors of eucaryotic translation initiation factors and/or IRS modulators offers a promising approach for developing precision cancer therapies, selectively suppressing the production of proteins that sustain tumor growth under low-oxygen conditions.
Nucleic acid ‑based next -generation therapeutics
Nucleic acid ‑based next -generation therapeutics
Nowadays, nucleic acid–based therapeutics can be produced in a personalized manner to support precision medicine. They exploit DNA and RNA molecules that act as trans-acting factors modulating gene expression by directly targeting specific sequences to treat diseases. These molecules including antisense oligonucleotides (ASOs), siRNA, microRNA, mRNA (RNA therapeutics), circular RNA, self-amplifying RNA, self-transfecting RNA, CRISPR or RNAi therapeutics are designed to interact with RNA or DNA cis-acting elements to regulate pathological processes, offering new avenues for personalized therapies. Their effects can modulate protein levels by silencing mutated gene copies, enhancing functional copies, or supplying a novel therapeutic protein to the cell.
Selected Reference Publications
Selected Reference Publications
Translational regulome–mediated control of translation efficiency
Translational regulome–mediated control of translation efficiency
The translational regulome (TR) comprises the full set of molecular and structural regulatory elements that govern protein synthesis, including translation efficiency (TE). Among these, RNA structures within the 5′UTR and 3′UTR have emerged as key determinants of TE. These features can be systematically analyzed and predicted using computational approaches, allowing the contribution of RNA structure to translational regulation to be quantified. Consequently, defining the TR provides a framework for in silico prediction of translation efficiency (TR → TE).
1) 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
2) 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. doi: 10.1371/journal.pone.0155359. PMID: 27171412
The epitranscriptome modifications influence RNA structure and function
The epitranscriptome modifications influence RNA structure and function
The epitranscriptome encompasses RNA modifications that influence RNA secondary structure formation and function and regulate gene expression.
Lewis CJ, Pan T, Kalsotra A. RNA modifications and structures cooperate to guide RNA-protein interactions. Nat Rev Mol Cell Biol. 2017 Mar;18(3):202-210. doi: 10.1038/nrm.2016.163. Epub 2017 Feb 1. PMID: 28144031; PMCID: PMC5542016.
Acute exercise promotes WAT browning by remodeling mRNA m6A methylation
Acute exercise promotes WAT browning by remodeling mRNA m6A methylation
Notably, CREBBP expression is extensively regulated by m6A modifications, enhancing its translation. Acute exercise promotes WAT beiging via BHBA-induced m6A upregulation, increasing m6A-dependent CREBBP translation and facilitating transcription of key thermogenic and glycolytic beige fat genes through chromatin remodeling, positioning CREBBP as a central mediator. These findings highlight a mechanistic link between metabolic stimuli, epitranscriptomic regulation, and chromatin remodeling.
Chen W, Liu Y, Liu J, Chen Y, Wang X. Acute exercise promotes WAT browning by remodeling mRNA m6A methylation. Life Sci. 2025 Jan 15;361:123269. doi: 10.1016/j.lfs.2024.123269. Epub 2024 Nov 22. PMID: 39581460.
N6-Methyladenosine Guides mRNA Alternative Translation during ISR
N6-Methyladenosine Guides mRNA Alternative Translation during ISR
This study demonstrates that N6-methyladenosine (m6A) plays a critical role in regulating alternative mRNA translation during the integrated stress response (ISR). The authors show that, in addition to the canonical eIF2α pathway, m6A modifications within the 5′ UTR control ribosome scanning and start codon selection, thereby modulating translation reinitiation of stress-responsive genes such as ATF4. Dynamic regulation of m6A, mediated by methyltransferases including METTL3 and demethylases (e.g., ALKBH5 and FTO), influences global patterns of alternative translation. These findings establish m6A as a key regulatory layer linking epitranscriptomic modifications to translational control under stress conditions.
Zhou J, Wan J, Shu XE, Mao Y, Liu XM, Yuan X, Zhang X, Hess ME, Brüning JC, Qian SB. N6-Methyladenosine Guides mRNA Alternative Translation during Integrated Stress Response. Mol Cell. 2018 Feb 15;69(4):636-647.e7. doi: 10.1016/j.molcel.2018.01.019. Epub 2018 Feb 8. PMID: 29429926
Prognostic role of circRNAs and RNA methylation enzymes in bladder cancer
Prognostic role of circRNAs and RNA methylation enzymes in bladder cancer
This systematic review and meta-analysis assessed the prognostic role of circRNAs and RNA methylation enzymes in bladder cancer. It found that high circRNA expression is linked to worse survival outcomes and higher recurrence risk, while elevated FTO levels are associated with shorter overall survival. These findings suggest their potential as prognostic biomarkers.
