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Update of the FANTOM web resource: enhancement for studying noncoding genomes
Tomoe Nobusada1, Chi Wai Yip1, Saumya Agrawal1
1RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa 230-0045, Japan.
Nucleic Acids Research
|November 26, 2024
Summary
The FANTOM resource now offers expanded annotations for long non-coding RNAs (lncRNAs) and transcribed cis-regulatory elements (CREs), enhancing mammalian genome research. These updates provide new insights into non-coding regions and their functions.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- The FANTOM (Functional ANnoTation Of the Mammalian genome) project has established a comprehensive web resource for mammalian genome research.
- Previous iterations focused on annotating various genomic features.
Purpose of the Study:
- To update and expand the FANTOM web resource with enhanced annotations for long non-coding RNAs (lncRNAs) and transcribed cis-regulatory elements (CREs).
- To provide researchers with improved tools and data for investigating the functional roles of non-coding genomic regions.
Main Methods:
- Expanded lncRNA annotations using large-scale lncRNA perturbations in induced pluripotent stem cells (iPSCs) and Hi-C data analysis (FANTOM6).
- Developed a new platform, fanta.bio, to collect transcribed CREs identified from an extended dataset of CAGE profiles.
- Integrated genetic and epigenetic information for CREs.
Main Results:
- Enhanced annotations for lncRNAs, detailing their impact on cellular/molecular phenotypes and potential RNA-chromatin interactions, accessible via ZENBU-Reports.
- New platform fanta.bio provides access to transcribed CREs with comprehensive annotations.
- CRE data is available through a dedicated interface and the UCSC Genome Browser Database.
Conclusions:
- The updated FANTOM resource offers significantly enhanced capabilities for studying mammalian non-coding genome functions.
- These advancements facilitate deeper investigation into the roles of lncRNAs and CREs in cellular processes and disease.
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