Human RNome Project 2025 Meeting Report

Human RNome Project 2025 Meeting Report
The Human RNome Project aims to sequence full-length RNA transcripts with all their chemical modifications. The technologies we develop will enable direct sequencing of any RNA from any organism. These advances will have wide-ranging impact—from fundamental biology to applications in manufacturing, data storage and therapeutics.
Our 2025 Consortium meeting took place on August 4–8th at Goethe University Frankfurt, Germany, focusing on identifying and quantifying RNA chemical modifications. Parallel breakout sessions covered non–mass spectrometry direct RNA sequencing methods, biological implications, and data storage.
Human RNome Project - A Global Collaborative Consortium
RNA biology has entered a new era with the recognition that RNA molecules carry a rich repertoire of chemical modifications that regulate their processing, localisation, translation and stability . More than 180 modifications have been identified across organisms, with at least 50 distinct chemical marks identified in humans, yet their precise roles and distribution across tissues remain incompletely understood. The Human RNome Project (HRP) is a global effort to reveal the complete landscape of human RNA biology. The 2025 Human RNome Project Consortium Meeting, held from August 4-8, at Goethe University Frankfurt, Germany, brought together a global, multidisciplinary community of researchers in RNA biology, epitranscriptomics and RNome. The five-day meeting featured interactive morning breakout discussions and hands-on mass spectrometry laboratory sessions, followed by afternoon plenary lectures from leading experts, fostering a comprehensive exploration of the current field. As a cornerstone event for the HRP, the meeting aimed to evaluate the current landscape of RNA modification research through both scientific discussions and hands-on experimentation. Throughout the breakout sessions, participants consistently emphasised technical innovation, novel computational approaches and collaborative strategies vital for advancing RNA modification research. Key topics included modification-specific and direct RNA sequencing (such as nanopore-based technologies), quantitative mass spectrometry, data analysis pipelines and functional annotation of RNA modifications. HRP aims to deliver a complete atlas of RNA molecules and their modifications in human cells, analogous in ambition to the Human Genome Project but with added complexity arising from the dynamic nature of the transcriptome and its chemical marks.
To explore these themes in depth, the meeting combined focused breakout discussions with hands-on laboratory sessions to encourage both targeted dialogue and practical collaboration. Over five days, participants conducted experiments across three independent LC–MS/MS platforms, gaining valuable experience in sample preparation and the detection of RNA modifications in total RNA. In parallel, ten breakout sessions were led by experts at different career stages, with designated note-takers capturing key insights to inform future planning for the Human RNome Project. The table below summarizes the session topics and facilitators.
Hands-on laboratory sessions
Mass spectrometry plays a vital role in uncovering RNA modifications. While widely used, researchers often rely on distinct protocols for sample preparation and data analysis, leading to challenges in data quality and reproducibility. To address these issues, we have developed a standardized, optimized protocol (SOP) designed to enhance consistency and reliability. This SOP has been tested across multiple mass spectrometry platforms—including the ThermoFisher Scientific Orbitrap Eclipse, Agilent Technologies U-HPLC coupled with QQQ, and the Bruker Impact II—using samples prepared with our optimized methodology. Our goal is to provide the research community with a robust framework for more trustworthy and comparable results in RNA modification analysis.
Breakout sessions
Key topics included modification-specific and direct RNA sequencing (such as nanopore-based technologies), quantitative mass spectrometry (LC-MS/MS), data analysis pipelines, and functional annotation of RNA modifications. HRP aims to deliver a complete atlas of RNA molecules and their modifications in human cells, analogous in ambition to the Human Genome Project but with added complexity arising from the dynamic nature of the transcriptome and its chemical marks.
Day 1: RNA Modification Detection Methods
Session 1: Modification-specific sequencing
This session examined advances and challenges in methods designed to detect individual RNA modifications with high specificity. Participants discussed pulldown strategies, naturally or chemically induced reverse transcription signatures, and newly developed multiplexed approaches.
Recent technologies such as eTAM-Seq were highlighted for their compatibility with low RNA input, while pulldown-based methods, including EpiPlex and m6A-Seq2, were recognized for enabling multiplexing or reducing assay noise through upstream barcoding.
