FANTOM5 miRNA atlas paper is published!

By applying short RNA-sequencing and Cap Analysis of Gene Expression (CAGE) we have generated expression profiles of mature miRNAs and their primary transcripts across a large collection of primary cell types. CAGE has also allowed us to map their promoters. We show that miRNA promoters are highly conserved, that the expression profiles of the mature and the primary transcript are correlated and that miRNAs originating from the same polycistron are highly correlated. We present the data as a web resource to the research community.

The FANTOM5 collection on NPG

A collection of articles, including research papers and data descriptors, on the FANTOM5 project published in the Nature Publishing Group (NPG) is provided here .
This is also picked up by RIKEN’s web site.

FANTOM5 long non-coding RNA paper is published!

There is a strong debate on whether the thousands of long non-coding RNAs transcribed from our genomes are functional or simply byproducts of a noisy transcriptional machinery. Scientists from the RIKEN-led FANTOM5 consortium used a technology known as Cap Analysis of Gene Expression (CAGE) to build an atlas of human long non-coding RNAs with accurate 5’ ends and summarized their expression patterns across the major cell types. In the work, published in Nature, they intersected this expression atlas with other genetic and genomic datasets and suggested many of these long non-coding RNAs might be functional.

FANTOM5 "Phase 2" paper has been published!

Using a comprehensive analysis of RNA expression in different cell types, scientist from the RIKEN-led FANTOM5 consortium have made major strides toward resolving an outstanding mystery in biology. In the work, published in Science, they showed that when cells undergo phenotype changes such as differentiation into specialized cell types, the initial activation happens at DNA regions called enhancers, a type of regulatory “switches” which are typically located far from the genes that they activate.

FANTOM5 papers have been published!

Using Cap Analysis of Gene Expression (CAGE) we have mapped the sets of transcripts, transcription factors, promoters and enhancers active in the majority of mammalian primary cell types. We have also complemented this with profiles from cancer cell lines, and tissues. The results are described in two landmark papers in Nature describing the promoterome and enhancerome of mammalian cells. An additional 16 publications cover areas as diverse as primary cells, gene families, genome wide observations on promoter features and new bioinformatics tools.

FANTOM5

In FANTOM5 we are expanding the efforts made in FANTOM3 and 4 and aim to generate both a map of the majority of human promoters and comparative transcriptional regulatory network models of each cellular state. To achieve this we are carrying out deepCAGE sequencing on the Heliscope true single molecule sequencer on RNA isolated from every major human organ, over 200 cancer cell lines, 30 time courses of cellular differentiation, mouse developmental time courses and over 200 primary cell types.

FANTOM4

FANTOM4 used deepCAGE to monitor the dynamics of transcription start site (TSS) usage during a time course of monocytic differentiation. The expression levels from each promoter and transcription factor binding site predictions were then used to build a transcriptional regulatory network model (Suzuki et al. 2009). Additionally, transcription intitiation RNAs, the expression of the 'repeatome' and at atlas of combinatorial TF regulation were published in FANTOM4.

FANTOM3

FANTOM consortium utilized a new technology, CAGE, to reveal that more than 63% of the genome — instead of the known ~1.5% fraction of protein coding exons — is transcribed as RNA. We also confirmed the existence of over 23,000 non-coding RNAs (ncRNAs) and that >73% of the transcriptional units show sense-antisense transcription. This work was published in a couple of papers in the “RNA special issue” of Science in 2005 (Carninci et al. 2005; Katayama et al. 2005)

FANTOM2

During the second phase of the FANTOM activities, we determined the base sequences and assigned functional annotations to a set of 60,770 full-length mouse cDNAs. This was the first project worldwide to standardize full-length mammalian cDNAs. The research was published in a special issue of Nature on the decoding of the mouse genome in 2002 (Okazaki et al. 2002)

FANTOM1

The consortium developed an effective system for functional gene annotation by designing appropriate rules and methods. The result was mainly published in Nature in 2001(Kawai et al. 2001). The paper was followed by the draft sequence of human genome (Lander et al. 2001) week later because they used our cDNA for gene number prediction.