- Library Home /
- Search Collections /
- Open Collections /
- Browse Collections /
- UBC Faculty Research and Publications /
- Relatively frequent switching of transcription start...
Open Collections
UBC Faculty Research and Publications
Relatively frequent switching of transcription start sites during cerebellar development Zhang, Peter; Dimont, Emmanuel; Ha, Thomas; Swanson, Douglas J.; Hide, Winston; Goldowitz, D.
Abstract
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.
Item Metadata
Title |
Relatively frequent switching of transcription start sites during cerebellar development
|
Creator | |
Contributor | |
Publisher |
BioMed Central
|
Date Issued |
2017-06-13
|
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.
|
Subject | |
Genre | |
Type | |
Language |
eng
|
Date Available |
2017-12-13
|
Provider |
Vancouver : University of British Columbia Library
|
Rights |
Attribution 4.0 International (CC BY 4.0)
|
DOI |
10.14288/1.0361998
|
URI | |
Affiliation | |
Citation |
BMC Genomics. 2017 Jun 13;18(1):461
|
Publisher DOI |
10.1186/s12864-017-3834-z
|
Peer Review Status |
Reviewed
|
Scholarly Level |
Faculty
|
Copyright Holder |
The Author(s).
|
Rights URI | |
Aggregated Source Repository |
DSpace
|
Item Media
Item Citations and Data
Rights
Attribution 4.0 International (CC BY 4.0)