Journal article
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
E Valen, G Pascarella, A Chalk, N Maeda, M Kojima, C Kawazu, M Murata, H Nishiyori, D Lazarevic, D Motti, TT Marstrand, MHE Tang, X Zhao, A Krogh, O Winther, T Arakawa, J Kawai, C Wells, C Daub, M Harbers Show all
Genome Research | COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT | Published : 2009
Abstract
Finding and characterizing mRNAs, their transcription start sites (TSS), and their associated promoters is a major focus in post-genome biology. Mammalian cells have at least 5-10 magnitudes more TSS than previously believed, and deeper sequencing is necessary to detect all active promoters in a given tissue. Here, we present a new method for high-throughput sequencing of 5' cDNA tags-DeepCAGE: merging the Cap Analysis of Gene Expression method with ultra-high-throughput sequence technology. We apply DeepCAGE to characterize 1.4 million sequenced TSS from mouse hippocampus and reveal a wealth of novel core promoters that are preferentially used in hippocampus: This is the most comprehensive ..
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Awarded by European Commission
Funding Acknowledgements
P. C. and Y.H. are supported by the National Project on Protein Structural and Functional Analysis from MEXT and the National Project on Genome Network Analysis and the RIKEN Genome Exploration Research Project from the Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government. P. C. is also supported by a grant by the EU 6th Framework Program (NFG project). Authors affiliated with the Bioinformatics Centre are supported by a grant from the Novo Nordisk Foundation. The European Research Council has provided financial support to A. S. under the EU 7th Framework Programme (FP7/20072013)/ERC grant agreement 204135. S. G. is supported by a career development grant from "The Giovanni Armenise-Harvard Foundation.'' We thank Susan Sunkin for help with in situ images and scientific discussion, Kazuho Ikeo and Toshitsugi Okayama for developing and sharing the CAGE mapping procedures before publication, and Akira Hasegawa for technical support.