A recurring theme was the urgent need for community-wide benchmarking. Participants proposed testing a single modification, such as m6A, across multiple laboratories and platforms to define a "gold standard."
Session 2: Nanopore sequencing
The nanopore sequencing session provided a broad overview of ONT's role in RNA modification detection. It was apparent that m6A, m5C, and pseudouridine (Ψ) were the most popular modifications studied by participants using this technology.
Participants highlighted the inherent bias of ONT's poly(A)-dependent sequencing and the need for expanded protocols that accommodate non-polyadenylated RNAs. Computational tools for modification detection are advancing rapidly, but concerns remain around reproducibility, resource demands, and the need for consensus-based approaches.
There was consensus that direct RNA sequencing with ONT will play a huge role in the detection of RNA modifications due to the ability to detect RNA modifications in sequence context, which is more difficult with Mass Spectrometry.
1
Antibody-based Methods
Including m6A MeRIP, m6A-seq2, and m6A-CLIP/eClip. These methods use antibodies to pull down modified RNA fragments.
2
Chemical Conversion Methods
Including ICE-seq, CMC-seq, Bisulfite-seq, and GLORI. These methods chemically convert or modify specific nucleotides to create detectable signatures.
3
Enzymatic Methods
Including SAC-seq, eTAM-seq, and Matzer Seq. These methods use enzymes to specifically target or convert modified nucleotides.
4
Direct RNA Sequencing
Using nanopore technology to directly detect RNA modifications in their native context without conversion or antibody enrichment.
Day 2: Comprehensive Detection and Biological Implications
Session 1: Complete Detection and Quantification
This session addressed the multifaceted challenges associated with achieving comprehensive detection and quantification of RNA modifications. Discussions centered on:
Need for methodological stringency
Biological relevance considerations
Development of standardized frameworks
Importance of rigorous data collection
Consideration of RNA abundance when interpreting significance
Session 2: Biological Implications
This session explored the biological roles and consequences of RNA modifications across diverse cellular contexts:
Modifications often operate in combinatorial and context-dependent manner
Rare modifications in mRNAs may represent collateral activity of tRNA/rRNA-modifying enzymes
Homologous enzymes across species can evolve new functions
Annotation of modification writers, readers, and erasers is still incomplete
A framework was proposed where the biological relevance of RNA modifications is tied to a measurable phenotype. The group advocated for the development of a decision tree to guide researchers through modification-specific analytical pathways, recognizing that a universal protocol may not yet be feasible with available technologies.
Participants stressed that while technological advances now enable increasingly precise mapping of modified nucleotides, the functional interpretation of these marks remains a major challenge. The group agreed that developing a human tissue- and cell-type atlas of modifications, starting with m6A, would provide an invaluable framework for connecting chemical marks to gene regulation, cellular physiology, and disease.
The session concluded that the key biological implications of RNA modifications will only be revealed through careful integration of multiple orthogonal methods, rigorous benchmarking across laboratories, and systematic mapping efforts spanning tissues and developmental states.
Day 3: Databases and Data Management
Session 1: Modomics and SciModom Databases
The foundational discussion established MODOMICS and Sci-ModoM as complementary, yet functionally distinct infrastructures vital to the epitranscriptomics community and large-scale initiatives like the Human RNome Project.
MODOMICS
A qualitative "encyclopedia" built on rigorous expert manual curation, offering verified knowledge on RNA modifications, including their chemical structures, associated enzymes (writers, erasers, readers), and genomic locations.
Sci-ModoM
A quantitative "atlas," designed to standardize and disseminate high-throughput sequencing data at single-nucleotide resolution, formatted into a computable, human-readable bedM format.
MODOMICS
Sci-ModoM
Session 2: Data Repository Challenges
A qualitative "encyclopedia" built on rigorous expert manual curation, offering verified knowledge on RNA modifications, including their chemical structures, associated enzymes (writers, erasers, readers), and genomic locations. The data repository session addressed the infrastructural and collaborative challenges of managing mass spectrometry data and raw ONT reads in RNA modification research, as no suitable repository or database currently exists. 
