Two independent transcription initiation codes overlap on vertebrate core promoters

Single-nucleotide resolution analysis of mRNA sequences with CAGE by the FANTOM project revealed earlier the existence of different ways to initiate the transcription of genes, in particular one called sharp, with a strong tendency to always start at the same nucleotide, and one called broad, where the start nucleotide varies withing a window that can be as large as a hundred of bases. The sequences governing the use of one way or the other are the initiation codes featured in the title.

This new article reconciles these different classes and shows that the same genes can be transcribed in sharp or broad manners in different biological contexts, here, the development of zebrafish embryos. This is explained in more details in the press releases at RIKEN and at the MRC.

The following part describes more in detail the contribution of the Genomics Miniaturization Technology Unit. For the validation of the findings in transgenic animals where the initiation codes were altered, we developed the Single-locus CAGE method. The picture below is the figure 3C in the article.

In brief, the Single-locus CAGE method is a gene-specific version of CAGE. The start position (5′ end) of target RNAs is accurately detected by the CAP Trapper method like in CAGE. However, the RNA is reverse-transcribed with gene-specific primers and not random or oligo-dT primers, and therefore the method guarantees a large number of sequence reads for a high coverage of the transcription start site of interest. Lastly, the experimental procedure is simplified by sequencing 5′ ends directly instead of cleaving tags with a restriction enzyme, and the libraries can easily be multiplexed on benchtop sequencers (Illumina MiSeq), allowing for the parallel study of experimental replicates.


Haberle V, Li N, Hadzhiev Y, Plessy C, Previti C, Nepal C, Gehrig J, Dong X, Akalin A, Suzuki AM, van Ijcken WF, Armant O, Ferg M, Strähle U, Carninci P, Müller F, Lenhard B. Two independent transcription initiation codes overlap on vertebrate core promoters. Nature. 2014 Mar 20;507(7492):381-5 PubMed: 24531765