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Linking FANTOM5 CAGE peaks to annotations with CAGEscan.
Nicolas Bertin1,2, Mickaël Mendez1,2, Akira Hasegawa1,2
1RIKEN Center for Life Science Technologies, Division of Genomics Technologies, Yokohama 230-0045, Japan.
Scientific Data
|October 4, 2017
Summary
The FANTOM5 expression atlas now links thousands of gene promoter regions to their transcripts using CAGEscan. This method provides experimental evidence to associate core promoter regions with cognate transcripts, enhancing the atlas.
Area of Science:
- Genomics
- Transcriptomics
- Bioinformatics
Background:
- The FANTOM5 expression atlas quantifies activity across ~200,000 human promoter regions in ~2,000 cell/tissue types.
- Cap Analysis of Gene Expression (CAGE) technology enables single-nucleotide resolution of transcription start sites.
- A significant portion of CAGE-defined promoters (~100,000) remained unassociated with known genes (gene-orphan).
Purpose of the Study:
- To associate the remaining gene-orphan promoter regions with their corresponding transcripts.
- To enhance the FANTOM5 expression atlas with experimental evidence linking core promoters to transcripts.
- To present the production and quality control of CAGEscan libraries for this purpose.
Main Methods:
- Utilized the CAGEscan method involving paired-end sequencing of random-primed 5'-cDNAs.
- Assembled sequencing reads into transcript models known as CAGEscan clusters.
- Generated and quality-controlled CAGEscan libraries from 56 FANTOM5 RNA sources.
Main Results:
- Successfully produced and validated CAGEscan libraries from 56 FANTOM5 RNA sources.
- Generated experimental evidence associating previously gene-orphan promoter regions with specific transcripts.
- Significantly enhanced the FANTOM5 expression atlas by resolving promoter-transcript associations.
Conclusions:
- CAGEscan effectively addresses the challenge of gene-orphan promoters identified by CAGE.
- The enhanced FANTOM5 atlas provides a more comprehensive understanding of human gene expression regulation.
- This work validates CAGEscan as a powerful tool for promoter-transcript mapping in large-scale expression atlases.
