Monitoring transcription initiation activities in rat and dog

Marina Lizio,Shoko Watanabe,Chung Chau Hon,Hideya Kawaji,Akira Hasegawa,Jessica Severin,Takeya Kasukawa,Imad Abugessaisa,Mizuho Ohno,Piero Carninci,Masayoshi Itoh,Jayson Harshbarger,Abdul Kadir Mukarram,Timo Lassmann,Alistair R.R Forrest,Yoshihide Hayashizaki

doi:10.1038/sdata.2017.173

Abstract

The promoter landscape of several non-human model organisms is far from complete. As a part of FANTOM5 data collection, we generated 13 profiles of transcription initiation activities in dog and rat aortic smooth muscle cells, mesenchymal stem cells and hepatocytes by employing CAGE (Cap Analysis of Gene Expression) technology combined with single molecule sequencing. Our analyses show that the CAGE profiles recapitulate known transcription start sites (TSSs) consistently, in addition to uncover novel TSSs. Our dataset can be thus used with high confidence to support gene annotation in dog and rat species. We identified 28,497 and 23,147 CAGE peaks, or promoter regions, for rat and dog respectively, and associated them to known genes. This approach could be seen as a standard method for improvement of existing gene models, as well as discovery of novel genes. Given that the FANTOM5 data collection includes dog and rat matched cell types in human and mouse as well, this data would also be useful for cross-species studies.

Highlights

Background & SummaryThe recent years have seen a renewed interest in non-human model organisms, mainly thanks to the advances in DNA sequencing technologies
We identified Cap Analysis of Gene Expression (CAGE) peaks and associated them to the existing gene models as a part of our quality assessment; this highlighted the utility of CAGE to refine incorrectly characterized gene models
The full sets of CAGE promoters are available both via DDBJ data repository and via the functional annotation of the mammalian genome (FANTOM) web resource, which can be accessible at http:// fantom.gsc.riken.jp

Summary

Introduction

Background & SummaryThe recent years have seen a renewed interest in non-human model organisms, mainly thanks to the advances in DNA sequencing technologies. In order to improve the definition of gene models for the less-studied organisms, the FANTOM consortium generated CAGE data for several other species, like dog (Canis lupus familiaris) and rat (Rattus norvegicus). The full sets of CAGE promoters are available both via DDBJ data repository (mapping results) and via the FANTOM web resource (expression and genomic visualization), which can be accessible at http:// fantom.gsc.riken.jp.

Results

Conclusion