A survey conducted during the meeting revealed persistent friction between wet lab and computational teams, often due to inconsistent sample labeling, incomplete metadata, and ambiguous terminology. These issues contribute to reproducibility problems and miscommunication. Data storage emerged as a major concern, as there is no centralized database or repository for RNA modification data. Current cloud-based solutions prove costly and are inadequate for long-term needs.
Expand Database Scope
Incorporate MS quantification, miRNA datasets, synthetic modifications, fluorescent analogues, and cross-species comparative data.
Improve Visualization
Integration with the UCSC Genome Browser and addition of confidence scores for modification sites.
Secure Long-term Funding
Shift from short-term project grants to permanent, community-anchored infrastructure capable of evolving alongside the field's demands.
Day 4: Future Vision and Next Steps
Session 1: Future Vision: The Human RNome in 2030
This forward-looking session invited participants to imagine the state of RNome science in the year 2030. Discussions were structured around three guiding questions: what will we be able to do technologically, what will we know scientifically, and what will we have changed clinically and societally?
Technology & Capability
Single-molecule methods capable of identifying all isoforms and associated modifications at base-level resolution, with precision and error rates approaching those of DNA sequencing.
Scientific Knowledge
Comprehensive maps of modification distributions across tissues and cell types, including their spatial localization and co-occurrence patterns, with causal links to RNA metabolism, translation, and protein abundance.
Clinical & Societal Impact
RNA modifications as biomarkers and therapeutic targets in cancer, metabolic disorders, rare "RNA modopathies," and antimicrobial resistance, as well as translational opportunities in agriculture and biotechnology.
Next Steps
The foundational workshop for the HRP culminated in a clear action plan, centering on a first collaborative project to map RNA modifications. The consortium agreed to use a common stock of total RNA from ENCODE GM12878 B-cells as a standardized reference sample.
1
Oct 15, 2025
Shipping GM12878 RNA
2
Jan 1, 2026
Wet-lab experiments completed
3
Mar 1, 2026
Data uploaded to common repository
4
Apr-May 2026
Joint data mining and analysis
5
Aug-Sep 2026
Report results at next HRP workshop
Vision Exercise
It's 2030. We're looking at the cover of a major journal celebrating the success of the HRP. What's the headline? What's the main image?" This exercise rapidly surfaces the group's highest aspirations.
Technology & Capability
What can we DO? In 2030, what is the one technological capability that has fundamentally changed the game for RNome research?
Scientific Knowledge
What do we KNOW? In 2030, what is the single most important piece of fundamental biological knowledge we will have gained thanks to the HRP?
Clinical & Societal Impact
What have we CHANGED? In 2030, what is the most significant real-world impact the HRP has had on a specific human disease?
Grand Challenge
What is the single most important "Grand Challenge" project the HRP community needs to launch in the next 18 months to meet the above goals?
Summary:
This forward-looking session invited participants to imagine the state of RNome science in the year 2030. Discussions were structured around three guiding questions: what will we be able to do technologically, what will we know scientifically, and what will we have changed clinically and societally? From a technological perspective, the community envisioned single-molecule methods capable of identifying all isoforms and associated modifications at base-level resolution, with precision and error rates approaching those of DNA sequencing. Improved nanopore chemistries, novel ligases, and more sensitive mass spectrometry platforms were highlighted as areas for innovation. A critical milestone will be the establishment of robust community standards, including benchmarking of synthetic and biological RNA references across laboratories, enabling comparability and reproducibility. In terms of scientific knowledge, participants anticipated that by 2030, the field would have achieved comprehensive maps of modification distributions across tissues and cell types, including their spatial localisation and co-occurrence patterns. Importantly, the group emphasised the need to link modifications causally to RNA metabolism, translation, and protein abundance, with particular focus on the extent of crosstalk between different marks. Fundamental questions include whether modifications are heritable, how they vary across populations, and how they contribute to cell fate decisions. The clinical and societal vision is centred on the potential of RNA modifications as biomarkers and therapeutic targets. Participants highlighted applications in cancer, metabolic disorders, rare "RNA modopathies," and antimicrobial resistance, as well as translational opportunities in agriculture and biotechnology. The group emphasised that whether modifications are causal drivers of disease, manipulating them may enable therapeutic reprogramming of cells. A grand challenge proposed for the next 18 months was a systematic functional screen of all RNA modification enzymes, combining epitranscriptomic profiling with transcriptomic, genomic, and metabolic readouts. Such a resource would establish the foundation for understanding modification biology at scale. The session concluded with broad agreement that realising the vision of the Human RNome Project requires coordinated infrastructure, transparent data sharing, and an international commitment to standards and benchmarking.
