Antisense-oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types
We perform a large-scale knockdown of 200 long non-coding RNAs (lncRNAs) in human induced pluripotent stem (iPS) cells and find 36 lncRNAs (18%) exhibiting cell growth inhibition. From the knockdown of 123 lncRNAs with transcriptome profiling, 36 lncRNAs (29.3%) show molecular phenotypes. Integration with chromatin-interaction assays further reveals cis- and trans- interacting partners as potential primary targets. Additionally, cell type enrichment analysis identifies lncRNAs associated with pluripotency. We compare our results with previously published fibroblasts phenotyping data and find that 2.9% of the lncRNAs exhibit consistent cell growth phenotype, whereas we observe 58.3% agreement in molecular phenotypes. This highlights the consistency of lncRNA function at the molecular level and molecular phenotyping is more comprehensive in revealing affected pathways.
Yip, C.W. et al. Cell Reports
DOI: 10.1016/j.celrep.2022.111893
Functional annotation of human long noncoding RNAs via molecular phenotyping
We published a pilot study of FANTOM6, the latest edition of the project. looking at human long non-coding RNAs, which outnumber protein-coding genes in mammals but whose function is still poorly understood. We selectively targeted nearly 300 long non-coding RNAs for suppression in human fibroblast cells using an automated robotics system (Figure 1), and combined live cell imaging with CAGE to observe how cells respond at both the cellular and the molecular level. Based on the analysis, over 25 percent of long non-coding RNAs were found to affect cell growth and morphology, as well as cell migration.
Ramilowski J. A., et al. Genome Research
DOI: 10.1101/gr.254219.119
Introduction to FANTOM6
FANTOM (Functional ANnoTation Of the Mammalian genome) is a worldwide collaborative project aiming at identifying all functional elements in mammalian genomes. The goal of the sixth edition of the FANTOM project (FANTOM6) is to systematically elucidate the function of long non-coding RNAs (lncRNAs) in the human genome.
We envision the following as the main experimental strategy for FANTOM6.
- We are generating a reference set of genome-wide profiles to establish the basal state of the transcriptome and epigenome in each cell type.
- We are perturbing a set of lncRNAs in each cell type, and evaluating the molecular phenotype of the perturbation by CAGE profiling followed by bioinformatics analysis. The lncRNAs selected for perturbation are based on published transcripts as well as yet unpublished RNAseq assemblies specific to the cell types in the FANTOM5 collection.
- A selected subset of lncRNAs will be functionally characterized in more detail using other complementary technologies.
Views and data
FANTOM6 Analysis Viewer with ZENBU-Reports
The view provides an interface to interactively access to analysis results performed in the FANTOM6 project. It is implemented with ZENBU-Report.
FANTOM6 Experiment Index
The view provides an interface to search for experiments and produced raw data files by the experiments.
FANTOM6 Data download site
The data files including sequences, mapping results, expression tables obtained in the FANTOM6 project are available via the FANTOM6 web site.