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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
Relatively frequent switching of transcription start sites during cerebellar development
BMC Genomics, Volume 18, No. 1, Article 461, Year 2017
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Description
Background: Alternative transcription start site (TSS) usage plays important roles in transcriptional control of mammalian gene expression. The growing interest in alternative TSSs and their role in genome diversification spawned many single-gene studies on differential usages of tissue-specific or temporal-specific alternative TSSs. However, exploration of the switching usage of alternative TSS usage on a genomic level, especially in the central nervous system, is largely lacking. Results: In this study, We have prepared a unique set of time-course data for the developing cerebellum, as part of the FANTOM5 consortium (http://fantom.gsc.riken.jp/5/) that uses their innovative capturing of 5' ends of all transcripts followed by Helicos next generation sequencing. We analyzed the usage of all transcription start sites (TSSs) at each time point during cerebellar development that provided information on multiple RNA isoforms that emerged from the same gene. We developed a mathematical method that systematically compares the expression of different TSSs of a gene to identify temporal crossover and non-crossover switching events. We identified 48,489 novel TSS switching events in 5433 genes during cerebellar development. This includes 9767 crossover TSS switching events in 1511 genes, where the dominant TSS shifts over time. Conclusions: We observed a relatively high prevalence of TSS switching in cerebellar development where the resulting temporally-specific gene transcripts and protein products can play important regulatory and functional roles. © 2017 The Author(s).
Authors & Co-Authors
Dimont, Emmanuel
United States, Boston
Harvard T.h. Chan School of Public Health
United States, Cambridge
Harvard Stem Cell Institute
Ha, Thomas J.
Canada, Vancouver
The University of British Columbia
Swanson, Douglas James
Canada, Vancouver
The University of British Columbia
Hide, Winston A.
United States, Boston
Harvard T.h. Chan School of Public Health
United States, Cambridge
Harvard Stem Cell Institute
United Kingdom, Sheffield
The University of Sheffield
Goldowitz, Daniel
Canada, Vancouver
The University of British Columbia
Statistics
Citations: 16
Authors: 5
Affiliations: 4
Identifiers
Doi:
10.1186/s12864-017-3834-z
ISSN:
14712164
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study