Session 2: What are the next steps?
Vision to Reality
To make that 2030 vision a reality, what must we prioritise now? This section is about defining our immediate marching orders.
Working Groups
What specific, action-oriented working groups need to be formed or commissioned by the people in this room?
Action Items
"Before We Meet Again" List: What are the top 3-5 concrete action items this group must accomplish before the next HRP workshop?
Summary
Session leader summarises the key next steps, the newly formed working groups, and the shared commitment to turning the 2030 vision into a tangible research plan.
The foundational workshop for the HRP culminated in a clear action plan, centering on a first collaborative project to map RNA modifications. The consortium agreed to use a common stock of total RNA from ENCODE GM12878 B-cells as a standardised reference sample. For this project to succeed, key resources and infrastructure must be established. An urgent priority is securing a central, funded data repository for both raw and processed data, with RMDB suggested as a potential solution. Furthermore, the consortium plans to develop a shared resource on the HRP website for standardised protocols, kit recommendations, and sources for reagents. The need for dedicated project management to oversee this complex logistics and infrastructure was also clearly identified.
Proposed actions and deadlines for benchmarking collaboration:
Parallel to the scientific work, a major focus will be on community engagement and communication. Plans are underway to maintain momentum through regular community gatherings, the first of which is suggested for January 2026 or sooner. The group will explore communication platforms for ongoing discussion and may record talks for a YouTube channel to increase exposure. A key initiative is the formation of subgroups, particularly for Early Career Researchers (ECRs), which will include activities like a monthly journal club. To effectively organise these efforts, a Google Form will be circulated to survey members' skills and resources, creating a valuable skill matrix for the entire consortium. Two critical writing projects were initiated to document and promote the consortium's efforts. First, there is a strong drive to publish a report on this foundational workshop to formalise the project and attract broad attention. ECRs have volunteered to lead the writing, with a target draft deadline of November 1st, though the challenge remains to find a journal that accepts meeting reports. Second, and crucial for funding, is the creation of a compelling Impact Statement. All members are encouraged to contribute points with citations to a shared Google Doc, which will be synthesised by Majd Abdulghani into a final statement accessible to the public and funding agencies. The discussions also highlighted several open questions for future resolution. The very nature of the consortium, whether it is a project, a society, or something else, needs further definition. Funding models, including the possibility of paid membership, and formal legal frameworks for international data sharing and privacy, will need to be addressed as the project evolves beyond its initial unofficial status.
Additional actions determined by workshop participants with proposed leads and deadlines:
Day 5: Collaborative Projects
The final breakout session successfully fostered dynamic interaction among consortium members to identify shared scientific interests and catalyze the design of actionable collaborative projects. Through a structured exercise, participants proposed ideas that coalesced into three thematic clusters: technology-driven, functional/mapping-focused, and disease-oriented.
A consistent message across sessions was that no single technology or lab can capture the full scope of RNA modifications. Instead, success will require benchmarking across platforms, standardized reference samples, and interoperable computational pipelines. Proposals such as the "epitranscriptome in a bottle" and the use of common RNA stocks reflect a strong community drive toward shared standards and reproducibility.
Technology Project
"From Molecule to Modification"
Core goal: Develop a standardized, benchmarked system for detecting any RNA modification across any species or RNA type using multiple analytical platforms.
Approach: Four work packages covering synthesis of standards, benchmarking existing technologies, cross-platform harmonization, and computational pipeline development.
Funding: Horizon Europe
Mapping & Function Project
"The Functional RNome Atlas"
Core goal: Create a complete, dynamic map of the modified transcriptome across time, from cell to organ to organism.