Ren H, Zou L, Jiang L, Zhang P, Li C, Li Z, Niu H, Zhang X, Liao H, Cheng L, Yang F, An S, Ge X, Ren F, Pan H, Rong S, Ma H. Prognostic role of circRNAs and RNA methylation enzymes in bladder cancer: A systematic review and meta-analysis of Chinese studies. Urol Oncol. 2025 Nov;43(11):628-638. doi: 10.1016/j.urolonc.2025.06.005. Epub 2025 Jun 26. PMID: 40579335.
RNA modifications in cancer
RNA modifications in cancer
RNA modifications, including N6‑methyladenosine (m6A) and 5‑methylcytosine (m5C), have emerged as crucial regulators of cancer by influencing RNA stability, splicing, translation, and degradation through specific writer, eraser, and reader proteins. These modifications impact key cellular processes such as metabolic reprogramming, signaling, and cell cycle control, which are essential for tumor growth and survival. Although mechanisms remain incompletely understood, current research links RNA modifications to cancer proliferation, metastasis, and programmed cell death (apoptosis, autophagy, ferroptosis), as well as epithelial–mesenchymal transition and the tumor immune microenvironment. The review also discusses the therapeutic potential of targeting RNA modifications to enhance conventional, immuno‑, and targeted cancer therapies.
Wu H, Chen S, Li X, Li Y, Shi H, Qing Y, Shi B, Tang Y, Yan Z, Hao Y, Wang D, Liu W. RNA modifications in cancer. MedComm (2020). 2025 Jan 10;6(1):e70042. doi: 10.1002/mco2.70042. Erratum in: MedComm (2020). 2025 Sep 30;6(10):e70397. doi: 10.1002/mco2.70397. PMID: 39802639.
More about RNA Modifications and their Therapeutic Implications and Therapeutic Targets
The role of RNA methylation in glioma progression
The role of RNA methylation in glioma progression
This narrative review discusses the crucial role of RNA methylation in glioma progression, highlighting how modifications such as m6A, m5C, m7G, and m1A regulate RNA processing and contribute to tumor development. Dysregulation of these processes is associated with glioma pathogenesis, while RNA methylation-related enzymes may serve as potential diagnostic biomarkers and therapeutic targets. The article also outlines key milestones in the RNA methylation field (click the adjacent figure on the left).
Zhang SZ, Liu SY, Cheng MD, Zhang YF, Tian JW. The role of RNA methylation in glioma progression: mechanisms, diagnostic implications, and therapeutic value. Front Immunol. 2025 May 21;16:1583039. doi: 10.3389/fimmu.2025.1583039. PMID: 40469294
RNA Modifications Differentially Regulate dsRNA-Mediated Innate Immunity
RNA Modifications Differentially Regulate dsRNA-Mediated Innate Immunity
Excess double-stranded RNA (dsRNA), generated during viral infections, activates innate immune responses, leading to inflammation and growth inhibition, but can also act without inducing inflammation. RLR, OAS/RNase L, and PKR pathways function independently: 5′ dsRNA ends drive inflammation, while the duplex structure activates growth-inhibitory pathways. RNA modifications generally do not affect dsRNA immunogenicity, except m6A, which specifically inhibits OAS/RNase L signaling.
Drazkowska K, et al. Effective recognition of double-stranded RNA does not require activation of cellular inflammation. Sci Adv. 2025 Apr 11;11(15):eads6498. doi: 10.1126/sciadv.ads6498. Epub 2025 Apr 9. PMID: 40203104;
Cieslicka J, Pianka K, Drazkowska K, Sikorski PJ. Sensing of double-stranded RNA in human cells: molecular mechanisms and cellular consequences. Biochem Soc Trans. 2026 Mar 25;54(3):BST20250259. doi: 10.1042/BST20250259. PMID: 41873699.
RNA modification: mechanisms and therapeutic targets
RNA modification: mechanisms and therapeutic targets
This narrative review summarized the potential functions of RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders.
Qiu L, Jing Q, Li Y, Han J. RNA modification: mechanisms and therapeutic targets. Mol Biomed. 2023 Aug 24;4(1):25. doi: 10.1186/s43556-023-00139-x. PMID: 37612540; PMCID: PMC10447785.
METHODS: GLORI enables absolute quantification of m6A methylome
METHODS: GLORI enables absolute quantification of m6A methylome
GLORI (Glyoxal- and Nitrite-mediated Deamination of Unmethylated Adenosines) is a novel chemical-based sequencing method for the absolute quantification of the -methyladenosine (M6A) methylome at single-base resolution across the entire transcriptome. GLORI 2.0 enhances sensitivity for both transcriptome-wide and locus-specific m6A detection.
