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Sci Data. 2017 Nov 28;4:170173. doi: 10.1038/sdata.2017.173.

Monitoring transcription initiation activities in rat and dog.

Author information

1
RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama 230-0045, Japan.
2
RIKEN Yokohama Institute, Omics Science Center, Yokohama 230-0045, Japan.
3
Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE-171 76, Sweden.
4
RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan.
5
Telethon Kids Institute, Telethon Kids Institute, The University of Western Australia, Subiaco WA 6008, Australia.
6
Harry Perkins Institute of Medical Research, Nedlands WA 6009, Australia.
7
RIKEN Advanced Center for Computing and Communication, Preventive Medicine and Applied Genomics Unit, Yokohama 230-0045, Japan.

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.

PMID:
29182598
PMCID:
PMC5704677
DOI:
10.1038/sdata.2017.173
[Indexed for MEDLINE]
Free PMC Article

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