Approach: Combine NGS-based detection in key cell lines to study development, aging, and immune response, followed by studies in engineered mouse models and human tissues.
Funding: Horizon Europe 
Disease Project
"RNA Epitranscriptomic Landscape in Immune Regulation (ReLi)"
Core goal: Understand how RNA modifications shape immunological responses in cancer and autoimmunity.
Approach: Map the baseline epitranscriptomic landscape in patient-derived tissuoids and organoids, followed by functional validation through knockdown experiments and immune cell response assays.
Funding: Horizon Europe 
Key Challenges and Solutions
Technical Challenges
Standardization
No single technology can capture all modifications; need for benchmarking across platforms and laboratories.
Data Storage
No centralized repository exists for large datasets like LC-MS and ONT RNA reads; current solutions are costly and inadequate.
Sensitivity
Detecting low-stoichiometry modifications remains challenging, especially in complex biological samples.
Proposed Solutions
"Epitranscriptome in a bottle"
Combining synthetic oligonucleotides and RNA across multiple protocols to establish ground truths for modification detection.
Collaborative Infrastructure
Regular cross-disciplinary meetings, shared communication platforms, and a common glossary to reduce ambiguity.
Shared Resources
Creating a central repository for protocols, reagents, and computational tools on the HRP website.
Biological interpretation of modifications remains a major challenge. Discussions highlighted the complexity of modification patterns, the limitations of current detection tools, and the need for orthogonal validation. Functional mapping efforts, including tissue- and cell-type specific atlases, were seen as essential next steps, alongside improved annotation of writer, reader, and eraser enzymes.
The chart represents the approximate distribution of discussion topics across all breakout sessions, highlighting the primary challenges facing the HRP consortium.
Community Building and Communication
Parallel to the scientific work, a major focus will be on community engagement and communication. Plans are underway to maintain momentum through regular community gatherings, the first of which is suggested for January 2026 or sooner.
Regular Gatherings
Community zoom meetings starting January 2026, with potential for recorded talks on a YouTube channel to increase exposure.
ECR Subgroup
Formation of Early Career Researcher subgroups led by Rami Bechara, Rebekah Penrice-Randal, and Bennett Henzeler.
Documentation
Two critical writing projects: a report on the foundational workshop and a compelling Impact Statement to support funding efforts.
The discussions also highlighted several open questions for future resolution. The very nature of the consortium, whether it is a project, a society, or something else, needs further definition. Funding models, including the possibility of paid membership, and formal legal frameworks for international data sharing and privacy, will need to be addressed as the project evolves beyond its initial unofficial status.
Workshop Conclusions
Technological Integration
A consistent message across sessions was that no single technology or lab can capture the full scope of RNA modifications. Instead, success will require benchmarking across platforms, standardised reference samples, and interoperable computational pipelines. Proposals such as the "epitranscriptome in a bottle" and the use of common RNA stocks reflect a strong community drive toward shared standards and reproducibility.
Biological Complexity
Biological interpretation of modifications remains a major challenge. Discussions highlighted the complexity of modification patterns, the limitations of current detection tools, and the need for orthogonal validation. Functional mapping efforts, including tissue- and cell-type specific atlases, were seen as essential next steps, alongside improved annotation of writer, reader, and eraser enzymes.
Collaborative Framework
Sessions proposed concrete solutions, such as collaborative checklists and regular cross-functional meetings. The workshop concluded with the formation of three flagship collaborative projects focusing on technology benchmarking, functional mapping, and disease applications, demonstrating strong momentum for action.
Future Vision
Looking ahead to 2030, participants envision a research environment where modifications are mapped with single-molecule precision, linked to biological outcomes, and translated into clinical insights. Realising this vision will require immediate progress on infrastructure, benchmarking, and funding. But the tone of the meeting was optimistic and unified: the Human RNome Project is no longer just an idea, it is a growing, global movement poised to unlock a new dimension of RNA biology.
References
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This report was prepared by Bennett Henzeler, Rami Bechara, and Rebekah Penrice-Randal (RNome ECR steering committee) based on notes collected during the 2025 Human RNome Project Consortium Meeting