Sun H, Lu B, Zhang Z, Xiao Y, Zhou Z, Xi L, Li Z, Jiang Z, Zhang J, Wang M, Liu C, Ma Y, Peng J, Wang XJ, Yi C. Mild and ultrafast GLORI enables absolute quantification of m6A methylome from low-input samples. Nat Methods. 2025 Jun;22(6):1226-1236. doi: 10.1038/s41592-025-02680-9. Epub 2025 May 5. PMID: 40325216.
Other methods for epitranscriptome analysis: 1) Illumina miCLIP-m6A, 2) Merk Magna MeRIP m6A kit, 3) EpiNext CUT&RUN RNA m6A-Seq Kit, 4) The EpiPlex assay from AlidaBio, Software, ref.: PMID: 41332709, PMID: 41164819 PMID: 39416026 5) CHEUI (CH3 (methylation) Estimation Using Ionic current), 6) LC-MS/MS, 7) Arraystar Inc Epitranscriptomic Array, 8) New England Biolabs, Epitranscriptomic nanopore sequencing, 9) i) Thermofisher N6-Methyladenosine (m6A) Monoclonal Antibody,10) Epigentek Elisa, 11) Abcam Anti-N6-methyladenosine (m6A) antibody and l) other tools.
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Mapping RNA modifications by proximity barcode sequencing
Mapping RNA modifications by proximity barcode sequencing
The EpiPlex platform enables reliable, simultaneous mapping of multiple RNA modifications, supporting comprehensive epitranscriptomic analyses. Using this approach, studies confirmed a key role of EIF4A3, an RNA helicase and core component of the exon junction complex (EJC), in shaping the m6A landscape during alternative splicing. Depletion or knockdown of EIF4A3 leads to increased global m6A levels, particularly at DRACH motifs within short internal exons and near exon–exon junctions. Mechanistically, EIF4A3, as part of the EJC, is required to protect these regions from methylation by the METTL3 complex. Dysregulation of EIF4A3 has been linked to multiple cancers, however, its effects are pleiotropic and depend on both global and local sequence-specific contexts, where it functions as a regulator of alternative splicing, locally modulating m6A -dependent exon usage.
Sendinc E, Yu H, Hwang Fu YH, Santos J, et al. Mapping multiple RNA modifications simultaneously by proximity barcode sequencing. bioRxiv [Preprint]. 2024 Oct 10:2024.10.09.617509. doi: 10.1101/2024.10.09.617509. PMID: 39416026.
Single-cell analysis of the epitranscriptome ...
Single-cell analysis of the epitranscriptome ...
This review highlights RNA modifications as an additional regulatory layer of gene expression, collectively known as the epitranscriptome. It focuses on recent advances in next-generation sequencing and single-cell technologies that enable high-resolution mapping of modifications, particularly N6-methyladenosine (m6A) in mRNA. These developments have improved understanding of how RNA modifications influence processes such as cap-independent translation, alternative splicing, nuclear export and RNA stability.
Crespo-García E, Bueno-Costa A, Esteller M. Single-cell analysis of the epitranscriptome: RNA modifications under the microscope. RNA Biol. 2024 Jan;21(1):1-8. doi: 10.1080/15476286.2024.2315385. Epub 2024 Feb 18. PMID: 38368619; PMCID: PMC10877985.
Nature Portfolio - The Epitranscriptome Collection
Nature Portfolio - The Epitranscriptome Collection
A role for DNA modification in gene regulation is well established, but much less is known about how RNA modification affects RNA fate and influences the way genes are expressed. This web collection features articles from various Nature journals that highlight this exciting new research area of epitranscriptomics.
Xu X, Wang Y, Zhu H, Lam M, Luo W, Teng M, Liu Y, Guo WY, Aastha A, Xu X, Chen S, Ci X, Wang S, Zeng Y, Zhu G, Kislinger T, Lupien M, Tsao MS, He HH. METTL3-based epitranscriptomic editing screening identifies functional m6A sites in cancers. Nat Cancer. 2026 Feb 6. PMID: 41652220.
Translational control in biology and medicine
Translational control in biology and medicine
This book provides a comprehensive overview of the mechanisms and regulation of protein synthesis in both bacteria and eukaryotes, incorporating advances in ribosome structure and insights into RNA- and protein-mediated control. With a new emphasis on the role of translational control in human development and disease, its 30 chapters, written by leading experts, explore how dysregulation of translation contributes to pathology. It is an essential resource for anyone studying translation, its regulation, and its implications in health and disease. ISBN 978-087969767-9.
For further information, see the project References
29 refereed publications, 30 > abstracts, 4 patents
H-Index range: 12–17 (2025), 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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